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Questionnaire

Summary of the main activities of a scientific Orga nisation

of the Slovak Academy of Sciences

Period: January 1, 2003 - December 31, 2006

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 compo sition

Directoriat name age years in the position

director Prof. Ing. Jozef Timko, DrSc. 64 12

deputy director Ing. Andrej Godány, CSc. 58 9

scientific secretary RNDr. Gabriela Bukovská, CSc. 49 9

3. Head of the Scientific Board

Ing. Eva Kutejová, CSc.

4. Basic information about the research personnel

i. Number of employees with a university degree (Ph D students excluded)

engaged in research and development and their full time equivalent work

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capacity (FTE) in 2003, 2004, 2005, 2006 and averag e number during the

assessment period

2003: 53 employees (47.07 FTE)

2004: 51 employees (46.37 FTE)

2005: 52 employees (47.44 FTE)

2006: 53 employees (47.50 FTE)

(see also table bellow)

ii. Organisation units/departments and their FTE em ployees with the university

degree engaged in research and development

No. FTE No. FTE No. FTE No. FTE No. FTE

organisation in whole 53 47.067 51 46.367 52 47.443 53 47.499 52.25 47.094

Department of Bochemistry 5 4.1665 4 3.5 4 4 5 4.083 4.5 3.9374

Department of Gene Expression 7 7 7 7 7 7 7 5.7495 7 6.6874

Department of Genomics andBiotechnology

14 11.5 13 11.7 13 11.03 15 11.916 13.75 11.537

Department of Microbial Genetics 8 6.7 8 6.7 7 6.1665 6 6 7.25 6.3916

Department of Microbiology 10 8.7 9 8.05 9 9 9 8.75 9.25 8.625

Department of Molecular Apidology N/A N/A N/A N/A 3 2.33 6 3 4.5 2.665

Department of Protein Structure andFunction

7 7 8 7.9165 7 6.25 6 6 7 6.7916

Laboratory of Neurobiology 2 2 2 1.5 2 1.6665 2 2 2 1.7916

Research staff2003 average200620052004

5. Basic information on the funding

i. Total salary budget 1 of the Organisation allocated from the institution al

resources of the Slovak Academy of Sciences (SAS) i n 2003, 2004, 2005, 2006,

and average amount for the assessment period

Salary budget 2003 2004 2005 2006 average

total salary budget (millions of SKK) 14.717 14.943 16.406 17.117 15.796

1 Sum of the brutto salaries without the fund contributions.

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6. URL of the Organisation’s web site

http://imb.savba.sk

II. General information on the research and development activity of

the Organisation:

1. Mission Statement of the Organisation as present ed in its Foundation

Charter

1. Research activities of the Institute of Molecular Biology are focused on basic research

of molecular principles in leaving systems. Molecular biology and microbiology are the

main directions of the Institute’s activity. Primary attention is focused on genetics and

physiology of microorganisms, metabolism of microorganisms and regulation of gene

expression and on the structure of expressed proteins.

2. The Institute offers consultancy and expertise that are closely related to the main

activities.

3. The Institute implements scientific education in terms of generally valid regulations.

4. The Institute guarantees publication of the results of R&D activities in periodical and

non-periodical press. The periodical and non-periodical press publishing is

administrated in accordance with regulation of the Presidium of SAS resolution.

2. Summary of R&D activity pursued by the Organisat ion during the assessed

period, from both national and international aspect s and its incorporation in

the European Research Area (max. 10 pages)

Molecular biology, as a very dynamic research field oriented toward understanding the cell mechanisms in the living systems at the molecular level, has high implication in evolution, medicine, pharmacology, food industry and biotechnology. Institute of Molecular Biology belongs to the modern and prosperous establishments with high national and international impact. Broad international collaborations with the leading institutes from Europe as well as from the USA reflect the high quality of research teams. In last four years many international grant projects have been awarded to the members of the Institute. Among those, the most important were/are the following - three projects of 5th Framework Programmes from EU, three projects of 6th Framework Programme from EU, two projects from The Wellcome Trust, one projects from European Science Foundation, Twining project the USA and Volkswagen project. The grant projects from national agencies APVV and VEGA and cooperation with the universities (Comenius University in Bratislava, Slovak Technical University in Bratislava, Slovak University of Agriculture in Nitra, University of SS Cyril and Methodius in Trnava and University of Veterinary Medicine in Košice), research institutes (Institute of Chemistry, Institute of Neuroimmunology, Institute of Virology and Institute of Animal Physiology SAS) and

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companies (Biotika a.s) in Slovakia stress the importance of the research activities national level. The Institute was the member of the Centre of Excellence of Molecular Medicine SAS (2003-2006) and still is member of Centre of Excellence of Biochemistry of Saccharides SAV -GLYCOBIOS (2005-2008). The Institute has currently 7 departments with 9 laboratories and one independent laboratory. Research activities are focused mainly on basic research in molecular biology and microbiology. The back-bone programmes of the Institute covers research of regulation of expression and function of proteins on a different levels like transcription (regulones, sigma factors, anti-sigma factors), modification (phosphorylation of DNA binding proteins, glycosylation of the amylolytic enzyme), structural changes (crystal structure, protein evolution), complex formation and proteolysis (neurotransmitters, cell migration and homeostasis of mitochondria). In addition, these basic research activities have been already directed towards possible applications in medicine (detection of pathogens, nanotechnology) and biotechnology (antibiotic and antibacterial peptides production, spore coat protein characterization, honeybee proteins with the role in immunostimulation and antimicrobial properties). Research activities in last four years are summarized in 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 Majority of these research activities have had long term tradition at the Institute and they are further developed into newly arising topics of basic science and applied research, respectively. Cell Division and Differentiation Cell division and differentiation are the most important stages in life of every cell. In the Institute Streptomyces and Bacillus subtilis have been used as model systems. Streptomyces are soil bacteria that undergo an exceptional process of morphological differentiation which is connected with production of more than 70% known antibiotics. Department of Gene Expression proved essential role of several sigma factors in particular developmental stages of Streptomyces. Using an optimized two-plasmid system, regulons (the genes that are directed by particular sigma factors) of two sigma factors: SigG and SigH with a dual role in stress-response and development of Streptomyces coelicolor have been identified and characterized. Moreover, regulatory mechanisms of SigH activation in response to stress and development have been investigated. The project belongs to the intensively studied topics worldwide, comprising investigation of molecular biology of the organisms producing antibiotics. The project is therefore included in the scope of wide international collaboration within European research area including partners from U.K., Germany and France. Head of the Department, Jan Kormanec is internationally recognized scientist in this field, reflected by his invitations to the international conferences and seminars. Streptomyces aureofaciens produces several intra- and extra-cellular enzymes with deoxyribonuclease activities. These nuclease genes have probably an important function related with the hydrolysis (recycling) of the substrate mycelium DNA during the programmed cell death which accompanies the development (differentiation in aerial mycelium) of this strain. Because of the investigation and analyses of their role in the development of Streptomyces aureofaciens strain, the genes coding for exodeoxyribonuclease ExoSa and exonuclease ExoVII large subunit were amplified, sequenced, cloned and expressed in E. coli expression system in Laboratory of Biology of Prokaryotes. Bacillus subtilis is a Gram-positive microorganism which is able to differentiate during process called sporulation. First clear morphological manifestation of sporulation is the

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formation of an asymmetric septum which partitions the cell into two compartments, the mother cell and forespore. The main aims of the projects of the Department of Microbial Genetics have been to understand the process of initiation and assembly of asymmetric sporulation septum on the molecular level. The first part of this research is focused on study of the relation between structure and function of Spo0A protein, one of the key proteins in the initiation of the sporulation. Spo0A protein belongs to a large group of so called response regulators, which are able to receive the signal through phosphorelay and change its own tertiary structure and to act as transcription activator or repressor of genes involved in sporulation. Structure of Spo0A should answer an important question, how phosphorylation of one part of the protein can change the ability of the other part of protein to bind on specific promoter sequences. Other parts of these projects have been devoted to study of the sporulation septum assembly. Many proteins take part in this process and the research has been focused on study of the localization, interactions and structures of some of these proteins, as SpoIIE, MinC, MinD, DivIVA, RacA, Spo0J or Soj. In case of programmed cell death the research has been directed to biochemical, genetic and structural studies of toxin-antitoxin, SpoIISA-SpoIISB system. These proteins were identified for the first time as part of sporulation process in Bacillus subtilis. Genetic and biochemical experiments and especially the tertiary structure determination of above mentioned proteins is a great contribution for our understanding of basic bacterial cell processes. The Department of Microbial Genetics belongs to the leading groups in the field of bacterial sporulation and it was internationally recognized also by entrusted to organize two European Spores Conferences (2004 and 2006). Head of the Department, Imrich Barák, was the main organizer of both these meetings. He is also a Coordinator of the Consortium of Central and Eastern European Structural Biology Groups (2000 – present). Protein Structure-function Relationships and Protein Evolution Laboratory of Protein Biochemistry and Laboratory of Protein Crystallography closely co-operate in studies of several classes of proteins. The former is oriented to production and biochemical studies of native as well as recombinant enzymes and their mutants, while the main effort of the latter is determination of three-dimensional structures using diffraction methods. The endeavour of both groups leads to protein characterization and structure-function relationship studies, resulting in production of enzymes with novel properties giving them an application potential. The main research activity of both laboratories was to study structure-function relationship of exo-acting amylolytic enzymes, belonging to various sequence-based families of glycoside hydrolases (GHs), which release glucose from starch, namely the family GH15 glucoamylases and GH31 α-glucosidases produced by food-born yeast Saccharomycopsis fibuligera, and another GH13 α-glucosidase from thermotolerant bacterium Thermomonospora curvata. The significant contribution to the structures of amylases, one of the most important groups of technologically exploited enzymes, is a priority in describing a structurally new type of raw starch-binding site in S. fibuligera GH15 glucoamylase, which is directly integrated into the catalytic domain. This property distinguishes the glucoamylase from all other amylolytic enzymes possessing a starch-binding domain (SBD) as a distinct unit. These findings were discovered on the basis of a high-resolution structure of glucoamylase-acarbose complex and were verified by molecular modelling and point mutations followed by probing their electrophoretic mobility in the gels containing starch. The GH13 α-glucosidase from T. curvata was purified to high homogeneity and crystals suitable for X-ray data collection were prepared. Laboratory of Protein Crystallography is the only laboratory in Slovakia which has been actively working for more than two decades in structure determination of proteins using diffraction methods. The structures of ribonucleases, glucoamylases, actin binding domain of plectin and monoclonal antibodies contributed to study of catalytic mechanism of enzymes, the mechanism of protein-ligand recognition, conformational stability and flexibility of proteins. The work of the laboratory has been internationally recognized, we

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have taken part in NASA project oriented to crystallization of proteins in the space (our proteins were crystallized in space shuttle Atlantis and Columbia), we were awarded Howard Hughes Medical Institute grant (1995-2000) and organized a world conference on ribonucleases (2005). The work of the Laboratory of Protein Evolution has been focused on protein bioinformatics. This in silico work is oriented mainly to a detailed study and analysis of amino acid sequences and three-dimensional structures of proteins with the aim of: (i) identifying the sequence regions conserved from the protein evolution point of view; (ii) revealing the sequence-structural features responsible for the properties of proteins (e.g., specificity and stability); and (iii) indicating the targets in the primary structure of proteins hit by the methods of site-directed mutagenesis in an effort to prepare the proteins with desired properties (protein engineering and design). The main interest has been focused on the amylolytic enzymes, especially the α-amylase family. This enzyme family covers three glycoside hydrolase (GH) families GH13, GH70 and GH77 forming thus a clan GH-H with almost 30 different enzyme specificities. The interest has also been expanded to “cousin” amylolytic families GH31 and GH57. All these enzymes operate on starch and related poly- and oligo-saccharides that are important as both the source of the energy for life and the subject of industrial application. The research aimed at the studying the relationships between the primary and tertiary structures of these enzymes as well as the questions concerning their evolution is therefore highly justified. The recent principal scientific contribution of the Laboratory of Protein Evolution can be summarized as follows: (i) describing the relation between domain evolution, specificity and taxonomy of the α-amylase family members containing a C-terminal starch-binding domain (SBD); (ii) revealing the fact that within the entire α-amylase family only the catalytic triad constitutes the invariant residues; (iii) indicating the horizontal gene transfer events in the α-amylase family based on the three α-amylase copies found in the genome of the marine bacterium Saccharophagus degradans; (iv) elucidating for the first time the evolutionary relationships within the family GH57, especially the establishing the conserved sequence regions; (v) proposal to create a new SBD clan from the carbohydrate-binding module (CBM) families CBM20 and CBM21; and (vi) describing a new “intermediary” CBM group related to the SBD families CBM20 and CBM21. Head of the Department, Stefan Janecek, has established the series of international symposia on the Alpha-Amylase Family (ALAMYs) held traditionally in the Smolenice Castle, Slovakia. The Third Symposium on the Alpha-Amylase Family will be held 23-27 September, 2007; ALAMY_3 (http://imb.savba.sk/~janecek/Alamys/alamy_3/). Microbial Ecology The research in the field of Microbial Ecology is focused on defence mechanisms of bacteria against stresses and diversity of bacterial assemblages in the contaminated environments. In the first research area, the ability of YodA protein (YodA was found previously as a new cadmium stress protein in our laboratory) to bind cadmium was achieved in vivo. The results in Laboratory of Microbial Ecology suggested that the role of YodA protein may be to decrease the concentration level of cadmium ions in E. coli cells during cadmium stress by its ability to bind heavy metal. In the second research area, E. coli isolated from Danube river water were assigned to the competent bacterial clones on the base of the outer membrane protein analysis, and the horizontal transfer of genetic resistance determinants against different classes of antibiotics inside of E. coli population as well as among different bacterial species was confirmed. In addition, cadmium-resistant bacterial assemblage isolated from the cadmium-contaminated sewage sludge was characterized, and 15 bacterial species belonging to 9 genera were isolated from heavy-metal contaminated soils. The representatives of Acinetobacter spp., Pasteurella spp. and Pseudomonas spp. contained czc- and ncc-like heavy-metal-resistance genes. On the other hand, non-cultivable bacterial assemblage represented 13 different unknown, phylogenetically distant bacterial clones, i. e. bacterial species, and 18

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different, phylogenetically distant ncc-like heavy-metal-resistance determinants with considerable genetic variability. The Laboratory collaborate with Department of Cellular and Molecular Biology-Microbiology of the Göteborg University in Sweden. Laboratory of Cell Biology evaluated the expression and diversity of catalases in isolates of genus Comamonas and the fungi Aspergillus niger in response to oxidative stress of polluted environment. Isolates exhibit much higher total catalase activity than the same species from laboratory collection culture. The environmental isolates exhibited also much higher resistance to exogenous oxidative stress. The role of monofunctional heme-containing catalase encoded by cat-1 gene from the soil bacterium C. terrigena N3H in response to various forms of oxidative stress has been studied. Our results indicate that this constitutively expressed catalase represents the major source for the defence of C.terrigena cells against toxic peroxides. These cells can express also a second form of catalase that is bigger and its regulation is probably more complicated. The sequence analysis confirmed the presence of highly conserved catalase sequence motifs in two environmental strains of Comamonas terrigena but in those strains that were not exposed to oxidative stress of environment no such sequence motif could be detected. Our results underline the importance of catalase expression, including alteration in expression of isozymes and regulation of catalase activity in the defence mechanisms against oxidative stress of polluted environment. Evolutionary lines of fungal cytochrome c peroxidases belonging to the superfamily of bacterial, fungal and plant heme peroxidases were also studied. Functional genomics, bioinformatics and biotechnology Functional genomics and bioinformatics have been implemented in research of pathogenic bacteria, antibiotics production, honeybee and bacteriophages characterization. Outcomes of functional genomic research have started to be transfered to modern bio-nanotechnologies. Pathogenic bacteria have been studied on several models. Basic research has been focused on regulation of gene expression (Salmonella typhimurium, Staphylococcus aureus, Mycobacterium tuberculosis, and Coxiella burnetii) and characterization of surface immunogenic protein (Streptococcus agalactiae). Modern detection techniques (fluorescent ITS-PCR, ddl-PCR, REP-PCR, AFLP) and systems (biochips) have been optimized and developed. Recombinant production of human antimicrobial peptides is in progress. In the Department of Gene Expression the role of three sigma factors in pathogenicity of essential human pathogens; RpoE of Salmonella typhimurium, SigB of Staphylococcus aureus, and SigF of Mycobacterium tuberculosis has been characterized. Applying the previously established efficient method for identification of promoters recognized by a particular sigma factor, regulons of all these sigma factors have been identified and characterized. Many of the genes dependent upon these sigma factors have been shown to play a crucial role in virulence and in the process of adhesion to host eukaryotic cells. Sequence comparison of the localized promoters recognized by particular sigma factors revealed a consensus sequence of the promoters. The expression of the identified genes was characterized, and for several of them their role in pathogenicity of the particular pathogen was investigated. For RpoE of S. typhimurium, its expression in response to stress conditions and regulatory mechanisms of recognition of cognate promoter by the sigma factor has been characterized. For comparison, we have identified and characterized regulon of its homologous sigma factor RpoE in non-pathogenic Escherichia coli. Coxiella burnetii, the etiologic agent of Q fever, is the only one known obligate intracellular pathogen with biphasic life cycle, that is able to survive and replicate inside of the phagolysosome in eukaryotic host cell. Low pH and presence of phagolysosomal enzymes activating Coxiella burnetii metabolism are important for replication process. The way of surviving particles in the phagolysosome determines progress of Q fever, it means if it manifests as an acute or chronic disease. It is known, that stress responsible sigma factor RpoS plays an important role in regulation of protein

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synthesis during post-exponentional phase, cooperates with other regulators in induction of virulence in many pathogens and regulates expression of the proteins in adaptive processes as a response to the influences of the stress environmental conditions such as acid pH. At the Department of Microbial Genetics, in collaboration with Department of Riskettsiae, Institute of Virology SAS, RpoS function in C. burnetii has been studied with clear aim to explain the mechanisms used by this microorganism for surviving bactericidal conditions of the phagolysosome in eukaryotic host cell. This project also involves the development and introduction of new methodologies for Coxiella burnetii as DNA transformation and homologous recombination. Department of Microbial Genetics is involved in projects focused on detection of tick borne pathogens using newly developed oligo chips. Unique DNA biochip for detection of bacterial pathogens from single tick isolates has been developed. This DNA chip uses laser DNA array reader and belongs to one of the most sensitive detection method for tick borne bacterial pathogens, where in one sample all chosen bacterial pathogens are detected by a single PCR reaction. The preliminary results clearly show the advantages of this methodology in comparison with other approaches and it should have wide use in medical, veterinary and epidemiological practices in near future. Laboratory of Genomics has developed a new method for detection and analysis of various clinical isolates of Salmonella using DNA oligochips („Salmonella-specific ResistoPathoCHIP“). The best conditions, i.e. protocols for isolation of the genetic material, fluorescent labelling, hybridization and computer analysis of the DNA chips were selected. The final oligochip was tested for twenty four clinical isolates of various Salmonella serovar and/or phagotypes. Our results correlated with the results of phenotype analysis. The results were proved and completed using the simultaneously developed PCR method for salmonella genotype determination. One of the research areas at the Laboratory of Biology of Prokaryonts are bovine isolates of Streptococcus agalactiae (GBS). These strains are highly infectious bovine mastitis pathogens that can rapidly spread throughout a herd from single infected animal. The majority of these strains express one or more characteristic surface-anchored proteins. These proteins can induce cross-protective immunity against S. agalactiae infections and emphasize its potential as universal vaccine candidates. Two new genes encoding putative alpha-like protein 6, encoded by alp6, and alpha-like protein 7, encoded by alp7, were identified in bovine isolates of S. agalactiae. A surface immunogenic protein, named SIP protein, which is distinct from the previously mentioned ones, was also identified in bovine isolates of S. agalactiae. All new identified genes encoding surface proteins were characterized, cloned and expressed in E. coli plasmid and T7 Phage-display expression systems. The purified recombinant proteins will be tested as candidates inducing protective immunity against various S. agalactiae serotypes. The results of this project eventuated in developing of a procedure for specific and rapid detection of bacterial pathogens in diary products by PCR for State Veterinary and Food Administration of the Slovak Republic: The main aim of the research at the Laboratory of Biotechnology and Bioinformatics was to monitor the variability of enterococci isolated from various environments and to asses their probiotic as well as pathogenic potential. Strains originated from food, water environment and human clinical isolates were included into the study. Species identification was provided by combination of phenotypic (Micronaut System, Merlin) and molecular detection methods (fluorescent ITS-PCR, ddl-PCR, REP-PCR, AFLP). A good correlation between molecular methods was observed, however several discrepancies were recognized during comparison of molecular and biochemical identification. Six enterococcal species were identified; E. faecium, E. hirae and E. casseliflavus were the most abundant ones. E. mundtii, E. faecalis, E. durans and E. gallinarum were detected in connection with several strains. The variability between strains measured by AFLP differed according to the source of isolation. The strains were characterized also by the detection of virulence factors, antibiotic resistance, and enterocins genes. Different strains were detected that contain virulence genes (cylA, gelE and esp). The resistance

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of enterococci strains to eleven antimicrobial substances (Penicillin, Ampicillin, Vancomycin, Erythromycin, Tetracycline, Ciprofloxacin, Rifampin, Chloramphenicol, Gentamicin, Nitrofurantoin, Amoxicillin / clavulanic acid) was also investigated. The presence of different enterocin genes (entA, entB, entP, ent31, entL50AB) was frequently observed in our isolates. The distribution of enterocin genes varied according to the species, the genes were present mainly in E. hirae and E. faecium. In the enterocin spot assay, several strains showed antilisterial activity and they were selected to be perspective for application in food production. Bioinformatics research at the Department has shifted from application of genome annotation and protein function prediction techniques to development of new bioinformatics tools and databases, mainly in the field of gene regulatory networks in prokaryotes. A unique database collecting all available data about phage genomes, genes, coded proteins and regulatory elements has been developed and maintained. Laboratory of Protein Biochemistry has a long-term international co-operation within the biotechnological project “Recombinant production of human antimicrobial peptides”, in co-operation with pharmaceutical company CPN limited, Dolni Dobrouc, Czech republic. The main goal of this research is preparing the recombinant expression systems based on Escherichia coli and Saccharomyces cerevisiae suitable for the follow-up technological processes. Education of external PhD students was also covered by this co-operation. An antibiotics production has been studied on two levels. Basic research has been focused on regulation of new antibiotics production and biotechnological research on improvement of quality of penicillin production. As streptomycetes are the main producers of antibiotics, Department of Gene Expression has investigated production of new antibiotics in the model organism, Streptomyces aureofaciens CCM3239 with emphasis on the regulation of production capabilities of the strain. Three polyketide clusters responsible for production of two polyketide antibiotics and spore pigment have been identified and characterized where. regulation of the production of polyketide antibiotic auricin in S. aureofaciens CCM3239 was characterized. A gene encoding an activator of expression of genes responsible for auricin production was identified and its role in auricin activation investigated. The Institute has long-term co-operation with Biotika a.s. that started within the research directed to development of strains for aminoacids production, with focus on recombinant strain of Escherichia coli L-theonine producer. In 2004, the project „Production efficiency improvement of Penicillium chrysogenum“ has been started. Using methods of molecular biology, production strain Penicillium chrysogenum NM, represented independent branch of strain improvement was analysed. The main goal was to determine the production potential of the strain (the strain is part of Biotika a.s. "know-how") and to improve its actual production using the metabolic engineering methods. We gain the knowledge about the biosynthetic cluster organization and its gene dose. Other crucial genes involved in β-lactamate antibiotics production were also analysed. The final product is the new Penicillium chrysogenum strain able to produce the cephalosporine antibiotics. Department of Molecular Apidology uses the honey bee, Apis mellifera carnica as a model, to understand mechanisms governing antimicrobial defensive system based on the nutrition. The research was designed to characterize proteins secreted by honeybee into its products (royal jelly, honey and honeybee pollen) and to explain their function. Owing to the findings obtained in the research of antibiotic peptides and proteins of royal jelly (RJ), which contributed to the molecular biology and functional genomics of honeybee and its products, the Department joined leading centres of apidology worldwide. We participated in the initiation of the project on sequencing of honeybee genome and became part of its international scientific consortium (Jozef Simuth and Katarina Bilikova) that published its results in October 2006. The bio-informational potential of nucleotide sequences of the honeybee genome in characterization of the genes encoding antimicrobial peptides and proteins has been exploited. It has been found out that RJ from different healthy honeybee colonies could differ in both, the level

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and the activity of antimicrobial peptides. This phenomenon could be caused by genetic variability of honeybees from different colonies, which might be important for practical bee keeping, particularly for the selection of colonies naturally resistant to microbial pathogens, especially to Paenobacillus larvae. Certain properties of RJ proteins might play a role in the cytokine-induced activation of genes important for immune response of honeybees and humans. Our attention is focused on physiological properties of major proteins of RJ with the aim to determine whether the protein part of major RJ glycoprotein, apalbumin 1, which also represents major protein of the honey, exerts immunostimulatory effect on the production of TNF-ά in mouse macrophages. It has been found that apalbumin-1, apalbumin-2, and apisimin induce release of TNF-α in mouse macrophages. A recombinant apalbumin1 (rApa1) and its fragments (rApa1-F1, rApa1-F2, rApa1-F3, and rApa1-F4) were prepared by heterologous expression in E. coli with the aim to characterize the minimum structure, responsible for the physiological activity of Apa1. The testing of stimulation of TNF-secretion by murine macrophages induced by the native protein and recombinant protein fragments revealed a N-terminal fragment of the protein, rApa-F1 as most effective. It was also demonstrated that these proteins are regular components of honey and honeybee pollen. Thus, honeybee secretes RJ proteins into their own food that could induce self-defence mechanisms in honeybees mainly during larval development. These findings, together with our methodical potential, enabled us to participate at active international cooperation within EU. In this regard, our long-term cooperation with the Max-Planck Institute for Molecular Genetics, Berlin, Germany, in common research project “Functional Genomics of Honeybee” within the Partner Group (01/2006-12/2010) represented an important condition. At present, the Department participates in the FP6 EU-STREP project and the FP6 Integrated Project EU, which deal with the genomics, proteomics and physiomics of honeybee and its products with an aim to eliminate the application of antibiotics in bee keeping. The Department also collaborates with the Institute of Apiculture, Liptovsky Hradok, Slovakia, and the Faculty of Chemical and Food Technology, Slovak Technical University, Bratislava, Slovakia. The bacteriophage genome sequencing projects of corynephage BFK20 and phage µ1/6 belong to the field of functional genomics. Corynephage BFK20 is a lytic phage of Brevibacterium flavum CCM 251, the previous industrial producer of L-lysine and phage µ1/6 is a temperate phage of Streptomyces aureofaciens. The entire double-stranded DNA genome of bacteriophage BFK20 was sequenced and analyzed in the Laboratory of Genomics. BFK20 is not only the first corynephage with an entirely sequenced genome, but also with accomplished global gene expression analysis using DNA microarray approach. Several bioinformatics approaches helped to identify 55 ORF on its genome and to predict their functions. Clusters of functionally related putative genes were defined (structural, lytic, replication and regulatory). Using DNA microarray method the expression profile of all 55 individual genes was constructed to investigate transcription of BFK20 genes during bacteriophage life cycle after the host infection. Our bioinformatics analyses indicated quite extensive homology between BFK20 and other bacteriophages (particularly those infecting Mycobacterium spp.) and to the prophage regions of Corynebacterium spp. genomes. The most significant are the similarities between the BFK20 genome and the mycobacteriophage Rosebush early genes, prophages from C. efficiens YS-314 and C. diphtheriae NCTC 13129 and C. glutamicum strain specific island 8, strain R. Current research is focused on elucidation of bacteriophage BFK20 lytic and replication mechanism and characterization of lytic and replication genes and their protein products. The study of endolysin and holin will contribute to the understanding of mechanism of host cell lysis and how this lytic process is regulated. The elucidation of the complicated interplay of phage-encoded replication factors with ‘host’ factors could be a contribution to the understanding of DNA replication in general. The entire double-stranded DNA genome of the Streptomyces aureofaciens phage µ1/6 was sequenced and analyzed in the Laboratory of Biology of Prokaryotes. The size

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of phage genome is 38 194 bp with an overall molar G+C content of 71.19%. Bioinformatics analysis revealed the presence of 52 putative protein coding regions, constituting about 92% of the whole µ1/6 genome sequence. Blast search did not predicted homologous for twenty-two gene products. The µ1/6 genome is apparently organized into two oppositely transcribed regions. In the left arm of the µ1/6 genome putative integrase and possible regulation proteins were identified. The rightwards transcribed region contains genes organized into four functional units responsible for replication, DNA packaging and head assembly, tail morphogenesis and lysis. Experimental evidence of function is available for lysis genes (endolysin and holine), integrase, prohead protease and major capsid protein. Department of Microbial Genetics has been oriented toward bio-nanotechnologies like development of oligo chip for detection of tick borne bacterial pathogens and specifically designed electronic devices for detection of DNA hybridization reaction. In co-operation with Italian physics, an universal electronic DNA biochip for detection of bacterial pathogens has been developed. This approach is based on CMOS technology and our preliminary results clearly point out the advantages comparing with present methods. Research and usage of spore coat proteins in different bio-nanotechnological processes is starting up. Molecular Cell Biology Investigation of some processes in eukaryotes belongs to research area that is relatively new at the Institute. There are three spheres of interest: (i) neurotransmitter transporters, (ii) cell migration, (iii) ATP-dependent proteolysis in mitochondria and peptides. Glycine transporters belong to the protein family named "sodium dependent neurotransmitter transporters". Their name cames from the fact they transport neurotransmitter substances across the membrane, where transport is coupled to cellular sodium gradient. Most of the family members are located in the central nervous system and their impairment leads to the serious neurological diseases. Laboratory of neurobiology investigates role of calpain in physiology of glycine transporters. The project was previously awarded by a grant from Volkswagen foundation (Germany). In the present time the project is further pursued under funding of Slovak Academy of Sciences and continuing international collaboration. 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. Migration is a multistep process that includes pericellular proteolysis, cell adhesion, signal transduction and chemotaxis. Although there is considerable knowledge of how these processes are initiated, less is known of molecules executing their down-regulation. The major aim of research at the Department of Biochemistry is discovery of mechanisms controlling migration towards the final goal to define targets and tools for pharmacologicall modulation of unwanted cell migration in cancer development. Our aim is to affect tumor-associated angiogenesis, a prerequisite for the growth of a primary tumor and metastases, and to directly target spreading of cancer cells. The Department focuses mainly on the mannose 6-phosphate/insulin-like growth factor 2 receptor (M6P/IGF2R, CD222) since the present data strongly indicate its negative regulatory role in the cell migration; particulary its inhibitory effects on the pro-migratory urokinase receptor (uPAR, CD87). It is studied in detail how this receptor exerts its regulatory functions, its membrane partners and implicated pathways. Basically, the loss-of-function and gain-of-function experiments using siRNA and transfection technology as well as biochemical, functional and imaging methods were applied. The peptides derived from M6PR have been already identified that can block cell migration in vitro and they are currently tested in vivo. It is the major goal of the Department to investigate whether there are possibilities to block tumor progression and tumor-associated angiogenesis with use of these peptides. The obtained knowledge will allow the design of novel strategies for therapeutic interventions in cancer. We have very intensive collaboration with the Institute

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of Immunology, Medical University of Vienna. The research projects are closely related and Austrian - Slovak bilateral project has been accomplished. ATP-dependent proteases are important not only for the protein quality control but play important role in the regulation of many biological processes in the cell. The endogenous substrates of the mitochondrial ATP-dependent protease Lon were characterised. At the Department of Biochemistry the subunits of the mitochondrial processing peptidase were found to be the substrates for the yeast and human Lon protease, and StAR protein (responsible for the cholesterol delivery to the mitochondrial membrane) was found to be the substrate for the human Lon protease. Based on the MS analysis of the peptides formed during the time dependent degradation of the substrates and their structures, the mitochondrial Lon protease was found to recognize specific surface determinants or folds, initiating proteolysis in solvent-accessible sites. Generated unfolded polypeptides are then processively degraded. This degradation mechanism is unique for the Lon proteases since till now unfolding of the substrate and transport to the proteolytic cavity was postulated as a mechanism of degradation by the ATP-dependent proteases. The human Lon binding to the mitochondrial DNA was characterized. All activities are closely connected to the research C.K.Suzuki's laboratory in UMDNJ NJ USA. (Twinning grant National Academy of Sciences, National Research Council’s Twinning Program). This cooperation started in Prof. G. Schatz group at the University of Basel, Switzerland. From 1999 the Institute has a mandate from Slovak government to serve as a National EMBnet Node. EMBnet is a science-based group of collaborating nodes throughout Europe and a number of nodes outside Europe. The combined expertise of the nodes allows EMBnet to provide services to the European molecular biology community which encompasses more than can be provided by a single node. The main activities of the Node are focused on education (on both, graduate and post graduate level), international cooperation in building of necessary bio-computing infrastructure (world wide biological database network based on SRS and recently on MRS database systems) and research activities in field of bioinformatics (gene identification, protein function prediction, gene regulatory networks). The Node facilitate a small computing grid composed of 5 PC based servers and a data storage of 2 TB in total. The EMBnet activities were supported by 5th Framework Programme EU. Institute of Molecular Biology is the owner of the section Cellular and Molecular Biology of the journal Biologia (http://www.springer.com/11756), which consists of three independent sections. Biologia is an international journal covering various aspects of botany, zoology and cellular and molecular biology. Since 1946 the journal serves to publish the newest results from research in life sciences. It provides to the authors a credible and efficient peer-review and is in a front to theirs expectations of high scientific standards. From over twenty years Biologia is indexed by Abstracting and Indexing Services and evaluated by receiving a first IF in 1994. Accordingly to the three subjects sections (botany, zoology and cellular and molecular biology) the papers are published bimonthly. Each section has its own Editorial Office, Editorial Board and Advisory Boards. Actual 2007 the efforts of all teams are increased and unified because the journal is starting in the co-publishing program with Versita (http://www.versita.com) and Springer-Verlag (http://www.springer.com). By this step in the development Biologia introduces into electronic publishing. For the authors it benefits in a faster and broader visibility of their results."

13

3. Concept of R&D activity of the Organisation for the next four years (max. 5

pages)

i. Present state of knowledge and status of ongoing research related to the subject

of the Concept, from both international and nationa l perspective

N/A

ii. Organisation’s role or significance in the over all research effort within the field

of the Concept on both the national and internation al scales

N/A

iii. Objectives of the Concept

N/A

iv. Proposed strategies and methods to be applied, and time schedule

N/A

III. Partial indicators of the main activities:

1. Research output

i. List of the selected publications documenting the m ost important results of

basic research. Total number of publications in the whole assessed period

should not exceed the average number of the researc h employees

monographs and proceedings [1] Timko, J., Siekel, P., Turňa, J. Geneticky modifikované organizmy (Geneticaly

modified organisms). Bratislava: VEDA 2004. 100s. ISBN 80-224-0834-4 [2] Turňa, J., Stuchlík, S., Drahovská, H., Gálová, Z., Timko, J. Techniky

rekombinantných DNA (Recombinant DNA techniques). Bratislava: VEDA, 2004. 160 s. ISBN 80-224-0835-2

[3] Valkova D., Turňa J., Timko J.Úvod do molekulárnej biotechnológie. (Introduction to molecular biotechnology) VEDA, 2005. 167 s. ISBN 80-224-0845-X

[4] Janeček, Š. (editor): 2nd Symposium on the Alpha-Amylase Family. VEDA, Bratislava, 2005, 185 pp. Biologia Supplement Issue No. 16, ISSN 0006-3088.

[5] Kuchta, T., Drahovská, H., Pangallo D., Siekel P.: Application of polymerase chain reaction to food analysis. VUP Food Research Institute, Bratislava, 2006. ISBN 80-969608-5-7

chapters in monographs [6] Barák I.: Regulation of morphology and gene expression asymmetry during

sporulation process in Bacillus subtilis. Chapter in: Recent Research Development in

14

Bacteriology. (2003), pp 179-200. Ed.: S.G.Pandalai, Tranworld Research Network, ISBN: 81-7895-082-0.

[7] Barák, I. Sporulation in Bacillus subtilis and other bacteria. In: Bacterial Spore Formers: Probiotics and Emerging Applications Ed.: E. Ricca, A.O. Henriques and S.M. Cutting, Horizon Bioscience, 2004. ISBN: 1-904933-02-5. pp 53 –64.

[8] Cutting, S.M. – Ricca, E. – Barák, I.: Bacterial Spores in Bionanotechnology. In Microbial Bionanotechnology: Biological self-assembly systems and biopolymer-based nanostructures. Ed. B. Rehm, Horizon Scientific Press, Norwich, 2006 ISBN: 1-904933-16-5. p. 223-251.

papers [9] Weinstock, G.M., The Honeybee Genome Sequencing Consortium (Members),

Bilikova, K., Simuth, J. et al. Insights into social insects from the genome of the honeybee Apis mellifera. (2006) Nature 443(7114): 931-947. [IF 29.273] [MIF 0.445] [AP 0.009] [NP 0.57]

[10] Rowley, G., Spector, M., Kormanec, J., Roberts, M. Pushing the envelope: extracytoplasmic stress responses in bacterial pathogens. (2006) Nat. Rev. Microbiol. 4(5): 383-394. [IF 13.989] [MIF 2.197] [AP 0.25] [NP 1.592]

[11] Leksa, V., Godar, S., Schiller, H.B., Feurtbauer, E., Muhammad, A., Slezakova, K., Horejsi, V., Steinstein, P., Weidle, U.H., Binder, B.R. et al. TGF-beta induced apoptosis in endothelial cells mediated by M6P/IGFII-R and mini-plasminogen. (2005) J. Cell Sci. 118(19): 4557-4586. [IF 6.543] [MIF 2.383] [AP 0.182] [NP 0.499]

[12] Howe, D., Melnicakova, J., Barak, I., Heinzen, R.A. Maturation of the Coxiella burnetii Parasitophorous vacuole requires bacterial protein synthesis but not replication. (2003) Cell Microbiol. 5: 469-480. [IF 6.333] [MIF 2.197] [AP 0.5] [NP 1.441]

[13] Barak, I., Ricca, E., Cutting, S. From fundamental studies of sporulation to applied spore research. (2005) Mol. Microbiol. 55: 330-338. [IF 6.203] [MIF 2.197] [AP 0.333] [NP 0.941]

[14] Barak, I., Wilkinson, A.J. Where asymmetry in gene expression originates. (2005) Mol. Microbiol. 57: 611-620. [IF 6.203] [MIF 2.197] [AP 0.5] [NP 1.412]

[15] Muchova, K., Lewis, R.J., Perecko, D., Brannigan, J.A., Ladds, J.C., Leech, A., Wilkinson, A.J., Barak, I. Dimer induced signal propagation in Spo0A. (2004) Mol. Microbiol. 53(3): 829-842. [IF 6.203] [MIF 2.197] [AP 0.375] [NP 1.059]

[16] Stahlberg, H., Kutejova, E., Muchova, K., Gregorini, M., Lustig, A., Muller, S.A., Olivieri, V., Engel, A., Wilkinson, A.J., Barak, I. Oligomeric structure of the Bacillus subtilis cell division protein DivIVA determined by transmission electron microscopy. (2004) Mol. Microbiol. 52: 1281-1290. [IF 6.203] [MIF 2.197] [AP 0.3] [NP 0.847]

[17] Liu, T., Lu, B., Lee, I., Ondrovicova, G., Kutejova, E., Suzuki, C.K. DNA and RNA binding by the mitochondrial Lon protease is regulated by nucleotide and protein substrate. (2004) J. Biol. Chem. 279: 13902-13910. [IF 5.854] [MIF 2.323] [AP 0.333] [NP 0.84]

[18] Ondrovicova, G., Liu, T., Singh, K., Tian, B., Li, H., Gakh, O., Perecko, D., Janata, J., Granot, Z., Kutejova, E. et al. Cleavage site selection within a folded substrate by the mitochondrial ATP dependent Lon protease. (2005) J. Biol. Chem. 280: 25103-25110. [IF 5.854] [MIF 2.323] [AP 0.25] [NP 0.63]

[19] Baliova, M., Betz, H., Jursky, F. Calpain-mediated proteolytic cleavage of the neuronal glycine transporter, GlyT2. (2004) J. Neurochem. 88: 227-232. [IF 4.604] [MIF 2.323] [AP 0.667] [NP 1.321]

15

[20] Da Lage, J.L., Feller, G., Janecek, S. Horizontal gene transfer from Eukarya to Bacteria and domain shuffling: the alpha-amylase model. (2004) CMLS-Cell. Mol. Life Sci. 61(1): 97-109. [IF 4.582] [MIF 2.323] [AP 0.333] [NP 0.657]

[21] Machovic, M., Janecek, S. Starch-binding domains in the post-genome era. (2006) CMLS-Cell. Mol. Life Sci. 63(23): 2710-2721. [IF 4.582] [MIF 2.323] [AP 1] [NP 1.972]

[22] Alston, R.W., Urbanikova, L., Sevcik, J., Lasagna, M., Reinhart, G.D., Scholtz, J.M., Pace, C.N. Contribution of single tryptophan residues to the fluorescence and stability of ribonuclease Sa. (2004) Biophys. J. 87: 4036-4047. [IF 4.507] [MIF 2.193] [AP 0.286] [NP 0.587]

[23] Bischoff, M., Dunman, P., Kormanec, J., Macapagal, D., Murphy, E., Mounts, W., Berger-Bachi, B., Projan, S. Microarray-based analysis of the Staphylococcus aureus �ăB regulon. (2004) J. Bacteriol. 186(13): 4085-4099. [IF 4.167] [MIF 2.197] [AP 0.125] [NP 0.237]

[24] Ghorbel, S., Kormanec, J., Artus, A., Virolle, M.J. Transcriptional studies and regulatory interactions between the phoR/phoP operon and the phoU, mtpA and ppk genes of Streptomyces lividans TK24. (2006) J. Bacteriol. 188(2): 677-686. [IF 4.167] [MIF 2.197] [AP 0.25] [NP 0.474]

[25] Senn, M.M., Giachino, P., Homerova, D., Steinhuber, A., Strassner, J., Kormanec, J., Fluckiger, U., Berger-Bachi, B., Bischoff, M. Molecular analysis and organization of the sB operon in Staphylococcus aureus. (2005) J. Bacteriol. 187(3): 8006-8019. [IF 4.167] [MIF 2.197] [AP 0.222] [NP 0.421]

[26] Rowley, G., Stevenson, A., Kormanec, J., Roberts, M. Effect of inactivation of degS on Salmonella enterica serovar Typhimurium in vitro and in vivo. (2005) Infect. Immun. 73(1): 459-463. [IF 3.933] [MIF 2.301] [AP 0.25] [NP 0.427]

[27] Machovic, M., Janecek, S. The evolution of putative starch-binding domains. (2006) FEBS Lett. 580(27): 6349-6356. [IF 3.415] [MIF 2.193] [AP 1] [NP 1.557]

[28] Zamocky, M., Dunand, C. Divergent evolutionary lines of fungal cytochrome c peroxidases belonging to the superfamily of bacterial, fungal and plant heme peroxidases. (2006) FEBS Lett. 580: 6655-6664. [IF 3.415] [MIF 2.193] [AP 0.5] [NP 0.779]

[29] Harraghy, N., Kormanec, J., Wolz, C., Homerova, D., Goerke, C., Ohlsen, K., Qazi, S., Hill, C.P., Herrmann, M. Sae is essential for expression of the staphylococcal adhesins Eap and Emp. (2005) Microbiology-(UK) 151: 1789-1800. [IF 3.173] [MIF 2.197] [AP 0.222] [NP 0.321]

[30] Novakova, R., Homerova, D., Feckova, L., Kormanec, J. Characterization of a regulatory gene essential for the production of the angucyclinelike polyketide antibiotic auricin in Streptomyces aureofaciens CCM 3239. (2005) Microbiology-(UK) 151(8): 2693-2706. [IF 3.173] [MIF 2.197] [AP 1] [NP 1.444]

[31] Skovierova, H., Rowley, G., Rezuchova, B., Homerova, D., Lewis, C., Roberts, M., Kormanec, J. Identification of the sE regulon of Salmonella enterica serovar Typhimurium. (2006) Microbiology-(UK) 152(5): 1347-1359. [IF 3.173] [MIF 2.197] [AP 0.571] [NP 0.825]

[32] Janecek, S., Svensson, B., MacGregor, E.A. Relation between domain evolution, specificity, and taxonomy of the a-amylase family members containing a C-terminal starch-binding domain. (2003) Eur. J. Biochem. 270: 635-345. [IF 3.164] [MIF 2.323] [AP 0.333] [NP 0.454]

16

[33] Machovic, M., Svensson, B., MacGregor, E.A., Janecek, S. A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21. (2005) FEBS J. 21: 5497-5513. [IF 3.164] [MIF 2.323] [AP 0.5] [NP 0.681]

[34] Sevcik, J., Urbanikova, L., Kostan, J., Janda, L., Wiche, G. Actin-binding domain of mouse plectin: crystal structure and binding to vimentin. (2004) Eur. J. Biochem. 271: 1873-1884. [IF 3.164] [MIF 2.323] [AP 0.6] [NP 0.817]

[35] Ševcik, J., Hostinova, E., Solovicova, A., Gasperik, J., Dauter, Z., Wilson, K.S. Structure aof the complex of a yeast glucoamylase with acarbose reveals the presence of a raw starch binding site on catalytic domain. (2006) FEBS J. 273(10): 2171-2171. [IF 3.164] [MIF 2.323] [AP 0.667] [NP 0.908]

[36] Zamocky, M. Phylogenetic relationships in class I of the superfamily of bacterial, fungal, and plant peroxidases. (2004) Eur. J. Biochem. 271: 3297-3309. [IF 3.164] [MIF 2.323] [AP 1] [NP 1.362]

[37] Zona, R., Chang-Pi-Hin, F., O'Donohue, M.J., Janecek, S. Bioinformatics of the family 57 glycoside hydrolases and identification of catalytic residues in amylopullulanase from Thermococcus hydrothermalis. (2004) Eur. J. Biochem. 271(14): 2863-2872. [IF 3.164] [MIF 2.323] [AP 0.5] [NP 0.681]

[38] Hostinova, E., Solovicova, A., Dvorsky, R., Gasperik, J. Molecular cloning and 3D structure prediction of the first raw-starch-degrading glucoamylase without a separate starch-binding domain. (2003) Arch. Biochem. Biophys. 411: 189-195. [IF 3.152] [MIF 2.193] [AP 1] [NP 1.437]

[39] Bukovska, G., Klucar, L., Vlcek, C., Adamovic, J., Turna, J., Timko, J. Complete nucleotide sequence and genome analysis of bacteriophage BFK20 - A lytic phage of the industrial producer Brevibacterium flavum. (2006) Virology 348(1): 57-71. [IF 3.080] [MIF 2.667] [AP 0.667] [NP 0.77]

[40] Janata, J., Hola, K., Kubala, M., Gakh, O., Parkhomenko, N., Matuskova, A., Kutejova, E., Amler, E. Substrate evokes translocation of both domains in the mitochondrial processing peptidase alpha-subunit during which the C-terminus acts as a stabilizing element. (2004) Biochem. Biophys. Res. Commun. 316(1): 211-217. [IF 3.000] [MIF 2.193] [AP 0.125] [NP 0.171]

[41] Barbaro, M., Bonfiglio, A., Raffo, L., Alessandrini, P., Facci, P., Barak, I. A CMOS, fully integrated sensor for electronic detection of DNA hybridization. (2006) IEEE Electron Device Lett. 27(7): 595-597. [IF 2.825] [MIF 0.696] [AP 0.167] [NP 0.676]

[42] Barbaro, M., Bonfiglio, A., Raffo, L., Alessandrini, P., Facci, P., Barak, I. Fully electronic DNA hybridization detection by a standard CMOS biochip. (2006) Sens. Actuator B-Chem. 118(1-2): 41-46. [IF 2.646] [MIF 0.799] [AP 0.167] [NP 0.552]

[43] Brezna, B., Kweon, O., Stingley, R.L., Freeman, J.P., Khan, A.A., Polek, B., Jones, R.C., Cerniglia, C.E. Molecular characterization of cytochrome P450 genes in the polycyclic aromatic hydrocarbon degrading Mycobacterium vanbaalenii PYR-1. (2006) Appl. Microbiol. Biotechnol. 71(4): 522-532. [IF 2.586] [MIF 1.634] [AP 0.25] [NP 0.396]

[44] Hostinova, E., Solovicova, A., Gasperik, J. Cloning and expression of a gene for an alpha-glucosidase from Saccharomycopsis fibuligera homologous to family GH31 of yeast glucoamylases. (2005) Appl. Microbiol. Biotechnol. 69: 51-56. [IF 2.586] [MIF 1.634] [AP 1] [NP 1.583]

[45] Brnakova, Z., Godany, A., Timko, J. An extracellular endodeoxyribonuclease from Streptomyces aureofaciens.

17

(2005) Biochim. Biophys. Acta-Gen. Subj. 1721: 116-123. [IF 2.418] [MIF 2.193] [AP 1] [NP 1.103]

[46] Baliova, M., Jursky, F. Calpain Sensitive Regions in the N-terminal Cytoplasmic Domains of Glycine Transporters GlyT1A and GlyT1B. (2005) Neurochem. Res. 30: 1093-1100. [IF 2.187] [MIF 2.323] [AP 1] [NP 0.941]

[47] Mazurakova, V., Sevcikova, B., Rezuchova, B., Kormanec, J. Cascade of sigma factors in streptomycetes: identification of a new extracytoplasmic function sigma factor sigmaJ that is under the control of the stress-response sigma factor sigmaH in Streptomyces coelicolor A3(2). (2006) Arch Microbiol. 186(6): 435-446. [IF 2.135] [MIF 2.197] [AP 1] [NP 0.972]

[48] Halgasova, N., Majtan, T., Ugorcakova, J., Timko, J., Bukovska, G. Resistance of corynebacterial strains to infection and lysis by corynephage BFK 20. (2005) J. Appl. Microbiol. 98: 184-192. [IF 2.127] [MIF 1.634] [AP 1] [NP 1.302]

[49] Blaskovic, D., Barak, I. Oligo-chip based assay for detection of tick-borne bacteria causing diseases in humans. (2005) FEMS Microbiol. Lett. 243: 473-478. [IF 2.057] [MIF 2.197] [AP 1] [NP 0.936]

[50] Ladds, J.C., Muchova, K., Blaskovic, D., Lewis, R.J., Brannigan, J.A., Wilkinson, A.J., Barak, I. The response regulator Spo0A from Bacillus subtilis is efficiently phosphorylated in Escherichia coli. (2003) FEMS Microbiol. Lett. 223: 153-157. [IF 2.057] [MIF 2.197] [AP 0.429] [NP 0.401]

[51] Rezuchova, B., Miticka, H., Homerova, D., Roberts, M., Kormanec, J. New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system. (2003) FEMS Microbiol. Lett. 225: 1026-1027. [IF 2.057] [MIF 2.197] [AP 0.8] [NP 0.749]

[52] Skovierova, H., Rezuchova, B., Homerova, D., Roberts, M., Kormanec, J. Characterization of the sigmaE-dependent rpoEp3 promoter of Salmonella enterica serovar Typhimurium. (2006) FEMS Microbiol. Lett. 261(1): 53-59. [IF 2.057] [MIF 2.197] [AP 0.8] [NP 0.749]

ii. List of monographs/books published abroad

iii. List of monographs/books published in Slovakia

[1] Kuchta, T., Drahovska, H., Pangallo D., Siekel P.: Application of polymerase chain

reaction to food analysis. VUP Food Research Institute, Bratislava, 2006. ISBN 80-

969608-5-7

[2] Timko, J., Siekel, P., Turňa, J. Genetický modifikované organizmy. Bratislava: VEDA

2004. 100s. ISBN 80-224-0834-4

[3] Valková D., Turňa J.: Postup hodnotenia rizika z používania geneticky

modifikovaných organizmov. Veda, Bratislava, 2003, ISBN 80-224-0770-4

[4] Valkova D., Turňa J., Timko J. Úvod do molekulárnej biotechnológie. VEDA, 2005.

167 s. ISBN 80-224-0845-X

18

iv. List of other scientific outputs specifically impor tant for the Organisation

[1] Jozef Timko was the coordinator and principal investigator of the partial task of the

State program R&D No. 2003SP51/0280700/0280701 “Prediction of development and

exploitation of research and technology till 2015 in Slovakia”. 8 experts from Slovakia

participated on this programme. Special protocol was prepared to create research

policies in Slovakia till 2015. Protocol was published in the following report:

• Timko J. at al., SWOT analýza – Genetika a biotechnológie (SWOT analysis-Genetics

and biotechnology), Bratislava 2003, 45 pages.

• Timko at al., Identifikácia trendov rozvoja vedy a techniky v SR v podmienkach

Európskeho výskumného priestoru – Genetika a biotechnológie,(Identification of

trends of development of the research and biotechnology in Slovakia in terms of

European research territory - Genetics and biotechnology) Bratislava 2003, 107

pages.

• Timko J. at al., Genetika a biotechnológie (Genetics and biotechnology), Bratislava,

2004, 53 pages.

[2] Our Institute has excellent results in preparation of highly purified proteins from

various biological materials. We have co-operated with the Institute of Virology, SAS

on separation of biologically active proteins from tick salivary gland extracts; with the

Department of Microbiology, Faculty of Natural Sciences, Comenius University on

isolation of proteins from Candida albicans; with Department of Biochemistry, Faculty

of Natural Sciences, Comenius University on thioredoxin and thioredoxin reductase;

with Dairy research institute, Žilina on isolation of milk proteins and with

Microbiological Institute, Academy of Sciences of Czech Republic on purification and

characterization of mitochondrial processive peptidase and its mutants.

[3] In cooperation with the University of Veterinary Medicine in Košice, bovine microbial

and bacteriophage isolate were characterised.

[4] The project "Investigation of microbial communities in art objects: New molecular

biological tools for a rapid and reliable diagnostic" was oriented on the isolation and

identification of biodegradative microflora present on wooden art objects exposed in

indoor environment (Slovak National Gallery, Bratislava, Slovakia). The isolated

microflora was tested, by different molecular methods and plate assays, for its abilities

to degrade cellulose and lignin. A series of molecular techniques (T-RFLP, RAPD,

and REP-PCR) were used to improve the detection of art pathogenic microflora.

[5] The Institute, together with Institute for Plant Research in Wageningen, has

participated on development and building of the "Gene Files" database, in scope of

19

the project "Introduction of National Biosafety Frameworks in Pre-integrated Countires

in Central and East Europe", funded by Dutch government.

v. Table of research outputs

Table Research outputs shows research outputs in number of specified entries; these

entries are then divided by FTE employees with a university degree (from Tab. Research

staff) for all Organisation at the respective year; finally these entries are divided by the

total salary budget (from Tab. Salary budget).

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

aver

aged

num

ber

per

year

av. N

o. /

FT

E

av. N

o. /

sala

ry

budg

et

chapters in monographs, books published abroad

1 0.02 0.07 2 0.04 0.13 0 0.00 0.00 1 0.02 0.06 4 1.0 0.02 0.06

chapters in monographs, books published in Slovakia

4 0.08 0.27 7 0.15 0.47 1 0.02 0.06 1 0.02 0.06 13 3.3 0.07 0.21

CC publications 25 0.53 1.70 44 0.95 2.94 36 0.76 2.19 30 0.63 1.75 135 33.8 0.72 2.14

scientific publications indexed by other databases (specify)

N/A N/A N/A N/A

scientific publications in other journals

3 0.06 0.20 7 0.15 0.47 4 0.08 0.24 4 0.08 0.23 18 4.5 0.10 0.28

publications in proc. of international scientific conferences

23 0.49 1.56 58 1.25 3.88 40 0.84 2.44 58 1.22 3.39 179 44.8 0.95 2.83

publications in proc. of nat. scientific conferences

8 0.17 0.54 1 0.02 0.07 8 0.17 0.49 8 0.17 0.47 25 6.3 0.13 0.40

active participations at international conferences

29 0.62 1.97 65 1.40 4.35 44 0.93 2.68 64 1.35 3.74 202 50.5 1.07 3.20

active participations at national conferences

9 0.19 0.61 1 0.02 0.07 12 0.25 0.73 8 0.17 0.47 30 7.5 0.16 0.47

total

Research outputs

2003 2004 2005 2006

20

vi. Renormalized publications 2

Renormalized publications = number of CC publications in the given year times

authorship’s portion of the Organisation times the journal impact factor in 2005 divided by

the median impact factor in the research field

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

Renormalized publications 15.8 0.34 1.07 23.4 0.50 1.56 17.3 0.36 1.06 17.6 0.37 1.03

2006

Renormalised publications

2003 2004 2005

vii. Standard manuscript page count 3

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

page count 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0 0 0.0 0.0

2006

Standard manuscript page count

2003 2004 2005

viii. List of patents and patent applications

[1] Streptomyces albus strain producing salinomycin and method of producing

salinomycin the same.

Authors: Gondova Blanka, Gajdošíková Jana, Cikosová Miroslava, Borošová

Gabriela, Zelenák Vasil, Turňa Ján, Timko Jozef, Kormanec Ján. 2 This information is required only from the Organisations of the Section 2 of the Slovak Academy of Sciences. 3 This information is required only from the Organisations of the Section 3 of the Slovak Academy of Sciences.

21

Owner of patent: Biotika a. s., (SK)

Patent number: SK3182004

ix. Supplementary information and/or comments on the sc ientific output of the

Organisation

Renormalisation of publications exclude all articles published in newly formed journals

without Impact Factor. For this reason, our article published in Acta Crystallographica

Sect. F-Struct. Biol. Cryst. Commun. is not counted towards the total sum of renormalized

publications for the year 2005.

2. Responses to the scientific output

Table Citations shows specified responses to the scientific outputs; these entries are

then divided by the FTE employees with a university degree (from Tab. Research staff)

for all Organisation at the respective year; finally these entries are divided by the total

salary budget (from Tab. Salary budget).

22

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

No.

/ F

TE

No.

/ sa

lary

bud

get

num

ber

aver

aged

num

ber

per

year

av. N

o. /

FT

E

av. N

o. /

sala

ry

budg

et

Web of Science 275 5.8 18.7 287 6.2 19.2 302 6.4 18.4 390 8.2 22.8 1254 313.5 6.7 19.8

(specify Database 1) N/A N/A N/A N/A

(specify Database 1) N/A N/A N/A N/A

in monographs, conf. proceedings and other publications abroad

N/A N/A N/A N/A

in monographs, conf. proceedings and other publications in Slovakia

N/A N/A N/A N/A

Citations

total2002 2003 2004 2005

Note: we have corrected the formula in column "av. No. / FTE", now it refers to "averaged

number per year" instead of "total number".

i. List of 10 top-cited publications and number of their citations in the

assessment period

[1] MacGregor, E.A., Janecek, S. & Svensson, B.: Relationship of sequence and

structure to specificity in the α-amylase family of enzymes. Biochim. Biophys. Acta

2001, 1546, 1-20. (66 citation)

[2] Lewis, R., Brannigan, J.A., Muchova, K., Barak, I., Wilkinson, A.J., J. Mol. Biol.

Phosphorylated Aspartate in the Structure of a Response Regulator Protein.1999,

294, 9-15. (42 citation)

[3] Janecek, S.: Alpha-Amylase family: molecular biology and evolution. Progr. Biophys.

Mol. Biol. 1997, 67, 67-97. (31 citation)

[4] Frandsen, N., Barak, I., Karmazyn-Campelli, C., Stragier, P. Transient gene

asymmetry during sporulation and establishment of cell specificity in Bacillus

subtilis.1999 Genes Dev. 13, 394-399. (24 citation)

23

[5] Janecek S, Sevcik J The evolution of starch-binding domain 1999 FEBS Lett.

456,119-125, (19 citation)

[6] Leveque, E., Janecek, Š., Haye, B. & Belarbi, A.: Thermophilic archaeal amylolytic

enzymes. Enzyme Microb. Technol. 2000, 26, 3-14. (17 citation)

[7] Stahlberg H, Kutejova E, Suda K, Wolpensinger B, Lustig A, Schatz G, Engel A,

Suzuki CK Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease

with seven flexible subunits. 1999 Proc. Natl. Acad. Sci. U.S. A. 96, 6787-6790 (17

citation)

[8] Lewis, R.J., Scott, D.J., Brannigan, J.A., Cervin, M.A., Spiegelman, G.B., Hoggett,

J.G., Barak, I. Dimer formation and transcription activation in the sporulation-

response regulator Spo0A. 2002 J. Mol. Biol. 316: 235-245. (16 citation)

[9] Pace CN, Hebert EJ, Shaw KL, Schell D, Both V, Krajcikova D, Sevcik J, Wilson KS,

Dauter Z, Hartley RW, Grimsley GR Conformational stability and thermodynamics of

folding of ribonucleases Sa, Sa2 and Sa3. 1998 J. Mol. Biol. 279, 271-286. (16

citation)

[10] Rezuchova B, Miticka H, Homerova D, Roberts M, Kormanec J. New

members of the Escherichia coli sigmaE regulon identified by a two-plasmid system.

2003 FEMS Microbiol. Lett. 225 1-7. (16 citation)

ii. List of top-cited authors from the Organisation (at most 10 % of the research

employees) and their number of citations in the ass essment period

[1] Janeček 306

[2] Barák 185

[3] Kormanec 164

[4] Ševčík 116

[5] Kutejová 68

iii. Supplementary information and/or comments on r esponses to the scientific

output of the Organisation

Department of Molecular Apidology has been at the Institute for two years now. The

Department continues in its research activities started at the Institute of Chemistry. However,

we can not count the citations for the papers published before the Department joined the

24

Institute, but the salary budget is involved in calculation for these two years (2005-2006). The

number of these extra citations is 24 for the year 2004 and 32 citations for 2005.

We would like to stress the fact that researchers at the Institute have not

systematically monitored the citations other then WOS. They were not required before and

we have found it not effective to search for them retrospectively. There is no equivalent

database for citations in monographs (comparing to WOS), so there are no possibilities to

assess it systematicaly.

3. Research status of the Organisation in the inter national and national

context

• International/European position of the Organisation

i. List of the most important research activities d ocumenting international

importance of the research performed by the Organis ation, incl. major projects

(details of projects should be supplied under Indic ator 4). Collective

membership in the international research organisati ons, in particular within the

European Research Area

[1] The member of The Honeybee Genome Sequencing Consortium

[2] Slovak National EMBnet node

[3] Collective membership of SSBMB (Slovak Society of Biochemistry and Molecular

Biology) that is member of FEBS

[4] Collective membership in Biotechnological Society, that is member of EFB (European

Federation of Biotechnology)

ii. List of international conferences (co-) organis ed by the Organisation

[1] 19th EMBnet Business Meeting

September 16–17, 2005, Smolenice Castle, Slovakia

Organized by: Ľuboš Kľučár, http://www.embnet.sk/agm2005/

[2] 7th International Meeting on Ribonucleases

June 16-20, 2005, Stará Lesná, Slovakia

Organized by: Jozef Ševčík

[3] XXII International Conference on Yeast Genetics and Molecular Biology

August 2005, Bratislava, Slovakia

25

Organized by: Department of Biochemistry Faculty of Natural Sciences Comenius

University, Bratislava, Eva Kutejová was one of the local organizers

http://www.yeast2005.org/committees.php

[4] ALAMY_2 - The Second Symposium on the Alpha-Amylase Family (Druhé

sympózium o alfa-amylázovej rodine).

October 3-7, 2004, Smolenice Castle, Slovakia

Organized by: Štefan Janeček

web: http://imb.savba.sk/~janecek/Alamys/alamy_2/

[5] EMBnet Collaborative Workshop

September 15. 2005, Smolenice Castle, Slovakia

Organized by: Ľuboš Kľučár, http://www.embnet.sk/agm2005/

[6] European Spores Conference

June 17-20, 2004, Smolenice Castle, Slovakia

Organized by: Imrich Barák

[7] European Spores Conference

June 15-18, 2006, Smolenice Castle, Slovakia

Organized by: Imrich Barák

[8] INYS - International networking of young scientists (workshop)

September 17-19, 2006, Smolenice Castle, Slovakia

Organised by: Jozef Ševčík, http://imb.savba.sk/INYS2006/

iii. List of international journals edited/publishe d by the Organisation

[1] Biologia, Bratislava, section Cellular and Molecular Biology

Two Issues per year and supplement until 2006; as of 2007, co-published by Versita

and Springer

web: http://www.springer.com/11756/.

[2] EMBnet.news, (published by EMBnet), Two Issues in the year 2006

http://www.embnet.org/download/embnetnews/index.html

iv. List of edited proceedings from international s cientific conferences and other

proceedings

[1] :2nd Symposium on the Alpha-Amylase Family. VEDA, Bratislava, 2005, 185 pp.

Janeček, Š. (editor) Biologia Supplement Issue No. 16, ISSN 0006-3088.

26

[2] 7th International Meeting on Ribonucleases: programme and abstracts, June 16-20,

2005, Stará Lesná. Ed.: Ľ. Urbániková. Bratislava: Ústav molekulárnej biológie SAV,

2005, 102 pp.

[3] ALAMY_2: The Second Symposium on the Alpha-Amylase Family (Program and

Abstracts). 3-7 October 2004, Smolenice Castle, Slovakia. Ed.: Š. Janeček.

Bratislava: Asco Art & Science, 100 pp. ISBN 80-88820-29-4.

[4] European Spores Conference Proceeding from European spores conference, June

15-18, 2006, Smolenice Castle, 17pp.

[5] INYS - International networking for young scientists: Structural Biology - From Genes

to Structures, Sept. 17-19, 2006, Smolenice Castle, 32 pp.

[6] Proceedings of the 9th Interdisciplinary Slovak-Czech Toxicology Conference held in

Píla – Častá, Slovakia, September 15–17, 2004. Biologia, Bratislava 2005, vol. 60,

Suppl. 17, 168 pp.

• National position of the Organisation

i. List of selected most important national project s (Centres of Excellence,

National Reference Laboratories, Agency for the Pro motion of Research and

Development (APVV/APVT), National Research Programm es, Scientific Grant

Agency of the Slovak Academy of Sciences and the Mi nistry of Education

(VEGA), and others )

[1] Centre of Excellence for Molecular Medicine of Slovak Academy of Scienece (2003-

2006)

Coordinator: Jaroslav Pastorek, Inst. of Virology, SAS

Principal investigator: Jozef Timko

Funding in 2003: 300 000 SKK

Funding in 2004: 250 000 SKK

Funding in 2005: 250 000 SKK

Funding in 2006: 225 000 SKK

[2] BITCET - Biotechnological Centrum. National project of R&D, that has been focused

on the support of infrastructure for research in Life Sciences. Institute was involved in

first stage of the project (2003 – 2006) as the co-guarantee of two sections: 1.

Genomics (J. Turňa, J. Timko) and 2. Bioinformatics (J. Turňa, Ľ. Kľučár).

[3] ENGL - European Network of GMO Laboratories. The Institute is representative for

plan to be establishment of GMO reference laboratory Slovakia, based on Agreement

No “20126-2002-11 SOSC ISP BE” between The European Community and the

27

European Laboratories Responsible for Genetically Modified Organisms sampling,

detection, identification and quantification.

[4] Centre of excellence of biochemistry of saccharides (GLYCOBIOS)

Coordinator: Vladimír Farkaš (Institute of Chemistry SAS)

Principal Investigator: Jozef Ševčík

Funding in 2005: 100 000 SKK

Funding in 2006: 50 000 SKK

[5] Biological variability of the pathogen GBS strains, and their detection during

transmission into diary products. National Research Programme: Foods, Quality and

Safety.

Registration number: 2003 SP 27/028 0E 02/028 0E 02

Principal investigator: Andrej Godány

Cooperation: 1 (UVL Košice)

Duration: 09/2003-12/2005

Grant agency: National Research Programme

Funding: 2003 - 2005: 2 720 000,- SKK

[6] 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")

Principal investigator: Ján Turňa

Registration number: 2004 SP26/ 028 0A 00/028 0A 03

Duration: 07/2004- 12/2007

Grant agency: National Research Programme

Funding: in 2004: 10 425 000.- SKK. (released in November 2004)

Funding: in 2005 - 2006: 23 250 000,- SKK

[7] The quality of the Life-health, nutrishment, education, State program R&D

“Foodstuffs-quality and safety” No 16 “ Enterococcus sp. in Foodstuffs, the study and

exploitation of their variability

Principal investigator: Jozef Timko

Cooperation investigator: Faculty of Sciences UK, Bratislava

Duration: 03/2003-12/2005

Grant agency: National Research Programme

Registration number: 2003 SP 27/0280 0E 1028 0E 01

Funding: 2003 - 2005: 7 800 000,- SKK

[8] A new natural bacterial strains containing genes of catabolic and detoxication

pathways (cat, yodA, czc, ncc) perspective for remediation biotechnology

Principal investigator: Bystrík Polek

28

Duration: 1/2005-12/2007

Grant agency: APVV, Bratislava

Registration number: APVT-51-024804

Funding: 2005 - 2006: 2 406 000,- SKK

[9] Bacterial programmed cell death as a tool for development of alternative drugs

Principal investigator: Imrich Barák

Duration: 1/2005-12/2007

Grant agency: APVT, Bratislava

Registration number: APVT-51-027804

Funding: 2005 - 2006: 1 747 000,- SKK

[10] Bioinformatics approach to discovery of gene regulatory networks in

bacteriophages

Principal investigator: Ľuboš Kľučár

Duration: 1/2005-12/2007

Grant agency: APVT, Bratislava

Registration number: APVT-51-02504

Funding: 2005 - 2006: 956 000,- SKK

[11] Heavy metals resistance as a virulence factor of pathogenic bacteria

Principal investigator: Ján Turňa

Cooperation investigator from IMB SAS: Peter Ferianc

Duration: 03/2006-02/2009

Grant agency: APVV

Registration number: 20-054005

Funding: in 2006: 120 000,- SKK

[12] Identification of novel Mycobacterium tuberculosis genes under the control of

RNA polymerase sigma factor SigF

Principal investigator: Ján Kormanec

Cooperation:

1, Katarína Mikušová, CSc, KB PríF UK, Bratislava

2, Patrick J. Brennan, Colorado State University, Fort Collins, USA

Grant agency: APVT, Bratislava

Duration: 07/2002 – 06/2005

Registration number: 032/2001

Funding: 2003 - 2005: 900 000,- SKK

[13] Mechanism of the substrates recognition by the Lon protease

Principal investigator: Eva Kutejová

Duration: 1/2005-12/2007

29

Grant agency: APVT, Bratislava

Registration number: APVT-51-029604

Funding: 2005 - 2006: 746 000,- SKK

[14] Study of basic cell processes in model microorganism Bacillus subtilis: Cell

division and programmed cell death

Principal investigator: Imrich Barák

Duration: 11/2006-11/2010

Grant agency and Registration number: APVT LPP-0218-06, <EXPR10>

Funding: in 2006: 369 000,- SKK

[15] The manose 6-phosphate receptor as the regulator of fibrinolysis on the cell

surface

Principal investigator: Vladimír Leksa

Duration: 1/2005-12/2007

Grant agency: APVT, Bratislava

Registration number: APVT-51-026204

Funding: 2005 - 2006: 730 000,- SKK

[16] The role of RpoE regulon in pathogenesis of Salmonella typhimurium

Principal investigator: Ján Kormanec

Cooperation: Mark Roberts, University of Glasgow, Glasgow, U.K.

Grant agency: APVV, Bratislava

Duration: 01/2005 – 12/2007

Registration number: APVT-51-012004

Funding: 2005 - 2006: 1 581 000,-SKK

[17] Bioinformatics of amylolytic enzymes

Principal investigator: Štefan Janeček

Duration: 1/2005-12/2007

Grant agency: VEGA

Registration number: 2/5067/25

Funding: 2005 – 2006: 299 000,- SKK

[18] Cloning and characterization the function of restriction-modification and other

nuclease-coding genes from Streptomyces aureofaciens and Streptomyces

antibioticus

Principal investigator: Andrej Godány

Grant agency: VEGA

Registration number: 2/2059/22

Duration: 01/2002-12/2004

Funding: 2003 – 2004: 280 000,-SKK

30

[19] Complex calcium role in regulation of glycine transporters

Principal investigator: František Jurský

Duration: 1/2004-12/2006

Grant agency: VEGA

Registration number: 2/4054/24

Funding: 2004 – 2006: 356 000,- SKK

[20] Function and structural analysis of bacteriophage BFK20 genome

Principal investigator: Gabriela Bukovská

Duration: 01/2002-12/2004

Grant agency: VEGA

Registration number: 2/2058/22

Funding: 2003 – 2004: 252 000,- SKK

[21] Molecular and biological engineering of amylolytic systems for agrofood

application

Principal investigator on ÚMB SAV: Eva Hostinová

Duration: 1/2003-12/2005

Number of cooperation institutes including: 3

Grant agency: VEGA

Registration number: 1/0101/03

Funding: 2003 - 2005: 122.000.- SKK

[22] Structural study of proteins

Principal investigator: Jozef Ševčík

Duration: 1/2004-12/2006

Grant agency: VEGA

Registration number: 2/4044/04

Funding: 2004 – 2006: 364 000,-SKK

ii. List of national scientific conferences (co)-or ganised by the Organisation

[1] Biologická bezpečnosť v agropotravinárstve. (Biological safety in agro - food industry)

10. jún 2003. Nitra. Kongresové centrum SPU

[2] Proceedings of the project No. C519/3-D118-VTPC/1998. Preservation and

conservation of the gene pool of old- and land-races of Slovak plant species . Nitra.

Kongresové centrum SPU

[3] Symposium on genetics modified microorganisms, Smolenice, 3 -4 December 2003

[4] Transcriptional analyses in genomic era - the use of microarray’ in frame of European

Social Fund programme allocated at Institute of Animal Biology and Genetics, SAS.

31

The practical course and lecture was organized in frame of ESF for PhD students and

other scientists. The main aim of the course was the introduction to DNA array

technology for selected student and scientist. There were 34 participants at the

lecture and 12 at the practical course.

[5] As a part of ESF project "Biotechnology Project Management" there was a course in

the Institute of Molecular Biology with participation of Italian lecturers.

iii. List of national journals published by the Org anisation

iv. List of edited proceedings of national scientif ic conferences/events

[1] Brindza, J., Tóth, D. (eds.). Proceedings of the project No. C519/3-D118-VTPC/1998.

Preservation and conservation of the gene pool of old- and land-races of Slovak plant

species. Biologia 58/Suppl. 12, 2003. Bratislava, 86 pp.

[2] Timko, J., Peťko, B. (eds.) Konferencia o geneticky modifikovaných

mikroorganizmoch. (Conference on genetically modified microorganisms) Zborník,

Smolenice-Kongresové centrum SAV, 3-4 decembra 2003, 73 pp. ISBN 80-224-

0790-9

[3] Tóth, D., Brindza, J. (eds.) Biologická bezpečnosť v agropotravinárstve. (Biosafety in

agro - food industry) Zborník referátov z celošt. seminára. 10. jún 2003. Nitra.

Kongresové centrum SPU, 43 pp.

• International/European position of the individual r esearchers

i. List of invited/keynote presentations at interna tional conferences, documented

by an invitation letter or programme

[1] Barák I Max Planck Institute symposium. Cell division and differentiation in Bacillus

subtilis. Berlin 22.-24. June 2005. (Invited speaker)

[2] Barak I Transcription Regulation of Potential Virulence Factors in Coxiella burnetii.

Detection of Tick-Borne Pathogens by DNA Chips and Electronic Devices 2006

NIAID Research Conference, Opatija, Croatia, June 24-30 2006. (Invited speaker)

[3] Hostinová, E. Production of recombinant proteins for crystallography. INYS 2006, 17

– 19 September 2006. (key-note lecture)

[4] Janeček, Š. Microbial starch-binding domains of glycoside hydrolases: focus on

Archaea. In International Thermophiles Conference - From Evolution to Revolution.

32

18-22 September 2005, Surfers Paradise, Gold Coast, Australia. Gold Coast: Griffith

University, 2005, p. 25-26.

[5] Kľučár Ľ. Principles of genome annotation and protein function prediction. INYS

2006, 17 – 19 September 2006. (key-note lecture)

[6] Kormanec, J., Mitická, H., Rowley, G., Řežuchová, B., Roberts, M.: New targets for

Salmonella treatment: RpoE regulon of Salmonella typhimurium. Proceedings of

World conference on Magic bullets, Nurnberg, Germany 2004, p.A69. (invited

presentation)

[7] Kormanec, J.: The role of sigma factors of RNA polymerase in differentiation of

Streptomyces”. Streptomyces workshop, Interdisciplinary programme for Cellular

Regulation (IPCR), University of Warwick, U.K (2005). (invited presentation)

[8] Kormanec, J., Nováková, R., Bistáková, J., Fecková, Ľ.: Gene cluster for an

angucycline-like polyketide auricin in Streptomyces aureofaciens CCM3239. VAAM

International meeting on the Biology of bacteria producing natural products in

conjunction with the European symposium Drug research in Actinomycetes.

Tubingen, 2006, Abstract book: T5. (invited keynote presentation)

[9] Ševčík J. Flexibility of proteins observed in structures determined by diffraction

methods. 2nd Central European Conference Chemistry towards Biology, Seggau,

Austria, Sept. 24-29, 2004, pp. 16

[10] Ševčík J. Flexibility observed in structures determined by X-ray diffraction.

INYS 2006, 17 – 19 September 2006. (key-note lecture)

[11] Urbániková Ľ. Protein as the main variable in crystallization. FEBS Advanced

Course: Advanced methods in protein crystallization II, 6.-13. 10. 2006, Nové Hrady,

CZ, Materials structure in Chemistry, Biology, Physics and Technology 2006, vol. 13,

No. 4, pp 199

[12] Urbániková Ľ. Art and science in protein crystallization. INYS 2006, 17 – 19

September 2006. (key-note lecture)

[13] Urbániková Ľ. Protein modifications for crystallogenesis. Proceedings from

Crystallization Course CC2005, 10.-12. 10. 2005, Nové Hrady, CZ, pp. 3

[14] Urbániková Ľ. Mutations for crystallization. Proceedings from FEBS Advanced

Course: Advanced methods in protein crystallization, 2.-9. 10. 2004, Nové Hrady, CZ,

pp. 19

ii. List of employees who served as members of the organising and/or programme

committees for international conferences

33

[1] Imrich Barák, the main organizer of European Spores Conference, Smolenice castle,

19-21 jún 2004.

[2] Imrich Barák, the main organizer of European Spores Conference, Smolenice castle,

15-18 jún 2006.

[3] Štefan Janeček, chairman of the Program Committee: The Second Symposium on

the Alpha-Amylase Family, Smolenice Castle, Slovakia, October 3-7, 2004.

[4] Štefan Janeček, member of the International Organising Committee: Thermophiles

05, Surfers Paradise, Gold Coast, Australia, September 18-22, 2005.

[5] Eva Kutejová. member of organization committee, co-chairman of Workshop 9.

Protein biosynthesis, maturation, modification and degradation (2005)

http://www.yeast2005.org/programme.php,

[6] Ľuboš Kľučár Chairman of the Program and Organising Committee: EMBnet

Collaborative Workshop and 19th EMBnet Business Meeting, 15–17 September

2005, Smolenice Castle, Slovakia

[7] Ľuboš Kľučár, member of Program Committee: XX. Czech and Slovak Biochemical

Meeting, Piešťany, September 12-16. 2006:

[8] Ján Kormanec, member of Biotechnology Strategy Group of European Academies

Science Advisory Council

[9] Ján Kormanec, member of Program Committee: XX. Czech and Slovak Biochemical

Meeting, Piešťany, September 12-16. 2006:

[10] Katarína Slezáková member of registration team of Workshop 9. Protein

biosynthesis, maturation, modification and degradation (2005)

[11] Jozef Ševčík, coordinator INYS workshop, Structural Biology, Smolenice

castle, Sept. 17-19,2006

[12] Jozef Ševčík, Ľubica Urbániková, Anna Varcholová, organising committee,

Jozef Ševčík - member of International scientific committee, 7th International meeting

on ribonucleases, Stara Lesna, June 16-20, 2005

[13] Jozef Timko, member of Local Organising Committee of the 10th International

Symposium on the Genetics of Industrial Microorganisms 2006, Prague, Czech

Republic

[14] Jozef Timko, member of Program Committee: XX. Czech and Slovak

Biochemical Meeting, Piešťany, September 12-16. 2006:

[15] Ľubica Urbániková, organiser of the 263rd Discussions: Crystallography of

large and small molecules - news from our laboratories, Bratislava, June 29th 2004.

34

iii. List of employees who served as members of imp ortant international scientific

bodies (e.g. boards, committees, editorial boards o f scientific journals)

[1] Imrich Barák

• Coordinator of the Consortium of Central and Eastern European Structural

Biology Groups, from 2000

[2] Štefan Janeček, DrSc • Managing Editor Biologia, Section Cellular and Molecular Biology (from 1997),

web: http://www.springer.com/11756/

• Member of the Editorial Board (from 2006): Journal of Applied Glycoscience

(http://wwwsoc.nii.ac.jp/jsag/index_e.html)

• Member of the Editorial Advisory Panel (from 2005): Biochemical Journal

(http://www.biochemj.org/bj/bjedavpanel.htm)

[3] Ľuboš Kľučár

• EMBnet National Node manager

• EMBnet Publicity & Public Relations committee secretary

[4] Ján Kormanec

• Member of „Biotechnology Strategy Group of EASAC (European Academies

Science Advisory Council) 2004

[5] Bystrík Polek

• Member of Editorial Board: Biologia, Section Cellular and Molecular Biology web:

http://www.springer.com/11756/

[6] Jozef Ševčík

• Editor CEJB (Central European Journal of Biology)

[7] Jozef Šimúth

• Member of Governing Council European Science Foundation, Strasbourg (2001-

2006)

[8] Jozef Timko

• Member of Editorial Board: Biologia, Section Cellular and Molecular Biology, web:

http://www.springer.com/11756/

• Member of General Assembly of the European Federation of Biotechnology

(EFB), from 1997

• Member of Applied Genome Research working group at EFB, from 1997

• Member (deputy of SR) EU KBBE ( Knowledge Based Bio-Economy) from 2006

[9] Dezider Tóth, DrSc

• Member of Editorial Board: Biologia, Section Cellular and Molecular Biology,

web: http://www.springer.com/11756/

35

iv. List of international scientific awards and dis tinctions

[1] AWARD by the United Nations Environment Programme (UNEP) and the Global

Environment Facility (GEF) at „Meeting of the Parties to the Cartagena Protocol on

Biosafety“, Montreal, Canada, May 31st, 2005

• National position of the individual researchers

i. List of invited/keynote presentations at nationa l conferences documented by

an invitation letter or programme

[1] Kormanec, J.: The role of sigma factors of RNA polymerase in stress response,

pathogenicity and differentiation of bacteria. 57. Zjazd chemických spoločností.

Tatranské Matliare, Vysoké Tatry 2005, Supplement: ChemZi 2005, vol. 1, No. 1, p.

63. (invited presentation)

ii. List of employees who served as members of orga nising and programme

committees of national conferences

[1] Gabriela Bukovská,

• Member of Organisation Committee „Študentskej vedeckej konferencie“, April 9.-

10. 2003, Bratislava, SR.

[2] Bystrík Polek,

• Member of Organisation Committee „Študentskej vedeckej konferencie“, April 9.-

10. 2003, Bratislava, SR.

[3] Jozef Timko

• Member of Organisation Committee „Študentskej vedeckej konferencie“, April 9.-

10. 2003, Bratislava, SR.

iii. List of employees serving in important nationa l scientific bodies (e.g. boards,

committees, editorial boards of scientific journals )

[1] Imrich Barák

• Secretary of the Scientific Advisory Board for Molecular Biology and Genetics of

the Slovak Academy of Sciences

• Member of committee for Programme of Center of Excellence

36

• Member of Evaluation committee for chemistry and biology sciences.

• Member of Committee for Molecular and Cellular Biology (VEGA)

• Member of Committee for PhD study programme at Faculty of Natural Sciences,

Comenius University, Bratislava and Faculty of Chemical and Food Technology,

SUT, Bratislava

[2] Juraj Gašperík

• Member of Committee for PhD study programme at Faculty of Chemical and

Food Technology, SUT, Bratislava)

[3] Andrej Godány

• Member of coordination committee of National Programme of Science and

Research (NPSR): Foods, Quality and Safety

• Member of Committee for PhD study programme at Slovak Agriculture University,

Nitra

[4] Štefan Janeček, DrSc

• Member of Committee for Molecular and Cellular Biology (VEGA)

[5] Ľuboš Kľučár

• Member of Parallel Computer Origin 2000 Users Board

[6] Ján Kormanec

• Member of Committee for Programs of Centres of Excellence of Slovak Academy

of Sciences

• Member of Committee: The Slovak Society for Biochemistry and Molecular

Biology

• Member of the Slovak committee for scientific degrees in Molecular Biology at the

Ministry of Education of Slovak Republic.

• Member of Committee for PhD study programme at Faculty of Chemical and

Food Technology, SUT, Bratislava, Faculty of Natural Sciences, Comenius

University, Bratislava

[7] Bystrík Polek

• Member of Committee: The Slovak Society for Biochemistry and Molecular

[8] Jozef Šimúth

• Member of Scientific Board: Faculty of Chemical and food technology Slovak

technical University Bratislava

• Member of Presidium SAS (until 31. 5.2005)

• Deputy of head council of international scientific cooperation SAS (until

31.5.2005)

• Member of council for international scientific cooperation SAS (from 1.6.2005)

37

• Member of council for international contact SAS (from 1.6.2005 until now)

• Vice-president of National council for nutritional science

[9] Jozef Ševčík

• Member of the Accreditation subcommittee for biological and chemical sciences

(1999-2001 and 2003-2005)

• Member of Committee for PhD study programme at the Faculty of Mathematics

and Physics and Informatics, Comenius University, Bratislava

[10] Jozef Timko

• President of the Biotechnology Society of Slovakia

• Chairman of the Scientific Advisory Board for Molecular Biology and Genetics of

the Slovak Academy of Sciences

• Member of the Board of State Program of R&D for progressive technology and

economy in Ministry of Education Slovak Republic

• Member of the Board of Biosafety Committee in Ministry of Environment Slovak

Republic

• Member of Scientific Board: Faculty of Biotechnology and Food Sciences, Slovak

University of Agriculture, Nitra

• Vice-president of the Slovak Society for Biochemistry and Molecular Biology

• Member of the Committee for Environment SAS

• Member of the Committee of Sciences policies and Prognostic of Sciences and

Society SAS

• Secretary of the Committee of Ethics SAS

• Member of committee for Development of advanced technology for executive

economy (NPSR)

• Chairman for National Programs of Science and Research, Biotechnology

(NPSR)

• Member of Committee for PhD study programme at Faculty of Natural Sciences,

Comenius University, Bratislava, Slovak Agriculture University, Nitra, Faculty of

Medicine Bratislava Faculty of Chemical and Food Technology, SUT, Bratislava

[11] Dezider Tóth

• Member of the Scientific Advisory Board for Molecular Biology and Genetics of

the Slovak Academy of Sciences

• Member of the Committee for Environment SAS

iv. List of national awards and distinctions

38

[1] Ján Kormance, Scientist of the year in Slovak Republic, 2004

[2] Eva Kutejová

• Honourable mention for “Characterization of nature, structure, role and unique

process of recognition of endogenous substrate by the mitochondrial ATP-

dependent Lon protease”, administrated by Journalist-Studiom Bratislava within

the national award „Scientist of the year 2005 in Slovakia”

[3] Jozef Ševčík, Ľubica Urbániková, Vladena Hlinková and Radovan Dvorský - Award

SAS to the research group for scientific activities in the field of ribonuclease

structures, 2005

[4] Jozef Šimúth

• Important person of SAS for 2006

• Medal of SAS for supporting of science

[5] Jozef Timko – Honour Guard of SAS for credits in Biological Sciences, 2003

Supplementary information and/or comments documenti ng 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 fun ding resources

• International projects and funding

i. List of major projects within the European Resea rch Area – 5th and 6th

Framework Programme of the EU, European Science Fou ndation, NATO, COST,

INTAS, CERN, etc. (here and in items below please s pecify: type of project, title,

grant number, duration, funding, responsible person in the Organisation and

his/her status in the project, e.g. coordinator, pr incipal investigator,

investigator)

[1] 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

Coordinator: R. Moritz, Martin-Luther –University, Halle-Wittenberg,

Principal investigator: Jozef Šimúth

39

Number of cooperation institutions including SR: 10

Max-Planck Institute for Molecular Genetics, Berlin, DE

Martin-Luther –University, Halle-Wittenberg, DE

Swedish University of Agricultural Sciences, Uppsala, SE

Queen´s University, Belfast, UK

University Paul Sabatier, Toulouse, FR

University Paris Sud, Orsay, FR

CEBAS, Murcia, ES

University Hohenheim, Stuttgart, DE

Italian National Institute of Apiculture, Bologna, IT

Bee Research Institute, Dol, CZ

Funding in 2006: EÚ 956 459.- SKK

SR 1 184000.- SKK

[2] Biomolecular recognition by integrated smart-sensor technology

Grant agency: 5th Framework Programme

Grant registration number: IST-2001-39266

Duration: 1/2003-12/2003

Coordinator: Luigi Raffo

Number of cooperation institutions including SR: 2

Responsible person in IMB SAS: Imrich Barák – Principal Investigator

Funding in 2003: EU 1 000 000,- SKK

SR 228 000,- SKK

[3] BPM – Biotechnology Project Management“

Grant agency: European Social Foundation

Grant registration number: JPD BA Cieľ 3 2005/ 1-038,

Project number: 13120200081

Duration: 02/2006-12/2006

Coordinator of the project: Jozef Timko

Cooperation: Eupolis Slovakia Ltd. Bratislava

Funding: in 2006: EU: 4 198 177 SKK

[4] 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

Principal investigator: Jan Maarten van Dijl, University of Groningen, Holandsko

Responsible person IMB SAS: Imrich Barák – Principal investigator

Duration: 01/2006-12/2009Funding in 2006: SR 880 000,- SKK

40

[5] Development of the Biosafety system for identification and sampling of genetically

modified organisms in Bosnia and Herzegovina

Grant agency: Ministry of Foreign Affairs Slovak Republic

Grant registration number: ACU/2004/02BA/12

Duration: 01/2005 – 06/2007

Principal investigator: Peter Siekel

Funding in 2006: SR: 54 000.- SKK

[6] Engineered Radionuclide Labelled Antibodies (Proteinovo-inžinierske protilátky

značené rádionuklidmi)

Grant agency: EUREKA

Grant registration number: E! 3537

Coordinator: Juraj Sedláček, Institute of molecular genetics of CAS, Prague

Principal investigator from IMB SAS: Marcela Múdra

Duration: 01/ 2006 – 12/ 2009

Number of cooperation institutions including SR: 4

Funding in 2006: SR 400 000,- SKK

[7] International Consortium on Ticks and Tick-Borne Diseases

Grant agency: 5th Framework Programme

Grant registration number: ICA4-CT-2000-30006

Duration: 7/2000-7/2004

Coordinator: Franz Jongejan

Number of cooperation institutions including SR: 31

Responsible person in IMB SAS: Imrich Barák. – Principal Investigator

Funding in 2003: EU 370 000,- SKK

SR 74 000,- SKK

Funding in 2004: EU 60 000,- SKK

SR 30 000,- SKK

[8] 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

Coordinator: Franz Jongejan

Number of cooperation institutions including SR: 55

Responsible person in IMB SAS: Imrich Barák – Principal investigator

Funding in 2005: EU 360 000,- SKK

SR 91 000,- SKK

Funding in 2006: EU 360 000,- SKK

41

SR 91 000,- SKK

[9] 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

Number of cooperation institutions including SR: 9

Coordinator: Simon Cutting, Royal Holloway and Bedford New College, London, UK;

Responsible person in IMB SAS: Imrich Barák – Principal investigator

Funding in 2005: EU 1 484 400,- SKK

SR 545 000,- SKK

Funding in 2006: EU 2 584363,- SKK

SR 737 000,- SKK

[10] The core European bioinformatics research infrastructure in the life sciences

(EMBCORE)

Grant agency: 5th Framework Programme

Grant registration number: QLRI-CT-2001-01363

Duration: 01/2002 –12/2004

Coordinator: Jack A.M. Leunissen, Katholieke Universiteit Nijmegen, the Netherlands

Number of cooperation institutions including SR: 40

Responsible person in IMB SAS: Ľuboš Kľučár – Principal investigator

Funding in 2003: EU 350 000,- SKK

SR 107 000,- SKK

Funding in 2004: EU 350 000.- SKK

SR 148 000.- SKK

[11] United Nations Environment Programme: Global Environment Facility, UNEP-

GEF Project on Development of National Biosafety Frameworks

National project title: Development on National Biosafety Framework for Slovakia

Grant agency: UNEP-GEF

National project number: GFL/2716-02-4573

Duration: 01/ 2003 – 10/2004

Coordinator: Christopher Briggs, Global Project Manager, UNEP/GEF Programme,

Geneva, Switzerland

Principal investigator in SR: Peter Siekel, - National Project Co-ordinator

Funding in 2004: EU: 136 000.- USD

ii. List of other international projects incl. fund ing

42

[1] Advance of Common project of Institute of molecular biology SAS and Max-Planck-

Institute for molecular genetics, Berlin, Germany

Principal investigator: Katarína Bíliková

Duration: 07/2004-31/2005

Funding in 2005: DE: 1 039 500.- SKK.

[2] Cell Division in Bacillus subtilis: Genetic and Structural studies of Proteins Involved

Grant agency: The Wellcome Trust, (Collaborative Research Initiative Grant)

Grant registration number: 066732/Z/01/Z

Duration: 2/2002-2/2005

Principal investigator: Imrich Barák

Cooperation: University of York, Department of Chemistry, York

Funding in 2003: UK: 1 280 000,- SKK

Funding in 2004: UK: 1 296 000.- SKK

Funding in 2005: UK: 250 000.- SKK

[3] Cleavage of the M6PR and characterization of the proteolytic fragments of the M6PR

(Štiepenie M6PR a charakterizácia proteolytických fragmentov M6PR)

Grant agency: Wissenschaftlich-Technische Zusamenarbeit

Österreich – Slowakei

Grant registration number: SK-AT-01106

Principal investigator: Hannes Stockinger Department of Molecular Immunology,

Centre for Biomolecular Medicine and Pharmacology, Medical University of Vienna

Principal investigator in IMB SAS: Eva Kutejová;

Duration: 01/2006-12/2007

Funding in 2006: SR 60 000.- SKK

[4] Cooperation of ATP-dependent Lon protease with DnaK/DnaJ chaperone system

Grant agency: National Academy of Sciences, National Research Council’s Twinning

Program

Grant registration number: CFDA 47.075

Duration: 02/2003-02/2006

Principal investigator: Eva Kutejová

Cooperation: Carolyn K. Suzuki, Ph.D., New Jersey Medical School

University of Medicine and Dentistry of New Jersey, Department of Biochemistry and

Molecular Biology, Newark, New Jersey, USA

Funding in 2003: from USA 3 000,- USD

Funding in 2004: from USA: 3 000,- USD

Funding in 2005: from USA 3 000.- USD

[5] Crystal structure of plectin's multifunctional amino- and carboxy-terminal domains.

43

Grant agency: Austrian Federal Ministry of Education, Science and Culture Research

Contract

Duration: 6/2002-6/2004

Coordinator: G. Wiche

Principal investigator: Jozef Ševčík

Funding 2002-2004: Austria 1 064 000,- SKK

[6] Functional genomics of honeybee

Grant agency: Max-Planck Society, Munchen, Germany

Coordinator: Katarína Bíliková

Duration 01/2006 – 12/2010

Funding in 2006: DE: 856 713.- SKK

[7] Glycine transporters in the central nervous system

Grant agency: Volkswagen Stiftung, Germany

Grant registration number: I/75 950

Duration: 4/2000-1/2004

Principal investigator: František Jurský

Cooperation: Max-Planck-Institut for Brain Research, Frankfurt am Main

Funding in 2003-2004: Germany 610 000,- SKK

[8] Identification of novel Salmonella typhimurium genes under the control of RNA

polymerase sigma factor, SigE

Grant agency: The Wellcome Trust, Collaborative Research Initiative Grant

Grant registration number: 065027/Z/01/Z

Duration: 09/2001-08/2004

Principal investigator: Ján Kormanec

Cooperation: Mark Roberts, University of Glasgow, Glasgow, U.K.

Funding in 2003: UK 480 000,- SKK

Funding in 2004: UK: 480 000.- SKK

iii. List of other important projects and collabora tions without direct funding

[1] Characterization of expression of genes encoding adhesins in Staphylococcus

aureus

Principal investigator in IMB SAS: Ján Kormanec

Cooperation: Mathias Herrmann, Institut fur Mikrobiologie und Hygiene, Universität

des Saarlandes, Homburg/Saar, Germany

Duration: no time limit

Funding in 2005: Germany: 4 000,- EUR

44

[2] Identification and characterization of genes controlled by stress-response sigma

factor SigB in Staphylococcus aureus

Principal investigator in IMB SAS: Ján Kormanec

Cooperation: Markus Bischoff, Institute of Medical Microbiology, University of Zurich,

Zurich, Switzerland

Duration: from 2003 (no time limit)

Funding in 2003: Switzerland: 2 000,- CHF

Funding in 2004: Switzerland: 2 000,- CHF

Funding in 2005: no funding

[3] 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

[4] SRS Federation

Principal investigator: Ľuboš Kľučár

Cooperation:

a) Robert Herzog, ULB, Bruxelles, Belgium

b) Erik Bongcam, Sweden Biomedical Centre, Uppsala, Sweden

c) Piotr Zielenkiwicz, Institute of Biochemistry and Biophysics Polish Academy of

Sciences, Warszawa, Poland

d) Martin Sarachu, IBBM Fac. Cs. Exactas Universidad Nacional de La Plata, La

Plata Argentina

e) Gonçalo Guimarães Pereira, Departamento de Genética e Evolução-IB,

Campinas-SP, Brazil

f) Dan Staines, LION Bioscience AG, Cambridge, UK

Duration: 2004-2006

No funding

[5] Structure - function relationship studied by point mutations in model proteins

Principal investigator: Jozef Ševčík

Cooperation:

a) C.N. Pace, Texas A&M University, College Station, USA

b) EMBL Hamburg, Germany

Duration: 1995 – no time limit

No funding

45

• National projects and funding

i. List of projects supported by the Agency for the Promotion of Research and

Development (APVV/APVT), National Research Programm es, and their funding

[1] A new natural bacterial strains containing genes of catabolic and detoxication

pathways (cat, yodA, czc, ncc) perspective for remediation biotechnology

Principal investigator: Bystrík Polek

Duration: 1/2005-12/2007

Grant agency: APVV, Bratislava

Registration number: APVT-51-024804

Funding: 2005 - 2006: 2 406 000.- SKK

[2] Bacterial programmed cell death as a tool for development of alternative drugs

Principal investigator: Imrich Barák

Duration: 1/2005-12/2007

Grant agency: APVT, Bratislava

Registration number: APVT-51-027804

Funding: 2005 - 2006: 1 747 000.- SKK

[3] Bioinformatics approach to discovery of gene regulatory networks in bacteriophages

Principal investigator: Ľuboš Kľučár

Duration: 1/2005-12/2007

Grant agency: APVT, Bratislava

Registration number: APVT-51-02504

Funding: 2005 - 2006: 956 000.- SKK

[4] Biological variability of the pathogen GBS strains, and their detection during

transmission into diary products. National Research Programme: Foods, Quality and

Safety

Registration number: 2003 SP 27/028 0E 02/028 0E 02

Principal investigator: Andrej Godány

Cooperation: 1 (UVL Košice)

Duration: 09/2003-12/2005

Grant agency: National Research Programmes

Funding: 2003 - 2005: 2 720 000.- SKK

[5] 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")

Principal investigator: Ján Turňa

46

Registration number: 2004 SP26/ 028 0A 00/028 0A 03

Duration: 07/2004- 12/2007

Funding: in 2004: 10 425 000.- SKK. (released in November 2004)

Funding: 2005 - 2006: 23 250 000.- SKK

[6] Heavy metals resistance as a virulence factor of pathogenic bacteria

Principal investigator: Ján Turňa

Cooperation investigator from IMB SAS: Peter Ferianc

Duration: 03/2006-02/2009

Grant agency: APVV

Registration number: 20-054005

[7] Identification of novel Mycobacterium tuberculosis genes under the control of RNA

polymerase sigma factor SigF

Principal investigator: Ján Kormanec

Cooperation:

1, Katarína Mikušová, CSc, KB PríF UK, Bratislava

2, Patrick J. Brennan, Colorado State University, Fort Collins, USA

Grant agency: APVT, Bratislava

Duration: 07/2002 – 06/2005

Registration number: 032/2001

Funding: 2003 - 2005: 900 000,- SKK

[8] Mechanism of the substrates recognition by the Lon protease

Principal investigator: Eva Kutejová

Duration: 1/2005-12/2007

Grant agency: APVT, Bratislava

Registration number: APVT-51-029604

Funding: 2005 - 2006: 746 000.- SKK

[9] Molecular diagnostics of tick-borne pathogens and development of DNA chip.

continuation of stages

Principal investigator: Marketa Derdákova, Zoologicky ústav SAV

Cooperation investigator from IMB SAS: Imrich Barák

Grant agency and Registration number: APVV-51-009205

Duration: 1/2006-12/2008

Funding: in 2006: 817 000,- SKK

Funding: in 2006: 120 000.- SKK

[10] Selected zoonoses in Slovakia in the era of genomics with the emphasis on

ticks and tick-borne infections

Principal investigator: Milan Labuda

47

Cooperation investigator from IMB SAS: Imrich Barák

Duration: 1/2002-12/2004

Grant agency: APVT, Bratislava

Registration number: APVT-51-004702

Funding: 2003: 362 000 SKK

Funding: 2004: 630 000 SKK

[11] Partial task: Monitoring, isolation and diagnostics of the bacterial component of

the plant microflora, in the framework of the project: Conservation and use the

genetic resources of neglected fruit plant species and their microflora in nutrition,

agriculture and rural development

Principal investigator: Ján Brindza

Cooperation investigator from IMB SAS: Peter Ferianc

Duration: 09/2002-08/2005

Grant agency: APVT, Bratislava

Registration number: 20-016602

Funding: 2003 - 2005: 382 000.- SKK

[12] Study of basic cell processes in model microorganism Bacillus subtilis: Cell

division and programmed cell death

Principal investigator: Imrich Barák

Duration: 11/2006-11/2010

Grant agency and Registration number: APVV-LPP-0218-06, <EXPR10>

Funding: in 2006: 369 000,- SKK

[13] The study of variability in salmonella clinical isolates from the SR

Principal investigator: Viktor Majtán

Cooperation investigator from IMB SAS: Jozef Timko

Duration: 01/2004-12/2006

Grant agency: APVV (APVT), Bratislava

Registration number: APVT-21-052602

Funding: 2004 - 2006: 300 000,- SKK

[14] Use of antigenic properties of polysaccharides and mannoproteins from

pathogenic yeasts in diagnosis and prevention of candidiasis

Principal investigator: Slavomír Bystrický, DrSc (CHI SAS)

Cooperation investigator from IMB SAS: Juraj Gašperík

Duration: 1/2003-12/2003

Grant agency: APVT, Bratislava

Registration number: 20-01590

Funding: in 2003: 27 000,- SKK

48

[15] The manose 6-phosphate receptor as the regulator of fibrinolysis on the cell

surface

Principal investigator: Vladimír Leksa

Duration: 1/2005-12/2007

Grant agency: APVT, Bratislava

Registration number: APVT-51-026204

Funding: 2005 - 2006: 730 000.- SKK

[16] The role of RpoE regulon in pathogenesis of Salmonella typhimurium

Principal investigator: Ján Kormanec

Cooperation: Mark Roberts, University of Glasgow, Glasgow, U.K.

Grant agency: APVV, Bratislava

Duration: 01/2005 – 12/2007

Registration number: APVT-51-012004

Funding: 2005 - 2006: 1 581 000.-SKK

[17] The quality of the Life-health, nutrishment, education, State program R&D

“Foodstuffs-quality and safety” No 16 “ Enterococcus sp. in Foodstuffs, the study and

exploitation of their variability”

Principal investigator: Jozef Timko

Cooperation investigator: KMB PríF UK Bratislava

Duration: 03/2003-12/2005

Grant agency: National Research Programmes

Registration number: 2003 SP 27/0280 0E 1028 0E 01

Funding: 2003 - 2005: 7 800 000.- SKK

[18] The Prognosis of the development and exploitation of sciences and

technology until 2015. Part: Genetics and Biotechnology

Principal investigator IMB SAS: Jozef Timko

Duration: 4/2003 – 12/2004

Grant agency: National Research Programmes

Registration number: 2003SP51/0280700/0280701

Funding: 2003 - 2004: 975 000.- SKK

ii. 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

49

VEGA 2003 2004 2005 2006

number 16 16 18 14

funding (millions of SKK) 1.481 1.536 1.873 1.817

• Summary of funding from external resources

External resources 2003 2004 2005 2006 total average

external resources (millions of SKK) 8.724 19.922 15.584 37.033 81.263 20.316

external resources transfered to coooperating research organisations (millions of SKK)

0.000 4.000 0.592 7.993 12.585 3.146

ratio between external resources and total salary budget 0.593 1.333 0.950 2.164 1.260

overall expenditures (millions of SKK) 32.749 44.892 45.624 70.114 193.379 48.345

Supplementary information and/or comments on resear ch projects and funding

resources

During the assessed period there is an increasing ration between external and

institutional funding, where international resources (mainly from EU) play the crucial part.

The Institute has collaborated in 22 internationally funded projects.

5. Organisation of PhD studies, other pedagogical a ctivities

i. List of accredited programmes of doctoral studie s (as stipulated in the

previously effective legislation as well as in the recently amended Act on the

Universities)

4.2 Life science

4.2.3 Molecular Biology

in cooperation with Faculty of Natural Sciences, Comenius University, Bratislava, and

with Slovak Agriculture University, Nitra (Guarantee from the Institute: Ján Kormanec)

4.2.7 Microbiology

in cooperation with Faculty of Natural Sciences and Faculty of Pharmacy, Comenius

University, Bratislava (Guarantee from the Institute: Imrich Barák)

(The head of PhD training centre at the Institute: Jozef Timko)

50

ii. Summary table on doctoral studies (number of inter nal/external PhD students;

number of students who completed their study by a s uccessful thesis defence;

number of PhD students who quitted the programme)

PhD study

number of potential PhD supervisors

PhD students

num

ber

defe

nded

thes

is

stud

ents

qui

tted

num

ber

defe

nded

thes

is

stud

ents

qui

tted

num

ber

defe

nded

thes

is

stud

ents

qui

tted

num

ber

defe

nded

thes

is

stud

ents

qui

tted

internal 10 1 1 10 1 2 13 0 1 13 3 3

external 9 1 0 8 1 0 7 2 2 4 3 4

supervised at external institution by the research employees of the assessed organisation

5 0 0 7 0 0 8 1 0 6 1 0

31.12.200531.12.2003 31.12.2004 31.12.2006

23 23 27 27

iii. Postdoctoral positions supported by

a) external funding (specify the source)

• one full time position of senior scientist Magda Lukáčová funded by the 6th FP

EU grant project NAS-SAP – Nano Arrayed Systems based on Self Assembling

Proteins.

b) internal funding - the Slovak Academy of Sciences Supporting Fund of Stefan

Schwarz

iv. Summary table on pedagogical activities in unde rgraduate programmes for

each year

51

Teaching 2003 2004 2005 2006

lectures (hours/year) 158 270 285 265

practicum courses (hours/year) 1138 1053 1389 3305

supervised diploma works (in total) 8 8 6 10

members in PhD committees (in total) 3 3 9 6

members in DrSc. committees (in total) 2 2 3 4

members in university/faculty councils (in total) 1 1 2 2

members in habilitation/inauguration committees (in total)

1 2 2 1

v. List of published university textbooks

[1] Turňa, J., Stuchlík, S., Drahovská, H., Gálová, Z., Timko, J. Techniky

rekombinantných DNA (Recombinant DNA techniques). Bratislava: VEDA, 2004. 160

s. ISBN 80-224-0835-2.

vi. Number of published academic course books

vii. List of joint research laboratories/facilities with the universities

[1] BITCET– Biotechnological Centrum of Slovak Republic (National R&D project,

http://www.bitcet.sk/)

[2] Join research laboratory of Faculty of Natural Sciences and Institute of Molecular

Biology

viii. Supplementary information and/or comments on doctoral studies and

pedagogical activities

Institute of Molecular Biology has accreditation for supervising PhD students in two

programmes of Life sciences: "Molecular Biology" and "Microbiology". There are two

forms of PhD study, internal (at least 3 and at most 4 years) or external (at most 5

52

years). The Institute supervised also PhD students working at external institutions - Food

Research Institute in Bratislava; State Health Institute in Bratislava; CPN s.r.o. in Dolní

Dobrouč, ČR; Siemens Bratislava. Totally we have 27 scientists with scientific degree

required for supervising PhD students. During the assessed period 14 scientists

participated in the PhD program.

There is a special seminar for PhD students once a year were they present results of

their work. The aim of the seminar is to evaluate the progress of their work. PhD students

present the results of their dissertation, status of their work and problems related with

their PhD study. They have possibility to become familiar with work of other colleagues.

Moreover, the PhD students are due to have individual seminars within the scope of

institutional scientific seminars.

To improve the skills, PhD students attended specialised courses in methods of

molecular biology and/or crystallography in Slovakia as well as abroad (Crystallization

Course CC2005, Nové Hrady, ČR, 10-12. 10. 2005, FEBS Advanced Course: Advanced

methods in macromolecular crystallization II, Nové Hrady, ČR, 6.-13. 10. 2006).

Most of our internal and external PhD students finish their study with successful

defending of their dissertation theses. PhD students from the Slovak Academy of

Sciences need to be registered at particular universities since 2005. This regulation

creates obstacles for PhD students. Difficulties are for example with financing of their

travelling costs to conferences and mobility in general.

At the Institute there is also a very good experience with a number of students

working on their diploma thesis among our research groups. During the period

2003 - 2006 thirty six of our scientists were supervising university students in preparation

of their diploma theses. The students are mainly from the Faculty of Natural Sciences,

Faculty of Pharmacy of Comenius University Bratislava and the University of SS Cyril

and Methodius in Trnava. Many researchers from the Institute are involved as lecturers

in educational programs at these Universities. The Institute also facilitated education and

training of several foreign PhD students and postdoctoral scientists.

Dr. Barak, as an exceptional PhD supervisor, has been awarded by the National

Agency for R&D grant for two PhD student positions ("Study of basic cell processes in

model microorganism Bacillus subtilis: Cell division and programmed cell death",

11/2006-11/2010, APVV-LPP-0218-06T, <EXPR10>, Funding in 2006: 369 000,- SKK).

6. Direct output to the society

(applications of results, popularisation and outrea ch activities)

53

i. List of the most important results of applied re search projects

[1] Institute of Molecular Biology supervises cooperation with industrial partner Biotika

a.s., Slovenská Ľupča (national R&D project)

[2] Co-operation with the pharmaceutical company CPN, Limited, Dolní Dobrouč, Czech

Republic: education of two external PhD students, consulting activities in the field of

the recombinant protein production and construction of the recombinant host strains

for production of the human antimicrobial peptides (hBD1 - 9 strains; dermcidin - 1

strain).

Principal investigator: Juraj Gašperík

[3] The main result of the project “Investigation and Improvement of the Strain Bacillus

polymyxa” is development and establishment specific new PCR method. The cell

cultures of Bacillus polymyxa were tested for presence of particular DNA segments

without necessity of chromosomal DNA isolation. The Bacillus genome library was

also prepared and sequences some of the significant DNA fragments obtained. The

cooperation still continues.

Principal investigator: Gabriela Bukovská

ii. List of the most important studies commissioned for the decision-making

authorities, the government and NGOs, international and foreign organisations

[1] Development of specific and rapid detection of bacterial pathogens in diary products

by PCR. For disposition of State Veterinary and Food Administration of the Slovak

Republic. (Andrej Godany)

[2] Expert's reports for Ministry of Environment SR for experimental work with GMO

(Jozef Timko)

[3] Expert´s reports for Ministry of Education SR within preparation of State

biotechnology program of R&D (Jozef Timko)

iii. List of the most important popularisation acti vities

press

[1] Barák I. (2003) Biologický výskum v období genomiky. (Biological research in

genomic era) Domino fórumXII/37

[2] Barák I. and Blaškovič D. (2005) Biočip ich odhalí. (Biochip detection) Quark/1

[3] Florek P. and Barák I. (2003) Stavbu veľkých biomolekúl treba odhaliť. Už vieme ako.

(Structure of big biomolecules) Quark/2

54

[4] Kutejová, E., „Likvidátori alebo pomocníci?“ Nobelova cena za chémiu 2004.

(“Assessors or supporters?” Nobel price for chemistry in 2004), Quark(1) (2005)

[5] Pangallo D. Podpora vedy na Slovensku (Support of Science in Slovakia), TREND

1.jún 2006

[6] Siekel, P. Ad. Kukuričná story (The corn story). TERČ, časopis na ochranu

spotrebiteľa. VIII, č.8. 2003-11-26 p. 7

[7] Ševčík J.: Poznávanie biologických procesov na atómovej úrovni (Learning biological

processes at atomic level), QUARK, 3, 6-7, 2006

[8] Šimúth, J., Bíliková, K.: Molekulárno-biologický výskum včiel (Molecular biology

research of honeybee), SME 26.10.2006, p 31.„

[9] Šimúth, J.: Certificate of birth of honeybee line Hontianka according Jozef Pollák

Včelár 12, LXXX., 2006, p.18

[10] Šimúth, J. Med ako liek – nie sladidlo..(Honey as a medicine - not sweetnes),

Slovenský magazín ROVINA, Nr. 1-vol. 13, p.11-13, 2006. Národná biblioteka Srbije,

Beograd, Srbsko, COBISS.SR-ID 17620482, ISSN 0354-8929 98

[11] Timko J.: Moderné biotechnológie prinášajú úžitok, (Modern biotechnology

bring profit.), Polnohospodar 50,8 , 13.1.2006, SPU Nitra

lectures

[12] Imrich Barak (2005) Detekcia patogénnych baktérií pomocou DNA biočipov.

(Detection of pathogenic bacteria using DNA biochips) Národné múzeum, Banská

Bystrica, marec, 22, 2005.

[13] Imrich Barak (2005) Detection of bacterial pathogens by DNA chip. Návšteva

predstaviteľov NATO na Ministerstve obrany SR. (Visit of NATO members at the

Ministry of Defence) 7 Janury, 2005.

[14] Imrich Barak (2005) Detekcia patogénnych baktérií pomocou DNA biočipov.

(Detection of pathogenic bacteria using DNA biochips) Syndikát novinárov. Apríl, 4,

2005.

[15] Michal Chotar, B. Vidová B, Andrej Godány Streptococcus agalactiae Surface

Immunogenic Proteins Lecture 2006 Institute of Biochemistry and Animal Genetic,

Ivanka pri Dunajii

[16] Jozef Timko (2005) : Geneticky modifikované mikroorganizmy. (Geneticaly

modified organisms) Národné múzeum, B.Bystrica, marec 22.

[17] Jozef Timko: Súčasný stav, trendy a výzvy v oblasti vedeckého poznania

GMO. (Present stage, trends and calls in scientific know-how of GMO) Agrofilm,

28.september 2005, Nitra.

55

TV

[18] Jozef Šimúth

• „Information on project of FP EU - BeeShop.“ 20.9.2006, STV2

• ,Bioinfopotential of honeybee genome for apiculture research and beekeeping".

21.11.2006, TA3

[19] Jozef Timko: "Microorganisms in sheep cheese", 2005, STV

other

[20] European Science and Technology Week (Science Week Slovakia) 8.

November 2005

IMB Lectures

• Jozef Timko: Geneticky modifikované organizmy (Genetically modified

microorganisms).

• Ján Kormanec: Regulácia diferenciácie a patogenita (Regulation of differentiation

and pathogenicity)

• Eva Kutejová: Proteázy ako dôležité regulátory v bunke (Proteases as an

important regulators in the cell)

• Peter Ferianc: Stres v baktériách (Stress in bacteria)

• Ľuboš Kľučár: Počítače a molekulárna biológia (Computing and Molecular

Biology)

• František Jurský: Ako sa rozprávajú mozgové bunky na úrovni molekúl? (How

neurons talk to each other on molecular level?)

[21] European Science and Technology Week ( Science Week Slovakia) 20 -

21.November 2006

IMB Lectures:

• Jozef Timko: Geneticky modifikované potraviny – Áno alebo Nie (Genetically

modified organisms – Yes or No?).

• Jozef Šimúth: Med ako liek (Honey as a medicine)

• Ján Kormanec: Bunková diferenciácia (Cell differentiation)

• Jozef Ševčík: Bielkoviny – stavebné jednotky živých organizmov (Proteins -

building blocs of living organisms)

• Ján Turňa: Koľko génov má človek (How many genes has man?)

[22] Jozef Šimúth and Katarína Bíliková

PANEL: Research in SAS Exhibition in Slovenské národné muzeum, Bratislava,

November 2006

56

iv. List of patents issued abroad, incl. revenues

v. List of the patents issued in Slovakia, incl. re venues

[1] Streptomyces albus strain producing salinomycin and method of producing

salinomycin the same.

Patent No.: SK3182004

Authors: Blanka Gondova, Jana Gajdošíková, Miroslava Cikosová, Gabriela Borošová,

Vasil Zelenák, Ján Turňa, Jozef Timko, Ján Kormanec

Owner: Biotika a.s., (SK)

vi. List of licences sold abroad, incl. revenues

vii. List of licences sold in Slovakia, incl. reve nues

viii. List of contracts with industrial partners, i ncl. revenues

ix. List of research projects with industrial partn ers, incl. revenues

[1] Agreement about Investigation and Improvement of the Strain Bacillus polymyxa

Principal investigator: Gabriela Bukovská

Coordinator: S&D Chemicals Limited

Duration: 1/2005-06/2005

Funding in 2005: UK 160.000.- SKK

[2] Agreement about Investigation and Improvement of the Strain Bacillus polymyxa -

Continue

Principal investigator: Gabriela Bukovská

Coordinator: S&D Chemicals Limited

Duration: 11/2005 - 04/2006

Funding in 2006: UK 153 000.- SKK

[3] BIOTIKA, a.s.

The Institute continues execution of the national R&D programme with Biotika a.s.

[4] Production of pharmaceutical significant recombinant human antimicrobial peptides

57

Principal investigator: Juraj Gašperík

Coordinator: CPN Limited, Dolní Dobrouč, CZ

Duration: 1/2003-12/2006

Funding in 2003-2006: 1 000 000,- SKK

x. Summary of outreach activities

Outreach activities 2003 2004 2005 2006 total

studies for the decision sphere, government and NGO s, international and foreign organisations

29 29 36 45 139

articles in press media/internet popularising resul ts of science, in particular those achieved by the Organi zation

3 8 6 5 22

appearances in telecommunication media popularising results of science, in particular those achieved by the Organization

5 11 4 7 27

public popularisation lectures 4 8 17 6 35

xi. Supplementary information and/or comments on ap plications and

popularisation activities

The techniques used in molecular biology and microbiology are highly specific and the

result of basic research is not always easily understandable to general public The

organization of European Science and Technology Week (Science Week Slovakia) is

a very good opportunity how to popularise the science and how to make it more

accessible for students and others. We have organised the Day of Science in the year

2005 and 2006 in form of a conference with lectures. These lectures were extensively

visited by about 40 (in 2005) and 60 (in 2006) students from secondary schools, not

only from Bratislava. The students were interested in many topics and discussed many

questions.

7. Background and management. Staffing policy and i mplementation of

findings from previous assessments

58

i. Summary table of personnel

Personnel 2003 2004 2005 2006

all personel 92 88 82 96

research employees from Tab. Research staff 53 51 52 53

FTE from Tab. Research staff 47.0665 46.3665 47.443 47.4985

averaged age of research employees with university degree 46.2 46 47.1 45.6

ii. Professional qualification structure

Number of 2003 2004 2005 2006

DrSc. 6 5 5 6

PhD / CSc. 32 33 30 36

Prof. 1 2 3 3

Doc./Assoc. Prof. 4 2 1 2

iii. Status and development of research infrastruct ure incl. experimental,

computing and technical base (description of the pr esent infrastructure,

premises, and material and technical resources. Inf rastructure, instrumentation

and major technical equipment necessary for the ach ievement of the objectives

specified in the research Concept)

Institute of Molecular Biology possesses essential research infrastructure. Each

laboratory is an independent unit with the basic equipments (centrifuges, incubators,

shakers, pH meters, PCR machine, water baths, etc.) as well as special instruments

demanded for the appropriate project like DNA array reader, PCR machines,

fluorescence microscope (Olympus BX60) with digital camera and related software for

image analysis, ultramicrotome for thin sectioning, laminar boxes, CO2 incubators,

vacuum concentrator, etc. In the last years laboratory equipment has been modernised

59

thanks to the external resources. In addition there are several common used instruments

like FPLC, HPLC, ultracentrifuges, refrigerators for -80°C etc. During evaluated period

the reference GMO laboratory was build up and fully equipped.

As a member of BITCET (http://www.bitcet.sk) we have built up the facility for

genomics and bioinformatics with the overall impact in Slovakia. Service is focused on

sequencing, fragment analysis of DNA and bioinformatic analysis of collected data. We

are able to use several other modern techniques like MS analysis Q-Tof Premier™ mass

spectrometer with nanoACQUITY UPLC™ (Waters), 2D electrophoresis with the

software Image Master Platinum (Amersham Biosciences), DNA sequencing, protein-

protein interactions BIACORE3000. We have also a full access to the state-of-art

confocal microscope Zeiss LSM 510 Meta, already used for most advanced fluorescent

techniques as FRAP, FRET and FLIM.

Based on our broad cooperation with the prestigious institutes in Europe and USA we

have possibility to extend our research also to X-ray analysis of proteins, up-to-date

techniques like transmission electron microscopy, SAXS, fluorescent techniques (FRAP,

FRET, FLIM). Institutional premises have started to be renovated as well. Several

laboratories were reconstructed and newly equipped.

During the past few years the Institute has build a reliable computing network based

on 100 Mbps and 1 Gbps Ethernet technology and structural cabling. Two WiFi Access

points are installed for wireless clients. The institute is interconnected to the SAS

campus via dedicated 100 Mbps optical line. Central PC based server running MS

Windows 2003 OS (Primary Domain Controller) is used as a 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 localised in air-conditioned room together with other 4 Linux based server

interconnected with 1 Gbps Sun Grid Engine, all on UPS. These are primarily used for

bioinformatics computing at the Laboratory of biotechnology and bioinformatics and also

as a main storage and application servers for National EMBnet Node. The institute

maintains (as the only institution in Slovakia) the full set of all major biological databases

(EMBL, Uniprot, Prosite, Pfam, Prints. Interpro, OMIM, the full KEGG set and

Taxonomy), together with several dozens of analysing tools mostly gathered in the

EMBOSS software package (http://www.embnet.sk:8080/srs81/). The Iinstitute maintains

about hundred PC workstation (majority are MS Windows and few Linux based).

60

iv. Status and development of bibliographic resourc es, activities of the

Organisation’s library and/or information centre

Library at the Institute has collected 32 books and 7 titles of scientific journals during

the assessed period (2003-2006). Full list of available journals is accessible at the web

pages (http://imb.savba.sk/journals.html). Management of bibliographic resources is de-

centralised, which means that each department/laboratory buys new titles according to

their needs and resources. Thanks to the different bibliographic services, the most of

required papers are available in a full version on-line.

v. Describe how the results and suggestions of the previous assessment were

taken into account

The last accreditation of the Institute (period 2000-2003) was in 2004 and there were

no negative responses from all three reviewers. Not only research results but also

increasing scientific activities at the Institute, education of young scientists, international

co-operation as well as personal policy and management at the Institute had high impact.

It was suggested to upgrade the infrastructure at the Institute in near future. The

government support of the science in Slovakia is low and we focused our effort to obtain

external financial resources - national (APVV project and state grants R&D) as well as

foreign (The Wellcome Trust, Volkswagen, programs 5th and 6th FP EU, European

Science Foundation). Moreover, we were successful in supplying the Institute with the

modern equipment thanks to funding from PHARE and EU projects (more than 30 mil.

SKK). Without such a support we could not obtain the scientific results we present in this

questionnaire.

vi. Supplementary information and/or comments on ma nagement, research

infrastructure, and trends in personnel development

In the assessed period there were several independent laboratories at the Institute,

based on the research projects. Recently, seven departments were created from these

laboratories on the basis of their research activities. However, these specialised

laboratories still keep their independence in their research work. The present structure is

as follows:

Department of Biochemistry (Head: Ing. Eva Kutejová, CSc.)

Department of Gene Expression (Head: RNDr. Ján Kormanec, DrSc.)

Department of Genomics and Biotechnology (Head: Prof. Ing. Jozef Timko, DrSc.)

Laboratory of Biology of Prokaryotes (Head: Doc. Ing. Andrej Godány, CSc.)

61

Laboratory of Biotechnology and Bioinformatics (Head: Prof. RNDr. Ján Turňa, CSc.)

Laboratory of Genomics (Head: RNDr. Gabriela Bukovská, CSc.)

Laboratory of GMO (Head: Dr. Domenico Pangallo, PhD.)

Department of Microbial Genetics (Head: RNDr. Imrich Barák, DrSc.)

Department of Microbiology (Head: Ing. Bystrík Polek, CSc.)

Laboratory of Cell Biology (Head: Ing. Bystrík Polek, CSc.)

Laboratory of Microbial Ecology (Head: RNDr. Peter Ferianc, CSc.)

Department of Molecular Apidology (Head: Doc. Ing. Jozef Šimúth, DrSc.)

Department of Protein Structure and Function (Head: Ing. Štefan Janeček, DrSc.)

Laboratory of Protein Biochemistry (Head: Ing. Juraj Gašperík, DrSc.)

Laboratory of Protein Crystallography (Head: Ing. Jozef Ševčík, DrSc.)

Laboratory of Protein Evolution (Head: Ing. Štefan Janeček, DrSc.)

Laboratory of Neurobiology (Head: RNDr. František Jurský, CSc.)

The Presidium of the Slovak Academy of Sciences decided (November 4, 2004, the

resolution No. 1123) to relocate the Laboratory of Genetic Engineering (J. Šimúth, Head,

K. Bíliková, A. Kostrian, J. Majtán student and M. Krupcová) from the Institute of

Chemistry SAS, to the Institute of Molecular Biology, SAS effective from January 2005.

The newly formed Department of Molecular Apidology continues its research of functional

genomics of the honeybee, which is currently funded by three international projects.

The Scientific board and the Institutional board use to have regular meetings. The

boards are advisory bodies for the director of the Institute. Scientific board initiated

preparation of the agreement "Long-term policy for governing the scientific potential at

the Institute of Molecular Biology SAS", defining the basic fair-play rules between

researchers and the Executive body of the Institute. Regular evaluation of researchers

takes place at the end of each year. A flexible database system has been developed that

collects and assesses scientific activities of each department and laboratory. One of the

future aims of the Scientific board is to ensure that each scientist engaged in research

and development is rewarded according to the quantity and quality of his/her scientific

outputs.

The Institute organises bi-weekly scientific seminars where our researchers and

researchers from other Slovak and foreign laboratories present up-to-date results of their

work. Scientists from the Institute improve their knowledge and skills during short-term

and long-term visits in prestigious foreign laboratories. If possible, we offer the a job

position also to researchers returning from long-term sojourns abroad.

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Other information relevant to the assessment

National funding for research and science in Slovakia is one of the smallest among all

EU countries. Therefore only International co-operations, projects and personal contacts

significantly enhance scientific activities at the Institute.