Program brochure of
First African Virtual Conference on Bioinformatics
(Afbix rsquo09)
Organized by
Bioinformaticsorg
In collaboration with
RSGshyAfrica and RSGshy Morocco
February 19shy20 2009
httpwikibioinformaticsorgAfbix09
afbix09bioinformaticsorg 1
Contents
Prologue
Concept of virtual hubs
Keynote speakers
Program
Program Chairs ndash Committee
Abstracts
List of participating hubs and confirmed participants
afbix09bioinformaticsorg 2
Prologue
We are delighted to bring you this brochure containing a list of abstracts for the first African
Virtual Conference on Bioinformatics (Afbix rsquo09) In addition to research on tropical diseases
pathogenesis and their vectors the field of bioinformatics has become an important part of life
science studies in Africa But with the great geographical expanse of the continent it is often
impractical or uneconomical for African researchers to come together for conferences That is in
person The Bioinformatics Organization (BioinformaticsOrg) has therefore collaborated with
the African Society of Bioinformatics amp Computational Biology (ASBCB) and Regional Student
Groups (RSGs) in Africa to develop a bioinformatics conference that utilizes local institutions in
Africa as virtual hubs
At the outset we would like to thank all of the keynote and other invited speakers for having
accepted our kind invitation to present a talk And thanks you to the workaholics of all
committee members and reviewers who planned this event well and made this a fruitful
beginning for virtual conferences in Africa
We look forward to see you during the virtual conference
Have a great conference ahead
Sincerely
Chairs and the Team Afbix lsquo09
afbix09bioinformaticsorg 3
Concept of virtual hubs
Considering the fact that there is still time to open affordable bandwidth in Africa we at
BioinformaticsOrg thought of distributing this virtual conference through hubs across all parts
of Africa In that process 20shy30 participants per hub can pay a fee for the hub which would act
as a cumulative reduced registration fee for the individual This may be the first of its kind in
the virtual world where this concept is introduced
BioinformaticsOrg has a subscription to an online meeting system which allows users to
connect and form a virtual classroom
Hub
BioinformaticsOrgrsquos virtual world
through the online meeting system
Hub
Individual participant(s)
Prototype of virtual conference
afbix09bioinformaticsorg 4
Keynote speakers
Dr Trevor Sewell Dr Richard F Wintle
Dr Ivan Gerling Dr Dan Masiga
afbix09bioinformaticsorg 5
Program(All times Greenwich Meridian time GMT)
February 19
Morning session
bull 0900shy0920 shy Welcome By Mtakai Ngara and Segun Fatumo
Subshytheme 1 Structural Biology Applied to Infectious Diseases
bull 0930shy1030 shy Keynote 1 Dr Trevor Sewell Title TBA bull 1040shy1100 shy Coffee break with virtual posters bull 1100shy1140 shy Invited Speaker 1 Dr Ezekiel Adebiyi Computational Biologists in
Malaria Research SignificanceChallenges and Suggestions on way forward bull 1150shy1210 shy Oral presenter 1 Khalid Moum bull 1220shy1240 shy Presentation about achievements from BioinformaticsOrg ndash Jeff Bizzaro bull 1250shy1350 shy LunchDinner (virtual) networking )
Afternoon session
SubshyTheme 2 Applied Genomics to Infectious Diseases
bull 1400shy1500 shy Keynote 2 Dr Richard Wintle Title TBA bull 1510shy1550 shy Invited speaker 2 Dr Raphael D Isokpehi Aquaporins at the Hostshy
Parasite Interface in Malaria1550shy1610 shy Coffee break with Virtual posters bull 1600shy1630 ndash Oral presenter 2 Segun Fatumobull 1640shy1710 ndash Oral presenter 3 John Tan
afbix09bioinformaticsorg 6
February 20
Morning session
SubshyTheme 3 Career Development in Bioinformatics and Opportunities for Researchers in Africa
bull 0900shy1000 shy Keynote 3 Dr Dan MasigashyChair ASBCB bull 1000shy1100 shy ISCB Student Council shy SC Chair Abhishek Pratap amp RSGs in Africa shy
RSG regional leaders bull 1100shy1130 shy Coffee break with virtual posters bull 1130shy1210 ndash LunchDinner NetworkingAdvertisements
Afternoon session
bull 1220shy1350 shy A tutorial on Mitochondrial systems biology a sequel to Mitochondriomics by Prashanth Suravajhala Bioinformatics Organization
SubshyTheme 4 Proteomic applications to Tropical Diseases
bull 1400shy1500 shy Keynote 4 Dr Ivan Gerling bull 1510shy1550 shy Invited speaker 3 Dr Lawrence Okoror Proteomics a major tool for
vaccine preparation Lassa virus as a case study bull 1600shy1730 ndash A tutorial on the UCSC Genome Browser by Warren Lathe
OpenHelixcom bull 1740shy1820 ndash Invited speaker 4 Dr Scott Emrich bull 1830shy1920 shy Invited speaker 5 Dr Michael Ferdigbull 1930shy2000 shy Noura Chelbat Vote of thanks conference wrapshyup and adieu
afbix09bioinformaticsorg 7
Program Chairs and Committee
Chairs Mtakai Ngara (ILRI Kenya) Noura Chelbat (Austria) JW Bizzaro (President BioinformaticsOrg ) Prashanth Suravajhala (Associate Director BioinformaticsOrg)
Program Committee
Chair Segun Fatumo (Covenant University Nigeria)
Noura Chelbat (Institute of Bioinformatics JKU Linz shyAustria) Sarath Chandra Janga (University of Cambridge UK) Abhishek Pratap (USA) Prashanth Suravajhala Sheila Ommeh (Kenya) Kavisha Ramdayal (SANBI South Africa) Souiai Ouissem (Tunisia)
Technical Committee
Chair Nelson Ndegwa
Working group Sheila Ommeh Kavisha Ramdayal Kenneth Babu Souiai Ouissem Stanley Mbandi Amina El Gonnouni Geoffrey Siwo Marion Adebiyi Dennis Zofou Amal Maurady
afbix09bioinformaticsorg 8
Abstracts
All the abstracts are in accordance with the ones that the authors communicated with us and
therefore DO NOT contain the revisions The readersrsquo discretion is advised However
scientific and technical revisions for abstracts if any have been amended by authors upon
receiving comments from reviewers Should you require the full length articles you could
communicate with authors directly after the conference The full length articles of select
abstracts will be communicated to the Journal of Bioinformatics and Computational Biology
and Bioinformation
afbix09bioinformaticsorg 9
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Contents
Prologue
Concept of virtual hubs
Keynote speakers
Program
Program Chairs ndash Committee
Abstracts
List of participating hubs and confirmed participants
afbix09bioinformaticsorg 2
Prologue
We are delighted to bring you this brochure containing a list of abstracts for the first African
Virtual Conference on Bioinformatics (Afbix rsquo09) In addition to research on tropical diseases
pathogenesis and their vectors the field of bioinformatics has become an important part of life
science studies in Africa But with the great geographical expanse of the continent it is often
impractical or uneconomical for African researchers to come together for conferences That is in
person The Bioinformatics Organization (BioinformaticsOrg) has therefore collaborated with
the African Society of Bioinformatics amp Computational Biology (ASBCB) and Regional Student
Groups (RSGs) in Africa to develop a bioinformatics conference that utilizes local institutions in
Africa as virtual hubs
At the outset we would like to thank all of the keynote and other invited speakers for having
accepted our kind invitation to present a talk And thanks you to the workaholics of all
committee members and reviewers who planned this event well and made this a fruitful
beginning for virtual conferences in Africa
We look forward to see you during the virtual conference
Have a great conference ahead
Sincerely
Chairs and the Team Afbix lsquo09
afbix09bioinformaticsorg 3
Concept of virtual hubs
Considering the fact that there is still time to open affordable bandwidth in Africa we at
BioinformaticsOrg thought of distributing this virtual conference through hubs across all parts
of Africa In that process 20shy30 participants per hub can pay a fee for the hub which would act
as a cumulative reduced registration fee for the individual This may be the first of its kind in
the virtual world where this concept is introduced
BioinformaticsOrg has a subscription to an online meeting system which allows users to
connect and form a virtual classroom
Hub
BioinformaticsOrgrsquos virtual world
through the online meeting system
Hub
Individual participant(s)
Prototype of virtual conference
afbix09bioinformaticsorg 4
Keynote speakers
Dr Trevor Sewell Dr Richard F Wintle
Dr Ivan Gerling Dr Dan Masiga
afbix09bioinformaticsorg 5
Program(All times Greenwich Meridian time GMT)
February 19
Morning session
bull 0900shy0920 shy Welcome By Mtakai Ngara and Segun Fatumo
Subshytheme 1 Structural Biology Applied to Infectious Diseases
bull 0930shy1030 shy Keynote 1 Dr Trevor Sewell Title TBA bull 1040shy1100 shy Coffee break with virtual posters bull 1100shy1140 shy Invited Speaker 1 Dr Ezekiel Adebiyi Computational Biologists in
Malaria Research SignificanceChallenges and Suggestions on way forward bull 1150shy1210 shy Oral presenter 1 Khalid Moum bull 1220shy1240 shy Presentation about achievements from BioinformaticsOrg ndash Jeff Bizzaro bull 1250shy1350 shy LunchDinner (virtual) networking )
Afternoon session
SubshyTheme 2 Applied Genomics to Infectious Diseases
bull 1400shy1500 shy Keynote 2 Dr Richard Wintle Title TBA bull 1510shy1550 shy Invited speaker 2 Dr Raphael D Isokpehi Aquaporins at the Hostshy
Parasite Interface in Malaria1550shy1610 shy Coffee break with Virtual posters bull 1600shy1630 ndash Oral presenter 2 Segun Fatumobull 1640shy1710 ndash Oral presenter 3 John Tan
afbix09bioinformaticsorg 6
February 20
Morning session
SubshyTheme 3 Career Development in Bioinformatics and Opportunities for Researchers in Africa
bull 0900shy1000 shy Keynote 3 Dr Dan MasigashyChair ASBCB bull 1000shy1100 shy ISCB Student Council shy SC Chair Abhishek Pratap amp RSGs in Africa shy
RSG regional leaders bull 1100shy1130 shy Coffee break with virtual posters bull 1130shy1210 ndash LunchDinner NetworkingAdvertisements
Afternoon session
bull 1220shy1350 shy A tutorial on Mitochondrial systems biology a sequel to Mitochondriomics by Prashanth Suravajhala Bioinformatics Organization
SubshyTheme 4 Proteomic applications to Tropical Diseases
bull 1400shy1500 shy Keynote 4 Dr Ivan Gerling bull 1510shy1550 shy Invited speaker 3 Dr Lawrence Okoror Proteomics a major tool for
vaccine preparation Lassa virus as a case study bull 1600shy1730 ndash A tutorial on the UCSC Genome Browser by Warren Lathe
OpenHelixcom bull 1740shy1820 ndash Invited speaker 4 Dr Scott Emrich bull 1830shy1920 shy Invited speaker 5 Dr Michael Ferdigbull 1930shy2000 shy Noura Chelbat Vote of thanks conference wrapshyup and adieu
afbix09bioinformaticsorg 7
Program Chairs and Committee
Chairs Mtakai Ngara (ILRI Kenya) Noura Chelbat (Austria) JW Bizzaro (President BioinformaticsOrg ) Prashanth Suravajhala (Associate Director BioinformaticsOrg)
Program Committee
Chair Segun Fatumo (Covenant University Nigeria)
Noura Chelbat (Institute of Bioinformatics JKU Linz shyAustria) Sarath Chandra Janga (University of Cambridge UK) Abhishek Pratap (USA) Prashanth Suravajhala Sheila Ommeh (Kenya) Kavisha Ramdayal (SANBI South Africa) Souiai Ouissem (Tunisia)
Technical Committee
Chair Nelson Ndegwa
Working group Sheila Ommeh Kavisha Ramdayal Kenneth Babu Souiai Ouissem Stanley Mbandi Amina El Gonnouni Geoffrey Siwo Marion Adebiyi Dennis Zofou Amal Maurady
afbix09bioinformaticsorg 8
Abstracts
All the abstracts are in accordance with the ones that the authors communicated with us and
therefore DO NOT contain the revisions The readersrsquo discretion is advised However
scientific and technical revisions for abstracts if any have been amended by authors upon
receiving comments from reviewers Should you require the full length articles you could
communicate with authors directly after the conference The full length articles of select
abstracts will be communicated to the Journal of Bioinformatics and Computational Biology
and Bioinformation
afbix09bioinformaticsorg 9
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Prologue
We are delighted to bring you this brochure containing a list of abstracts for the first African
Virtual Conference on Bioinformatics (Afbix rsquo09) In addition to research on tropical diseases
pathogenesis and their vectors the field of bioinformatics has become an important part of life
science studies in Africa But with the great geographical expanse of the continent it is often
impractical or uneconomical for African researchers to come together for conferences That is in
person The Bioinformatics Organization (BioinformaticsOrg) has therefore collaborated with
the African Society of Bioinformatics amp Computational Biology (ASBCB) and Regional Student
Groups (RSGs) in Africa to develop a bioinformatics conference that utilizes local institutions in
Africa as virtual hubs
At the outset we would like to thank all of the keynote and other invited speakers for having
accepted our kind invitation to present a talk And thanks you to the workaholics of all
committee members and reviewers who planned this event well and made this a fruitful
beginning for virtual conferences in Africa
We look forward to see you during the virtual conference
Have a great conference ahead
Sincerely
Chairs and the Team Afbix lsquo09
afbix09bioinformaticsorg 3
Concept of virtual hubs
Considering the fact that there is still time to open affordable bandwidth in Africa we at
BioinformaticsOrg thought of distributing this virtual conference through hubs across all parts
of Africa In that process 20shy30 participants per hub can pay a fee for the hub which would act
as a cumulative reduced registration fee for the individual This may be the first of its kind in
the virtual world where this concept is introduced
BioinformaticsOrg has a subscription to an online meeting system which allows users to
connect and form a virtual classroom
Hub
BioinformaticsOrgrsquos virtual world
through the online meeting system
Hub
Individual participant(s)
Prototype of virtual conference
afbix09bioinformaticsorg 4
Keynote speakers
Dr Trevor Sewell Dr Richard F Wintle
Dr Ivan Gerling Dr Dan Masiga
afbix09bioinformaticsorg 5
Program(All times Greenwich Meridian time GMT)
February 19
Morning session
bull 0900shy0920 shy Welcome By Mtakai Ngara and Segun Fatumo
Subshytheme 1 Structural Biology Applied to Infectious Diseases
bull 0930shy1030 shy Keynote 1 Dr Trevor Sewell Title TBA bull 1040shy1100 shy Coffee break with virtual posters bull 1100shy1140 shy Invited Speaker 1 Dr Ezekiel Adebiyi Computational Biologists in
Malaria Research SignificanceChallenges and Suggestions on way forward bull 1150shy1210 shy Oral presenter 1 Khalid Moum bull 1220shy1240 shy Presentation about achievements from BioinformaticsOrg ndash Jeff Bizzaro bull 1250shy1350 shy LunchDinner (virtual) networking )
Afternoon session
SubshyTheme 2 Applied Genomics to Infectious Diseases
bull 1400shy1500 shy Keynote 2 Dr Richard Wintle Title TBA bull 1510shy1550 shy Invited speaker 2 Dr Raphael D Isokpehi Aquaporins at the Hostshy
Parasite Interface in Malaria1550shy1610 shy Coffee break with Virtual posters bull 1600shy1630 ndash Oral presenter 2 Segun Fatumobull 1640shy1710 ndash Oral presenter 3 John Tan
afbix09bioinformaticsorg 6
February 20
Morning session
SubshyTheme 3 Career Development in Bioinformatics and Opportunities for Researchers in Africa
bull 0900shy1000 shy Keynote 3 Dr Dan MasigashyChair ASBCB bull 1000shy1100 shy ISCB Student Council shy SC Chair Abhishek Pratap amp RSGs in Africa shy
RSG regional leaders bull 1100shy1130 shy Coffee break with virtual posters bull 1130shy1210 ndash LunchDinner NetworkingAdvertisements
Afternoon session
bull 1220shy1350 shy A tutorial on Mitochondrial systems biology a sequel to Mitochondriomics by Prashanth Suravajhala Bioinformatics Organization
SubshyTheme 4 Proteomic applications to Tropical Diseases
bull 1400shy1500 shy Keynote 4 Dr Ivan Gerling bull 1510shy1550 shy Invited speaker 3 Dr Lawrence Okoror Proteomics a major tool for
vaccine preparation Lassa virus as a case study bull 1600shy1730 ndash A tutorial on the UCSC Genome Browser by Warren Lathe
OpenHelixcom bull 1740shy1820 ndash Invited speaker 4 Dr Scott Emrich bull 1830shy1920 shy Invited speaker 5 Dr Michael Ferdigbull 1930shy2000 shy Noura Chelbat Vote of thanks conference wrapshyup and adieu
afbix09bioinformaticsorg 7
Program Chairs and Committee
Chairs Mtakai Ngara (ILRI Kenya) Noura Chelbat (Austria) JW Bizzaro (President BioinformaticsOrg ) Prashanth Suravajhala (Associate Director BioinformaticsOrg)
Program Committee
Chair Segun Fatumo (Covenant University Nigeria)
Noura Chelbat (Institute of Bioinformatics JKU Linz shyAustria) Sarath Chandra Janga (University of Cambridge UK) Abhishek Pratap (USA) Prashanth Suravajhala Sheila Ommeh (Kenya) Kavisha Ramdayal (SANBI South Africa) Souiai Ouissem (Tunisia)
Technical Committee
Chair Nelson Ndegwa
Working group Sheila Ommeh Kavisha Ramdayal Kenneth Babu Souiai Ouissem Stanley Mbandi Amina El Gonnouni Geoffrey Siwo Marion Adebiyi Dennis Zofou Amal Maurady
afbix09bioinformaticsorg 8
Abstracts
All the abstracts are in accordance with the ones that the authors communicated with us and
therefore DO NOT contain the revisions The readersrsquo discretion is advised However
scientific and technical revisions for abstracts if any have been amended by authors upon
receiving comments from reviewers Should you require the full length articles you could
communicate with authors directly after the conference The full length articles of select
abstracts will be communicated to the Journal of Bioinformatics and Computational Biology
and Bioinformation
afbix09bioinformaticsorg 9
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Concept of virtual hubs
Considering the fact that there is still time to open affordable bandwidth in Africa we at
BioinformaticsOrg thought of distributing this virtual conference through hubs across all parts
of Africa In that process 20shy30 participants per hub can pay a fee for the hub which would act
as a cumulative reduced registration fee for the individual This may be the first of its kind in
the virtual world where this concept is introduced
BioinformaticsOrg has a subscription to an online meeting system which allows users to
connect and form a virtual classroom
Hub
BioinformaticsOrgrsquos virtual world
through the online meeting system
Hub
Individual participant(s)
Prototype of virtual conference
afbix09bioinformaticsorg 4
Keynote speakers
Dr Trevor Sewell Dr Richard F Wintle
Dr Ivan Gerling Dr Dan Masiga
afbix09bioinformaticsorg 5
Program(All times Greenwich Meridian time GMT)
February 19
Morning session
bull 0900shy0920 shy Welcome By Mtakai Ngara and Segun Fatumo
Subshytheme 1 Structural Biology Applied to Infectious Diseases
bull 0930shy1030 shy Keynote 1 Dr Trevor Sewell Title TBA bull 1040shy1100 shy Coffee break with virtual posters bull 1100shy1140 shy Invited Speaker 1 Dr Ezekiel Adebiyi Computational Biologists in
Malaria Research SignificanceChallenges and Suggestions on way forward bull 1150shy1210 shy Oral presenter 1 Khalid Moum bull 1220shy1240 shy Presentation about achievements from BioinformaticsOrg ndash Jeff Bizzaro bull 1250shy1350 shy LunchDinner (virtual) networking )
Afternoon session
SubshyTheme 2 Applied Genomics to Infectious Diseases
bull 1400shy1500 shy Keynote 2 Dr Richard Wintle Title TBA bull 1510shy1550 shy Invited speaker 2 Dr Raphael D Isokpehi Aquaporins at the Hostshy
Parasite Interface in Malaria1550shy1610 shy Coffee break with Virtual posters bull 1600shy1630 ndash Oral presenter 2 Segun Fatumobull 1640shy1710 ndash Oral presenter 3 John Tan
afbix09bioinformaticsorg 6
February 20
Morning session
SubshyTheme 3 Career Development in Bioinformatics and Opportunities for Researchers in Africa
bull 0900shy1000 shy Keynote 3 Dr Dan MasigashyChair ASBCB bull 1000shy1100 shy ISCB Student Council shy SC Chair Abhishek Pratap amp RSGs in Africa shy
RSG regional leaders bull 1100shy1130 shy Coffee break with virtual posters bull 1130shy1210 ndash LunchDinner NetworkingAdvertisements
Afternoon session
bull 1220shy1350 shy A tutorial on Mitochondrial systems biology a sequel to Mitochondriomics by Prashanth Suravajhala Bioinformatics Organization
SubshyTheme 4 Proteomic applications to Tropical Diseases
bull 1400shy1500 shy Keynote 4 Dr Ivan Gerling bull 1510shy1550 shy Invited speaker 3 Dr Lawrence Okoror Proteomics a major tool for
vaccine preparation Lassa virus as a case study bull 1600shy1730 ndash A tutorial on the UCSC Genome Browser by Warren Lathe
OpenHelixcom bull 1740shy1820 ndash Invited speaker 4 Dr Scott Emrich bull 1830shy1920 shy Invited speaker 5 Dr Michael Ferdigbull 1930shy2000 shy Noura Chelbat Vote of thanks conference wrapshyup and adieu
afbix09bioinformaticsorg 7
Program Chairs and Committee
Chairs Mtakai Ngara (ILRI Kenya) Noura Chelbat (Austria) JW Bizzaro (President BioinformaticsOrg ) Prashanth Suravajhala (Associate Director BioinformaticsOrg)
Program Committee
Chair Segun Fatumo (Covenant University Nigeria)
Noura Chelbat (Institute of Bioinformatics JKU Linz shyAustria) Sarath Chandra Janga (University of Cambridge UK) Abhishek Pratap (USA) Prashanth Suravajhala Sheila Ommeh (Kenya) Kavisha Ramdayal (SANBI South Africa) Souiai Ouissem (Tunisia)
Technical Committee
Chair Nelson Ndegwa
Working group Sheila Ommeh Kavisha Ramdayal Kenneth Babu Souiai Ouissem Stanley Mbandi Amina El Gonnouni Geoffrey Siwo Marion Adebiyi Dennis Zofou Amal Maurady
afbix09bioinformaticsorg 8
Abstracts
All the abstracts are in accordance with the ones that the authors communicated with us and
therefore DO NOT contain the revisions The readersrsquo discretion is advised However
scientific and technical revisions for abstracts if any have been amended by authors upon
receiving comments from reviewers Should you require the full length articles you could
communicate with authors directly after the conference The full length articles of select
abstracts will be communicated to the Journal of Bioinformatics and Computational Biology
and Bioinformation
afbix09bioinformaticsorg 9
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Keynote speakers
Dr Trevor Sewell Dr Richard F Wintle
Dr Ivan Gerling Dr Dan Masiga
afbix09bioinformaticsorg 5
Program(All times Greenwich Meridian time GMT)
February 19
Morning session
bull 0900shy0920 shy Welcome By Mtakai Ngara and Segun Fatumo
Subshytheme 1 Structural Biology Applied to Infectious Diseases
bull 0930shy1030 shy Keynote 1 Dr Trevor Sewell Title TBA bull 1040shy1100 shy Coffee break with virtual posters bull 1100shy1140 shy Invited Speaker 1 Dr Ezekiel Adebiyi Computational Biologists in
Malaria Research SignificanceChallenges and Suggestions on way forward bull 1150shy1210 shy Oral presenter 1 Khalid Moum bull 1220shy1240 shy Presentation about achievements from BioinformaticsOrg ndash Jeff Bizzaro bull 1250shy1350 shy LunchDinner (virtual) networking )
Afternoon session
SubshyTheme 2 Applied Genomics to Infectious Diseases
bull 1400shy1500 shy Keynote 2 Dr Richard Wintle Title TBA bull 1510shy1550 shy Invited speaker 2 Dr Raphael D Isokpehi Aquaporins at the Hostshy
Parasite Interface in Malaria1550shy1610 shy Coffee break with Virtual posters bull 1600shy1630 ndash Oral presenter 2 Segun Fatumobull 1640shy1710 ndash Oral presenter 3 John Tan
afbix09bioinformaticsorg 6
February 20
Morning session
SubshyTheme 3 Career Development in Bioinformatics and Opportunities for Researchers in Africa
bull 0900shy1000 shy Keynote 3 Dr Dan MasigashyChair ASBCB bull 1000shy1100 shy ISCB Student Council shy SC Chair Abhishek Pratap amp RSGs in Africa shy
RSG regional leaders bull 1100shy1130 shy Coffee break with virtual posters bull 1130shy1210 ndash LunchDinner NetworkingAdvertisements
Afternoon session
bull 1220shy1350 shy A tutorial on Mitochondrial systems biology a sequel to Mitochondriomics by Prashanth Suravajhala Bioinformatics Organization
SubshyTheme 4 Proteomic applications to Tropical Diseases
bull 1400shy1500 shy Keynote 4 Dr Ivan Gerling bull 1510shy1550 shy Invited speaker 3 Dr Lawrence Okoror Proteomics a major tool for
vaccine preparation Lassa virus as a case study bull 1600shy1730 ndash A tutorial on the UCSC Genome Browser by Warren Lathe
OpenHelixcom bull 1740shy1820 ndash Invited speaker 4 Dr Scott Emrich bull 1830shy1920 shy Invited speaker 5 Dr Michael Ferdigbull 1930shy2000 shy Noura Chelbat Vote of thanks conference wrapshyup and adieu
afbix09bioinformaticsorg 7
Program Chairs and Committee
Chairs Mtakai Ngara (ILRI Kenya) Noura Chelbat (Austria) JW Bizzaro (President BioinformaticsOrg ) Prashanth Suravajhala (Associate Director BioinformaticsOrg)
Program Committee
Chair Segun Fatumo (Covenant University Nigeria)
Noura Chelbat (Institute of Bioinformatics JKU Linz shyAustria) Sarath Chandra Janga (University of Cambridge UK) Abhishek Pratap (USA) Prashanth Suravajhala Sheila Ommeh (Kenya) Kavisha Ramdayal (SANBI South Africa) Souiai Ouissem (Tunisia)
Technical Committee
Chair Nelson Ndegwa
Working group Sheila Ommeh Kavisha Ramdayal Kenneth Babu Souiai Ouissem Stanley Mbandi Amina El Gonnouni Geoffrey Siwo Marion Adebiyi Dennis Zofou Amal Maurady
afbix09bioinformaticsorg 8
Abstracts
All the abstracts are in accordance with the ones that the authors communicated with us and
therefore DO NOT contain the revisions The readersrsquo discretion is advised However
scientific and technical revisions for abstracts if any have been amended by authors upon
receiving comments from reviewers Should you require the full length articles you could
communicate with authors directly after the conference The full length articles of select
abstracts will be communicated to the Journal of Bioinformatics and Computational Biology
and Bioinformation
afbix09bioinformaticsorg 9
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Program(All times Greenwich Meridian time GMT)
February 19
Morning session
bull 0900shy0920 shy Welcome By Mtakai Ngara and Segun Fatumo
Subshytheme 1 Structural Biology Applied to Infectious Diseases
bull 0930shy1030 shy Keynote 1 Dr Trevor Sewell Title TBA bull 1040shy1100 shy Coffee break with virtual posters bull 1100shy1140 shy Invited Speaker 1 Dr Ezekiel Adebiyi Computational Biologists in
Malaria Research SignificanceChallenges and Suggestions on way forward bull 1150shy1210 shy Oral presenter 1 Khalid Moum bull 1220shy1240 shy Presentation about achievements from BioinformaticsOrg ndash Jeff Bizzaro bull 1250shy1350 shy LunchDinner (virtual) networking )
Afternoon session
SubshyTheme 2 Applied Genomics to Infectious Diseases
bull 1400shy1500 shy Keynote 2 Dr Richard Wintle Title TBA bull 1510shy1550 shy Invited speaker 2 Dr Raphael D Isokpehi Aquaporins at the Hostshy
Parasite Interface in Malaria1550shy1610 shy Coffee break with Virtual posters bull 1600shy1630 ndash Oral presenter 2 Segun Fatumobull 1640shy1710 ndash Oral presenter 3 John Tan
afbix09bioinformaticsorg 6
February 20
Morning session
SubshyTheme 3 Career Development in Bioinformatics and Opportunities for Researchers in Africa
bull 0900shy1000 shy Keynote 3 Dr Dan MasigashyChair ASBCB bull 1000shy1100 shy ISCB Student Council shy SC Chair Abhishek Pratap amp RSGs in Africa shy
RSG regional leaders bull 1100shy1130 shy Coffee break with virtual posters bull 1130shy1210 ndash LunchDinner NetworkingAdvertisements
Afternoon session
bull 1220shy1350 shy A tutorial on Mitochondrial systems biology a sequel to Mitochondriomics by Prashanth Suravajhala Bioinformatics Organization
SubshyTheme 4 Proteomic applications to Tropical Diseases
bull 1400shy1500 shy Keynote 4 Dr Ivan Gerling bull 1510shy1550 shy Invited speaker 3 Dr Lawrence Okoror Proteomics a major tool for
vaccine preparation Lassa virus as a case study bull 1600shy1730 ndash A tutorial on the UCSC Genome Browser by Warren Lathe
OpenHelixcom bull 1740shy1820 ndash Invited speaker 4 Dr Scott Emrich bull 1830shy1920 shy Invited speaker 5 Dr Michael Ferdigbull 1930shy2000 shy Noura Chelbat Vote of thanks conference wrapshyup and adieu
afbix09bioinformaticsorg 7
Program Chairs and Committee
Chairs Mtakai Ngara (ILRI Kenya) Noura Chelbat (Austria) JW Bizzaro (President BioinformaticsOrg ) Prashanth Suravajhala (Associate Director BioinformaticsOrg)
Program Committee
Chair Segun Fatumo (Covenant University Nigeria)
Noura Chelbat (Institute of Bioinformatics JKU Linz shyAustria) Sarath Chandra Janga (University of Cambridge UK) Abhishek Pratap (USA) Prashanth Suravajhala Sheila Ommeh (Kenya) Kavisha Ramdayal (SANBI South Africa) Souiai Ouissem (Tunisia)
Technical Committee
Chair Nelson Ndegwa
Working group Sheila Ommeh Kavisha Ramdayal Kenneth Babu Souiai Ouissem Stanley Mbandi Amina El Gonnouni Geoffrey Siwo Marion Adebiyi Dennis Zofou Amal Maurady
afbix09bioinformaticsorg 8
Abstracts
All the abstracts are in accordance with the ones that the authors communicated with us and
therefore DO NOT contain the revisions The readersrsquo discretion is advised However
scientific and technical revisions for abstracts if any have been amended by authors upon
receiving comments from reviewers Should you require the full length articles you could
communicate with authors directly after the conference The full length articles of select
abstracts will be communicated to the Journal of Bioinformatics and Computational Biology
and Bioinformation
afbix09bioinformaticsorg 9
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
February 20
Morning session
SubshyTheme 3 Career Development in Bioinformatics and Opportunities for Researchers in Africa
bull 0900shy1000 shy Keynote 3 Dr Dan MasigashyChair ASBCB bull 1000shy1100 shy ISCB Student Council shy SC Chair Abhishek Pratap amp RSGs in Africa shy
RSG regional leaders bull 1100shy1130 shy Coffee break with virtual posters bull 1130shy1210 ndash LunchDinner NetworkingAdvertisements
Afternoon session
bull 1220shy1350 shy A tutorial on Mitochondrial systems biology a sequel to Mitochondriomics by Prashanth Suravajhala Bioinformatics Organization
SubshyTheme 4 Proteomic applications to Tropical Diseases
bull 1400shy1500 shy Keynote 4 Dr Ivan Gerling bull 1510shy1550 shy Invited speaker 3 Dr Lawrence Okoror Proteomics a major tool for
vaccine preparation Lassa virus as a case study bull 1600shy1730 ndash A tutorial on the UCSC Genome Browser by Warren Lathe
OpenHelixcom bull 1740shy1820 ndash Invited speaker 4 Dr Scott Emrich bull 1830shy1920 shy Invited speaker 5 Dr Michael Ferdigbull 1930shy2000 shy Noura Chelbat Vote of thanks conference wrapshyup and adieu
afbix09bioinformaticsorg 7
Program Chairs and Committee
Chairs Mtakai Ngara (ILRI Kenya) Noura Chelbat (Austria) JW Bizzaro (President BioinformaticsOrg ) Prashanth Suravajhala (Associate Director BioinformaticsOrg)
Program Committee
Chair Segun Fatumo (Covenant University Nigeria)
Noura Chelbat (Institute of Bioinformatics JKU Linz shyAustria) Sarath Chandra Janga (University of Cambridge UK) Abhishek Pratap (USA) Prashanth Suravajhala Sheila Ommeh (Kenya) Kavisha Ramdayal (SANBI South Africa) Souiai Ouissem (Tunisia)
Technical Committee
Chair Nelson Ndegwa
Working group Sheila Ommeh Kavisha Ramdayal Kenneth Babu Souiai Ouissem Stanley Mbandi Amina El Gonnouni Geoffrey Siwo Marion Adebiyi Dennis Zofou Amal Maurady
afbix09bioinformaticsorg 8
Abstracts
All the abstracts are in accordance with the ones that the authors communicated with us and
therefore DO NOT contain the revisions The readersrsquo discretion is advised However
scientific and technical revisions for abstracts if any have been amended by authors upon
receiving comments from reviewers Should you require the full length articles you could
communicate with authors directly after the conference The full length articles of select
abstracts will be communicated to the Journal of Bioinformatics and Computational Biology
and Bioinformation
afbix09bioinformaticsorg 9
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Program Chairs and Committee
Chairs Mtakai Ngara (ILRI Kenya) Noura Chelbat (Austria) JW Bizzaro (President BioinformaticsOrg ) Prashanth Suravajhala (Associate Director BioinformaticsOrg)
Program Committee
Chair Segun Fatumo (Covenant University Nigeria)
Noura Chelbat (Institute of Bioinformatics JKU Linz shyAustria) Sarath Chandra Janga (University of Cambridge UK) Abhishek Pratap (USA) Prashanth Suravajhala Sheila Ommeh (Kenya) Kavisha Ramdayal (SANBI South Africa) Souiai Ouissem (Tunisia)
Technical Committee
Chair Nelson Ndegwa
Working group Sheila Ommeh Kavisha Ramdayal Kenneth Babu Souiai Ouissem Stanley Mbandi Amina El Gonnouni Geoffrey Siwo Marion Adebiyi Dennis Zofou Amal Maurady
afbix09bioinformaticsorg 8
Abstracts
All the abstracts are in accordance with the ones that the authors communicated with us and
therefore DO NOT contain the revisions The readersrsquo discretion is advised However
scientific and technical revisions for abstracts if any have been amended by authors upon
receiving comments from reviewers Should you require the full length articles you could
communicate with authors directly after the conference The full length articles of select
abstracts will be communicated to the Journal of Bioinformatics and Computational Biology
and Bioinformation
afbix09bioinformaticsorg 9
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Abstracts
All the abstracts are in accordance with the ones that the authors communicated with us and
therefore DO NOT contain the revisions The readersrsquo discretion is advised However
scientific and technical revisions for abstracts if any have been amended by authors upon
receiving comments from reviewers Should you require the full length articles you could
communicate with authors directly after the conference The full length articles of select
abstracts will be communicated to the Journal of Bioinformatics and Computational Biology
and Bioinformation
afbix09bioinformaticsorg 9
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
1
MDM2 promoter SNP309 is not associated with risk of nasopharyngeal carcinoma in North African population
LAANTRI N19 NAJI F 1 MOUMAD K1 JALBOUT M 2 CORBEX M2 KANDIL M 9
BENIDER A3 BEN AYED F4 CHOUCHANE L5 BOUAOUINA N6 BOUALGA K7
CHEacuteRIFH8 KHYATTI M1
Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Abou Chouaib Doukkali El Jadida Maroc
PURPOSE MDM2 is a major negative regulator of p53 and a single nucleotide polymorphism in the MDM2 promoter region SNP309 (rs2279744) has been shown to increase the affinity of the transcriptional activator Sp1 resulting in elevated MDM2 transcription and expression in some cancers We examined whether the SNP309 was related to the risk of developing nasopharyngeal carcinoma (NPC) among North african populations
EXPERIMENTAL DESIGN We genotyped the SNP309 in 436 patients with NPC and 432 healthy control subjects in North africa by polymerase chain reaction based restriction fragment length polymorphism Multivariate logistic regression analysis was used to calculate adjusted odds ratio (OR) and 95 confidence interval (95 CI)
RESULTS No association was found between genetic variation in MDM2shy309 and the risk of NPC occurrence The OR were respectivelly (OR 1031 IC 075shy 142 P 085 for TG genotype) and (OR 088 IC 052shy 15 P 062 for GG genotype) The same results was found in the distibution of the genotypes by sexe and age
CONCLUSIONS Our findings suggest that MDM2 SNP309 is not a strong factor in Nasopharyngeal carcinogenesis In addition this is the first MDM2 SNP309 reported in North african populations
Key Words Nasopharyngeal carcinomaMDM2shy309 PCRshyRFLP
afbix09bioinformaticsorg 10
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
2
Inferring the metabolic network of Plasmodium falciparum in the host
Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
In a recent publication [Ginsburg 2008 TREPARshy784] shy a critical comparison of a manual
reconstruction of the metabolic pathways for Plasmodium (Malaria Parasite Metabolic Pathways)
with databases comprising of computationally inferred pathways like PlasmoCyc MetaSHARK
and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done The study disclosed that
the automatic reconstruction of pathways generates manifold paths that need an expert manual
verification as eg In the PlasmoCyc database there may be pathways incomplete or not
completely correct In this paper we support the hypothesis that the gaps in PlasmoCyc could be
filled by an elaborated comparison to the human metabolic network as the parasite may take
advantage of human enzymes The parasite may use them outside the parasitersquos organism in the
red blood cell and in the apicoplast organelle We reconstructed the metabolic network of
Plasmodium falciparum and found that the network got more complete when including the
human enzymes Furthermore we could show that the metabolism got more robust as the
number of essential reactions was substantially reduced when taking human enzymes into
account
Keywords chokepoints essential reactions Plasmodium Drug targets
afbix09bioinformaticsorg 11
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
3 Genetic polymorphism of Interleukin-10 promoter in North African EBV-associated Nasopharyngeal Carcinoma patients
K MOUMAD1 2 N LAANTRI1 F NAJI1 M CORBEX3 MM ENNAJI2 M JALBOUT1 W BEN AYOUB4 S DAHMOUL5 M AYAD6 M ABDOUN6 S MESLI6 M HAMDIshyCHERIF7 K BOUALGA6 N BOUAOUINA5
L CHOUCHANE8 A BENIDER9 F BEN AYED4 D GOLDGAR3 M KHYATTI1
1shy Institut Pasteur du Maroc 2shyFaculteacute des Sciences et Techniques Mohammedia Morocco 3shyInternational Agency for Research on Cancer Genetic Epidemiology unit Lyon France 4shyAssociation Tunisienne de Lutte Contre le Cancer Tunis Tunisia 5shy Service de Radiotheacuterapie CHU Farhat Hached Sousse Tunisia 6shy Centre Antishycancer de Blida service de radiotheacuterapie oncologique Blida Algeria 7shy Service deacutepideacutemiologie CHU de Seacutetif Seacutetif Algeria 8shy Laboratoire dImmunoshyOncologie Moleacuteculaire faculteacute de meacutedecine Monastir Tunisia 9shy Centre doncologie Ibn rochd Casablanca Morocco
Nasopharyngeal carcinoma (NPC) is a rare type of cancer in most populations The highest incidence has been
found in southern China with an annual ageshystandardized incidence rate of 30100000 However in North Africans
the incidence is intermediate with a rate of 3shy5100000 Accumulative data from epidemiological studies revealed
that NPC as a multishyfactorial disease might be caused by EpsteinshyBarr virus (EBV) infection genetic and
environmental factors
It is possible that part of susceptibility to NPC may be explained by variations in genes encoding immunoregulatory
molecules such as cytokines There is increasing evidence that genetic polymorphisms in interleukineshy10 are
important in determining individual susceptibility to NPC However despite the importance of the ILshy10 in NPC
pathogenesis the literature concerning the role of the ILshy10 polymorphism in relation to NPC is small On these
grounds the present study was designed to evaluate the importance of the functional pormoter polymorphisms of
ILshy10 (1082 GA and ndash592 AC) a key immunoregulatoryshyrelated gene in the development and disease onset of
NPC Polymorphisms of sites within the promoter region of ILshy10 gene were analyzed using polymerase chain
reactionshyrestriction fragment length polymorphism (PCRshyRFLP) technique on genomic DNA isolated from
peripheral lymphocytes
The results of the present study obtained from a large sample indicate that young patients from North Africa with
the shy1082 GG genotype (high ILshy10 production) in North Africa had 2shyfold increased risk of NPC (P=00217
OR=258) This difference in ILshy10 polymorphism association with different ages at onset suggests that the younger
and older onset patients are genetically different and may involve different mechanisms
Keywords Nasopharyngeal Carcinoma Cytokine ILshy10 Genetic polymorphism PCRshyRFLP Corresponding
author khalidmoumgmailcom
afbix09bioinformaticsorg 12
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
4
Designing of Vector and Vector map based on genome of Emiliania huxleyi phage
Neha Ojha1 Amit Kumar Singh2 Varsha Gupta3 Santosh Kumar3 Jitendra Naryan4
1Annie Besant College of Engineering amp Management Lucknow INDIA 2Amity University Uttar Pradesh Lucknow Campus India 3BCS Inshysilico Biology Lucknow India 4Departments of Bioinformatics Amity University Uttar Pradesh Noida India
Emiliania huxleyi virus (EHUX) a Coccolithovirus is a giant doubleshystranded DNA virus that infects Emiliania huxleyi a species of coccolithophore Its genome is 407 kbp long with a G+C content of 411 and contains 472 predicted coding sequences It attacks Emiliania huxleyi a singleshycelled phytoplankton which produces a group of chemical compounds like alkenones that are very resistant to decomposition Alkenones are used by earth scientists as a clue to past sea surface temperatures EHUX is largest known marine virus and after its genome sequencing ceramide a cell death controlling factor is discovered in it So EHUX as a vector can be used in different biotechnology process We have identified three restriction sites for commercial restriction enzymes in EHUX with distinct Open Reading Frames (ORFs) for their proper functioning as a vector by using SimVector 42 Finally we have designed vector map for EHUX to be used as a commercial vector for Emiliania huxleyi
afbix09bioinformaticsorg 13
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
5
Computational Evaluation of Some Malaria Drug Targets
Chinwe Ekenna1 Segun Fatumo1 Ezekiel Adebiyi1 and Rainer Koumlnig 2
1 Computer and Information Sciences Department Covenant University Ota Nigeria2 Bioinformatics and Functional Genomics Institute of Pharmacy and Molecular Biotechnology
University of Heidelberg Germany
The most severe form of malaria a disease that affects over 300 million people annually is
caused by the singleshycelled parasite Plasmodium falciparum It is most prominent in Africa and
has led to the death of millions both children and adult alike Although there are already existing
antishymalarial drugs but the development of resistance by the parasite against existing drugs has
necessitated the importance of identifying new drug targets In a recent publication [Fatumo et
al2008] 22 potential drug targets based on an automated metabolic pathway database called
PlasmoCyc [Karp et al 2005 ] were predicted However in a more recent publication by
[Ginsburg 2008] shy a critical evaluation of the comparison of a manual reconstruction database
(Malaria Parasite Metabolic Pathways) against pathways generated automatically like
PlasmoCyc MetaSHARK and KEGG (Kyoto Encyclopedia for Genes and Genomes) was done
The study shows that the automatically generated pathwaysdatabases need an expert manual
verification Consequently in this work we evaluated the drug targets predicted by Fatumo et
al (2008) via one of the automatically generated databases ndash PlasmoCyc We also built the
protein structures and identified the binding sites for the refined list of the drug targets
afbix09bioinformaticsorg 14
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
6 Abstract truncated
FUNCTIONAL ANNOTATION OF PROTEINS WITH UNSPECIFIED ROLE IN THE
HUMAN YshyCHROMOSOME
Lydia I Charles MSc Bio Informatics Bharathiar University Coimbatore
lydiajothigmailcom
Various genes across the human genome are found to be functionally related or
dependent Functional annotation of a few genes of the human Yshychromosome coding for
hypothetical proteins and those with unknown role can help us better understand the structure
and role of human genes thereby understanding sexshylinked male chromosome This could also
provide us new strategies to combat human diseases Of the307 genes of the human Y
chromosomes those coding for hypothetical proteins were short listed using bioinformatics
tools while function of proteins coded by these genes were predicted by manual annotation to
assign the most probable function This prediction was done using the tools JAFA CPH
PSORT GNF SymAtlas SMART and other comparative genomics approaches The confidence
score of the candidates were made based on similar results that were obtained from different
number of tools
The study can also be extended to the current build of the human genome and provide clue to the
various diseases linked to the human Y chromosome Out of the twenty five genes for which
functions were predicted three genes have their functions predicted with 90 percent accuracy
These can lead to a wet laboratory analysis where the predicted function for these three genes
can be verified
afbix09bioinformaticsorg 15
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
7
Modeling the Malaria ParasiteshyMosquito Midgut Cell Interactions
1 Oluwagbemi Olugbenga 1Ezekiel Adebiyi 2Seydou Doumbia
1Department of Computer and Information Sciences (Bioinformatics Unit)College of Science and Technology Covenant University
2Malaria Research and Training Centre (MRTC)University of Bamako Mali
Corresponding author ltOluwagbemi Olugbengagt
Background
Many inshyvitro and inshyvivo experiments had been performed to elucidate the interaction between mosquito and the malaria parasites (Baton et al In Programmed Cell Death in Protozoa Edited by Martin P Landes Bioscience Springer 2007 Garver et al In Insect Immunology Edited by Nancy Beckage Elsevier 2007 Osta et al Journal of Experimental Biology 207 2551shy2563 2004) and findings have shown that in and at the wall of the midshygut (henceforth inat the midshygut) of the mosquitoes a number of the malaria parasites at this crucial life cycle died while a number of them survive and move to the next stage of their life cycle that enable them to infect the human (the vertebrate host) with the malaria disease
Methodology
In this work we model using Agent Based Modeling (henceforth ABM) (Mansury et al Journal of theor Biol 219 343shy370 2002) how factors in inat the midshygut of the mosquito can be enhanced to enable the mosquito immune system destroy all the malaria parasites (the mosquito plays host to) at this crucial stage of their life cycle The tools used are the Java Programming language to simulate the dynamics of the interactions of the malaria parasites inat the midshygut cells of the mosquito and the use of an agentshybased modeling programmable language to model the corresponding interactions under different scenarios by employing highshycontent data
Results
The result of this work shows the simulation output of the Java programming implementations and the agentshybased programmable language This will be useful for the development of a novel chemotherapeutic strategy for transmission blocking of the malaria parasites inat the midshygut of the mosquito
afbix09bioinformaticsorg 16
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
8
Applied bioinformatics to optimize CGH microarray studies of Plasmodium falciparum genome variation
Plasmodium falciparum is the causative agent of the most severe and fatal form of human malaria Studying this organisms genome variation is an important step to understanding how it has successfully evaded efforts to eradicate malaria and how we can better combat it Comparative genomic hybridization (CGH) microarrays are one way to study entire parasite genomes in single experiments This technology effectively identifies large structural variation such as segmental amplifications and deletions but also can recognize more subtle variations such as SNPs and indels Not all SNPs and indels can be effectively assayed through hybridizationshybased approaches however it is possible to optimize the microarrayrsquos ability to detect SNPs through careful analysis
This presentation will outline one method to analyze publicly available sequence information in the form of trace reads and incomplete genome assemblies relying on basic bioinformatic tools such as formatdb blastall and bioperl scripts This information is crossshyreferenced with microarray data and applied towards SNP detection optimization Potential application of this analyzed data to in silico CGH approaches is also mentioned briefly The findings are currently being applied to design a unified microarray platform capable of effective SNP genotyping in addition to CGH capabilities
afbix09bioinformaticsorg 17
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
9 Abstract truncated
AfriPFdb The African Plasmodium falciparum database
1 Ewejobi Ilowast 1 Adebiyi E + 1Ekenna C+ 1Emebo O 2Rebai A 34Koenig R 34 Brors B 5Doumbia S 1Oyelade J 1Fatumo S 8Dike I 36Eils R and 7Lanzer M
IntroductionPresently the popular database that houses the Plasmodium falciparum (Pf) that causes mostly malaria that kills 15 to 3 million people annually is the PlasmoDB (wwwplasmodborg) Africa has suffered and is still suffering from the adverse socioshyeconomic effects of malaria caused mostly by Plasmodium falciparum The popular treatment to malaria is chloroquine which has become largely in effective as the parasite has grown resistance to it Therefore there is a huge need to discover and validate new drug or vaccine targets to enable the development of new treatments for malaria (Bulashevska S et al 2007) Genomics has the promise of ushering new generation of drugs and possibly vaccines and inshysilico analysis has recently been a useful tool in helping life science to speedshyup drug and vaccine discovery pipeline (Bulashevska S et al 2007 Fatumo S et al 2008) The publicly accessible database afriPFdb is to play a similar role to PlasmoDB just like KEGG Kyoto Encyclopedia of Genes and Genomes (wwwgenomejpkegg) developed using inshysilico analysis did to BioCyc (wwwbiocycorg) developed mostly with experimentally curated data We hope that the experimental results that will be obtained thanks to our data will drive work in malaria research and quicken the discovery pipeline of drugs and vaccines
As regards Plasmodium faciparum our database is designed to provide services with respect to its genomics enzymes biological metabolic pathways Furthermore we provide information (such as name sequence and 3D Structure) as regard important and current antimalaria lead compounds and will in the very near future provides potent structures docking results The added value services we provided are certainly in the bottom three points namely networks lead compounds and docking For networks we split the presentation into metabolic networks (from BioCyc) and genetic regulatory networks (for now as obtained from transcriptomics (Bulashevska S et al 2007) Furthermore we also provide another added value service under genomics where we provide a complete distribution of the Protein Data Bank (PDB) (wwwpdborg) 3D structures on all the chromosomes (Adebiyi EF 2007) Where a protein does not have a PDB Structure we provided an inshysilico 3D structure using MODELLER (Andrej Sali et al 1993) We plan soon also provide 3D structures for tRNA protein using our results from (Adebiyi EF 2007)
Apart from the above added values we strive also to present vital information as simple as possible with an inherent easy to find presentation
Key words Malaria Plasmodium falciparum Database Drugs and Vaccines
corresponding email aitee4real2000yahoocom second joint author afbix09bioinformaticsorg 18
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
10
FAS shy 844 TC polymorphism and the risk of Nasopharyngeal Carcinoma in North Africa
countries
Naji F19 Laantri N1 Moumad K1 Jalbout M 2 Corbex M2 Azeddoug H 9 Benider A3 Ben
Ayed F4 Chouchane L5 Bouaouina N6 Boualga K7 Cheacuterifh8 Khyatti M1
1shy Institut Pasteur du Maroc Casablancandash Morocco2shy International Agency for Research on Cancer Genetic Epidemiology unit Lyon ndash France3shy Centre doncologie Ibn Rochd Morocco4shyAssociation tunisienne de Lutte
contre le cancer Tunis ndash Tunisia5shyLaboratoire dImmunoshyoncologie moleacuteculaire Medicine Faculty of Monastir Tunisia6shyService de Radiotheacuterapie Oncologie du CHU Farhat Hached Sousse ndash Tunisia 7shyCentre anti cancer de
Blida shy Service de Radiotheacuterapie Oncologique shy BLIDA Algeria8shyService depideacutemiologie CHU de setif Algeria9shyFaculteacute des sciences Ain Chok Casablanca Maroc
Objective Singleshynucleotide polymorphism of the FASL _844TC gene may alter
transcriptional activity of this gene Recent evidence suggests an association of this
polymorphism with an increased risk of Nasopharyngeal Carcinoma (NPC) so we explored this
relationship
Methods Genotypes of 441 patients with NPC and 432 healthy control subjects from North
Africa countries Tunisia Algeria and Morocco were determined using polymerase chain
reaction based restriction fragment length polymorphism (PCRshyRFLP)
Results No Associations with cancer risk were estimated We observed a no significant
difference in distribution of the genotype CC and TC between cases and controls the OR was
respectively 171CI (062shy465) 073CI (053shy1) In the distribution by age we found a plt005
in subjects whose age exceeds 30 years hold with TC genotype but its not statistically significant
OR=061 In male we found a p=003 with an OR=066 the difference is significant between
cases and controls with TC genotype but this is not statistically significant
Conclusion FAS _844 TC polymorphism may not be associated with an increased risk of
nasopharyngeal carcinoma in Maghrebian population
Key Words NPC FAS L PCRshyRFLP
afbix09bioinformaticsorg 19
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
11
Plasmodium falciparum Chloroquine Resistance (Pfcrt) Mechanisms An IntrashyErythrocytic Developmental Stage
Marion Adebiyi1 Yah Clarence2
1Department of Computer and Information Sciences Covenant University Ota Nigeriaolumarionhotmailcom
2Department of Biological Sciences Covenant University Ota Nigeriayahclargmailcom
Correspondence Corresponding Author olumarionhotmailcomAbstract
Chloroquine (CQ) cheap and long history antimalaria has failed in the treatment of malariaThis work therefore sought to expose the resistance mechanism(s) of Plasmodium falciparum (Pf) at the Intrashyerythrocytic developmental stage By considering the activity involved at this stage and reviewing polymorphism within the food vacuolar membrane protein Pfcrt chloroquine resistance polymorphism at that level will be determined The biochemical network of Pf and the gene expression data were downloaded from the genebank NCBI EMBL plasmoDB and geneDB The data were performed as confirmed by the Blast and ClustalX programme using NCBI blast against the biochemical network of Pf and mapped onto the enzymatic reaction nodes of the metabolic network The result shows that there was a variation in the targeted metabolic pathways of the erythrocytic cycle likewise the genes that codes for the enzymes of the metabolic pathways These methods give a better understanding of how resistance process occurs as well as the important mechanisms that Pf deplores for resisting these antishymalaria drugs The knowledge therefore facilitates the rationale to design new effective and well tolerated antimalaria drugs
Key Words ChloroquineshyPfshyresistanceshymechanismshyErythrocytic stage
afbix09bioinformaticsorg 20
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
12
DESIGNING OF DRUG FOR REMOVAL OF METHYLATION EFFECT FROM TCF21 GENE IN LUNG CANCER
Shishir Kumar Gupta Archana Singh
Department of Bioinformatics CSJM University Kanpur India
eshymail shishirbioinfogmailcom
Tcf21 is one of the tumor suppressor gene associated with lung cancer It is a specific gene because it can alter the normal epithelial cells into amoeboid primordial mesenchymal cells This gene is inactivated due to CpG hypermethylation of promoter region Removal of methylation effect is one of the strategies to win over metastatic cancer This research explores two parallel approaches for removal of methylation effect ie proteinshyligand docking and DNAshyligand docking MeCPs are the proteins that bind to methylated transcription factor binding sites and block the recruitment of RNA polymerase MeCPs can be inhibited by FKshy228 Further the targeted methylated DNA is docked with the drugs that may remove the methylation by converting the 5shymethyl cytosine into cytosine Decitabine is one of the DNA binding drugs that may perform this task appreciably Wet lab experiments have also been proven the effectiveness of decitabine In other cancers these inshysilico approaches can be used to identify possible potential drugs that would be able for human welfare
KEY WORDS Computational Drug Discovery DNA methylation Tcf21 gene Lung cancer
afbix09bioinformaticsorg 21
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
13
Experimental study for PCRshybased detection of Malaria infection at the Liver stage
Victor Osamor1 Ezekiel Adebiyi1 Adedayo Oduola2 Conrad Omonhinmin3 Ijeoma Dike3 Samson Awolola2 and Seydou Doumbia4
1Department of Computer and Information Sciences Covenant University Ota Nigeria
2 Public Health Division Nigerian Institute of Medical Research Yaba Lagos Nigeria
3Department of Biological Sciences Covenant University Ota Nigeria
4Malaria Research Training Center (MRTC) University of Bamako Mali
Corresponding Author vcosamoryahoocom
Malaria transmission involves three different developmental stages namely Human liver stage
human blood stages and mosquito stage Symptoms of malaria are expressed at the human blood
stage Generally there is no doubt that there are some available drugs that can cure the disease
but the problem in most cases is poor or late diagnosis resulting to complications and even death
However most studies do not consider the genes that code for proteins expressed at the nonshy
infective liver stage of the parasite In vivo experimental access to liver organ for liver stages of
human malaria parasites is practically prohibited and therefore mouse model malaria parasites P
berghei have been used for in vivo studies The rationale of this study is to develop a diagnostic
technique based on regular Polymerase Chain Reaction (PCR) for detecting malaria at the liver
stage so that timely intervention can be made to alleviate the problem of the disease
Diagnostics on biochip has been making inshyroad into modern healthcare at a faster pedestal
especially PointshyofshyCare comparatively to the labshybased diagnostics The ultimate breakthrough
may be to translate the result of a livershybased malaria diagnostics into a biochip comparable to
diagnostic chip used for detecting other diseases like HIV
Keywords Diagnosis Nonshyinfective liver stage Pberghei PCR Biochip
afbix09bioinformaticsorg 22
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
14
Polphasic approach for phylogenetic analysis and classification of a bacterial strain
Rishika Bisariya
Bioinformatics VIT University Vellore Tamil Nadu India
Rishikabisariyagmailcom
A novel bacterial strain was isolated from a soil sample taken from the dumping grounds in the
parade ground South Delhi The strain was identified as a member of genus Herminiimonas by
polyphasic approach The 16S rRNA was amplified by the polymerase chain reaction using the
universal bacterial primers For phylogenetic analysis closely related reference strains alongwith
one outgroup were chosen from BLAST and RIBOSOMAL DATABASE PROJECT results For
the construction of the phylogenetic trees the software packages TREECON and CLUSTALX
version 18 were used Unrooted phylogenetic trees were constructed using the neighbourshyjoining
and maximum parsimony method and evaluated by bootstrap resampling (100 replications)
The nucleotide sequence was then translated into amino acid sequence by using the proteomics
tool TRANSLATE
Keywords Polyphasic approach phylogenetic analysis bootstrap resampling
afbix09bioinformaticsorg 23
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
15
Computational Identification of functional related gene in Malaria parasites
Jelili Oyelade1 Ezekiel Adebiyi1 Benedict Brors2 and Roland Eils2
1Department of Computer and Information SciencesCovenant University
PMB 1023 Ota Nigeria
2Theoretical BioinformaticsGerman Cancer Research Center(DKFZ)
69120 HeidelbergGermany
Plasmodium falciparum the most severe form of malaria causes 15shy27 million deaths annually The most commonly used computational method for analyzing microarray gene expression data is clustering This has been used by LeRoch et al 2003 and Bozdech et al 2003 The results obtained have been used to classify genes into functional modules namely metabolisms and pathways The results obtained have left us with many putative functional genes Experimental results in the Hagai database (accessible also from wwwplasmodborg) provides limited information about this Recent work like Gangman Yi Sing ndash Hoi Sze and Michael R Thon 2007 and Young et al 2008 introduce the use of Gene Ontology but the results are also still very limited in their application to Plasmodium falciparum (Oyelade et al 2008)
In this work for the first time with improved precision we identify functional modules (ie groups of functional related genes and protein ) using genomicsshytranscription factors and high throughput large scale data such as transcriptomic proteomic and metabolic data
Key words Plasmodium falciparum Gene Ontology Transcription factors Genomics
afbix09bioinformaticsorg 24
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
16
In silico studies of multi drug resistance [MDR] genetic markers of Plasmodium speciesYah Clarence Suh1 and Segun Fatumo2
1 Department of Biological Sciences Covenant University Ota Nigeria2 Department of Computer and Information sciences Covenant University Ota Nigeria
Rationale Malaria has been and stills the cause of much morbidity and mortality throughout the tropics and subtropics Epidemics have devastated large populations and posed a serious barrier to economic growth in developing countries The major obstacle however in malaria drug resistance is the prevention and treatment of malaria infections worldwide Therefore antishymalarial drug development needs to continue so that novel and highly effective antishymalarials can be plugged into recommended strategy of malaria therapies The sequencing of various MDR of Plasmodium should contribute substantially to our understanding of the multi drug resistance that permit the identification of novel therapeutic strategies and new malaria parasites targets for drug and vaccine development
Materials and Methods The current research engaged the use of inshysilico approach to seek new chemotherapeutic strategies in analyzing and proffering solutions to malaria therapies Four Plasmodium species two from rodents [Plasmodium chabaudi and Plasmodium yoelii] and two from human [Plasmodium vivax and Plasmodium falciparum] multi drug resistance genes were compared using the Atermis comparative tool (ACT) The phylogenetic relationships and species identification of the MDR genes of the parasites were down loaded from Genebank NCBI EMBL PlasmoDB and GeneDB and performed as confirmed by the BLAST and ClustalX programs
Results and conclusion The results showed a slight variation in the updown stream alignment within the genes likewise their phylogenetic relationships This therefore showed that same resistance genes within a population of the same site may vary within the same drug Through these efforts our goal is to better understand how drug resistance occurs and to develop new approaches to combat this global problem This knowledge therefore facilitated the rationale to design new effective and wellshytolerated antishymalarial drugs
afbix09bioinformaticsorg 25
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Participating Hubs
East Africa Hub ILRI Nairobi
South Africa SANBI Cape Town
West Africa Covenant University Nigeria
Morocco SMBI
USA University of Notre Dame
List of Confirmed Participants
Name Affiliation
Abhishek Tripathi University of Notre Dame
Abiodun Adebayo Covenant University
Adele Kruger SANBI
Adesola Ajayi Covenant University
Alecia Naidu SANBI
Allan Kamau SANBI
Amit Kumar India
Andrew Rider University of Notre Dame
Angela Eni Covenant University
Angela Makolo IITA
afbix09bioinformaticsorg 26
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Asako Tan University of Notre Dame
Becky Miller University of Notre Dame
Bisibori Bett Agricultural Research Institute
Bonaventure O Aman -
Changde Cheng University of Notre Dame
Chinwe Ekenna Covenant University
Dedan Githae University of Manchester
Dr Ashley Pretorius SANBI
Dr Gordon Harkins SANBI
Dr James Patterson SANBI
Dr Mandeep Kaur SANBI
Dr Mike Ferdig University of Notre Dame
Dr Scott Emrich University of Notre Dame
Dr Stuart Meier SANBI
Dr Sundararajan
Seshadri SANBI
Dr Sunil Sagar SANBI
Edwin Murungi SANBI
Edwin Siu University of Notre Dame
Ekow Oppon SANBI
Esther Kanduma -
Eunice Machuka Kenyatta UniversityKARITRCICIPE
Eva Kalemera
Aluvaala KEMRIITROMIDUniversity of Nairobi
Ezekiel Adebiyi Covenant University
Feziwe Mpondo SANBI
afbix09bioinformaticsorg 27
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Frederick Kamanu
Kinyua SANBI
Gbenga Oluwagbemi Covenant University
Geoffrey Siwo University of Notre Dame
George Tinega KARITRCUniversity of Nairobi
Huxley Makonde JKUAT
Irene Kasumba University of Notre Dame
Irene Njoki Kiiru Kenyatta University
Isaac Njaci University of Manchester
Itunu Ewejobi Covenant University
James Atika Kenyatta University
Jelili Oyelade Covenant University
Jenica Abdrudan University of Notre Dame
Jessica Hewitt University of Notre Dame
John Maduka UNN
John Smith University of London
John Tan University of Notre Dame
Joseph Njoroge Egerton University
Kamau Peter Kuria University of Jomo
Kiboi Muthui -
Kuda Kupara ICIPE
Kunle Ibikunle Covenant University
Lydia Charles India
Magbubah Essack SANBI
Maria Unger University of Notre Dame
Mario Jonas SANBI
afbix09bioinformaticsorg 28
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Marion Adebiyi Covenant University
Mark Wacker University of Notre Dame
Mark Wamalwa SANBI
Mary Ngendo Kenyatta University
Monique Maqungo SANBI
Mulongo Moses ILRI
Musa Nur Gabere SANBI
Mushal Allam SANBI
Olawande Daramola Covenant University
Olubanke Ogunlana Covenant University
Onyeka Emebo Covenant University
Pamela Tamez University of Notre Dame
Paul Ogongo Institute of Primate Research
Pauline Mcloone Covenant University
Pierre Mulamba
Mutombo SANBI
Ryne Gorsuch University of Notre Dame
Saleem Adam SANBI
Samson Machohi Tea Research Foundation of Kenya
Samuel Kojo Kwofie SANBI
Sarah Mwangi SANBI
Sean McLaughlin SANBI
Sebastian Fernandez University of Notre Dame
Sebastian Schmeier SANBI
Segun Fatumo Covenant University
Serah Waithira Kahiu JKUATILRI
afbix09bioinformaticsorg 29
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
Siah Habi Biomed Institute
Sonal Patel ILRI
Sumir Panji SANBI
Susanta Behura University of Notre Dame
Timothy Kuria
Kamanu SANBI
Tracey Kibler SANBI
Ulf Schaefer SANBI
Unizik Uzochukwu -
Upeka Samarakoon University of Notre Dame
Victor Osamor Covenant University
Watchman Kwesi National University of Ghana
FAOUZI Abdellah Pasteur Institut
HAMDI Salsabil Pasteur Institut
NAJI fadwa Pasteur Institut
MOUMAD Khalid Pasteur Institut
LAANTRI Nadia Pasteur Institut
BOUHALI ZRIOUIL Sanaacirc
Pasteur Institut
BOUNACEUR Safaa Pasteur Institut
BENRAHMA Houda Pasteur Institut
CHARIF Majida Pasteur Institut
ELOUALID Abdelmajid Pasteur Institut
OUATOU Sanaa Pasteur Institut
ANGA Latifa Pasteur Institut
BOUDABBOUCH Najma
Pasteur Institut
afbix09bioinformaticsorg 30
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31
BAKHOUCH Khadija Pasteur Institut
FARIAT Nadia Pasteur Institut
Fouzia Radouani Pasteur Institut
afbix09bioinformaticsorg 31