Bioinformatics Today Prof. A.S. Kolaskar Advisor National Knowledge Commission Data Escalation Full genome sequences Prokaryotes~350 Eukaryotes~125 Viruses~2,000 Proteomes~50 Microarray data ~80 3-D Structures~2,500 Metabolomes~10 ~50 TB Doubles every Twelve Months Data Explosion in Biology Combinatorial Chemistry Human Genome The Internet Mergers and Acquisitions Growth in Clinical Trials External Research Partnerships Medical Data Growth Metabolic Pathways Proteins Pharmacogenomics ESTs HTS SNPs Petabytes of Data Biodiversity Information System Species2000 Database Species 2000 & Integrated Taxonomic Information System (IT IS) have assembled 37 taxonomic databases - 880,000 species Also available on a free CD-ROM. Real time access to the Species 2000 array of 26 online taxonomic databases - 450,000 species Indian Bioresource Information Network (IBIN) Jeevsampada Sasyasampada Matsyasampada Plants of India Microbial Species Information System Forest Resource Information System B a c k t o I B I N J e v S a m p a d a B a c k t o I B I N J e e v S a m p a d a H O M E H O M E V e r n a c u l a r S e a r c h V e r n a c u l a r S e a r c h S c i e n t i f i c S e a r c h S c i e n t i f i c S e a r c h M a j o r C a t e g o r y M a j o r C a t e g o r y Matsya Sampada Fresh water Fin Fishes and Shell Fishes: Data on 1849 species include literature, distribution, common name, coloration, images, synonyms, remarks, references, morphology, economic importance, size etc. and the datasets are collated at National Bureau of Fish Genetic Resources, Lucknow. B a c k t o I B I N J e v S a m p a d a B a c k t o I B I N J e e v S a m p a d a H O M E H O M E V e r n a c u l a r S e a r c h V e r n a c u l a r S e a r c h S c i e n t i f i c S e a r c h S c i e n t i f i c S e a r c h M a j o r C a t e g o r y M a j o r C a t e g o r y Matsya Sampada Fresh water Fin Fishes and Shell Fishes: Data on 1849 species include literature, distribution, common name, coloration, images, synonyms, remarks, references, morphology, economic importance, size etc. and the datasets are collated at National Bureau of Fish Genetic Resources, Lucknow. Searching Matsyasampada Vernacular Search Scientific Search Major Category Chosen Vernacular Search Search a vernacular name Select Language Maharashtra Drop down menu: Marathi names of all the fish Chosen - Shingat Information Available Classification Common names Synonym Images Distribution Morphology References Taxonomic Information Taxonomic Heirarchy SuperOrderOstariophysi OrderSiluriformes ClassActinopterygii SubClassNeopterygii OrderSiluriformes FamilyBagridae SubFamily- GenusMystus Speciesmontanus Shingat You are looking for 'Mystus montanus Common Names English Wynaad Mystus Kerala Vari kallencoori Maharashtra Shingat Morphology (Mystus Montanus) Morphology Body elongate and compressed, its depth about 5 times in standard length. Head depressed; occipital process narrow, about 4 times as long as broad, reaching to basal bone of dorsal fin; median longitudinal groove on head not extending to occipital process Color In life, silvery above with a tinge of yellow along abdomen; a silvery line along the flank terminating in a dark spot at base of caudal fin, one or two light bands along the side above lateral line; a bluish spot on shoulder. Fins tinged with green Finformulae D 7; A iii 9; PI 6; Vi 5 Fishery This species which attains a length of 15 cm, is of minor interest to fisheries Synonyms ReferencesYear Bagrus montanus Jerdon1849 Macrones montanus (Jerdon)1849 Macrones montanus dibrugarensis Chaudhuri1913 Mystus montanus (Jerdon)1849 Mystus vittatus dibrugarensis (Chaudhuri)1913 Synonyms References Economic Importance - AuthorTalwar and Jhingran Book Inland Fisheries vol. 2 Page noPg.567 Images Distribution Shingta You are looking for 'Mystus cavasius Common Names Andhra Pradesh Muti-jhella Nahara-jella Thella jella Assam Barsingarah Singarah Bihar Palwa Tengra English Gangetic Mystus Karnataka Nai-kirle Maharashtra Katima Khirkirya Shingta Orissa Guntea Kontia Tengra Punjab Kinger Tamil Nadu Cutta Nai-kelunti Solai-kelunti Vazhappu Vella- kellette Uttar Pradesh Kala-tenguah Kavasi Shingti Singhara Tenguah West Bengal Kabasi-tengra Tengra Images Distribution Explore & Have Fun/ Understanding Biology using Metabolic Pathways Database Development of Metabolic Pathways and related tools Some of the major metabolic pathway databases are: KEGG Boehringer Mannheim WIT Ginsburg Malaria Database BioCyc PUMP-E KEGG KEGG LIMITATIONS Pathways are composites of pathways found in many organism (Unclear what sub- pathways occur in specific organism) Static visualization No detailed information about enzymes (inhibitors, subunits) No literature citations, no comments Boehringer Mannheim LIMITATIONS LIMITATIONS No query system Overloaded with information WIT Better representation but still readability needs to be improved PUMP-E: Salient Features Dynamic Representation of pathways Dynamically building the organism-specific pathways from genomic data Development of Software for Automated data updating (Perl scripts) Reformatting and organization of relevant information from different databases Drawing pathways diagrams Comparison of pathways Visualization of ligands, enzymes Prediction of enzyme-substrate interactions URL- PUMP-E Comparison of Metabolic Pathways Case studies Malarial parasite, Mosquito & Human Metabolome of Plasmodium falciparum Metabolic pathways of Plasmodium falciparum are known to be stage-specific. Asexual blood-stage parasites depend on glycolysis and conversion of pyruvate to lactate to derive energy. MS-MS studies carried out by Florens et.al(2002), revealed that gametocyte and sporozoite stages of the malarial parasite contain peptides of enzymes known to be involved in mitochondrial TCA cycle and oxidative phosphorylation. In Plasmodium falciparum EnzymeChromosome HsAgPf Citrate synthase123L10 Aconitase223R13 Isocitrate dehydrogenase22L13 Alpha-keto glutarate dehydrogenase (E1)72R8 Alpha-keto glutarate dehydrogenase (E2)143L13 Alpha-keto glutarate dehydrogenase (E3)73L12 Succinyl CoA ligase132L14 Succinate dehydrogenase (Cyt b560) (SDHA)13L- Succinate dehydrogenase ( Cyt b small) (SDHB)11X- Succinate dehydrogenase (flavoprotein) (SDHC)53L10 Succinate dehydrogenase (iron-sulfur) (SDHD)12L12 Fumarase1 *2R*9** Malate dehydrogenase73R6 Chromosomal locations of TCA cycle-enzymes * Class II non-iron dependent Fumarase ** Class I iron-dependent Fumarase Comparison of TCA cycle enzymes of Plasmodium falciparum-Anopheles gambiae-Homo sapiens Plasmodium contains only two SDH subunits in contrast to 4 SDH subunits in human & anopheles Fumarase class I is present in Plasmodium whereas Fumarase class II is present in human & anopheles Sequnece identity Enzyme TCA cycle: Comparison of proteome of host,vector and parasite revealed TCA cycle-specific enzymes of Homo sapiens and Anopheles gambiae have high degree of sequence identity. Aconitase and Fumarase enzymes of Plasmodium falciparum show very less similarity with their human and mosquito counterparts. An iron regulatory protein that has a C terminal domain similar to Aconitase is present in Plasmodium and it likely carries out the function of Aconitase enzyme. Fumarase (Class I) an iron-dependent enzyme is present in Plasmodium whereas Fumarase (Class II), an non-iron dependent enzyme is present in human and mosquito. Succinate dehydrogenase in Plasmodium contains only two subunits in contrast to its human & mosquito counterparts, which have four subunits. Homology models of Isocitrate dehydrogenase High sequence identity Structural similarities Comparative Metabolomics - Bacterial Identification Organism namePhylumGenome Size (Mbp) Total number of pathways Agrobacterium tumefaciens Bacillus anthracis Bacillus subtilis Caulobacter crescentus Chlamydia trachomatis Escherichia coli Francisella tularensis Haemophilus influenzae Helicobacter pylori Mycoplasma pneumoniae Mycobacterium tuberculosis CDC1551 Mycobacterium tuberculosis H37Rv Shigella flexneri Treponema pallidum Vibrio cholerae Proteobacteria Firmicutes Firmicutes Proteobacteria Chlamydiae Proteobacteria Firmicutes Actinobacteria Proteobacteria Spirochaetes Proteobacteria Total number of pathways in bacteria under study as per BioCyc 9.1 Pathways identical in all 15 bacteria under study w.r.t E.coli Aspartate biosynthesis and degradation Gluconeogenesis Glycolysis Pentose-Phosphate-Cycle Purine nucleotides de novo biosynthesis I De novo biosynthesis of pyrimidine ribonucleotides Salvage pathway of adenine, hypoxanthine and their nucleotides Salvage pathways of pyrimidine ribonucleotides Importance of identical pathways Aspartate is a constituent of proteins and participates in several biosyntheses pathways such as de novo biosynthesis of pyrimidine ribonucleotide, purine nucleotide de novo biosynthesis I, NAD biosynthesis I, pantothenate biosynthesis. Approximately 27 percent of the cell's nitrogen flows through aspartate. Gluconeogenesis is a process by which glucose is generated. Glucose is an important source of energy. Glycolysis is one of the most important metabolic processes. It is known to be present in all types of organisms. Pentose-Phosphate-Cycle is one of the essential pathways of central metabolism. This pathway is an important source of NADPH. Bases and nucleosides that are formed during degradation of RNA and DNA can be recovered through salvage pathways, which can be reconverted into nucleotides. All the above pathways are essential for survival of an organism Pathways similar but not identical in all 15 bacteria under study w.r.t E.coli Glycine biosynthesis I TCA FormylTHF biosynthesis I Superpathway of biosynthesis of aspartate and asparagine Colanic acid building blocks biosynthesis Organism nameIdentical Pathways Similar Pathways Pathways Absent Additional Pathways Agrobacterium tumefaciens (207) Bacillus anthracis (254) Bacillus subtilis (145) Caulobacter crescentus (176) Chlamydia trachomatis (61) Francisella tularensis (184) Haemophilus influenzae (127) Helicobacter pylori (123) Mycoplasma pneumoniae (48) Mycobacterium tuberculosis CDC1551 (186) Mycobacterium tuberculosis H37Rv (184) Shigella flexneri (179) Treponema pallidum (56) Vibrio cholerae (207) Comparison of pathways with respect to E.coli Hamming Distance Calculations Identical Pathways (0): Start and end products are identical; intermediate steps are same. Similar Pathways (1): Start and end products are identical; intermediate steps are different Pathways are absent (2): Start or end products are not same Metabolic pathway path profile Columns represents n number of pathways and rows represent 15 bacteria under study. Each column corresponds to a particular type of pathway. 2 denote pathway follows same path, 1 denotes pathway follows different path while 0 denotes absence of pathway. This represents a part of the organism specific metabolic pathway path profile. Metabolic pathway path profile based tree Acknowledgements Shweta Kohli Manjari Ms. Deshpande Sangita Sawant