1 Questionnaire Summary of the main activities of a scientific Organisation of the Slovak Academy of Sciences Period: January 1, 2007 - December 31, 2011 I. Formal information on the assessed Organisation: 1. Legal name and address Ústav molekulárnej biológie Slovenskej akadémie vied (Institute of Molecular Biology, Slovak Academy of Sciences) Dúbravská cesta 21, 845 51 Bratislava 45 Slovakia 2. Executive body of the Organisation and its composition Directoriat name age years in the position director RNDr. Imrich Barák, DrSc. 50 3 deputy director RNDr. Dagmar Homerová, CSc. 59 1 scientific secretary Mgr. Ľuboš Kľučár, PhD. 41 3 3. Head of the Scientific Board RNDr. Ján Kormanec, DrSc.
Transcript
1
Questionnaire
Summary of the main activities of a scientific Organisation
of the Slovak Academy of Sciences
Period: January 1, 2007 - December 31, 2011
I. Formal information on the assessed Organisation:
1. Legal name and address
Ústav molekulárnej biológie Slovenskej akadémie vied
(Institute of Molecular Biology, Slovak Academy of Sciences)
Dúbravská cesta 21, 845 51 Bratislava 45
Slovakia
2. Executive body of the Organisation and its composition
Directoriat name age years in the position
director RNDr. Imrich Barák, DrSc. 50 3
deputy director RNDr. Dagmar Homerová, CSc. 59 1
scientific secretary Mgr. Ľuboš Kľučár, PhD. 41 3
3. Head of the Scientific Board
RNDr. Ján Kormanec, DrSc.
2
4. Basic information about the research personnel
i. Number of employees with a university degree (PhD students excluded)
engaged in research and development and their full time equivalent work
capacity (FTE) in 2007, 2008, 2009, 2010, 2011 and average number during the
assessment period
2007: 56 employees (51.3 FTE)
2008: 61 employees (49.33 FTE)
2009: 60 employees (47.46 FTE)
2010: 57 employees (47.94 FTE)
2011: 59 employees (42.4 FTE)
ii. Organisation units/departments and their FTE employees with the university
Laboratory of Protein Evolution 2.0 1.0 2.0 1.7 3.0 1.9 3.0 2.5 4.0 2.8 2.8 2.0
Research staff2007 average201020092008 2011
5. Basic information on the funding
3
i. Total salary budget1 of the Organisation allocated from the institutional
resources of the Slovak Academy of Sciences (SAS) in 2007, 2008, 2009, 2010,
2011 and average amount for the assessment period
Salary budget 2007 2008 2009 2010 2011 average
total salary budget (milions of EUR) 0.641 0.633 0.677 0.675 0.645 0.654
6. URL of the Organisation’s web site
http://www.imb.savba.sk
II. General information on the research and development activity of
the Organisation:
1. Mission Statement of the Organisation as presented in its Foundation
Charter
1. The research activities of the Institute of Molecular Biology are focused on basic research into the molecular principles of living systems. The molecular biology of prokaryotes and eukaryotes and microbiology are the main focuses of the Institute’s activity. Primary attention is paid to the biological sciences (molecular biology, microbiology, structural biology, genetics, cell biology, neuroscience, and virology), chemical sciences (mainly biochemistry and bioorganic chemistry), biotechnology (environment, industry, medicine, and agriculture), earth and environmental sciences (ecology and biodiversity), bioinformatics, biophysics, and nanotechnology.
2. The Institute offers consultation and expertise that are closely related to its main activities.
3. The Institute implements PhD education in terms of generally valid regulations. 4. The Institute requires that the results of its R&D activities be published in periodical
and non-periodical presses. This is carried out according to regulations laid out by resolutions passed by the Presidium of SAS.
5. The Institute offers the following enterprise activities: - Contractual research in molecular biology, biology, microbiology, and biotechnology - Provision of consultation and expertise in the fields of molecular biology, microbiology, biotechnology, and GMO - Synthesis of specific bio-products and standards for research and development - Organization of specialized seminars, conferences, and educational meetings in molecular biology, microbiology, and biotechnology
2. Summary of R&D activity pursued by the Organisation during the assessed
period, from both national and international aspects and its incorporation in
the European Research Area (recommended 5 pages, max. 10 pages)
1 Objem mzdových prostriedkov bez odvodov do poisťovní so započítaním sumy miezd pracovníkov THS, ktorú
organizácii poskytne ETO Úradu SAV. Rozpočet v Sk prepočítajte na eurá podľa konverzného kurzu
1€ = 30,126. (Podobne aj v ďalších tabuľkách.)
4
Molecular biology is a very dynamic research field, oriented toward understanding the cellular mechanisms of living systems at the molecular level. It greatly influences applications in medicine, pharmacology, the food industry and biotechnology. The Institute of Molecular Biology is a modern and prosperous establishment with a substantial national and international impact. Its many international collaborations with leading institutes from Europe and USA supported by international grant projects, and their results, reflect the high quality of its research teams. The Institute currently has six departments and two independent laboratories. Its main research activities encompass basic research into molecular biology and microbiology. The Institute’s foundational programmes cover research on the regulation of gene expression, functions of proteins, impact of structural changes on protein biological functions. These basic research activities are also directed towards possible applications in medicine (pathogen detection) and biotechnology (antibiotic production, spore coat protein characterization, identification of honeybee proteins antimicrobial properties). Its research activities during the assessed period were in the following areas: 1. cell division and differentiation 2. protein structure-function relationships and protein evolution 3. microbial ecology 4. functional genomics, bioinformatics, and biotechnology 5. molecular cell biology Most of these areas have been studied at the Institute for many years and they have been further adapted for study into new topics of basic science and applied research. Cell Division and Differentiation
Cell division and differentiation are two essential features of life. They allow each cell to reproduce itself or to acquire different biological functions. The main aims of the projects of the Department of Microbial Genetics have been to understand the mechanisms of these processes, along with programmed cell death in Bacillus subtilis (a common model organism whose physiology, biochemistry and genetics have been studied intensively for decades) on the molecular level. One of the most important questions regarding cell division of B. subtilis concerns the mechanism that ensures correct placement of the division septum. For the first time, the Department identified and characterized specific phospholipid domains which form on helical trajectories from pole to pole in the B. subtilis cell membrane. Division inhibitory proteins recognize these helices and control cell division by forming a concentration gradient along the lipid helical track. This gradient is able to define the mid-cell plane with high precision for accurate cell division. Furthermore, formation and/or preservation of these unusual helical lipid domains are connected with the formation of peptidoglycan, the main component of the bacterial cell wall.
To survive hostile conditions, B. subtilis can enter a specific differentiation process, termed sporulation, in which two cells with different programmes of gene expression are formed after asymmetric cell division. SpoIIE is a crucial protein that links asymmetric cell division to activation of the first compartment-specific sigma factor. SpoIIE and its interaction partners were characterized, and the functional domains of SpoIIE were crystallized for structural investigations. Sporulation leads to the formation of a highly resistant spore wrapped with many different Cot proteins. It was shown that they could form self-assembled layers in vitro.
Other projects are devoted to studying programmed cell death and the biological role of a novel SpoIIS toxin-antitoxin system. The tertiary structure of a complex consisting of the cytosolic domain of SpoIISA and the entire SpoIISB at 2.5 Å resolution has been solved. This structure is an important contribution to understanding how the antitoxin binds its toxin and thus neutralizes its activity. Genetic and biochemical experiments and especially this tertiary structure determination have greatly contributed to our understanding of basic bacterial cell processes.
5
The Department is one of the leading groups in the field of bacterial sporulation. It has been internationally recognized by being entrusted to organize four European Spores Conferences (2004–2010). The Department Head, Imrich Barák, was the main organizer for two of these meetings and a member of the organizing committee for all four conferences. He is also one of the Coordinators of the Consortium of Central and Eastern European Structural Biology Groups (2000–present) and a member of the Bacell organization Steering group (2011–present). Bacell is the umbrella organization supporting Bacilli research in Europe.
Soil-dwelling bacteria of the genus Streptomyces undergo an exceptional process of morphological differentiation, which is connected with the production of more than 70% of known antibiotics. The Department of Gene Expression discovered the essential roles of several sigma factors in different developmental stages of Streptomyces and their connections to this stress response. The interconnectedness of the activation of several previously identified promoters which are recognized by nine homologous RNA polymerase sigma factors (SigB, SigF, SigG, SigH, SigI, SigK, SigL, SigM and SigN) was characterized during differentiation and stress in Streptomyces coelicolor. A complex cascade of mutual interactions among these homologues was found to activate promoters during differentiation and under stress, and new regulatory mechanisms of SigB and SigH activation in response to stress and development were found. Specifically, a new multi-domain regulator, OsaC, was discovered, which contains an anti-sigma factor domain which has a role in the feedback regulation of SigB. A specific anti-anti-sigma factor BldG and an anti-sigma factor UshX were found which play roles in the activation of SigH during osmotic stress using a partner-switching mechanism.
This project belongs to one of the most intensively studied topics worldwide, specifically, investigation of the molecular biology of antibiotic-producing organisms. Consequently, this project has attracted wide international collaboration from within the European research area, including partners from the U.K. The Department Head, Jan Kormanec, is an internationally recognized scientist in this field, as reflected by his invitations to international conferences and seminars.
Streptomyces produces several deoxyribonucleases, which have an important function in DNA recycling during the programmed cell death which accompanies cell differentiation. In order to investigate this function, the gene exoSa encoding exodeoxyribonuclease from Streptomyces aureofaciens was cloned and characterized by the Laboratory of Prokaryotic Biology. Its protein product has both exonuclease and 5´-phosphomonoesterase activities, but degrades only linear DNA. Disruption of this gene in both S. aureofaciens and S. coelicolor revealed that it is essential for growth.
Protein Structure-Function Relationships and Protein Evolution
Structural biology contributes to a better understanding of the biological processes in living organisms at the molecular level. Our institute has long history of determining the structure of proteins using diffraction methods. Nearly 60 different macromolecular objects in total have been crystallized and 37 structures determined at the Institute. The Department of Biochemistry and Structural Biology has focused its attention on medically interesting (the human ryanodine receptor 2, hRyR2, and the mitochondrial, ATP-dependent Lon protease), and biotechnologically significant proteins (amylolytic enzymes). Ryanodine receptors are vitally important ion channels, which play a key role in initiating muscle contraction. They are responsible for Ca2+ release from the lumen of the sarcoplasmatic reticulum into the cytoplasm. Bioinformatics and structural studies have been focused on the domain characterization of hRyR2. This analysis showed that the protein is composed of 14 domains. Particular attention was paid to the first three N-terminal domains. The idea that the domains can behave as separate, independent protein units was demonstrated using several techniques. The high amino-acid sequence similarity of hRyR2 to that of rabbit RyR1, whose X-ray structure is known, allowed a reliable homology model of the N-terminal part of hRyR2 to be constructed. This model was consistent with both the bioinformatics analysis and a CD spectroscopy study. This
6
model should allow a clearer insight into the possible influence of mutations on cardiac diseases to be developed.
To better understand how Lon protease recognizes and degrades its substrate, several truncated mutants were prepared and investigated. The results revealed that close cooperation between the N-terminal, ATPase, and the proteolytic domains is important for multimer formation and for all protease functions. In cooperation with the University of York, the crystal structure of the proteolytic domain of human Lon was determined and a mechanism relating the formation of Lon oligomers to the regulation of the proteolytic active site was suggested. It is thought that the movement of a loop in the oligomer interface is associated with a conformational shift in the active site region which converts a proteolytically inactive form to an active one.
The Department has also carried out molecular-genetic and structural characterizations of recombinant α-amylases and glucoamylases from the yeast Saccharomycopsis fibiligera with particular attention on the binding site of a glucoamylase which degrades raw starch.
The Laboratory of Prokaryotic Biology has also carried out structure-function studies. Its most notable result is the structure of xylanase from Erwinia chrysanthemi in complex with aldotetraouronic acid (a product of its enzymatic reaction) at 1.4 Å resolution. This structure provides a better understanding of enzyme specificity, its substrate recognition and its reaction mechanism.
The Laboratory of Protein Evolution has mainly been concerned with questions on the relationships between sequence, structure, function, specificity and evolution of the enzymes from the α-amylase families. These enzymes operate on starch and related α-glucans which are important both as biological energy sources and as subjects of wide industrial application. Interest has also been extended to in silico studies on the so-called starch/glycogen-binding domains. The recent major scientific contributions of this laboratory can be summarized as follows: (i) revealing the remote but still significant sequence homology between the α-amylase family (clan GH-H, containing the GH13, GH70, and GH77 families) and the GH31 family, which share the catalytic nucleophile; (ii) describing the sequentially unique GH77 family amylomaltases from borrelias which share only the invariantly conserved catalytic triad; (iii) elucidating the structural and evolutionary relatedness of CBM20 and CBM48, two families of starch and glycogen binding domains; (iv) documenting the ancestry of cystinuria-related proteins within the α-amylase family GH13 and describing their likely course of evolution; (v) defining the maltase clusters of the GH13 family in Drosophila genomes and proposing their evolutionary history; and (vi) identifying a new group of α-amylase-like homologues in the GH57 family containing putative proteins lacking one or both catalytic residues.
The laboratory is one of the leading research groups in the field of amylolytic enzymes and produces internationally recognized results. Its current activities are based on 20 years of research experience by the Laboratory Head, Stefan Janecek, which have yielded worldwide scientific collaborations and personal contacts. He established and has been the main organizer of a series of international conferences on the α-amylase enzyme family, ALAMYs (http://imb.savba.sk/~janecek/Alamys/), held every third year since 2001 in Slovakia. He is also the responsible curator for the families GH57 and GH77 in the Wikipedia-like project CAZypedia (http://www.cazypedia.org/) and a co-author for the family GH13. Microbial Ecology
Microbial Ecology research is focused on the defence mechanisms of bacteria against stresses and on the diversity of bacterial assemblages in natural and contaminated environments. The Laboratory of Microbial Ecology has studied the effects of different toxic metals on natural bacterial populations for the last four years. A phylogenetic analysis based on 16S rRNA and heavy-metal resistance genes was done to compare the structure and diversity of the cultivable and non-cultivable fractions of bacterial assemblages in heavy-metal-contaminated soil. The results suggested that heavy-metal-contaminated soil could be a very important reservoir of new and heretofore
unknown bacteria and heavy-metal-resistance determinants. This research area is an important and globally investigated topic. The Laboratory has participated in two projects funded by an agency of the Ministry of Education, Science, Research and Sport of the Slovak Republic using EU structural funds. The Laboratory collaborates with the Department of Cellular and Molecular Biology-Microbiology of Göteborg University in Sweden.
Soil bacteria of the family Comamonadaceae, which are known for their broad catabolic activity in polluted environments, exhibit differences in the expression of catalase and peroxidase activities in response to selective environmental pressure. The Laboratory of Molecular Microbiology showed essential role played by the catalase-peroxidase katG gene product of Comamonas spp. in both protection against oxidative stress and stress-response processes. A study on the potential use of catalases and peroxidases in the biotechnology of bioremediation was supported by the European Union.
The Laboratory of Environmental and Food Microbiology participated in different national and international projects which were mainly focused on studying the microbial communities responsible for the biodegradation of art objects and which are present in different kinds of fermented food (for example those found in bryndza cheese and in wine). Other topics included the diversity of Enterococci strains in several water environments, the degradation of polycyclic aromatic hydrocarbons (PAH) by different soil bacteria, and the DNA analysis of various kinds of historical parchments to discover which animal skin was used for their production. Its main focus was on the evaluation and development of PCR-based tools for analyzing, selecting and identifying the microflora present in particular environments or food matrices. Several molecular tools, such as AFLP (Amplified Fragment Length Polymorphism) and REP (Repetitive Extragenic Palindromic)-PCR, were optimized to enable the analysis of environmental microflora using culture-independent methods. Several different PCR-based assays (f-ITS-PCR; f-CBH-PCR; RAMP PCR) have been developed for the selection of intra-species clustering and the sub-typing of bacterial and fungal isolates. In addition, different agar plate assays were developed to detect the proteolytic, keratinolytic, cellulolytic and PAH-degradation activities of isolated microorganisms.
Functional genomics, bioinformatics and biotechnology
Functional genomics and bioinformatics were applied to research on pathogenic bacteria, antibiotics production, bacteriophages and honeybee characterization. Initial steps were made to transfer the results of this research to modern bio-nanotechnological applications. Several models were used to study pathogenic bacteria. Basic research was focused on the regulation of virulence gene expression. Modern detection techniques and systems were optimized and developed to detect pathogens.
Sigma factors of RNA polymerase were found to have a critical role in the pathogenicity of many bacterial organisms. The role of three sigma factors in the pathogenicity of three different human pathogens, Salmonella typhimurium RpoE, Staphylococcus aureus SigB, and Mycobacterium tuberculosis SigF, was characterized by the Department of Gene Expression. Several genes belonging to the regulons controlled by these sigma factors were characterized in detail and were found to play a crucial role in the virulence and stress responses of S. Typhimurium (pbpG, smpA, htrA, skp, rseP, micA) and S. aureus (arlRS, yaeJ, spoVG). In addition, the regulation of these genes and the genes encoding only the sigma factors alone were characterized. An investigation of the interactions between RpoE and its cognate promoters revealed an amino-acid residue essential for the recognition of a specific nucleotide in the cognate promoter, and a mutant of rpoE with altered promoter specificity was found. In M. tuberculosis, a regulon of SigF and SigJ was found and characterized. This project addresses one of the most intensively studied topics worldwide, that of finding new drug targets in human pathogens, and it was carried out in a wide international collaboration
8
within the European research area including partners from U.K, Germany, and Switzerland.
The Department of Microbial Genetics is involved in projects focused on the detection of tick borne pathogens using newly developed oligonucleotide chips. A unique DNA biochip for the detection of bacterial pathogens from single tick isolates has been developed. This DNA chip uses a laser DNA array reader which allows all chosen bacterial pathogens in one sample to be detected by a single PCR reaction and is one of the most sensitive methods for detecting tick-borne bacterial pathogens. This chip was used for epidemiological studies of the prevalence of tick-borne bacterial pathogens in different regions of Slovakia.
The Laboratory of Prokaryotic Biology focused on a method to rapidly detect pathogenic bacteria in food. Escherichia coli O157:H7 is a well known enterohemorrhagic pathogen. The main source of this bacterium is cattle, mostly asymptomatic, and through that E. coli O157:H7 can be simply transferred to food products. There is therefore a need for a simple and reliable detection method. The research activity of this laboratory was focused on the development of a rapid, sensitive and specific detection procedure based on the virulence genes of E. coli O157:H7 and employing a heptaplex polymerase chain reaction. The procedure was developed in cooperation with EL spol. s.r.o., Spišská Nová Ves, Slovakia.
The Laboratory of Genomics has analysed various clinical isolates of Salmonella using a novel oligonucleotide microarray method (“Salmonella-specific ResistoPathoCHIP”), which could become a useful tool for the detection of virulence and resistance genes and for monitoring their dissemination among salmonellae and closely related bacteria.
Antibiotics production has been studied in several aspects. Basic research has focused on screening techniques for identifying and regulating new antibiotics. Biotechnology research has focused on improving the quality of penicillin production. Because streptomycetes are the main antibiotic producers, the Department of Gene Expression has investigated the production of new antibiotics using the model organism Streptomyces aureofaciens CCM3239, with particular emphasis on regulating the production capabilities of this strain. The polyketide gene cluster responsible for the production of a new angucycline antibiotic auricin was identified and characterized. Auricin production was found to be carefully regulated by a unique and complex cascade process. Three regulatory genes were found to be critically important for this regulation. The negative regulator Aur1R directly binds to the promoters for two activator genes, aur1P and aur1PR3, and inhibits their expression during a specific growth stage. This inhibition is relieved by the binding of auricin intermediates to Aur1R. The salinomycin gene cluster containing multiple regulatory genes was also identified and characterized in Streptomyces albus.
There is an acute need for new antibiotics as resistance to currently available drugs is growing. To this end, the Laboratory of Molecular Microbiology has screened BAC metagenomic libraries for antibacterial activities. To detect antibacterial activities, an overlay assay was used with different bacterial strains. Sequence-based methodology employing PCR or hybridization was used as a complementary approach. This project started in 2011 and is done in collaboration with the laboratory of Dr. Christian Ottmann of the Chemical Genomic Centre in Dortmund with the support of a Humboldt Foundation Research Group Linkage Grant.
The Institute has a long-running collaboration with Biotika a.s. A collaborative project “Production efficiency improvement of Penicillium chrysogenum” was carried out at the Institute during the assessed period by several laboratories. Using the methods of molecular biology, a production strain of P. chrysogenum NM (part of Biotika’s “know-how”) was analysed in order to determine its production potential and to improve its actual production capabilities through metabolic engineering. During this project, knowledge about the biosynthetic cluster organization, its gene dose and its regulation were acquired.
9
Bacteriophages are the most abundant biological entities on earth and their extreme natural adaptability and strict or broad specificity in host bacterial infection make them ideal tools for combating human and other bacterial diseases (generally termed phage therapy). Several groups in the Institute study bacteriophages. The Laboratory of Genomics focused on genomic and proteomic studies of corynephage BFK20 and phage PhiBP. BFK20 is a lytic phage of Brevibacterium flavum CCM 251, the former industrial producer of L-lysine, whose whole genomic sequence had previously been determined and characterized. During the past five years, attention was focused on lytic and phage replication proteins. The BFK20 endolysin was isolated and characterized in detail. Its modular structure, consisting of an N-terminal amidase_2 domain (gp24CD) and a C-terminal cell wall binding domain (gp24BD), was elucidated. The lytic activities of endolysin and its catalytic domain were demonstrated on corynebacteria and bacillus substrates. The binding activity of its cell-wall binding domain to the cell surface of B. flavum CCM 251 and other corynebacteria was shown. The catalytic and binding domains can act independently, but the catalytic domain activity is inhibited in the presence of the cell wall binding domain. Purified gp24BD was crystallized in two crystal forms which diffracted to 3.15 and 1.34 Å. The BFK20 replication protein was investigated. It contains two different domains: a C-terminal helicase and a rare, N-terminal primase-polymerase domain. Both primase and DNA polymerase activities were detected in the N-terminal part of the protein and the phage primase used only dNTPs for both reactions. The primase was not highly sequence specific and does not require a specific trinucleotide for the initiation of primer synthesis. This makes it similar to Archaeal primases. This primase-polymerase domain is the first such domain studied as an individual heterologous protein.
PhiBP, a new bacteriophage which infects Paenibacillus polymyxa CCM 7400, was also discovered. Electron microscopy suggested that it belongs to a taxonomical group containing unclassified Siphoviridae. The PhiBP genome consists of 43-kbp of double-stranded DNA. A homology search of sequenced DNA fragments revealed regions with significant similarity to phage terminase genes and lytic genes. This bacteriophage is capable of triggering the lysis of a P. polymyxa PhiBP lysogen, despite the presence of phage DNA on the bacterial chromosome. It was concluded therefore that PhiBP is a virulent mutant phage.
Another bacteriophage, μ1/6, which affects Streptomyces aureofaciens and whose sequence had previously been determined, was studied in the Laboratory of Prokaryotic Biology. Two genes, lyt and hol, encoding endolysin and holin, respectively, were identified in the lysis module of μ1/6. An additional candidate holin gene, hol2, was found downstream from the hol gene. The genes were cloned and expressed in E. coli, and expression of hol1 or hol2 was found to cause cell death. Concomitant expression of endolysin and holin resulted in cell lysis, apparently due to the ability of endolysin to hydrolyze the peptidoglycan layer. In contrast, the simultaneous expression of hol2 and the endolysin gene did not cause cell lysis. The holin function was demonstrated in streptomycetes, where it was shown that holin produces holes in the membrane. The actinophage μ1/6 integrates into the chromosome of S. aureofaciens via a site-specific recombination process. The μ1/6 genome encodes an integrase that belongs to the family of site-specific tyrosine recombinases. It was shown to be functional in vivo in heterologous E. coli without any other factors. The actinophage attachment site (attP) was localized downstream of the int gene. Its attachment junctions (attL and attR) were determined, allowing identification of the bacterial attachment site (attB). An integration vector containing the μ1/6 int-attP region was stably inserted into many Streptomyces strains.
The recently formed Laboratory of Bioinformatics followed the previous activities of its members in the field of phage genomics. Its main focus was on building and maintaining the new and unique database phiSITE, which collects data about the regulation of gene expression and the general genomics of bacteriophages (http://www.phisite.org/). It presently contains detailed information on more than 700 experimentally confirmed or
10
predicted regulatory elements from 32 bacteriophages. An integral part of the phiSITE portal is phiGENOME, a web-based genome browser which generates dynamic and interactive graphical representations of the phage genomes stored in the database. It is optimised for visualisation of phage genomes with an emphasis on gene regulatory elements. phiGENOME consists of three components: (i) a genome map viewer, providing a dynamic and interactive graphical display of phage genomes; (ii) a sequence browser, allowing a detailed exploration of genome features and (iii) a regulation illustrator, designed for the graphical representation of gene regulations. Its more than 600 complete genome sequences, along with accompanying rich annotations and references, make phiGENOME a unique information resource in the field of phage genomics. This laboratory is also involved in the building of phiBIOTICS (http://www.phibiotics.org), another phage-related database which collects information about representative enzybiotics and relevant research studies regarding their practical application in the renewed field of phage therapy. The accompaning tool phiBiScan can reliably predict new potential enzybiotics based on their primary structure.
The honeybee offers many advantages as a model system for functional proteomics. A functional proteomic study into the physiological potential of royal jelly (RJ) identified RJ proteins which could be used to address a very critical situation in beekeeping. The Department of Molecular Apidology focused on the antimicrobial potential of RJ proteins, on their multifunctionality, and on how they can acquire new functions as a result of various posttranslational modifications on maternal, nutritive RJ proteins. The physisological properties of the major acidic RJ protein apalbumin1, the minor basic protein apalbumin2 and the peptides royalyzin and apisimin were studied. During these studies, a novel minority protein apalbumin2a was identified. The antibiotic properties of apalbumin2a were demonstrated against P. larvae, the primary honeybee pathogen. The results of this research also indicate that apalbumin1 is responsible for important physiological properties of honey. Apalbumin1 is a honeybee-specific major protein of honey, which makes it a useful standard for analyzing the quality and authenticity of honey. Consequently, a new, reproducible, and sensitive enzyme-linked immunoassay for the quantitative determination of apalbumin1 in honey was developed.
The proteins and peptides obtained by HPLC analysis from the milky venom Consours Consors library exhibited antimicrobial activity against P. larvae. Ninety native and recombinant analogues from this library were also tested for antiparasitic activity against Ixodex vicinius; the most effective were found to be conopresin, alfa-conotoxin, CcTx-l peptide, Conkunitzin-like, and Conomarhin-like propeptide. These results were achieved with the support of the following projects: 6.FP EU - BEESHOP, 6.FP EU - CONCO, 7.FP EU - BEEDOC and “Partner Group project” from the Max Planck Society.
Molecular Cell Biology
Investigation of eukaryotic cellular processes is a relatively new research area at our institute. There are several areas of interest, (i) neurotransmitter transporters, (ii) cell migration and cytokinesis, and (iii) mitochondrial biogenesis.
Neurotransmitter transporters are membrane proteins which regulate a pool of available neurotransmitters, mainly around neurons and glial cells. Their impairment frequently leads to serious neurological illnesses. Research in the Laboratory of Neurobiology focused on the regulation of neurotransmitter transporters, particularly on
those transporting glycine, -aminobutyric acid and dopamine. There are three major research achievements of the laboratory. A new polyclonal antibody was developed to demonstrate the existence of the glycine transporter GlyT2 in amphibian retina. Calcium-dependent proteolytic processing in the cytosolic regions of several neurotransmitter transporters was identified and characterized. Finally, benzophenanthridine alkaloids were found to be a new class of inhibitors of the glycine transporter GlyT1.
Septins constitute a group of GTP-binding proteins involved in cytokinesis and other essential cellular functions of eukaryotic cells. They form heterooligomeric linear complexes, which polymerize into nonpolar filaments. Septin biology is presently one of
the hot topics in the field of cytoskeletal studies worldwide. A very important step towards understanding septin molecular function was the solving of the crystal structure of SEPT2 bound to GppNHp in the Laboratory of Molecular Microbiology in close collaboration with Prof. Wittinghofer’s group at the Max-Planck Institute in Dortmund. GTP-binding was found to induce conformational changes in the switch regions at the G interfaces, which are then transmitted to the N-terminal helix and also affect the neighbouring NC interface. GTP–binding and hydrolysis and the nature of the nucleotide, whether GTP or GDP, were proposed to influence interface stability in heterooligomeric and polymeric septins. Proper septin filament assembly/disassembly requires the binding and hydrolysis of the correct nucleotide. These results also suggest a characteristic for subdividing human septins into different functional subgroups.
The ability of cells to migrate is crucial for a number of biological processes. Deregulated cell motility is one of the major characteristics of cancer diseases. The urokinase plasminogen activator (uPA) system is the mediator of cell surface controlled proteolysis and is thus involved in a number of patho/physiological processes including cell migration. The Department of Biochemistry and Structural Biology and the Institute for Hygiene and Applied Immunology of the Medical University of Vienna identified one important regulator of the uPA system: the mannose 6-phosphate/insulin-like growth factor 2 receptor (M6P/IGF2R). The department contributed by finding that the tumour necrosis factor α-convertase mediates the release of M6P/IGF2R’s ectodomain from human endothelial cells, and that sM6P/IGF2R binds plasminogen (Plg), thereby preventing Plg from binding to both the cell surface and uPA, effectively inhibiting Plg activation (This interaction has been found in the sera of liver disease patients). Furthermore, a peptide from the Plg-binding site of M6P/IGF2R mimics this inhibition of Plg activation and blocks cancer cell invasion in vitro and endothelial cell invasion and tumour growth in vivo. The interaction of M6P/IGF2R with Plg may be an important regulatory mechanism for inhibiting the migration of cells.
The Department has a long history of studying mitochondrial proteolysis. The ATP-dependent Lon protease plays a key role in protecting mitochondria from damage. In close cooperation with C.K.Suzuki of UMDNJ Newark NJ USA, the roles of human Lon in mitochondrial DNA maintenance were characterized. These studies showed that Lon was associated with the mitochondrial genome and that Lon binds specifically to single-stranded G-rich sequences and preferentially to the control region that overlaps the binding site for mitochondrial transcription factor A (TFAM). The results indicated that Lon is involved in TFAM regulation through controlled TFAM degradation. Because a high level of TFAM blocks transcription while a low level destabilizes mitochondrial DNA, it seems that Lon contributes to mitochondrial DNA biogenesis by controlling the TFAM level.
Since 1999, the Institute has had a mandate from the Slovak government to serve as a National EMBnet Node (www.embnet.org). EMBnet, The Global Bioinformatics Network, is a science-based group of collaborating nodes throughout the world. EMBnet’s mission is to provide education and training in bioinformatics; to exploit network infrastructures to investigate, develop and deploy public domain software; to assist biotechnology- and bioinformatics-related research, bridging commercial and academic sectors, promoting global cooperation through its community networks. The main activities of the National Node are education and international cooperation in the building of the necessary bio-computing infrastructure. It is also significantly involved in the activities of the Executive Editorial Board of EMBnet.journal, an international Open Access peer-reviewed journal. The Institute was involved in the planning stages of ELIXIR (European Life Sciences Infrastructure for Biological Information), a project funded by the EU under the European Strategy Forum on Research and Innovation (ESFRI), whose proposed activities are similar to those of the National Node.
The Institute of Molecular Biology is the owner of the international life-science international Biologia (http://www.springer.com/life+sciences/journal/11756), section Cellular and Molecular Biology. It provides credible and efficient peer-review to its
authors as well as high scientific standards. Biologia is indexed by Abstracting and Indexing Services (Current Contents and Web-of-Science) with an Impact Factor of 0.609 (2010). It is published bimonthly and all issues from 2006 are available on-line under a co-publishing program with Versita (http://www.versita.com/) and Springer-Verlag (http://www.springer.com/). Biologia, section Cellular and Molecular Biology, has its own Editorial Office and Editorial/Advisory Boards and uses the Editorial Manager online system for manuscript submission and handling (http://www.editorialmanager.com/biologia/).
3. Concept of R&D activity of the Organisation for the next four years
(recommended 3 pages, max. 5 pages)
i. Present state of knowledge and status of ongoing research related to the subject
of the Concept, from both international and national perspective
Molecular biology is a research domain which is essential for all aspects of life sciences. As shown above, the research activities at the Institute are focused on basic biological issues, including cell division and differentiation, protein structure-function relationships, protein evolution, microbial ecology, functional genomics, bioinformatics, biotechnology, and molecular cell biology. The departments at the Institute have excellent backgrounds for all these research activities. A brief review of the current state of knowledge in the major fields of research at the Institute follows. Several research projects involve close international co-operations while others have considerable importance for national industry. The mechanisms of cell division and differentiation are likely best characterised in the rod-shaped sporulating bacterium Bacillus subtilis. Despite the large amount of information available on the key proteins involved, a detailed description of the molecular mechanisms which determine where, how and when cells form the division septum is lacking. The discovery by the Department of Microbial Genetics of a higher level of membrane lipid organization and its role in cell division has led to further questions. Its goals are to determine the origin of these helical lipid domains in the cell membrane and their relationships to cytoskeletal and morphogenetic proteins and the peptidoglycan synthesizing machinery. In addition, the mechanism of programmed cell death caused by the toxin-antitoxin SpoIISA-SpoIISB system (which also exists in other Bacilli) will be studied with the aims of discovering why, how and when is the toxin unleashed, triggering cellular suicide.
The antibiotics-producing Streptomyces have been extensively studied all over the world with particular emphasis on the regulation of its antibiotics production and its morphological differentiation. They have a very large collection of 65 RNA polymerase sigma factors. The Department of Gene Expression has been studying the role of several of these sigma factors in stress-response and differentiation for 20 years. The presence of an exceptionally large number of closely related SigB stress-response sigma factors homologues (9) and huge number of regulators for them (a total of 122 anti-sigma factors, anti-anti-sigma factors, and activating phosphatases) illustrates the exceptional complexity of the stress-response process and its connection to differentiation. The aim of these studies is to further characterize this complex regulation.
During the next period, several laboratories will investigate protein structure-function relationships and evolution. The Department of Biochemistry and Structural Biology will continue its studies of the human ryanodine receptor 2 (hRyR2), mitochondrial protease Lon and glycoside hydrolases. The domains of hRyR2 are important for the allosteric regulation of channel opening; mutations in these domains lead to arrhythmia and sudden cardiac arrest. The goal is to determine the structure of the individual hRyR2 domains and to study their interactions in order to better understand the function of the hRyR2 channel.
ATP-dependent proteases are essential parts of the cellular stress response. To better understand the role of the proteolytic domain of human Lon in the overall function of the protease, we will prepare and test several point mutants based on the structure already determined.
Raw starch degrading glucoamylases are an important group of industrial enzymes. The plan is to describe the co-operation of the raw-starch binding site with the catalytic one to better understand the function of the enzyme.
Structural research on biotechnologically important proteins will also be continued in the Laboratory of Prokaryotic Biology and will focus mainly on the enzymes of the phage cell lytic system, on carbohydrate active enzymes, and on proteins relating to photosynthesis.
The Laboratory of Protein Evolution will continue to be focused on the bioinformatics of amylolytic enzymes in an effort to maintain leadership in this field. In addition to the main α-amylase family GH13, attention will also be paid to the GH57, GH119, and GH31 families. Other projects will be oriented on investigating the starch/glycogen-binding domains. These studies will be conducted with the aim of contributing significantly to the “amylase” research field by delivering in silico results that would be of help for the biochemical characterization of hypothetical amylolytic enzymes and their modification for potential use in starch-based industries.
Research in microbial ecology will be performed by two laboratories. The results of the Laboratory of Microbial Ecology suggested that heavy-metal-contaminated soil may be a very important reservoir of new and heretofore unknown bacteria, heavy-metal-resistance determinants and their products. The objective of the projects will be to obtain new, difficult to cultivate, and previously uncultured soil bacterial isolates carrying unusual resistance determinants against toxic metals. These could be exploitable in bioremediation technologies.
To facilitate the selection of isolated microflora, several different three-step strategies were developed by the Laboratory of Environmental and Food Microbiology as indicated in the previous section. These novel approaches will be used for the microbial investigation of different kinds of food and environmental samples.
Functional genomics, bioinformatics, and biotechnology have been pursued for many years at the Institute. This research includes studies on pathogenic bacteria, antibiotics production, bacteriophages, bionanotechnology, and honeybee characterization.
The Intracellular pathogen Salmonella typhimurium is a model for the study of pathogen-host interactions. Pathogen stress response directly affects its virulence, and stress response sigma factors were found to have a role in pathogenicity. The Department of Gene Expression has previously shown that sigma factor RpoE plays a critical role in S. typhimurium virulence. Its future goal is to investigate the regulation of RpoE and the role of its regulon in virulence. These results will increase our knowledge of pathogenesis and the mechanisms of defense against stress.
Bacteria of the genus Streptomyces produce a large amount of bioactive secondary metabolites, including the majority of antibiotics. The Department of Gene Expression has characterized several antibiotic gene clusters, including that of a new antibiotic, auricin. The cluster is located on a large linear plasmid called pSA3239. The main goal of this project is to characterize this plasmid and its genes in regard to secondary metabolism and horizontal gene transfer.
A significant fraction of secondary metabolites remains unknown due to a lack of cultivation techniques for more than 99% of environmental microorganisms. Recent improvements in metagenomics have enabled access to a tremendous resource of bioactive molecules contained in different biotopes. The Laboratory of Molecular Microbiology will further continue in this research with a focus on constructing BAC metagenomic libraries from different habitats. Sequence- and function-based techniques will be used to identify and characterize new natural products.
The possible use of bacteriophages in the treatment of infectious diseases has attracted the interest of scientists all over the world. Three laboratories have been
14
studying the genomics and bioinformatics of bacteriophages. The Laboratory of Genomics will continue to study the bacteriophage BFK20 lytic and replication proteins. Its goals are to complete the determination of the protein’s structure and the catalytic domains and to understand its biological activity. The expected results will include a likely description of the phage’s DNA replication mechanism. The study of the phage BFK20, PhiBP, and μ1/6 lytic proteins will result in the construction of recombinant endolysins with new properties. The bacteriophage μ1/6 of S. aureofaciens will also be further studied in the Laboratory of Prokaryotic Biology with the aim of better understand the regulation and structure of the proteins of the lytic system. The regulation module of μ1/6, which contains the integration region active in heterologous E. coli will also be further investigated to allow it to be used as a biotechnological tool for the integration of important target genes into the chromosomes of a wide range of microorganisms. Finally, the Laboratory of Bioinformatics will continue to maintain and enhance the phiSITE database bacteriophage gene regulation, with the goal of making this portal the most comprehensive resource in the field of phage genomics. Several new functionalities, mainly related to comparative genomics, will be added. Additionally, the increasing availability of new technologies (DNA arrays, NextGen sequencing, high-throughput Mass Spec) prompts us to develop and implement a broad range of statistical methodologies for analysing these high-throughput data.
In the field of nanotechnology, the B. subtilis coat proteins are objects of interest at the Department of Microbial Genetics. The coat proteins are self-assembling proteins that can generate extremely uniform structured surfaces. These can then be attached to effector elements, such as enzymes, DNA, antibodies, and drugs. Our main efforts will be on their structural characterization and on investigation of their potential use in new nano-biotechnological applications.
The Department of Molecular Apidology, as a part of the 7. FP EU consortium, has been investigating the honeybee as a model to elucidate the mechanisms governing its antimicrobial defence system. This international cooperation on the genomics, proteomics and physiomics of the honeybee will continue.
Three laboratories will continue their molecular cell biology research by studying neurotransmitter transporters, cell migration and cytokinesis, and mitochondrial biogenesis. The results of the Laboratory of Neurobiology revealed that glycine transporters are proteolytically truncated by calpain, and that this truncation modifies their activity and alters signalling homeostasis. It has been proposed that these phenomena could have both physiological and pathological significance. There is a big effort to find specific inhibitors of glycine transporters to treat several forms of neurological diseases. The discovery of the specific inhibitory effect of benzophenanthridine alkaloids on the Glyt1 glycine transporter will contribute to these studies. The Laboratory of Molecular Microbiology will continue to study the role of septins in cytokinesis and other essential cellular functions. Septins at the division plane serve as a scaffold for the assembly of various proteins. It is not well understood how the specific protein-protein interactions between these various proteins lead to changes in septin filament polymerization. The detailed characterization of the dynamics of septin assembly and the regulatory mechanisms involved in it will be important for understanding septin function. Finally, the Department of Biochemistry and Structural Biology will continue in its characterization of proteolytic systems. The urokinase plasminogen activator (uPA)/plasmin system is essential for cell migration and plays a key role in tumour progression. The aim will be to identify new molecules involved in the regulation of plasmin activity. The department will delineate those molecular regulatory pathways which might contribute to development of pharmacological tools useful for treating the pathological disorders associated with uncontrolled plasminogen activation. The other proteolytic system studied is associated with mitochondria. Previous studies have shown that Lon protease is a DNA binding protein found in the mitochondrial nucleoid. How Lon contributes to the regulation of
15
nucleoid protein function is not clear and identifying the nucleoid components that are either bound to or degraded by Lon may answer this question.
ii. Organisation’s role or significance in the overall research effort within the field
of the Concept on both the national and international scales
The Institute of Molecular Biology enjoys an excellent position within its research fields at both national and international levels. Presently, the Institute is either a principal investigator of or it participates in several different VEGA and APVV projects as well as in German–Slovak, Austrian–Slovak, and Czech–Slovak bilateral projects, and in 6th and 7th EU Framework Programmes. Its international position can also be seen in its numerous collaborations with excellent foreign institutes from around the world and in its various publications. Its national position can be seen through its presence in eight projects supported by the Research & Development Operational Programme funded by the ERDF.
iii. Objectives of the Concept
Molecular biology is a domain which encompasses biochemistry, structural biology, protein evolution, genomics and bioinformatics, all of which are part of the research Concept. We will focus on understanding the processes of living cells, as well as the structure and function of proteins which may be of interest or use to medicine, pharmacy, ecology, biotechnology and nanotechnology. The objectives of the Concept closely follow the previous results of research done at the Institute and are linked to running projects and projects in preparation. They represent the continuation of our previous research activities and at the same time open some new areas. A few projects are closing down and the results of these are efficiently being introduced into new ones. The overall concept includes five main spheres of research with the following objectives:
1. Studies of Cell Division and Differentiation
pursue basic research into bacterial cell division, differentiation and a particular example of bacterial programmed cell death
explore the role of the complex cascade of stress response sigma factors and their regulators in Streptomyces differentiation
2. Protein Structure-function Relationships and Protein Evolution
carry out structure-function studies on human ryanodine receptor domains, the Lon protease proteolytic domain, carbohydrate active enzymes, proteins participating in photosynthesis, and bacteriophage lytic enzymes
bioinformatics on catalytic and binding domains of carbohydrate active enzymes with an emphasis on identifying sequence features indicating unique enzyme specificities
3. Microbial Ecology
to obtain new uncultured soil bacterial isolates resistant to toxic metal pollutants with a high degree of detoxification activities against these metals
to gain knowledge on the complexity and interactions of microbial populations on the biochemical and genetic level during the production of bryndza cheese.
investigation of microbial communities from art objects and determining their degradative capacities to clarify their roles in the biodegradation of art objects
4. Functional Genomics, Bioinformatics and Biotechnology
regulation of the sigma factor RpoE and its regulon in salmonella with an emphasis on its pathogenicity and envelope stress response
the characterization of the complex regulation of the auricin gene cluster and its horizontal gene transfer through pSA3239, a large linear plasmid
16
structural characterization of spore coat proteins, their protein-protein contacts and self-assembly characteristics with the aim of using them in bio-nanotechnology
investigation of protein-protein interactions during bacteriophage BFK20 infection and a structural analysis of its replication proteins
molecular characterisation of honeybee royal jelly proteins, and the study of the molecular mechanisms of the antibiotic effects of their antimicrobial peptides on pathogens
construction of recombinant endolysins from bacteriophages BFK20, PhiBP, and μ1/6 with a broad spectrum of action; characterisation of the catalytic and cell wall binding domains of μ1/6 and phiBP endolysins
identifying and characterizing new bio-active natural products using a metagenomic approach
maintaining the phiSITE, phiGENOME and phiBIOTICS bioinformatics resources; computational genomics of selected organisms and high-throughput data analysis
5. Molecular Cell Biology
elucidation of the physiological significance of the calpain-mediated cleavage of glycine transporters and the identification of factors regulating this process
characterization of the molecular mechanisms of septin filament assembly
analysis of the additional components of the urokinase plasminogen activator (uPA)/plasmin system and identification of its function
characterization of selected components of the mitochondrial nucleoid in the context of their possible regulation by the Lon protease
iv. Proposed strategies and methods to be applied, and time schedule
The Institute is well prepared to proceed with the research activities described above and is ready to be a part of new national and international projects and programs. Within these projects the Institute plans to support transfer of present know-how to new and important spheres of research. In all research activities, both traditional and the most modern techniques of molecular biology, biochemistry, structural biology and genetics will be applied. Techniques to study gene expression (DNA microarray, S1-nuclease mapping, qRT-PCR etc.) are well established. Many available reporter systems (egfp, lux, lacZ etc.) to detect quantitative, temporal, and spatial expression, as well as expression systems for overproduction of proteins will be applied. In protein purification, different chromatographic methods will be used. HPLC will be used for the analysis and purification of secondary metabolites. ESI-MS and MALDI-MS spectroscopy will be used to investigate both proteins and secondary metabolites. Crystallization and X-ray analysis, transmission electron microscopy, SAXS analysis, and in silico approximations analysis will be used for structural studies. A wide range of techniques, including EMSA, DNase I footprinting, atomic force microscopy, and different fluorescence techniques will help us to characterize protein-protein and protein-DNA interactions. The time schedule will be closely connected to those of the national and international grant projects supported by the granting agencies for this period. As described in other parts of this form, VEGA projects, APVV projects, the 6th and 7th FP EU projects, and other bilateral collaborative projects will continue during this time period, and the research laboratories are well prepared to apply for new projects.
17
III. Partial indicators of the main activities:
1. Research output
i. Principal forms of research outputs of the Organisation
Research papers
ii. List of the selected publications documenting the most important results of
basic research. Total number of publications in the whole assessed period
should not exceed the average number of the research employees. The
principal science outputs (max. 5) underline
[1] Barak, I., Muchova, K., Wilkinson, A.J., O Toole, P.J., Pavlendova, N. Lipid spirals in
Bacillus subtilis and their role in cell division. (2008) Mol. Microbiol. 68: 1315-1327.
[IF2009 5.361]
[2] Gabrisko, M., Janecek, S. Looking for the ancestry of the heavy-chain subunits of
heteromeric amino acid transporters rBAT and 4F2hc within the GH13 alpha-amylase
family. (2009) FEBS J. 276(24): 7265-7278. [IF2009 3.042]
[3] Klucar, L., Stano, M., Hajduk, M. phiSITE: database of gene regulation in
iii. List of journals edited/published by the Organisation:
1. WOS (IF of journals in each year of the monitoring period)
Biologia (section Cellular and Molecular Biology); involved in WOS, SCOPUS and other databases. IF (2007) = 0.207; IF (2008) = 0.406; IF (2009) = 0.617; IF (2010) = 0.609;
EMBnet.journal - international, Open Access, peer-reviewed journal published by
EMBnet (http://journal.embnet.org)
iv. List of edited proceedings from international scientific conferences and other
proceedings
[1] ALAMY_3 (Janecek S., ed.): 3rd Symposium on the Alpha-Amylase Family.
Smolenice Castle, Slovakia, 23-27 SEP 2007. Programme and Abstracts. 102 pp.
ISBN 978-80-969750-0-6.
[2] ALAMY_4 (Janecek S., ed.): 4th Symposium on the Alpha-Amylase Family.
Smolenice Castle, Slovakia, 26-30 SEP 2007. Programme and Abstracts. 108 pp.
ISBN 978-80-88820-47-5.
National position of the Organisation
i. List of selected most important national projects (the EU Structural Funds,
Slovak Research and Development Agency (APVV), State Research
Programmes, Scientific Grant Agency of the Slovak Academy of Sciences and
the Ministry of Education (VEGA), Centres of Excellence, National Reference
Laboratories and others)
[1] Centre of excellence for translation research in molecular medicine – TRANSMED Grant agency: ASFEU Grant registration number: 26240120008 Duration: 06/2009 – 05/2011 Total Funding: 1 327 757 Eur Funding for IMB SAS: 7645,92 € Responsible person in IMB SAS: Ján Kormanec - Principal investigator Coordinator: Silvia Pastoreková, Institute of Virology SAS Number of cooperation institutions: 7
[2] New microbial isolates containig genes of catabolic and detoxication pathways and their use in biotechnology Grant agency: ASFEU Grant registration number: 26240220010 Duration: 09/2009 – 09/2012 Total Funding: 479 302,19 EUR Funding for IMB SAS : 96 535,75 Eur Responsible person in IMB SAS: Bystrík Polek - Coordinator Number of cooperation institutions: 1
[3] Centre of Excelence for the Use of Informational Biomacromolecules in Prevention of Diseases and for Improvement of the Quality of Life - BIOMAKRO Grant agency: ASFEU Grant registration number: ITMS 26240120003 Duration: 05/2009 – 10/2011 Total Funding: 1 391 315 Eur
Funding for IMB SAS: 0 Eur Responsible person in IMB SAS: Jozef Timko - Principal investigator Coordinator: Marta Kollárová, Faculty of Natural Sciences Comenius University Number of cooperation institutions: 6
[4] Development of the diagnostic methods for the detection of tick-borne pathogens and the techniques for the preparation of the vaccine development directed against ticks Grant agency: ASFEU Grant registration number: 26240220044 Duration: 11/2010 – 10/2013 Total Funding: 939 914,76 Funding for IMB SAS 2010 - 2011: 258 237 Eur Responsible person in IMB SAS: Imrich Barák - Principal investigator Coordinator: Dušan Žitňan, Institute of Zoology SAS Number of cooperation institutions: 3
[5] Developing a Competency Center for Research and Development in Molecular Medicine Grant agency: ASFEU Grant registration number: ITMS 26240220071 Duration: 10/2011 - 11/2014 Total Funding: 1 892 138,21 EUR Funding for IMB SAS: 64 514,21 EUR Responsible person in IMB SAS: Ľubica Urbániková - Project manager Coordinator: Prof. RNDr. Ján Turňa, CSc., Comenius University Bratislava Number of cooperation institutions including SR: 14
[6] Study of basic cell processes in model microorganism Bacillus subtilis: Cell division and programmed cell death Grant agency: APVV Registration number: APVT LPP-0218-06 Duration: 11/2006-10/2010 Funding 2007-2010: 153 422 EUR Principal investigator: Imrich Barák
[7] Structure-function relationship of the ryanodine receptor domains involved in CPVT arrhythmias Grant agency: APVV, Bratislava Registration number: APVV-0139-06 Duration: 02/2007-12/2009 Funding: 115 847 EUR Principal investigator: Jozef Ševčík
[8] Functional and structural analysis of corynephage BFK20 replication module Grant agency: APVV Registration number: APVV-0354-07 Duration: 06/2008-05/2011 Funding: 77 707 EUR Principal investigator: Gabriela Bukovska
[9] Molecular characterization of regulation and biosynthesis of polyketide antibiotic auricin in Streptomyces aureofaciens CCM3239 Grant agency: APVV Registration number: APVV-0017-07
33
Duration: 06/2008-12/2010 Funding: 110 469 EUR Principal investigator: Ján Kormanec
[10] The role of catalase-peroxidase genes of microbial isolates in processes of organic fraction solid waste degradation Grant agency: APVV Registration number: APVV- 0444-07 Duration: 09/2008-12/2010 Funding: 124 909 EUR Principal investigator: Bystrík Polek
[11] Molecular mechanisms implicated in the control of mitochondrial integrity in eukaryotic cells Grant agency: APVV Registration number: APVV-0024-07 Duration: 06/2008-12/2010 Funding: 57 657 EUR Principal investigator: Eva Kutejová Coordinator: Jozef Nosek, Faculty of Natural Sciences, Comenius University Bratislava
[12] Lipid domains in cell division and programmed cell death in Bacillus subtilis Grant agency: APVV Registration number: APVV-00335-10 Duration: 05/2011 - 10/2014 Funding 2011: 32839 EUR Principal investigator: Imrich Barák
[13] Structural and functional characterization of human ryanodine receptor regulation and its malfunction caused by mutations Grant agency: APVV Registration number: APVV-0628-10 Duration: 05/2011-10/2014 Funding 2011: 47 852 EUR Principal investigator: Jozef Ševčík
[14] Development of progressive technologies for powerful economics (area „Biotechnologies“ – "Increase of production of biologically active substances" "increase of economic efficiency of the strain Penicilium chrysogenum") Grant Agency: State Research Programmes Registration number: VaV 2004 SP26/028 0A 00/028 0A 03 Duration: 07/2004- 12/2007 Funding 2007: 165 970 Eur Principal investigator: Ján Turňa
[15] The role of sigma factors of RNA polymerase in stress response, pathogenicity and differentition of bacteria Grant Agency: VEGA Registration number: VEGA 2/0104/09 Duration: 01/2009 - 12/2011 Funding: 34 868 Eur Principal investigator: Ján Kormanec
34
[16] Role of septin complex in eukaryotic cell division Grant Agency: VEGA Registration number: VEGA 2/0038/08 Duration: 01/2008 - 12/2010 Funding: 11 070 Eur Principal investigator: Marian Farkašovský
[17] Lon protease and mtDNA binding proteins Grant Agency: VEGA Registration number: VEGA 2/0141/08 Duration: 01/2008 - 12/2010 Funding: 18 816 Eur Principal investigator: Eva Kutejová
[18] Transcriptional analysis of the Streptomyces aureofaciens phage μ1/6 Grant Agency: VEGA Registration number: VEGA 2/0121/08 Duration: 01/2008 - 12/2010 Funding: 21 093 Eur Principal investigator: Andrej Godány
[19] Building of phage gene regulatory networks and characterisation of phage elements with potential application in phage therapy Grant Agency: VEGA Registration number: VEGA 2/0100/09 Duration: 01/2009 - 12/2011 Funding: 13 650 Eur Principal investigator: Ľuboš Kľučár
[20] Evolutionary trends in amylases studied in the post-genome era Grant Agency: VEGA Registration number: VEGA 2/0114/08 Duration: 01/2008 - 12/2010 Funding: 16 651 Eur Principal investigator: Štefan Janeček
[21] Role of protease calpain in physiology of glycine transporters Grant Agency: VEGA Registration number: VEGA 2/7049/27 Duration: 01/2007 - 12/2009 Funding: 8 571 Eur Principal investigator: František Jurský
[22] Biorestoration: complex analysis of environmental microflora applied to innovative stone artwork restoration techniques. Grant Agency: VEGA Registration number: VEGA 2/0117/08 Duration: 01/2008 – 12/2010 Funding: 16407 Eur Principal investigator: Domenico Pangallo
[23] Centre of excellence of biochemistry of saccharides (GLYCOBIOS) Grant Agency: Centre of excellence SAS Duration: 01/2005- 12/2008
35
Total Funding: 101 573,39 EUR Funding 2007: 11 618 Eur Principal Investigator: Jozef Ševčík Coordinator: Vladimír Farkaš (Institute of Chemistry SAS) Number of cooperation institutions: 2
[1] In 2007 the National Reference GMO Laboratory was established in the Institute. The laboratory became the member of ENGL (European Network of GMO Laboratories) of the European Union. In 2009 the Laboratory of GMO received the "Certificate of Accreditation S-255" as a testing laboratory - Laboratory Type 1 granted by SNAS (Slovak National Accreditation Service). On June 30th 2010 the Laboratory of GMO was abolished and also the membership of the Institute in ENGL of the EU was terminated.
ii. List of national scientific conferences (co)-organised by the Organisation
None
iii. List of edited proceedings of national scientific conferences/events
None
International/European position of the individual researchers
i. List of invited/keynote presentations at international conferences, documented
by an invitation letter or programme
[1] Barák I., Barbaro M., Blaškovič D., Mullerová D., Campo A., Raffo L.: DNA biochips for microbial pathogen detection. NANOVED 2007 - 4th International Conference on Nanosciences and Nanotechnologies, Bratislava, Slovakia, 11-14 NOV 2007. (Barák I – Invited lecture)
[2] Barak I., Chromikova Z., Muchova K., Pavlendova N.: Compartment specific gene expression during differentiation of Bacillus subtilis. RNA club Biologicka konference nejen o RNA, Praha, Czech Republic, 28 Nov 2008. (Barák I – Invited lecture)
[3] Barak I., Muchova K., Pavlendova N., Chromikova Z.: Bacterial cell division - how the cell finds its center. XXI. Biochemical congress, Ceske Budejovice, Czech Republic, 14-17 SEP 2008. (Barák I – Invited lecture)
[4] Barak I., Krajcikova D., Lukacova M., Mullerova D.: Bacillus subtilis spore coat proteins as novel structures for nano-biotechnology research. Workshop in Bio-nanotechnologies, Ho Chi Minh City, Vietnam, 17 AUG 2009. (Barák I – Invited lecture)
[5] Barak I., Muchova K., Krajcikova D., Pavlendova N., Florek P., Mullerova D., Vavrova L., Resetarova, S.: Bacillus subtilis as a tool in basic science and applied research. International Conference on Emerging Trends In Biotechnology, Varanasi, India, 4-6 DEC 2009. (Barák I – Invited lecture)
[6] Barak I., Muchova K., Pavlendova N., Resetarova S., Vavrova L.: Bacillus subtilis as a tool in basic science and applied research. 2009 DELPHE* Workshop in Infectious Diseases, Hanoi, Vietnam, 10-14 AUG 2009. (Barák I – Invited lecture)
[7] Bilikova K., Simuth J.: New criteriom of evaluation of honey quality. XVl. Internationak congres of innovators and inventors in beekeeping, Bratislava, Slovakia, 17-19 OCT 2008. (Bílikova, K – Invited lecture)
36
[8] Bíliková K., Lehrach H., Šimúth J.: Why honeybee genome contains less genes for innate imunity as Drosophila melanogaster genome. 2nd International Conference on Crossroads between Innate and Adaptive Immunity, Crete, Greece, 17-22 JUN 2007. Šimuth J. – invited lecture)
[9] Bíliková K., Šimúth J.: Immunochemical approach to detction of adelturation of honey. Genes and Pathogenes in Honeybees-Satelite Symposium in conjuction with XI. ESEB Congres 2007, Uppsala, Sweeden, 26 AUG 2007. (Bílikova, K – Invited lecture)
[10] Bilikova K.: Multifunctionality of honeybee proteins - molecular properties of novel antimicrobial glycoprotein of royal jelly. The 2nd International Symposium on Antimicrobial Peptides, Saint-Maolo, France, 17-19 JUN 2009. (Bilikova, K – invited lecture)
[11] Bilikova K., Lehrach H., Simuth J.: Royal jelly proteins as a new class of physiologically active proteins with immunostimulatory and antimicrobial properties. Apimondia 2009 - 41st Congress, Montpellier, France, 15-20 SEP 2009. (Šimuth J. – invited lecture)
[12] Bilikova K., Simuth J.: Physiological plasticity of royal jelly proteins as a consequence of posttranslation modification - assumptions for application in medicine. 4th Medical Biotech Forum 2009, Dalian, China, 7-10 AUG 2009. (Bilikova, K – invited lecture)
[13] Bilikova K., Simuth J.: Honey as a drug. XVll. Internationak congress of innovators and inventors in beekeeping, Ostrava, Czech Republic, 10-12 SEP 2010. (Bilikova, K – invited lecture).
[14] Bukovska G.: The analysis of bacteriophage BFK20 genome. XXI. Biochemical congress, České Budejovice, Czech Republic, 14-17 SEP 2008. (Bukovska G. - keynote lecture)
[15] Farkasovsky M.: Structural insight into the septin filament assembly. XVI. Cytoskeleton club, Vranovska Ves, Czech Republic, 14-16 MAY 2008. (Farkasovsky M – Invited lecture)
[16] Garcia S., Ondrovicova G., Bauer J., Wilkinson A.J., Wilson K.S., Kutejova E.: Structure of the proteolytic domain of human mitochondrial Lon protease. 8th International Conference on AAA Proteins, Toronto, Canada, 12-16 JUL 2009. (Kutejova, E – Invited lecture)
[17] Hlinková V., Ling H.: The purification of PCNAs from Sulfolobus solfataricus - optimization of crystal growth. 4th Oulu summer school in Bioprocess Engineering - OSSIBE 4, Oulu, Finland, 11-15 JUN 2007. (Hlinkova V – Invited lecture)
[18] Janeček Š.: Bioinformatics of amylolytic enzymes in the post-genome era. International Conference on New Horizons in Biotechnology - NHBT-2007, Trivandrum, India, 26-29 NOV 2007. (Janeček S – Invited lecture)
[19] Janeček Š., Gabriško M., Urbániková Ľ.: A remote relatedness between the heteromeric amino acid transporters and enzymes from the alpha-amylase family. Biospectrum 2007 - International Symposium on Advances in Food Biotechnology and Nutrition, Tiruvalla, India, 30 NOV - 1 DEC 2007. (Janeček S – Invited lecture)
[20] Janecek S.: Classification and characterization of the alpha-amylase family. 2008 Agricultural Biotechnology Symposium, Seoul, Republic of Korea, 26-27 SEP 2008. (Janeček S – Invited lecture)
[21] Janecek S.: Alpha-amylase enzyme families - sequences, structures, specificities and evolution. International Conference on New Horizons in Biotechnology, Trivandrum, India, 21-24 NOV 2011. (Janeček S – Invited lecture)
37
[22] Kormanec J., Novakova R., Feckova L., Kutas P., Rehakova A.: A complex regulation of angucycline antibiotic auricin production in Streptomyces aureofaciens CCM 3239. International Conference on Emerging Trends In Biotechnology, Varanasi, India, 4-6 DEC 2009. (Kormanec, J. – invited lecture)
[23] Kutejova E.: Several aspects of the rule of the proteolytic domain of human LON protease in degradation process. Mitochondria: Function and Disfunction, Kibbutz Ein Gedi, Izrael, 21-24 NOV 2010. (Kutejova, E – Invited lecture)
[24] Kutejova E., Pevala V., Ondrovicova G., Ambro L., Bauer J.: ATP-dependent proteases and mitochondrial nucleoid. 7th International Conference Structure and Stability of Biomacromolecules, Kosice, Slovakia, 6-9 SEP 2011. (Kutejova, E – Keynote lecture)
[25] Nasso R., De Leo F., Bruno L., Krakova L., Pangallo D., Albertano P., Urzí C.: Microbial diversity on catacomb surfaces before and after biocide treatments. Sistemi Biologici e Beni Culturali, Palermo, Italy, 6-7 OCT 2009. (Pangallo, D – Invited lecture)
[26] Ondrovičová G., Adamušková H., Kutejová E.: Lon protease - new aspects in structure and function. 7th International Conference of AAA Protein, Cirencester, UK, 9-13 SEP 2007. (Kutejova, E – Invited lecture)
[27] Ondrovicova G., Bauer J., Pevala V., Ambro L., Augustinová E., Kutejova E.: Lon protease - dynamic protein with high flexibility and diverse functions. 6th International Conference Structure and Stability of Biomacromolecules SSB2009, Košice, Slovakia, 9-11 SEP 2009. (Kutejova, E – Invited lecture)
[28] Pevala V., Ondrovicova G., Ambro L., Sedo O., Zdrahal Z., Kutejova E., Bauer J.: Protease and peptidase activity of the mitochondrial ATP-dependent protease Lon can be separated. 9th International Conference on AAA Proteins, Kumamoto, Japan, 6-10 NOV 2011. (Kutejova, E – Invited lecture)
[29] Šimúth J., Bíliková K.: Apitherapy in the light of data from sequence of honeybee genome. XI. Phyto-apitherapy days with international participitation. Košice, Slovakia, 29-30 SEP 2007 (Šimuth, J - invited lecture)
[30] Simuth J., Bilikova K.: Multifunctionality of native and recombinant proteins of honeybee royal jelly: assumptions for application in pharmacy. 2nd World Conference, Celebrating the 100th Anniversary of the Nobel Prize Award to Paul Ehrlich, Nurnberg, Germany, 3-5 OCT 2008. (Šimuth, J - invited lecture)
[31] Simuth J, Bilikova K.: The physiological potential of proteins and peptides of honeybee royal jelly. 2nd National Apitherapy Congress, Expo and Workshops with International Participation, Apitherapy and Apipuncture, Iasi, Romania, 21-24 NOV 2008. (Šimuth, J - invited lecture)
[32] Simuth J., Bilikova K., Lehrach H.: A new view on honeybee defence system based on own proteinous antibiotics and phytochemicals. Apimondia 2009 - 41st Congress, Montpellier, France, 15-20 SEP 2009. (Šimuth, J - invited lecture)
[33] Šimúth J., Kraková T., Bíliková K.: Apiterapy and phytoapitherapy in postgenomics . Xll. Phyto-apitherapy days with international participitation. Košice, Slovakia, 26-27 SEP 2009. ( Šimúth, J - invited lecture)
[34] Simuth J., Bilikova K.: Functional proteomics of royal jelly proteins and their utilization in modern apitherapy. Apiculture in the XXl Century: Apiculture, Apitherapy and the Quality of Life, Moscow, Russia, 17-20 MAY 2010. ( Šimúth, J - keynote lecture)
[35] Simuth J., Bilikova K.: Rediscovery of medicinal effects of honey bee products. XII.Phyto-apitherapy days with international participations. Košice, Slovakia, 17-18 SEP 2011. (Šimúth J. - invited lecture)
38
[36] Urbanikova L.: Protein as the main variable in crystallization. FEBS Advanced Crystallization Course, Nové Hrady, Czech Republic, 3-10 OCT 2008. (Urbanikova, L - invited lecture)
[37] Urbanikova L.: Protein as the main variable in crystallization. FEBS Advanced Course Advanced Methods in Macromolecular Crystallization IV, Nové Hrady, Czech Republic, 25 JUN - 2 JUL 2010. (Urbanikova, L - invited lecture)
[38] Urbanikova L., Vrsanska M., Morkeberg Krogh K.B., Hoff T., Biely P.: Structural basis for substrate recognition by GH30 glucuronoxylanases. 12th Bratislava Symposium on Saccharides, Smolenice, Slovakia, 19-23 JUN 2011. (Urbanikova, L - invited lecture)
[39] Urbanikova L., Vrsanska M., Morkeberg Krogh K.B., Hoff T., Biely P.: Structural principles of substrate specificity in GH30 glucuronoxylanases. 7th International Conference Structure and Stability of Biomacromolecules, Kosice, Slovakia, 6-9 SEP 2011. (Urbanikova, L - invited lecture)
[40] Urzí C., De Leo F., Bruno L., Krakova L., Pangallo D., Albertano P.: How to control biodeterioration of cultural heritage: an integrated methodological approach for the diagnosis and treatment of affected monuments. Works of Art & Conservation Science Today, Thessaloniki, Greece, 26-28 NOV 2010. (Pangallo, D. - invited lecture)
ii. List of employees who served as members of the organising and/or programme
[10] Lubos Klucar - Information Technology in Bio- and Medical Informatics (ITBAM´10), Bilbao, Spain, 30AUG – 3 SEP 2010
[11] Lubos Klucar - Workshop on Human-Computer Interaction & Knowledge Discovery and Data Mining (HCI-KDD) at USAB 2011 Conference, Graz, Austria, 24 NOV 2011
[12] Imrich Barak - 4rd European Spores Conference, Cortona, Italy, 27-29 MAY 2010.
39
iii. List of employees who served as members of important international scientific
bodies (e.g. boards, committees, editorial boards of scientific journals)
[1] Jacob Bauer
European crystallographic association (member)
[2] Gabriela Bukovská
World Journal of Virology (Editorial board member)
[3] Katarína Bíliková
Eurbee - European Commission for Apidological Research (member)
International Honey Commission (member)
[4] Štefan Janeček
Biologia (Managing Editor, section Cellular and Molecular Biology)
Journal of Applied Glycoscience (Editorial Board member)
Biochemical Society, UK (member)
[5] František Jurský
Frontiers in Molecular Neuroscience (Review editor)
[6] Ján Kormanec
Biotechnology Strategy Group of European Academies Science Advisory Council (EASAC) (member)
[7] Luboš Kľučár
EMBnet National node (manager)
EMBnet.news (member)
[8] Bystrík Polek
Biologia (section Cellular and Molecular Biology, Advisory board member)
[9] Matej Stano
EMBnet (ETPC chairman)
[10] Jozef Šimúth
International Honey Commission (member, Apimedicine section chairman)
[11] Jozef Timko
European Federation of Biotechnology (committee member)
Applied Genome Research group at EFB (member)
EÚ Knowledge Based Bio-Economy (KBBE) (member; SR delegate)
Biologia (section Cellular and Molecular Biology, Advisory board member)
[12] Ľubica Urbániková
Czech and Slovak Crystallographic Association (member)
[13] Marcel Zámocký
The Open Biochemistry Journal (Editorial board member)
PeroxiBase (administrator)
iv. List of international scientific awards and distinctions
none
40
v. List of employees with the highest H – index indicating field of science by WOS
Ing. Štefan Janeček, DrSc. 25 RNDr Ján Kormanec, DrSc. 22 RNDr. Imrich Barák, DrSc. 17 Doc. Ing. Jozef Šimuth, DrSc. 16 Ing. Jozef Ševčík, DrSc. 16 RNDr. Marcel Zámocký, CSc. 15 Ing. Alexandra Záhradníková, DrSc. 14 Prof. Ing. Jozef Timko, DrSc. 12 RNDr. Dagmar Homerová, CSc. 12 Ing. Eva Kutejová, CSc. 11 Ing. Eva Hostinová, CSc. 11 Ing. Juraj Gašperík, CSc. 11 RNDr. František Jurský, CSc. 10 RNDr. Katarína Bíliková, PhD. 9 RNDr. Katarína Muchova, CSc. 9 RNDr. Gabriela Bukovská, CSc. 8 Mgr. Renáta Nováková, CSc. 8 Dr. Domenico Pangallo, PhD. 8 Ing. Andrej Godány, CSc. 7
National position of the individual researchers
i. List of invited/keynote presentations at national conferences documented by
an invitation letter or programme
[1] Barak I., Barbaro M., Blaskovic D., Mullerova D., Campo A., Raffo L.: DNA biochips for microbial pathogens detection. Nanoved 2007, Bratislava, Slovakia, 11-14 NOV 2007. (Barák I – Invited lecture)
[2] Šimúth J. and Bíliková K. (2007) „Bee diseases.“ National bee exhibition, Banská Bystrica, (21. 10. 2007) (Šimúth J - invited lecture)
[3] Godany A., Vidova B.: Variability of surface proteins of Streptococcus agalactiae. Security and quality of raw materials and food III. Scientific conference with international participation connected with 5th anniversary of foundation of FBP SPU in Nitra, Nitra, Slovakia, 31 JAN - 1 FEB 2008. (Godany A - invited lecture)
[4] Bíliková K.: Royal jelly proteins, a new criterion for evaluation of honey quality. National exhibition of beekeeping, Trnava, Slovakia, 14-15 NOV 2009. (Bíliková K - invited lecture)
[5] Krakova L., Pangallo D., Chovanova K., Simonovicova A.: Analysis of pergamen: study of contaminating microorganisms and molecular identification of origin – animal species used during preparation. Message in pergamen, Martin, Slovakia, 4-6 NOV 2009. ( Pangallo D - invited lecture)
[6] Vidova B., Godany A.: Rapid detection of pathogenic microorganism in food. Security and quality of raw materials and food III. Scientific conference with international participation, Nitra, Slovakia, 3-4 FEB 2010.
[7] Bíliková K.: Royal jelly proteins, a new criterion for evaluation of honey quality. 14.Exhibition of beekeeping materials and honeybee products, Trenčín, Slovakia, 14-17 APR 2010. (Bíliková K - invited lecture)
[8] Godany A., Farkasovska J.: Application of bacteriophages and their gene product in biotechnology and food safety. Security and quality of raw materials and food III. Scientific conference with international participation, Nitra, Slovakia, 3-4 FEB 2010.
41
[9] Simuth J., Bílikova K.: Bee and Man. XV. Medical congres of natural medicine, Trnava, Slovakia, 14-15 OCT 2011. (Šimúth J - invited lecture)
[10] Bílikova K.: New approach for evaluation of honeybee products quality. Agrokomplex 2011, Nitra, Slovakia, 20 AUG 2011. ( Bíliková K - invited lecture)
ii. List of employees who served as members of organising and programme
committees of national conferences
None
iii. List of employees serving in important national scientific bodies (e.g. boards,
committees, editorial boards of scientific journals)
[1] Peter Ferianc
Expert Panel on Biological Safety, Ministry of Environment of SR (member)
[2] Andrej Godány
Nova Biotechnologica (Editorial Board member)
[3] Štefan Janeček
Nova Biotechnologica (Editorial Board member)
[4] Ján Kormanec
Slovak Society for Biochemistry and Molecular Biology (Committee member)
Council Centres of Excellence Program (member)
[5] Jozef Šimúth
Expert Panel on Biological Safety, Ministry of Environment of SR (member)
Working Group III. - Environment - National Convent for EU at Slovak Foreign Policy Association (member)
Expert Session for Biotechnology - Slovak Academy of Engineering Sciences (guarantee)
[6] Jozef Timko
Slovak National Committee for Biochemistry and Molecular Biology (member)
Expert Panel on Biological Safety, Ministry of Environment of SR (member)
Commission for Collaboration with XFEL (European X-ray Free-Electron Laser Facility) - Ministry of Education, Science, Research and Sport of the Slovak Republic (member)
Working Group of Accreditation Commission for Life Sciences - Ministry of Education, Science, Research and Sport of the Slovak Republic (member)
6FP ESW Programme Committee - for research, technical development and demonstration activities of specific programme “Integrating and Strengthening the European Research Area” (independent expert)
State Programme Council for Science and Development - Development of Progressive Technologies for Powerful Economy (member)
Slovak Society for Biotechnology (chairman)
Slovak Society for Biochemistry and Molecular Biology (Committee vice-chairman)
iv. List of national awards and distinctions
2008
[1] Bystrík Polek - Commemorative Plaque; awarded by: Presidium of SAS
42
[2] Jozef Timko - Medal of SAS for Support of Science; awarded by: Presidium of SAS
[3] Ján Kormanec - Personality of Kysuce 2008 for Act of the Year in Science and Economy; awarded by: Kysuce Culture Foundation
[4] Jozef Šimúth - Award for Lifetime Achievements in the Field of Science and Technology; awarded by: Deputy Prime Minister and Minister of Education, Science, Research and Sport of the Slovak Republic
2010
[5] Katarína Bíliková - Scientist of the Year 2009 of SR - For Achievements in the 2009 EU Programmes; awarded by: Journalist-Studio - Club of scientific and technical journalists of the Slovak journalist syndicate
[6] Jozef Ševčík - Award of the Minister of Education, Science, Research and Sport of the Slovak Republic for Science and Technology; awarded by: Minister of Education, Science, Research and Sport of the Slovak Republic
v. Supplementary information and/or comments documenting international and
national status of the Organisation
Numerous scientists from the Institute are internationally recognized in their fields of
research. They are members of international scientific boards, reviewers for several
international grant agencies and international scientific journals. Scientists have been
invited to international conferences and seminars.
4. Project structure, research grants and other funding resources
International projects and funding
i. List of major projects within the European Research Area – 6th and 7th
Framework Programme of the EU, European Science Foundation, NATO, COST,
INTAS, CERN, etc. (here and in items below please specify: type of project, title,
grant number, duration, total funding and funding for the Organisation,
responsible person in the Organisation and his/her status in the project, e.g.
coordinator, work package leader, investigator)
[1] International Consortium on Ticks and Tick-Borne Diseases Grant agency: 6th Framework Programme Grant registration number: FP6-2002-INCO-DEV-1-510561 Duration: 10/2004-9/2008 Total Funding: 1 842 000,- EUR Funding for IMB SAS 2007 - 2008: 16 099,32 EUR Funding from SAS - MVTS: 3 485,36 EUR Responsible person in IMB SAS: Imrich Barák – Principal investigator Coordinator: Franz Jongejan, Faculty of Veterinary Medicine, Utrecht University Number of cooperation institutions including SR: 55
[2] Nano Arrayed Systems based on Self Assembling Proteins Grant agency: 6th Framework Programme Grant registration number: STREP 013523 NAS-SAP Duration: 3/2005-2/2008
43
Total Funding: 2 299 702,- EUR Funding for IMB SAS 2007 - 2008: 121 671,75 EUR Funding from SAS - MVTS: 19 451,63 EUR Responsible person in IMB SAS: Imrich Barák – Principal investigator Coordinator: Simon Cutting, Royal Holloway and Bedford New College, London, UK; Number of cooperation institutions including SR: 9
[3] Bees in Europe and Sustainable Honey Production – BEESHOP Grant agency: 6th Framework Programme Grant registration number: No. 022568 Contract FOOD-CT-2006-022568 Project Duration: 03/2006 – 02/2009 Total Funding: 1 865 000 EUR Funding for IMB SAS 2007 - 2009: 76 591,72 Eur Funding from SAS - MVTS: 16 862,11 Eur Responsible person in IMB SAS: Jozef Šimúth – Principal investigator Coordinator: R. Moritz, Martin-Luther University, Halle-Wittenberg, DE Number of cooperation institutions including SR: 15
[4] Applied venomics of the species Conus consors for the production of innovative biomedical drugs. - CONCO Grant agency: 6th Framework Programme Grant registration number: 037592 Duration: 02/2007 – 01/2013 Total Funding: 10 696 782 EUR Funding for IMB SAS: 106608,9 Eur Funding from SAS - MVTS: 31 301,74 Eur Responsible person in IMB SAS: Katarína Bíliková – Principal investigator Coordinator: Dr. R. Stöcklin, Atheris Laboratories, Switzerland Number of cooperation institutions including SR: 18
[5] Bees in Europe and the decline of honeybee colonies - BEEDOC Grant agency: 7th Framework Programme Grant registration number: 7RP EU 244956 Duration: 03/2010 – 02/2013 Total Funding: 2 991 577 EUR Funding for IMB SAS 2010 - 2011: 28 896,50 Eur Funding from SAS – MVTS: 4 000,- Eur Funding from SRDA: 13 540,41 Eur Responsible person in IMB SAS: Katarína Bíliková – Principal investigator Coordinator: R. Moritz, Institut fur Zoologie, Martin-Luther University Halle, DE Number of cooperation institutions including SR: 11
[6] Development and exploitation of Bacillus subtilis as a host for the production of protein complexes and membrane proteins (BACELL EuroSCOPE) Grant agency: European Science Foundation ESF Grant registration number: ESF-EC-0106 Duration: 01/2006-12/2009 Total Funding: 743 752,- EUR Funding for IMB SAS 2007 - 2009: 87418,17 Eur Responsible person in IMB SAS: Imrich Barák – Principal investigator Coordinator: Jan Maarten van Dijl, University of Groningen, Holandsko
[7] Engineered Radionuclide Labelled Antibodies Grant agency: EUREKA
44
Grant registration number: E! 3537 ENGRAB Duration: 01/ 2006 – 12/ 2009 Funding for IMB SAS 2007 - 2009: 19 916,56 Eur Principal investigator in IMB SAS: Marcela Múdra Coordinator: Juraj Sedláček, Institute of molecular genetics of CAS, Prague Number of cooperation institutions including SR: 4
[8] Next Generation Sequencing Data Analysis Network Grant agency: COST Grant registration number: BM1006 Duration: 03/2011-03/2015 Responsible person in IMB SAS: Ľ. Kľučár – Principal investigator Coordinator: Erik BONGCAM-RUDLOFF, The Swedish University of Agricultural Sciences BMC, Uppsala,Sweden Number of cooperation institutions including SR: 22
ii. List of other international projects incl. total funding and funding for the
Organisation
[1] Functional Genomic of honeybee Advance of Common project of IMB SAS and Max-Planck-Institute for Molecular Genetics, Berlin, Germany Duration: 07/2004 -03/2011 Total Funding: 120 000 EUR Funding for IMB SAS 2007 - 2011: 120 000 Eur Funding from SAS - MVTS: 17 277,78 Eur Responsible person in IMB SAS: Katarína Bíliková - Principal investigator Coordinator: Max-Planck-Institute for Molecular Genetics, Berlin, Germany Number of cooperation institutions including SR: 2
[2] Structure, function and interaction studies of the cell differentiation protein SpoIIE from Bacillus subtilis Grant agency: The Wellcome Trust, (Collaborative Research Initiative Grant) Grant registration number: 082829/Z/07/Z-The Wellcome Trust Duration: 01/2008 - 09/2010 Total Funding: 305 667,87 EUR (254 010 GBP) Funding for IMB SAS: 73121 Eur Responsible person in IMB SAS: Imrich Barák – Principal investigator Coordinator: University of York, Department of Chemistry, York Number of cooperation institutions including SR: 2
[3] Mining the metagenome for modulators of cell and protein activities Grant agency: Humboldt Foundation Grant registration number: 3.4 - Fokoop - DEU/1133283 Duration: 07/2011 – 06/2014 Total Funding: 55 000,- Eur Funding for IMB SAS 2011: 17000 € Responsible person in IMB SAS: Marian Farkašovský – Coordinator Number of cooperation institutions including SR: 2
[4] Electronic detection of biomolecular processes in integrated biosensors Bilateral Scientific Cooperation Grant registration number: 132.48.1 Duration: 01/2007 - 12/2009
45
Total Funding: 5 000 EUR Funding for IMB SAS: 2 545 EUR (CNR Italy) Responsible person in IMB SAS: Imrich Barák – Principal investigator Coordinator: Massimo Barbaro, University of Cagliari, Italy Number of cooperation institutions including SR: 2
[5] Self assembly and structure of light harvesting antennas Grant agency: International Visegrad Found Grant registration number: 20820159 Duration: 03/2009 – 03/2010 Total Funding: 10 000,- EUR Funding for IMB SAS: 1200,- EUR Responsible person in IMB SAS: Ľubica Urbaniková - Principal investigator Coordinator: Gyozo Garab, Biological Research Centre of Hungarian Academy of Sciences Number of cooperation institutions including SR: 4
[6] Cleavage of the M6PR and characterization of the proteolytic fragments of the M6PR Grant agency: Wissenschaftlich-Technische Zusamenarbeit Österreich – Slowakei Grant registration number: SK-11 AUT-9 Duration: 01/2006-12/2007 Total Funding: 3430,82 EUR Funding for IMB SAS 2007: 3 519 Eur Responsible person in IMB SAS: Eva Kutejová – Principal investigator Coordinator: Hannes Stockinger Department of Molecular Immunology, Centre for Biomolecular Medicine and Pharmacology, Medical University of Vienna
[7] Integrated structural biology infrastructure Grant agency: European Strategy Forum on Research Infrastructures (ESFRI) Duration: 04/2008 – 12/2012
Funding from SAS for IMB SAS 2008 - 2011: 7300 € Responsible person in IMB SAS: Jozef Ševčík - Principal investigator Coordinator: prof. David Stuart, University of Oxford, UK Number of cooperation institutions including SR: 25
iii. List of other important projects and collaborations without direct funding
[1] Molecular characterization of microbial communities involved in the biodegradation of culture heritage Bilateral Scientific Cooperation Grant registration number: CNR-SAV; 2/UNI11 Duration: 01/2007 – 12/2009 Responsible person in IMB SAS: Domenico Pangallo - Coordinator Number of cooperation institutions including SR: 2
[2] International collaboration Czech-Slovak Principal investigator: Eva Kutejová, ÚMB SAV, Bratislava Cooperation: Jiří Janata, Institute of Microbiology, Academy of Sciences Czech Republic, Praha Grant agency: Academy to Academy agreement Duration: Co-operation was not time-limited No funding
[3] Charakterization of the RpoE regulon in stress response and pathogenicity of Salmonella enterica
46
Bilateral Scientific Cooperation Principal investigator: Ján Kormanec, ÚMB SAV, Bratislava Cooperation: Prof. Mark Roberts, Institute of Comparative Medicine, Faculty of Veterinary Medicine, University of Glasgow, Glasgow, U.K. Duration: Co-operation was not time-limited No funding
[4] Charakterization of the SigB regulon in stress response and pathogenicity of Staphylococcus aureus Bilateral Scientific Cooperation Principal investigator: Ján Kormanec, ÚMB SAV, Bratislava Cooperation: Dr. Markus Bischoff, Prof. Mathias Herrmann, Institute for Medical Microbiology and Hygiene, University Hospital of Saarland, Homburg, Germany Duration: Co-operation was not time-limited No funding
National projects and funding2
i. List of State Research Programmes, and their funding
[1] Development of progressive technologies for powerful economics (area „Biotechnologies“ – "Increase of production of biologically active substances" "increase of economic efficiency of the strain Penicilium chrysogenum") Grant Agency: State Research Programmes Registration number: VaV 2004 SP26/028 0A 00/028 0A 03 Duration: 07/2004- 12/2007 Funding 2007: 165 970 Eur Principal investigator: Ján Turňa
ii. List of project supported by APVV
[1] A new natural bacterial strains containing genes of catabolic and detoxication pathways (cat, yodA, czc, ncc) perspective for remediation biotechnology Registration number: APVT-51-024804 Duration: 1/2005-12/2007 Funding 2007: 39 932 EUR Principal investigator: Bystrík Polek, IMB SAV
[2] Bacterial programmed cell death as a tool for development of alternative drugs Registration number: APVT-51-027804 Duration: 1/2005-12/2007 Funding 2007: 30 538 EUR Principal investigator: Imrich Barák, IMB SAV
[3] Bioinformatics approach to discovery of gene regulatory networks in bacteriophages Registration number: APVT-51-02504 Duration: 1/2005-12/2007 Funding 2007: 13 045 EUR Principal investigator: Ľuboš Kľučár, IMB SAV
[4] Mechanism of the substrates recognition by the Lon protease Registration number: APVT-51-029604
2 Excluding projects for the popularisation of science
47
Duration: 1/2005-12/2007 Funding 2007: 12 049 EUR Principal investigator: Eva Kutejová, IMB SAV
[5] The manose 6-phosphate receptor as the regulator of fibrinolysis on the cell surface
Registration number: APVT-51-026204 Duration: 1/2005-12/2007 Funding 2007: 12 614 EUR Principal investigator: Vladimír Leksa, IMB SAV
[6] The role of RpoE regulon in pathogenesis of Salmonella typhimurium Registration number: APVT-51-012004 Duration: 01/2005 – 12/2007 Funding 2007: 27 816 EUR Principal investigator: Ján Kormanec, IMB SAV Cooperation: Mark Roberts, University of Glasgow, Glasgow, U.K.
[7] Study of basic cell processes in model microorganism Bacillus subtilis: Cell division and programmed cell death Registration number: APVT LPP-0218-06 Duration: 11/2006-10/2010 Funding 2007-2010: 153 422 EUR Principal investigator: Imrich Barák, IMB SAV
[8] Heavy metals resistance as a virulence factor of pathogenic bacteria Registration number: 20/054005 Duration: 03/2006-02/2009 Funding in 2007 - 2009: 12 448 EUR Coordinator: Ján Turňa Principal investigator from IMB SAS: Peter Ferianc
[9] Molecular diagnostics of tick-borne pathogens and development of DNA chip. Registration number: APVV -51-009205 Duration: 01/2006-12/2008 Funding in 2007 - 2008: 59 782 EUR Principal investigator: Imrich Barák, IMB SAV Coordinator: M. Derdáková, Insitute of Zoology, SAS, Bratislava, Slovakia
[10] Cell volume and insuline secretion. Registration number: APVV-0235-06
Duration: 02/2007-12/2009 Funding: 45 807 EUR Principal investigator: Jozef Timko, IMB SAV Coordinator: Vladimír Štrbák, ÚEE SAV
[11] Structure-function relationship of the ryanodine receptor domains involved in CPVT arrhythmias Registration number: APVV-0139-06 Duration: 02/2007-12/2009 Funding: 115 847 EUR Principal investigator: Jozef Ševčík, IMB SAV
[12] Functional and structural analysis of corynephage BFK20 replication module
48
Registration number: APVV-0354-07 Duration: 06/2008-05/2011 Funding: 77 707 EUR Principal investigator: Gabriela Bukovská, IMB SAV
[13] Molecular characterization of regulation and biosynthesis of polyketide antibiotic auricin in Streptomyces aureofaciens CCM3239
Registration number: APVV-0017-07 Duration: 06/2008-12/2010 Funding: 110 469 EUR Principal investigator: Ján Kormanec, IMB SAV
[14] The role of catalase-peroxidase genes of microbial isolates in processes of oragnic fraction solid waste degradation
Registration number: APVV- 0444-07 Duration: 09/2008-12/2010 Funding: 124 909 EUR Principal investigator: Bystrík Polek, IMB SAV
[15] Molecular characterization of yeast communities in the production of typical Slovak wines
Registration number: APVV-0219-07 Duration: 06/2008-12/2010 Funding: 48 762 EUR Principal investigator: Domenico Pangallo, IMB SAV Coordinator: Tomáš Kuchta, Food Research Institute, Bratislava
[16] Molecular mechanisms implicated in the control of mitochondrial integrity in eukaryotic cells
Registration number: APVV-0024-07 Duration: 06/2008-12/2010 Funding: 57 657 EUR Principal investigator: Eva Kutejová, IMB SAV Coordinator: Jozef Nosek, Faculty of Natural Sciences, Comenius University Bratislava
[17] Occurence, mobilization and dissemination of resistance and virulence genes among Salmonellae
Registration number: APVV- LPP-0097-07 Duration: 06/2008-12/2008 Funding: 7 137 EUR Principal investigator: Jozef Timko, IMB SAV
[18] Structural studies of membrane proteins from photosynthetic bacteria Grant registration number: SK-HU-0022-08 Duration: 05/2009 – 12/2010 Total Funding: 2987,46 EUR Funding for IMB SAS: 2987,46 Eur Responsible person in IMB SAS: Ľubica Urbaniková, IMB SAV - Coordinator Number of cooperation institutions including SR: 2
[19] Use of selected autochthon yeasts with adsorption activities to improve the quality and safety of wine
Grant registration number: APVV SK-IT-0019-08
49
Duration: 06/2009 – 12/2011 Total Funding: 7966,54 EUR Funding for IMB SAS: 7554,15 EUR Responsible person in IMB SAS: Domenico Pangallo - Principal investigator Coordinator: Prof. Andrea Caridi Number of cooperation institutions including SR: 2
[20] Bioinformatics analysis of amylases Registration number: APVV- LPP-0417-09 Duration: 09/2009 - 08/2013 Funding 2009 - 2011: 41 970 EUR Principal investigator: Štefan Janeček, IMB SAV
[21] Rapid detection of pathogenic bacteria in food practice Registration number: VMSP-P-0111-09 Duration: 10/2009 - 07/2011 Funding: 26 600 EUR Principal investigator: Andrej Godány, IMB SAV Coordinator: EL spol. s r.o., Spišská Nová Ves
[22] Lipid domains in cell division and programmed cell death in Bacillus subtilis Registration number: APVV-00335-10 Duration: 05/2011 - 10/2014 Funding 2011: 32839 EUR Principal investigator: Imrich Barák, IMB SAV
[23] Structural and functional characterization of human ryanodine receptor regulation and its malfunction caused by mutations
Registration number: APVV-0628-10 Duration: 05/2011-10/2014 Funding 2011: 47 852 EUR Principal investigator: Jozef Ševčík¸ IMB SAV
[24] New bacteriophages and phage proteins for pathogen devitalization in foods prepared by synthetic biology approach
Registration number: APVV-0098-10 Duration: 05/2011 - 10/2014 Funding 2011: 23 165 EUR Principal investigator: Gabriela Bukovská, IMB SAV Coordinator: Hana Drahovská, Faculty of Natural Sciences, Comenius University Bratislava
[25] Molecular architecture, dynamics and evolution of chromosomes in yeast mitochondria
Registration number: APVV-0123–10 Duration: 05/2011 - 10/2014 Funding 2011: 14 000 EUR Principal investigator: Eva Kutejová, IMB SAV Coordinator: Jozef Nosek, Faculty of Natural Sciences, Comenius University Bratislava
[26] Broadening of scientific knowledge on quality and safety of Slovakian bryndza cheese using modern molecular, microbiological, and chromatographic methods
Registration number: APVV-0590-10
50
Duration: 05/2011-10/2014 Funding 2011: 14 180 EUR Principal investigator: Domenico Pangallo, IMB SAV Coordinator: Tomáš Kuchta, Food Research Institute, Bratislava
[27] Structure of foci and emerging diseases with emphasis on role of rodents in urban type of natural foci of diseases
Registration number: APVV -00267-10 Duration: 05/2011 - 10/2014 Funding 2011: 5 100 EUR Principal investigator: Imrich Barák, IMB SAV
Coordinator: Michal Stanko, Insitute of Zoology, SAS, Bratislava
iii. Number of projects supported by the Scientific Grant Agency of the Slovak
Academy of Sciences and the Ministry of Education (VEGA) for each year, and
their funding
VEGA 2007 2008 2009 2010 2011
number 16 18 19 18 16
funding in the year (EUR) 70736 80163 86035 114386 115834
Summary of funding from external resources
External resources 2007 2008 2009 2010 2011 total average
Summary of external resources of the EU Structural Funds (ERDF/ESF)
[1] Centre of excellence for protection and use of landscape and biodiversity Grant agency: ASFEU Grant registration number: ITMS 26240120014 Duration: 05/2009 – 11/2011 Total Funding: 1 327 757 Eur Funding for IMB SAS: 111 110,84 Eur Responsible person in IMB SAS: Peter Ferianc - Principal investigator Coordinator: Henrik Kalivoda, Institute of Landscape Ecology SAS Number of cooperation institutions: 7
51
[2] Centre of excellence for translation research in molecular medicine - TRANSMED Grant agency: ASFEU
Grant registration number: ITMS 26240120008 Duration: 06/2009 – 05/2011 Total Funding: 1 327 757 Eur Funding for IMB SAS: 7645,92 € Responsible person in IMB SAS: Ján Kormanec - Principal investigator Coordinator: Silvia Pastoreková, Institute of Virology SAS Number of cooperation institutions: 7
[3] Centre of Excelence for the Use of Informational Biomacromolecules in Prevention of Diseases and for Improvement of the Quality of Life - BIOMAKRO
Grant agency: ASFEU Grant registration number: ITMS 26240120003 Duration: 05/2009 – 10/2011 Total Funding: 1 391 315 Eur Funding for IMB SAS: 0 Eur Responsible person in IMB SAS: Jozef Timko - Principal investigator Coordinator: Marta Kollárová, Faculty of Natural Sciences Comenius University Number of cooperation institutions: 6
[4] Prionoses transferable to human: Research and development of cell model with potential in applications
Grant agency: ASFEU Grant registration number: ITMS 26240220008 Duration: 10/2009 – 09/2012 Total Funding: 494 082 EUR Funding for IMB SAS 2009 - 2011: 36 541,- Eur Responsible person in IMB SAS: Imrich Barák - Principal investigator Coordinator: Michal Novák, The Institute of Neuroimmunology SAS Number of cooperation institutions: 2
[5] New microbial isolates containig genes of catabolic and detoxication pathways and their use in biotechnology
Grant agency: ASFEU Grant registration number: ITMS 26240220010 Duration: 09/2009 – 09/2012 Total Funding: 479 302,19 EUR Funding for IMB SAS : 96 535,75 Eur Responsible person in IMB SAS: Bystrík Polek - Coordinator Number of cooperation institutions: 2
[6] Centre of excellence for translation research in molecular medicine - TRANSMED 2 Grant agency: ASFEU
Grant registration number: ITMS 26240120030 Duration: 06/2010 – 05/2012 Total Funding: 2 647 857 Eur Funding for IMB SAS 2010-2011: 1235,04 € Responsible person in IMB SAS: Ján Kormanec - Principal investigator Coordinator: Juraj Kopáček, Institute of Virology SAS Number of cooperation institutions: 7
52
[7] Centre of Excelence for the Use of Informational Biomacromolecules in Prevention of Diseases and for Improvement of the Quality of Life - BIOMAKRO 2
Grant agency: ASFEU Grant registration number: ITMS 26240120027 Duration: 02/2010 – 01/2013 Total Funding: 2 788 317 Eur Funding for IMB SAS 2010-2011: 0 Eur Responsible person in IMB SAS: Andrej Godány - Principal investigator Coordinator: Marta Kollárová, Faculty of Natural Sciences Comenius University Number of cooperation institutions: 6
[8] Development of the diagnostic methods for the detection of tick-borne pathogens and the techniques for the preparation of the vaccine development directed against ticks
Grant agency: ASFEU Grant registration number: ITMS 26240220044 Duration: 11/2010 – 10/2013 Total Funding: 939 914,76 Funding for IMB SAS 2010 - 2011: 258 237 Eur Responsible person in IMB SAS: Imrich Barák - Principal investigator Coordinator: Dušan Žitňan, Institute of Zoology SAS Number of cooperation institutions: 3
[9] Excellence centre for Glycomics Grant agency: ASFEU Grant registration number: ITMS 26240120031 Duration: 09/2010 – 05/2013 Total Funding: 3 977 975 EUR Funding for IMB SAS 2010 - 2011: 154 100 Eur Responsible person in IMB SAS: Juraj Gašperík - Principal investigator Coordinator: Ján Mucha, Institute of Chemistry SAS Number of cooperation institutions: 6
[10] Developing a Competency Center for Research and Development in Molecular Medicine
Grant agency: ASFEU Grant registration number: ITMS 26240220071 Duration: 10/2011 - 11/2014 Total Funding: 1 892 138,21 EUR Funding for IMB SAS: 64 514,21 EUR Responsible person in IMB SAS: Ľubica Urbániková - Project manager Coordinator: Prof. RNDr. Ján Turňa, CSc., Comenius University Bratislava Number of cooperation institutions including SR: 14
v. Supplementary info and/or comments on research projects and funding
resources
During the assessed period, the ratio between external and institutional funding
increased, with the great rise coming from international resources (mainly the EU).
The institute collaborated in 15 internationally funded projects. The other significant
source of external funding was from 27 APVV projects and VEGA grants. In addition,
53
the Institute also participated in 10 projects funded by EU Structural funds, and was a
coordinator in one of these.
5. Organisation of PhD studies, other pedagogical activities
i. List of accredited programmes of doctoral studies (as stipulated in the
previously effective legislation as well as in the recently amended Act on the
Universities). Period of validity of accredited scientific disciplines,
characterization of perspectives of PhD study on the Organisation
4.2 Life science 4.2.3 Molecular Biology in cooperation with: Faculty of Natural Sciences, Comenius University, Bratislava (2006 – present) Slovak Agriculture University; Nitra (2005 -31.8.2012) (Guarantee from the Institute: Ján Kormanec) 4.2.7 Microbiology in cooperation with: Faculty of Natural Sciences, Comenius University, Bratislava (2006 – present) Faculty of Pharmacy, Comenius University, Bratislava (2005 – 31.8.2010) (Guarantee from the Institute: Imrich Barák) (The head of PhD training centre at the Institute: Imrich Barák) Organization strongly encourages applying for PhD studies for candidates coming from following field of research – molecular biology, microbiology, genetics, biophysics, bioinformatics. The possible supervisors are evaluated by Scientific Board of the Institute.
54
ii. Summary table on doctoral studies (number of internal/external PhD students;
number of students who completed their study by a successful thesis defence;
number of PhD students who quitted the programme)
PhD study
number of potential PhD
supervisors
PhD students
nu
mb
er
de
fen
de
d t
he
sis
stu
de
nts
qu
itte
d
nu
mb
er
de
fen
de
d t
he
sis
stu
de
nts
qu
itte
d
nu
mb
er
de
fen
de
d t
he
sis
stu
de
nts
qu
itte
d
nu
mb
er
de
fen
ded
th
esis
stu
de
nts
qu
itte
d
nu
mb
er
de
fen
ded
th
esis
stu
de
nts
qu
itte
d
internal 13 0 2 13 1 2 15 1 1 15 4 2 13 5 1
external 9 2 0 8 0 1 5 2 1 1 5 0 1 0 1
supervised at external
institution by the research
employees of the assessed
organisation
1 0 0 1 0 1 0 0 0 0 0 0 1 0 0
12/31/2011
26
12/31/200912/31/2007 12/31/2008 12/31/2010
29 30 31 30
iii. Postdoctoral positions supported by
a) external funding (specify the source)
Full time position of Magda Lukáčová funded by the 6th FP EU grant project NAS-SAP – Nano Arrayed Systems based on Self Assembling Proteins.
Full time position of Jana Melničáková funded by EU Structural fund Development of the diagnostic methods for the detection of tick-borne pathogens and the techniques for the preparation of the vaccine development directed against ticks., No. 26240220044
Part time position (50%) of Bystrík Polek funded by The Agency of the Ministry of Education EÚ OPVaV-2008/4.2/01-SORO, No. 26240220010, New microbial isolates containig genes of catabolic and detoxication pathways and their use in biotechnology.
2 months contract of Roman Šmidák funded by integrated Project 6FP EU, Applied venomics of the species Conus consors for the production of innovative biomedical drugs.(CONCO), No. 037592
b) internal funding - the Slovak Academy of Sciences Supporting Fund of Stefan
Schwarz
Postdoctoral position - Naďa Pavlendová funded by the Slovak Academy of Sciences Supporting Fund of Stefan Schwarz (2011-2015)
supervised rigorous thesis (in total) N/A N/A N/A N/A N/A
members in PhD committees (in total) 3 4 5 6 3
members in DrSc. committees (in total) 3 2 1 2 1
members in university/faculty councils (in
total)2 2 2 2 1
members in habilitation/inauguration
committees (in total)1 0 2 2 1
3
v. List of published university textbooks
[11] Simonovicova, A., Ferianc, P., Frankova, E., Pavlickova, K., Pieckova, E.
Mikrobiológia pre environmentalistov Univerzita Komenského, Bratislava 2008. 156 s.
(ISBN 978-80-223-2314-7)
vi. Number of published academic course books
None
vii. List of joint research laboratories/facilities with the universities
[1] Joint research laboratory of Faculty of Natural Sciences of Comenius University,
Bratislava and Institute of Molecular Biology
[2] Joint research laboratory of Faculty of Pharmacy of Comenius University, Bratislava
and Institute of Molecular Biology
[3] Joint research laboratory of Faculty of Medicine of Comenius University, Bratislava
and Institute of Molecular Biology
[4] Joint research laboratory of Faculty of Natural Sciences of University of SS Cyril and
Methodius, Trnava and Institute of Molecular Biology
[5] Joint research laboratory of Faculty of medicine of Charles University, Prague and
Institute of Molecular Biology
3 Do not include time spent with bachelor, diploma or PhD students during their supervising
56
[6] Joint research laboratory of Faculty of Mathematics, Physics and Informatics of
Comenius University, Bratislava and Institute of Molecular Biology
viii. Supplementary information and/or comments on doctoral studies and
pedagogical activities
The Institute of Molecular Biology is accredited for supervising PhD students in two Life science programmes: “Molecular Biology” and “Microbiology”, Though all Slovak Academy of Sciences PhD students have needed to be registered at a university since 2005.There are two forms of PhD study, internal (4 years) and external (5 years). Internal PhD students are normally supported by internal SAS funding, but, during the period 2007–2011, three PhD students were funded by APVV-LPP project grants. External PhD students are usually employees of the Institute improving their qualification, but the Institute has also supervised PhD students carrying out working at external institutions: the Food Research Institute and the Public Health Authority of the Slovak Republic, both in Bratislava. During the assessed period there were 31 scientists in total with the scientific degree needed for supervising PhD students of which 16 actually participated in the supervision of PhD students. Each year, laboratory heads suggest 8-12 themes for PhD theses and 3 to 5 of these are usually chosen by the Scientific Board. The Scientific Board supervises the progress of these theses. As part of the evaluation of their work, a special seminar is held for the PhD students once a year, where they present the results of their dissertation, the status of their work and any problems related to their PhD study. In addition, the Scientific Board also organizes seminars for the students in which they inform the scientific staff about their results and plans. They are encouraged to prepare these presentations in English. These seminars are open to all scientists and students, allowing them to become familiar with work of other PhD students.
To improve their skills, the PhD students have the possibility to attend specialised courses in the methods of molecular biology, crystallography and bioinformatics in Slovakia as well as abroad (during the assessed period, these included Zeiss on your Campus 2010, 21-23 september, Bratislava; FEBS Biochemistry Education Workshop, 12-13 September 2011, Smolenice, Slovakia, Advanced methods in macromolecular crystalization III, FEBS Advanced course PLC08-0032, Nové Hrady, October 3-10, 2008 etc.). The Institute co-organised “The Bioinformatics Roadshow” (6-7 October 2010), a workshop headed by the EBI (European Bioinformatics Institute) in which 22 participants, mostly PhD students from our Institute and other Slovak academic institutions, were tutored by four EBI lecturers in the fields of Protein Structure, Protein Interactions and Mass Spec Proteomics. Most of our PhD students finish their study by successfully defending their dissertation thesis. The main reasons that students do not finish are because of family reasons, principally maternity leave, or because they leave Bratislava or Slovakia.
The Institute encourages its best PhD students to apply for Postdoctoral positions through the SAS Schwarz fund after successfully defending their thesis. In 2011, the Institute also established a new Postdoctoral fund to support 1–3 Postdoctoral positions each year. The positions are for two years with the possibility of renewal for an additional two years. These positions are open to candidates both from within the Institute or from outside; there were three successful candidates in 2011. Successful candidates are selected by the Institute’s Scientific Board. The organization also encourages successful PhD students to apply for Postdoctoral positions abroad.
The Institute’s research groups have also had a great deal of experience supervising students working on their bachelor theses and especially their diploma (Masters) theses. During 2007–2011, five of our scientists supervised university students in the preparation of their bachelor theses and nineteen of them supervised university students in the preparation their diploma theses. These students were mainly from the Faculty of Natural Sciences of Comenius University and the University of Cyril and Methodius in Trnava. Many researchers from the Institute also serve as lecturers in the educational programs of these Universities,
57
especially at the Faculty of Natural Sciences of Comenius University, Bratislava, the Faculty of Natural Sciences of the University of Cyril and Methodius, Trnava and the Faculty of Biotechnology and Food Sciences, Slovak Agriculture University, Nitra. The number of researchers serving as lecturers was as follows: 2007, eight researchers; 2008, nine researchers; 2009, seven researchers; 2010, nine researchers; and 2011; nine researchers. In 2008 and 2011 two researchers gave lecture courses abroad.
6. Applied research
(Applications of results)
i. List of the most important results of applied research projects
[1] APVV project VMSP-P-0111-09 "Rapid detection of pathogenic bacteria in food praxis" in co-operation with EL spol s r.o. Spišská Nová Ves. Principal investigator: Ing. Andrej Godány, CSc. Main results: Rapid and inexpensive PCR method was developed for detection of pathogenic bacteria in food. This method was approved by government authority.
[2] Project Structural Funds of EU (Bratislavsky kraj č. 26240220010) "New microbial isolates comprising genes of catabolite and detoxification pathways and their exploitation in biotechnology" in co-operation with Water Research Institute, Bratislava. Principal investigators: Ing. Bystrík Polek, CSc., RNDr. Peter Ferianc, CSc.
Main results: Several microbial isolates were isolated from contaminated soils. Currently, they have been tested for PAH biodegradation in field experiments.
[3] Institute of Molecular Biology supervised cooperation with industrial partner Biotika a.s., Slovenská Ľupča. National R&D project 2004 SP 26 028 OA 03 was focused on improvement of yield of biologically active products (e.g. in strain Penicilium
chrysogenum). Principal investigator: prof. RNDr. Ján Turňa, CSc. Main results: Strain Penicilium chrysogenum with increased production of penicillin was constructed and genetically characterized.
ii. List of the most important studies commissioned for the decision-making
authorities, the government and NGOs, international and foreign organisations
[1] Expert's reports for Ministry of Environment SR for experimental work with GMO Author: RNDr. Peter Ferianc, CSc. (2008 - 1x, 2009 - 3x, 2010 - 6x, 2011 – 7x)
[2] Expert's report for Ministry of Education: Project impulses for Research and development. Author: RNDr. Gabriela Bukovská, CSc. (2009)
[3] Expert's report for Slovak Centre of Scientific and Technical Information “Technical and functional requirements for Research and Development Information System” (2009) Author: Mgr. Ľuboš Kľučár, PhD.
[4] Expert's report for Slovak Centre of Scientific and Technical Information “Expert
assessment of the possibility of acquisition of software for data processing in the field of bioinformatics and determination of necessary requirements for operation in a Data center for research and development” (2010),
58
Author: Mgr. Ľuboš Kľučár, PhD.
iii. List of licences sold abroad, incl. revenues
None
iv. List of licences sold in Slovakia, incl. revenues
None
v. List of contracts with industrial partners, incl. revenues4
None
vi. List of research projects with industrial partners, incl. revenues4
[1] Co-operation with the S&D Chemicals Limited (Great Britain) focused on selection and characterization of probiotic strains Lactobacillus and Bifidobacterium.
Principal investigator: RNDr. Gabriela Bukovská, CSc.
Funding 2010 - 2011: 13 281 € Main results: The new strains of Lactobacillus and Bifidobacterium were selected and characterised by microbiology methods as a potential probiotics.
[2] Co-operation with the S&D Chemicals Limited (Great Britain) focused on investigation and improvement of strain Streptomyces laurentii. Principal investigator: RNDr. Gabriela Bukovská, CSc. Funding 2008 - 2010: 8776 €
Main results: The strain of Streptomyces laurentii with increased production of
thiostrepton was constructed and genetically characterized.
[3] Co-operation with the S&D Chemicals Limited, Great Britain - consulting activities in the field of investigation and improvement of strain Bacillus polymyxa and agreement about technical cooperation.
Principal investigator: RNDr. Gabriela Bukovská, CSc. Funding 2008: 4980 € Main results: The phage resistent antibiotic production strain of Bacillus polymyxa was constructed by molecular biology methods and a new phage PhiBP was characterised.
[4] Co-operation with the pharmaceutical company CPN, Limited, Dolní Dobrouč, Czech Republic withing biotechnological project: “Recombinant production of human antimicrobial peptides”
Funding 2007: 11900 €
Principal investigator: Juraj Gašperík Main results: His-tag and Nus-tag versions of recombinant human β – defensin 1 were prepared and tested for antimicrobial activity.
4 If not included in documentation of projects in chapter 4 (Projects structure, research grants and other funding
resources).
59
vii. Supplementary information and/or comments on applied activities
2007 2008 2009 2010 2011 total
studies for the decision sphere, government and NGOs,
international and foreign organisations0 1 5 7 7 20
7. Popularisation of Science (outreach activities)
i. List of the most important popularisation activities
Scientific events and festivals [1] Science festival Researchers’ night in Slovakia 2011 - IMB was presented in a form of an
exhibition stand "DNA chips- a new trends in diagnosis of diseases".
[2] European Science and Technology Week. Open Door Day at IMB (2011) New methods for diagnosis of bacterial diseases using DNA chip. 7.11.2011
[3] European Science and Technology Week. Open Door Day at IMB (2010). 9.11.2010
[4] European Science and Technology Week. Science festival Open Door Day at IMB.
(2009). World of microorganisms - research, detection and applications. How cells
specialize? Bacteriophages - when bacteria get a flue. 3.11.2009
[5] European Science and Technology Week. Open Door Day at IMB (2008). „Molecular
biology -DNA, genes, proteins., 25.11.2008
[6] European Science and Technology Week. Open Door Day at IMB (2007). What is a
molecular biology - from bacteria to bee. 14.11.2007
TV and radio broadcast [7] Bílíková K. and Šimúth J. (2011) There will be enough honey. STV1, Správy STV,
26.12.2011
[8] Bílíková K. (2011) Medical effect of bee products for human. Radio Lumen, session
Lumenáda, 3.11.2011
[9] Bílíková K. and Šimúth J. (2011) Everyday honey - not just for today. STV2, talk show
"Spectrum of science 22.6.2011
[10] Kormanec, J. (2011) Talk show about E. coli resistant strains. 5 minutes to 12, STV,
12.6.2011
[11] Kormanec J. (2010), A new bacteria which can grow using arsenic instead of
phosphor, TV Joj, Journal, 3.12.2010
[12] Bílíková K. (2010) Portrét - Talk show with distinguished persons of Slovakia.,
Televízia Ta3, 19.9.2010
[13] Bílíková K. (2010) Science of the year and where is the Slovak science now?, Slovak
radio, 24.3.2010
[14] Bílíková K. and Šimúth J. (2010), Honey and public health, Slovak radion - Radio
Devín-Solárium, 8.1.2010
[15] Šimúth J. (2008) Apitherapy, Slovak radion Banská Bystrica, 24.1.2008
[16] Šimúth J. (2008) Actual problems of apidological research, TV TA3, 20.11.2008
[17] Šimúth J. (2008) New horizon of molecular apidology, TV TA3, 21.11.2008
60
[18] Hostinová, E. and Gašperík J. „Yeast in modern biotechnologies.“ Slovak Radio,
SOLÁRIUM, 13.9.2007
[19] Godány A. (2007) „Bacteriophages for therapy.“ Slovak Radio (Rádio Devín),
SOLÁRIUM
Press
[20] Barák I. (2010) Soil bacteria could surprise, journal Pravda, 4.12.2010
[21] Bílíková K. and Šimúth J. (2010), Research of bee and its associates. Newspaper
Roľnícke noviny, 27.10.2010
[22] Kormanec J. (2010), Artificial life? journal Život, číslo 22, 29.5.2010
[23] Kormanec J. (2009), Human being versus microorganisms, journal Týždeň, 9.3.2009
[24] Barák I. (2008) There is a biological bomb ticking in countries of devils. Newspaper
Pravda
[25] Kormanec J. (2007) „Transcription - a key step for transfer of genetic information.“
QUARK, 4, 16-17, 2007
Lectures [26] Ambro Ľ. (2011) Recombinant DNA techniques., Gymnázium Pavla Horova
Michalovce, 3.11.2011
[27] Bílíková K. (2011), Application of the results of molecular biology research of bee and
bee products for public health. “Scientific coffee lounge” within a project APVV - „Science
in schools and coffee bars.“, Institute of Forest Ecology, SAV, Zvolen, 27.10.2011
[28] Bílíková K. (2011) A new technique for assessment of quality of bee products, invited
lecture, AGROKOMPLEX 2011, 20.8.2011
[29] Kormanec J. (2008) ,Human being and microorganisms - is there a threat? Quo Vadis
[30] Timko J. (2008), Genetically modified food., Faculty of social and natural sciences PU
Prešov
[31] Šimúth J. and Bíliková K. (2007) „Bee diseases. “ National bee exhibition, Banská
Bystrica, (21. 10. 2007) (invited lecture)
[32] Kutejová E., (2011) XV. Medical congress of natural medicine, Trnava15.10.2011
(invited lecture)
Internet [33] Bílíková K. and Šimúth J. (2011) Bee and human being, XV. Medical congress of
Outreach activities 2007 2008 2009 2010 2011 total
articles in press media/internet popularising results of
science, in particular those achieved by the Organization1 1 1 3 2 8
appearances in telecommunication media popularising
results of science, in particular those achieved by the
Organization
2 3 4 4 13
public popularisation lectures 2 3 1 1 5 12
iii. Supplementary information and/or comments on popularisation activities
During this period (2007-2011) we once again very actively participated in the European Science and Technology Week by organizing our annual Open doors at IMB. We offered to acquaint the public with our institute and its scientific projects. This event has become very popular, especially among high school students. We popularized our research work through popular lectures and in 2011 we also prepared practical demonstrations of some of the basic experiments carried out at our institute. The students showed interest in several topics and we discussed many of their questions with them. Another scientific festival which we took part in was the Researcher's Night organized by the European Commission. We prepared demonstrations of some simple experiments in which the audience could participate. Our scientists and PhD students discussed different aspects of our projects with visitors. We also contributed to radio and TV programs devoted to specific scientific issues. We published responses to real public concerns in national newspapers and magazines. Our scientists also repeatedly gave lectures on general or specific scientific topics either for students or at different events (exhibitions, fairs).
8. Background and management. Staffing policy and implementation of
recommendations from previous assessments
i. Summary table of personnel
Personnel 2007 2008 2009 2010 2011
all personnel 92 94 82 77 76
research employees from Tab. Research
staff56 61 60 57 59
FTE from Tab. Research staff 51.3 49.3 47.5 47.9 42.4
average age of research employees with
university degree47.5 48.3 48.1 48.5 44.7
62
ii. Professional qualification structure (as of 31.12. 2011)
iv. Status and development of research infrastructure incl. experimental,
computing and technical base (description of the present infrastructure,
premises, and material and technical resources. Infrastructure, instrumentation
and major technical equipment necessary for the achievement of the objectives
specified in the research Concept)
The Institute of Molecular Biology possesses substantial research infrastructure. Each laboratory forms an independent unit with basic equipment (centrifuges, incubators, shakers, pH meters, thermal cyclers, water baths, etc.) and the special instruments required for its particular projects. These include a microarray scanner, microplate readers, fluorescence microscopes (Olympus, Leica) equipped with digital cameras and image analysis software, an ultramicrotome for thin sectioning, a flow cytometer, special electrophoretic systems (Pulsed-field gel electrophoresis, 2D electrophoresis, Denaturing Gradient Gel Electrophoresis), laminar boxes, CO2 incubators, a vacuum concentrator, etc. All of these devices are available to all employees of the Institute. In recent years, much laboratory equipment has been updated thanks to external resources. There are also several commonly used instruments including an FPLC (Äkta Prime, Äkta FPLC), an HPLC (Shimadzu, Varian), a Dynamic Light Scattering device, a Real-time PCR machine, an automated pipetting
system (epMotion), a microarrayer (Genetix), ultracentrifuges, -80°C freezers, etc. As a
member of BITCET (http://www.bitcet.sk) we have built up a facility for genomics and bioinformatics which has a great impact in Slovakia. Its service is focused on sequencing,
5 Responsibility to organize PhD study
6 Responsibility to be a supervisor of PhD study
63
DNA fragment analysis, and the bioinformatics analysis of the collected data. We are able to use several other modern techniques including MS analysis with a Q-Tof Premier™ mass spectrometer attached to a nanoACQUITY UPLC™ (Waters), and DNA sequencing and protein-protein interactions can be characterized using label-free surface plasmon resonance (SPR) based technology (BIACORE3000). We also have a full access to a Zeiss LSM 510 Meta state-of-the-art confocal microscope, which is used for most advanced fluorescence techniques (FRAP, FRET and FLIM). A consequence of the Institute’s large number of international collaborations is that it also has the possibility to extend its research activities to include the X-ray analysis of proteins, the use up-to-date techniques like cryo-electron microscopy, SAXS, and additional fluorescence techniques (fluorescence titration, fluorescence polarization).
The Institute’s real property has also started to be renovated. Several laboratories were reconstructed and newly equipped. The Institute has a reliable computing network based on 100 Mbps and 1 Gbps Ethernet technology and structural cabling (1 Gbps for servers and internal backbone; 100 Mbps for workstations). The institute is interconnected to the SAS campus via a dedicated 1 Gbps optical line. A central PC-based server running MS Windows 2007 Server OS (Primary Domain Controller) is used as the main storage and application point (users home boxes, e-mail client space, centralised repository for documents and software, http and ftp server, print server, nightly backup). This central server is housed in an air-conditioned room along with 4 other, Linux based servers interconnected by a 1 Gbps Sun Grid Engine, all on a UPS. These are primarily used for bioinformatics computing and also serve as the main storage and application servers for the National EMBnet Node. The Institute maintains (and is the only institution in Slovakia to do so) a full set of all major biological databases (EMBL, Uniprot, Prosite, Pfam, Prints. Interpro, OMIM, the full KEGG set and Taxonomy), together with several dozen analysis tools mostly gathered from the EMBOSS software package (http://www.embnet.sk:8080/srs81/). The Institute maintains more than one hundred PC workstations (the majority are MS Windows with a few are Linux-based ones).
v. Describe how the results and suggestions of the previous assessment were
taken into account
For the assessment period 1.1.2003 to 31.12.2006, the Institute was evaluated as category “A”. Scientific output: It was stated that scientific output was good especially in that of 50 selected publications, a high number of them were in high impact factor journals. However, it was also noted that only three departments were responsible for the majority of these outputs: the Department of Gene Expression, the Department of Microbial Genetics and the Department of Protein Structure and Function. During the present assessment period, from 1.1.2007 to 31.12.2011, the scientific outputs were as follows: There were 142 publications which appeared in journals with an average impact factor of 3.102. This compares favourably with the previous assessment period when it was 136 publications with average impact factor of 2.649. It can be seen that while the overall scientific output (number of publications) is comparable, the average impact factor has increased substantially. During the present assessment period, a large rearrangement of departments and laboratories was completed. These changes should lead to a better distribution of manpower and other resources and they should also result in a better distribution of scientific output from each department and laboratory in the future.
64
Responses to the scientific output: For the previous period, it was stated that the number of citations reflected the quality of the publications and that some of the laboratories have exceptional number of citations. During the present assessment period, from 1.1.2007 to 31.12.2011, the number of citations increased from 1254 to 2693, which clearly indicates that publication quality has improved. It also shows that the Institute’s policy of publishing fewer but better articles in higher impact journals elicits a higher response from the scientific community. Research status of the Organization in the international and national context: It was stated that during the previous period the Institute had a large number of collaborations with many different foreign institutions. In addition, the organization had a key role in implementing molecular biology research on the national level and it had a high impact on the international level. During present assessment period, from 1.1.2007 to 31.12.2011, the Institution maintained this highly regarded status on both international and national levels. Project structure, research grants and other funding resources: It was stated that during the previous period the Institute had excellent success in obtaining additional financial resources from national and international agencies. During the present assessment period, from 1.1.2007 to 31.12.201, the Institute continued to enjoy this success. The key achievements in this assessment category follow: - Projects from 6th and 7th Framework Programmes - A Project from the European Science Foundation - A Project from The Wellcome Trust - National projects from APVV and EU structural funds. Organization of PhD studies, other pedagogical activities: It was stated that during the previous assessment period the Institute collaborated with different universities in the training and education of students and researchers. In addition, many researchers from the organization were active in the teaching of undergraduate students. Success rate of PhD students was average, however. During the present assessment period, from 1.1.2007 to 31.12.2011, the Institute was clearly more successful with its PhD students: twenty PhD students defended their theses successfully in comparison with twelve successful PhD students in the previous period. Direct output to the society (applications of results, popularization and outreach activities): It was stated that during the previous assessment period the Institute achieved excellent results relevant to applied research and it was very good in the popularization of science at the national level. During the present assessment period, from 1.1.2007 to 31.12.2011, the Institute has tried to maintain this high status. Background and management. Staffing policy: It was stated for the previous assessment period that the results produced by the Institute’s employees of the Institute showed that the organization functions properly and encourages good personal development. During the present assessment period, from 1.1.2007 to 31.12.2011, the Institute made great changes in the organization of its laboratories and departments. Particular attention was paid
65
to research quality to the age structure of the scientists employed. Both of these areas of emphasis were supported by the Presidium of SAS following the announcement that the budgets of the institutes would be reduced during the years 2011–2013. Although the budget cut was not as severe as initially declared, the Institute still made changes in its organizational structure, taking into consideration the likely scientific benefits and the age structure of its research staff. Summary of the assessment: IMB SAS is one of the most distinguished research institutes in the field of molecular biology and biotechnology in Central Europe. For the further development of the organization and to increase its scientific outputs, it was suggested that better conditions for collaboration amongst its different departments should be created. Accordingly, we have changed the structure of the organization. Some laboratories were merged and new departments were created. We believe that these changes will lead to a higher scientific output from each department and laboratory and will likely result in better collaboration between the laboratories and departments. It is clear, however, that some existing departments are working on very different topics and it is natural for them to have closer collaborators outside of the Institute. Suggestions for improvements:
1. Such a high level of research activities should have had a higher output in patents. 2. There is great unevenness among the departments, especially concerning publication
quality. The production of patents is usually very difficult in our field, especially since most of our projects are oriented toward basic science. However, to encourage the production of patents, the Director of the Institute signed a Directive of intellectual property protection and specific meetings related to this subject were organized with specialists from the Institute of Technology, SAS.
vi. Supplementary information and/or comments on management, research
infrastructure, and trends in personnel development
A reduction of the budget for the institutes of SAS during 2011 to 2013, including a 10–12% reduction in the wage bill, was announced in 2010. After negotiations with the Scientific Board, the director decided to reorganize the Institute’s laboratories and departments. From the 1st of January 2011, the following departments and laboratories were closed: The Department of Protein Structure and Function, the Laboratory of Protein Biochemistry and the Laboratory of Protein Crystallography. The Laboratory of Molecular Microbiology and the Laboratory of Food and Environmental Microbiology were integrated into the Department of Microbiology. The Laboratory of Protein Evolution remains as an independent laboratory. The new Department of Biochemistry and Structural Biology was created by merging the old Department of Biochemistry and the Laboratory of Protein Crystallography. Part of the Laboratory of Protein Crystallography staff moved to the Laboratory of Prokaryotic Biology. Following the Institute’s reorganization, the GMO Laboratory was closed from the 9th of January 2010. The Institute currently has 6 departments (two of them containing 6 laboratories total), and two independent laboratories. The organization structure is as follows:
66
Department of Biochemistry and Structural Biology (Head: Ing. Eva Kutejová, CSc.) Department of Gene Expression (Head: RNDr. Ján Kormanec, DrSc.) Department of Genomics and Biotechnology (Head: Doc. Ing. Andrej Godány, CSc.)
Laboratory of Bioinformatics (Head: Mgr. Ľuboš Kľučár. PhD.) Laboratory of Genomics (Head: RNDr. Gabriela Bukovská, CSc.) Laboratory of Prokaryotic Biology (Head: Doc. Ing. Andrej Godány, CSc.)
Department of Microbial Genetics (Head: RNDr. Imrich Barák, DrSc.) Department of Microbiology (Head: RNDr. Marian Farkašovský, CSc.) Laboratory of Environmental and Food Microbiology (Head: Domenico Pangallo, PhD.)
Laboratory of Microbial Ecology (Head: RNDr. Peter Ferianc, CSc.) Laboratory of Molecular Microbiology (Head: RNDr. Marian Farkašovský, CSc.)
Department of Molecular Apidology (Head: RNDr. Katarina Bíliková, PhD.) Laboratory of Neurobiology (Head: RNDr. Frantisek Jurský, CSc.) Laboratory of Protein Evolution (Head: Ing. Štefan Janeček, DrSc.) The management of the Institute together with the Scientific Board proposed to deal with the planned reduction of the wage bill by reducing staff. Specifically, the age structure of the researchers was improved and the number of other scientific staff was reduced based on their low publishing activity (evaluated over the last 6 years), and the number of technical and service staff was also cut. The employment of two technical workers and the director’s secretary, who also worked as a Human Resources assistant, were terminated.
The reduction in the wage bill was less dramatic than originally announced, however. This new situation allowed the creation of a Postdoctoral fund at the Institute which enables the hiring of one to three postdoctoral fellows each year and will allow at least one senior researcher to be hired in the next year. This new policy should allow the organization to not only significantly reduce the average age of its scientists, but may also open new fields of research.
As of 1 January 2011 RNDr. Dagmar Homerová, CSc. took over as deputy director of the Institute, replacing Ing. Juraj Gašperík, CSc.
Other information relevant to the assessment
A N N E X
2007
Vedecký výstup - bibliografické údaje výstupov za rok 2007
Zahraničné monografie
Nemáme
Kapitoly v zahraničných monografiách
1. Machovic, M., Janecek, S.: Amylolytic enzymes: types, structures and specificities,
pp. 3-18 in Industrial Enzymes: Structure, Function and Applications, ed. by J.
Polaina, A. P. MacCabe. Springer, Dordrecht 2007 (ISBN 978-1-4020-5376-4)
Domáce monografie
Kapitoly v domácich monografiách
1. Godany, A.: Geneticky modifikované mikroorganizmy, pp. 129-154 in Biologická
bezpečnosť, ed. by D. Toth. VES-SPU, Nitra 2007 (ISBN 978-80-8069-8461)
2. Mikula, I., Mlynarcik, D., Godany, A., Tkacikova, L.: Mikroorganizmy a rezistencia
na antibiotiká, pp. 75-106 in Klinická a veterinárna farmakológia, ed. by J. Šnirc, J.
Sokol, J. Seginko, A. Hera. Neografia, Martin 2007 (ISBN 978-80-88892-75-
ADCA Vedecké práce v zahraničných karentovaných časopisoch impaktovaných
ADCA01 BARAK, Imrich., WILKINSON, A.J. Division site recognition in Escherichia coli
and Bacillus subtilis. In Fems Microbiol. Rev. 2007, vol. 31: pp. 311-326. (8.691 -
IF2006)
ADCA02 BUČKOVÁ, Mária - GODOČÍKOVÁ, Jana - POLEK, Bystrík. Responses in the
mycelial growth of Aspergillus niger isolates to arsenic contaminated environments
and their resistance to exogenic metal stress. In Journal of Basic Microbiology :
international journal. ISSN 0233-111X (Print), 2007, vol. 47, no. 4, pp. 295-300..
(1.000 - IF2006).
ADCA03 BRNAKOVA Zuzana, - GODANY Andrej,- TIMKO Jozef An
exodeoxyribonuclease from Streptomyces coelicolor: Expression, purification and
biochemical characterization. In BIOCHIMICA ET BIOPHYSICA ACTA-
GENERAL SUBJECTS. ISSN 2007, vol.770, no.4, p. 630-637 (1.000 - IF2006).
ADCA04 DRAHOVSKA, H., MIKASOVA, E., SZEMES, T., FICEK, A., SASIK, M.,
MAJTAN, V., TURNA, J. Variability in occurrence of multiple prophage genes in
Salmonella Typhimurium strains isolated in Slovak Republic. In FEMS Microbiol.
Lett. 2007, vol. 270, no 2, pp. 237-244. (2.068 - IF2006)
ADCA05 FARKAŠOVSKÁ, Jarmila - KĽUČÁR, Ľuboš - VLČEK, C. - KOKAVEC, J. -
GODÁNY, Andrej. Complete Genome Sequence and Analysis of the Streptomyces
aureofaciens Phage µ1/6. In Folia Microbiologica. ISSN 0015-5632 (Print), 2007,
vol. 52, no. 4, pp. 347-358. (0.918 - IF2006).
ADCA06 HOMEROVÁ, Dagmar - SURDOVA, K. - MIKUSOVA, K. - KORMANEC, Ján.
Identification of promoters recognized by RNA polymerase containing
