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Program developing interdisciplinary research potential for the studies of biomolecular interactions (POSTBIOMIN)

Project summary

National Centre for Biomolecular Research (NCBR), Masaryk University Brno in the Czech Republic has become one of the leading laboratories for structural biology in the Central Europe. The institute is very well equipped by modern laboratory equipment and instruments. Project POSTBIOMIN will strengthen our research potential in theoretical and experimental research that focuses on the structural characterization of biomacromolecules and especially biomolecular interactions study through the scheme of support measures like recruitment of foreign experts, organization of international PhD courses and lectures given by top international scientists. Series of workshops, seminars, postdoctoral and expert inter-ships and visits will be organized. We suppose to reinforce our capacities related to transfer of technologies by hiring the West European specialist. This program will complement investments in research capacity co-financed through the EU cohesion policy programmes for 2007-2013, i.e., CEITEC - large project of Centro-European Institute of Technology focuses on biotechnologies and interdisciplinary medical research, and is prepared in Brno with political support of the Czech Government. Project POSTBIOMIN will contribute to the creation of human potential for modern research institutions and companies dealing with bio-medical research and biotechnologies within the region of Brno.

Funding source: FP7 - 7th Framework Programme for Research and Development

Beneficiary name: Masaryk University

Date enter project: 1.3.2008

Date exit project: 28.2.2011

Further information: Regional aspects of FP7

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Concept and project objectives

The global objective of this project is to further develop research potential of our institute (NCBR), which is important part of regional network of bio-sciences research institutions. This project will help us to gain knowledge and exchange experience within European regions. We will work on setting up strategic partnerships with other research teams elsewhere in the Europe as well. One of the greatest challenges to be achieved is the return of Czech scientist who would come back to pursue her/his independent career in our institute.

Apart from global objective we can identify technical and scientific objectives in POSTBIOMIN project. Due to the character of REGPOT-1 call, technical objectives are crucial and the most substantial for the project. However achievement of scientific goals and objectives is even more important, despite scientific objectives are rather hidden behind main content of work packages.

Technical objectives, i.e. organization of post-doc and PhD courses, appointment of foreign experts and scientists, organization of lectures, workshops, trainings both in Masaryk University in Brno and abroad (EU-15 countries) are described in details below within the description of particular work packages.

Scientific objectives will be targeted by all work packages. Structural biology is relatively young research area aiming at understanding the three-dimensional structures of biological macromolecules, proteins, nucleic acids and sugars. In recent years, the techniques of structural biology have significantly advanced and generated many structures of biomolecules. However, the visualization of isolated molecules is not the only goal. Biological molecules work in the context of cells and tissues, interacting with other proteins, nucleic acids and carbohydrates. Detailed knowledge of mutual interactions provides fundamental insights into molecular biology and feeds into the development of medical applications. We aim to enhance our research capacities to study biomolecular interactions and their structures with the ultimate goal to find the molecular basis behind a biological event. This requires interdisciplinary knowledge in physics, chemistry and biology and to be able to develop and apply the state-of-the-art techniques in this area. This program will enable us to obtain this interdisciplinary research experience through the scheme of support measures such as recruitment of foreign experts and postdocs, organization of international postdoctoral courses and lectures given by internationally recognized scientists. In general, we can describe scientific objectives as three research topics (see below).

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S/T methodology and associated work plan

Research Topic 1 - Repair of damaged DNA

Responsible Scientists: Dr. Krejci, Dr. Stefl, Prof. Sklenar, Prof. Koca

Relevance of this research topic:
Through this supporting scheme, we will establish single molecule techniques such as Total Internal Reflection Microscopy, Förster (Fluorescence) Resonance Energy Transfer, Atomic Force Microscopy, Surface Plasmon Resonance. These modern techniques are still under development and require highly trained experts. This programme will help us to attract well-trained experts who will transfer their expertise to our Institute. At present, there is several contradictory issues in the area of homology recombination. To resolve them, we urgently need more structural information about molecular assemblies involved in this mechanism. With these techniques we could obtain structural and mechanistic insights into the processes of homology recombination, which may significantly enhance the momentum in the research area.

Research Topic 2 - RNA quality control

Returning experienced researcher: Dr. Vanacova
Responsible Scientists: Dr. Stefl, Prof. Koca, Prof. Sklenar

Relevance of this research topic:
Despite the increasing amount of data on RNA quality control, there are still many questions to be answered. How does the quality-control machinery distinguish its RNA substrates from other RNA molecules? What allows the exosome to switch from the degradation mode to the processing mode? How exactly is the exosome stimulated by the TRAMP and Nrd1 complexes, and what other protein factors are required for its proper function in vivo? To answer these questions, we need to transfer know-how from West Europe to implement and further develop new techniques that includes NMR spectroscopy of large molecular assemblies, macroarray analysis, and single molecule techniques. With these techniques we will be able to dissect both the general mechanism and detailed features of the RNA surveillance apparatus, a universal machinery with the fundamental quest to seek and destroy damaged molecules.

Research Topic 3 - Pathogen-host recognition and interaction

Responsible Scientists: Dr. Wimmerova, Prof. Koca, Prof. Sklenar

Relevance of this research topic:
Through this supporting scheme, we will establish crystallization and X-ray diffraction techniques in our institute, which will be used to determine crystal structures of protein-carbohydrate complexes. These are highly advanced techniques that are usually located only at selected European sites where all the knowledge is accumulated. We wish to transfer most of these technologies to our institute to form a unique structural biology unit in central Europe region.
In addition, this program will unable us to gain know-how in other important techniques such as Surface Plasmon Resonance and Isothermal titration microcalorimetry. These techniques are used to study kinetics and termodynamics of biomolecular interactions which are essential parameters one has to fully understand when rationalizing interactions of biomolecules.

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Work package descriptions

WP1 - Return of experienced Czech scientist (start month 1)

Objective:

  • To recruit Czech scientist, who would return from abroad and continue in research at home country and to create new laboratory for returning scientist.

Activities:

  1. Return of experienced Czech scientist
    Dr. Štěpánka Vaňáčová (Biozentrum, University of Basel). She focuses on studies of RNA processing and degradation and is interested in coming back to CR to pursue her career. She will transfer a new technology & know-how for studying biomolecular interactions to our institute.
    Dr. Petr Kulhánek (Institute of Enzymology, Budapest, Hungary). He has expertise in molecular modeling and cluster and grid supercomputing with the main focus on the calculation of the free energies.
  2. Creation of new laboratory
    that will focus on studying the protein-RNA interactions involved in RNA surveillance apparatus (see detailes).

Current progress:

WP2 - Incoming Post-docs (start month 1)

Objective:

  • To attract experienced postdoctoral fellows who will bring missing know-how.

Activities:

  1. We will open six postdoctoral positions to bring experienced postdoctoral fellows from EU-15. Every one will work on different project that will last up to 2,5 years. Each postdoc will have a regular working contract.
    The following postdoctoral projects will be opened:
    • project 1 - Development and implementation of NMR methods for studies of biomolecular interactions of large assemblies.
    • project 2 - Structure-function analysis of carbohydrate-binding proteins from filamentous fungi, bacterial pathogens and viruses.
    • project 3 - Development and application of computational methods in the biomolecular interactions study.
    • project 4 - Implementation of microarray technology to search for new RNA targets.
    • project 5 - Structural studies of protein-RNA complexes involved in RNA quality control.
    • project 6 - Implementation o.f single molecule analysis tools (SMAT) to study interactions between proteins with DNA/RNA and other proteins to dissect the molecular details of recognition and repair of damaged DNA/RNA.

Current progress:

  1. Recruitment is open for the following positions:
  2. Recruited post-docs:

WP3 - PhD courses (start month 10)

Objective:

  • To upgrade human potential by employment of excellent international scientists as lecturers for our young scientists - PhD scholarship holders.

Activities:

  1. We will organise three PhD courses. Each PhD course will take five days and will include 2 tutors from Western Europe, each teaching two days. In the middle of these five days, the PhD students will take part in one-day workshop (WP6). We expect that each PhD course will be attended by 20 participants. The courses will be focused:
    • On Structure determination of biomolecular complexes using NMR spectroscopy.
    • On Biomolecular interactions study by molecular modelling tools.
    • On Structural and functional aspects of proteins involved in host oligosaccharide interactions and their biosynthesis.

Current progress:

  • The Ph.D. course on Biomolecular Interactions by Computational Chemistry Tools was held in November 3 - 7, 2008. The course was attended by approximately 44 participants.
    More info: www.ncbr.chemi.muni.cz/interactions08
  • The Ph.D. course on Biomolecular Interactions by Experimental Methods was held in November 2 - 6, 2009. The course was attended by approximately 40 participants.
    More info: www.ncbr.chemi.muni.cz/interactions09
  • The Ph.D. course was held in October 4 - 8, 2010. The course was attended by approximately 40 participants.
    More info: www.ncbr.chemi.muni.cz/interactions10

WP4 - Lectures given by international leaders of biomolecular interactions (start month 3)

Objective:

  • To facilitate knowledge and experience transfer from prestigious West European research centres and laboratories to scientists from MU (NCBR) and other centres in Brno region.

Activities:

  1. We will organise approximately 20 lectures that will be given by leaders in the field of biomolecular interactions. These lectures will follow a well-established series of Mendel lectures. These lectures will be held in the Augustinian Abbey of St Thomas, Brno. It is a place where Gregor Mendel lived and worked. The audience will include people from both academic institutions and industry from the Brno region. We expect that each lecture will be attended by an audience of about 60-80 participitant.

Current progress:

  1. Lecture: DNA strand-break repair and relationship to human disease.
    Given by: Prof. Stephen West, Cancer Research UK, Clare Hall Laboratories, UK (April 10, 2008)
  2. Lecture: Electrostatics and catalysis: Dissecting the pH-dependent mechanisms of model glycosidases.
    Given by: Prof. Lawrence McIntosh, EMBL, Grenoble, France (May 15, 2008)
  3. Lecture: Protein-protein interactions and molecular mechanisms of signal transduction.
    Given by: Annick Dejaegere, Institute of Genetics and Molecular and Cellular Biology-GBMC, ESBS, Strasbourg, France (November 5, 2008)
  4. Lecture: Modeling nucleosome positioning.
    Given by: Richard Lavery, Institut de Biologie et Chimie des Protéines-IBCP, Lyon, France, (November 5, 2008)
  5. Lecture: Computationally-guided Glycoscience: Predicting the Structures and Energies of Carbohydrate-Protein Interactions.
    Given by: Robert Woods, National University of Ireland at Galway, Ireland (November 6, 2008)
  6. Lecture: Hit Identification and Binding Mode Predictions by Rigorous Free Energy Calculations.
    Given by: Jonathan Essex, Department of Chemistry, University of Southampton, UK (November 6, 2008)
  7. Lecture: Structural biology - What structures of the ribosome have revealed about its central role in translating genetic information.
    Given by: Dr. Venki Ramakrishnan, Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, England (May 7, 2009)
  8. Lecture: 3' end processing of messenger RNA precursors and RNA quality kontrol.
    Given by: Prof. Walter Keller MD, PhD, Biocentrum, University of Basel, Switzerland (May 21, 2009)
  9. Prof. Iain Campbell, November 4 – 6, 2010, University of Oxford, Depatment of biochemistry, UK.
    Cell migration and protein – protein interactions.
  10. Prof. Linda Partridge, April 7 – 8, 2011, Max-Planck-Institute for Biology, Cologne, Germany.
    The new biology of ageing.
  11. Prof. David Scheratt, April 12 – 18, 2011, University of Oxford, Depatment of biochemistry, UK.
    A passion for DNA.

WP5 - Incoming Experts (start month 1)

Objective:

  • To enhance knowledge and experience of research teams from MU (NCBR) by transfer of knowledge by incoming experts.

Activities:

  1. Short-term stays (1-8 weeks) of incoming experts will help to implement and develop modern scientific methods in MU (NCBR). We would especially like to invite experts in the following scientific fields: structural methods, computational techniques, protein/protein, protein/nucleic acid and protein/carbohydrate interactions, thermodynamics of biomolecular interactions, single molecule analysis and microarrays. We expect at least two experts per each field to be invited (about 16 incoming experts).

Current progress:

  • Prof. Lawrence McIntosh, May 13 - 16, 2008, EMBL, Grenoble, France.
    NMR spectroscopy and structural biology of biomolecular interactions.
  • Dr. Jozef Hritz, March 31 - April 11, 2008, Vrije Universiteit, Amsterdam, The Netherlands.
    Molecular modelling and interpretation of NMR data.
  • Prof. Stephen West, April 8 - 10, 2008, Cancer Research UK, Clare Hall Laboratories, UK.
    DNA repair.
  • Prof. Serge Pérez, July 12 - 16, 2008, CERMAV, Grenoble, France.
    Glycobioinformatics.
  • Roberto Pergoli, September 3 - 6, 2008, RSCI - The Royal College of Surgeons in Ireland, Dublin, Ireland.
    Reaction mechanism of a novel cycloaddition reaction.
  • Maria Sanudo Arce, September 3 - 6, 2008, RSCI - The Royal College of Surgeons in Ireland, Dublin, Ireland.
    Preparation of a deoxyribose based synthon.
  • Charles Sabin, October 7 - November 2, 2008, EMBL Grenoble, France.
    X-ray analysis of proteins.
  • Premyslaw Ozdowy, December 6 - 8, 2008, University of Innsbruck, Austria.
    Study of labeled proteins by NMR methods.
  • Tamás Tereh, March 5 - 6, 2009, Budapest, Hungary.
    DNA Repair.
  • Prof. Serge Pérez, April 15 - 19, 2009, CERMAV, Grenoble, France.
    Glycobioinformatics.
  • Prof. Karl Klisch, April 14 – 19, 2009, The University of Nottingham, United Kingdom.
    Glycoproteins.
  • Doc. Katarina Mikušová, April 16 -17, 2009, Comenius University in Bratislava, Bratislava, Slovakia.
    Study of the activity of glycosyltransferases.
  • Dr. Ksenia Matlawska-Wasowska, April 28 – 30, 2009, National University of Ireland, Galway, Ireland.
    DNA Repair.
  • Ms. Ana Maria Leon Ortiz, April 30 - May 5 and May 15 - May 21, 2009, Institut Curie - Centre de Recherche, Paris, France.
    Expertise in genetics area.
  • Dr. Jacek Lichota, June 8 - 9, 2009, Laboratory of Neurobiology Biomedicine, Aalborg University, Denmark.
    Chromatin association and in vivo role of non-histone chromosomal proteins.
  • Dr. Mario Schubert, June 9 - 11, 2009, Institut of Molecular Biology and Biophysics, Zurich, Switzerland.
    Structure determination of protein-RNA complexes and glykoproteins.
  • Dr. Emil Damyanov Parvanov, June 18 - 19, 2009, Postdoctoral Associate, The Jackson Laboratory, Bar Harbor, ME, USA.
    DNA recombination.
  • Dr. Jürgen M. Plitzko, June 24 - 26, 2009, Department of Structural Biology, Max Planck Institute of Biochemistry, Martinsfried, Germany.
    Strategies and developments in cryo-electron microscopy.
  • RNDr. Dana Vigašová, August 10 – October 9, 2009, Cancer Research Institute, Slovak Academy of Science, Slovakia.
    Characterization of the role of Srs2 protein during repair of damaged.
  • Peter Burkovics Ph.D, September 21 – October 2, 2009, Institute of Genetics, BRC, HAS, Szeged, Hungary.
    Testing of influence of recombinating proteins to TLS polymers.
  • Dr. Helene Tourriere, October 15 – 17, 2009, IGH - Institute of Human Genetics, CNRS, France.
    Influence of DNA helikases on the procesivity of repliation.
  • Dr. Armelle Cau-Lengronne, October 15 – 17, 2009, Institute of Human Genetics, CNRS, France.
    Influence of DNA helikases on the procesivity of repliation.
  • Dr. Philippe Pasero, October 15 – 17, 2009, Institute of Human Genetics, CNRS, France.
    Influence of DNA helikases on the procesivity of repliation.
  • M.Sc. Wiktor Kozminsku, Ph.D, D.Sc., October 21 - 24, 2009, Fakulty of chemistry, University of Warsaw, Poland.
    Applications of Multidimensional Fourier Transform and random sampling.
  • Prof. Dr. Norbert Müller, October 25 - 27, 2009, Institute of Organic Chemistry, Johannes Kepler University , Linz, Austria.
    Non-coherent NMR spectrometry.
  • Dipl. Ing. Martin Nausner, October 25 - 29, 2009, Institute of Organic Chemistry, Johannes Kepler University , Linz, Austria.
    Non-coherent NMR spectrometry.
  • Dipl. Ing. Judit Schlagnitweit, October 25 - 29, 2009, Institute of Organic Chemistry, Johannes Kepler University , Linz, Austria.
    Non-coherent NMR spectrometry.
  • Dr. Vilko Smrecki, October 25 - 29, 2009, NMR Center, Rudjer Boskovic Institute, Zagreb, Croatia.
    Non-coherent NMR spectrometry.
  • RNDr. Dana Vigašová, October 26 – December 18, 2009, Cancer Research Institute, Slovak Academy of Science, Slovakia.
    Characterization of the role of Srs2 protein during repair of damaged
  • Dr. Andre Gerber, October 29 - 31, 2009, Institute of Pharmaceutical Sciences, ETH, Zutích, Switzerland.
    Global aspects of the RNA-Protein Interaction Network.
  • Prof. Gernot Längst, October 29 - 31, 2009, University of Regensburg, Germany
    Global aspects of the RNA-Protein Interaction Network.
  • Prof. Ten Feizi, October 3 - 6, 2009, Imperial College, London, UK.
    Excursion in Glycobiology with carbohydrate microarrays.
  • M.Sc. Mikael Akke, Ph.D, November 18-20, 2009, Dept. of Biophysical Chemistry, Lund University, Lund, Sweden.
    Dynamic aspects of biopolymers.
  • Dr. Peter Burkovics Ph.D, November 16 – December 14, 2009, Institute of Genetics, BRC, HAS, Szeged, Hungary.
    Testing of influence of recombinating proteins to TLS polymers.
  • Dr. Emil Damyanov Parvanov, December 3 - 23, 2009, Postdoctoral Associate at the Jackson Laboratory, Bar Barbor, USA.
    Start regulation of two-chain breaks.
  • Ing. Peter Bystrický, Ph.D, November 1 – December 23, 2009, Institute of chemistry, Slovak academy of Science, Bratislava, Slovakia.
    Introduction of STD-NMR Method to interactions protein / sugar.
  • Dr. Peter Burkovics Ph.D, February 1 - March 26, 2010, Institute of Genetics, BRC, HAS, Szeged, Hungary.
    Testing of influence of recombinating proteins to TLS polymers.
  • Madhusoodanan Urulangodi, March 22 – April 30, 2010, IFOM - The FIRC Institute of Molecular Oncology Foundation', IFOM-IEO campus, Milan, Italy.
    Role of recombination during DNA synthesis and replication.
  • Dr. Lajos Haraska, March 25 – 27, 2010, Institute of Genetics Laboratory of Mutagenesis and Carcinogenesis, Biological Research Center Hungarian Academy of Science, Szeged, Hungary.
    DNA repair and genome maintenance.
  • Ivan Krešimir Světec, March 25 – 27, 2010, University of Zagreb, Department of biochemical Engineering, Zagreb, Croatia.
    DNA repair and genomic instability.
  • Prof. RNDr. Lubomír Tomáška, Dr.Sc., April 8, 2010, Department of Genetics Faculty of Natural Sciences , Comenius University in Bratislava, Slovak republic.
    Evolution gadgetry and telenomers.
  • Clemens Uanschou , May 17 – 21, 2010, Department of Chromosome Biology MFPL - Max F. Perutz Laboratories, University of Vienna, Vienna, Austria.
    Expression and purification of proteins with low solubility.
  • Samy Ceciony, M.S., June 2 – July 1, 2010, CERMAV-CNRS, BP53, 38041 Grenoble cedex 9, France.
    Interactions of proteins with inhibitors.
  • Olga Jasnovidcova, June 16 – 18, 2010, University of Tartu, Estonia.
    Study of the carboxyl-terminal extension (CTE) of S. cerevisiae mitochondrial DNA polymerase Mip1p.
  • Prof. Michael Lisby, July 3 – 4, 2010, University of Copenhagen, Copenhagen, Denmark.
    In vivo characterization of recombination factors and the effect of their post-translational modification by SUMOylation.
  • Mgr. Lucia Pánčiová, August 1 – 31, 2010, Faculty of Natural Sciences of Comenius University, Bratislava, Slovakia.
    Introduction of gene expression of heterogenous proteins in high-density cultures.
  • M.Sc. Pathan Meerakhan, October 3 - 9, 2010, University of Lille, France.
    NMR Biomolecul expertise.
  • Dr. Jürgen M. Plitzko, October 5 - 8, 2010, Department of Structural Biology, Max Planck Institute of Biochemistry, Martinsfried, Germany.
    3 dimensional cryo – elektron microscopy – Voyages to uncharted molecular territories, Correlative cryo – microscopy: From cellular territories to molecular landscapes.
  • Dr. Anne Imberty, October 16 – 19, 2010, Molecular Glycobiology, CNRS – CERMAV, Grenoble, France.
    Expertise in sacharide docking.
  • Dr. Peter Lukavský, October 20 – 22, 2010, Laboratory of Molecular Biology Medical research council, Cambridge, UK.
    A´- form RNA helices drive microtubule – based mRNA transport in Drosophila.
  • Dr. Peter Burkovics Ph.D, November 1 – 14, 2010, Institute of Genetics, BRC, HAS, Szeged, Hungary.
    Characterization of Rad5-Srs2 protein interaction.
  • Prof. Marek Potrzebowski, November 22 – 25, 2010, Department of Structural Studies, Laboratory for Analysis of Organic Compounds and Polymers, Łódź. Poland.
    Aplication of Solidstate NMR spectroscopy to studyof structure, dynamics and polymorphism of selected peptides and proteins.
  • Dr. Václav Veverka, November 25 - 28, 2010, Leicester, UK.
    NMR spectroscopy as a versatile tool in knowledge-based drug development.
  • Dr. Lukáš Trantírek, December 7 – 11, 2010, Cellular Protein Chemistry , Utrecht University, The Netherlands.
    A holistic approach to stuctural biology.
  • RNDr. Vladimir Pevala, January 31 – February 4, 2011, Slovak Academy of Sciences, Slovakia.
    Analysis of DNA binding.
  • Prof. Martin Zacharias, February 23 – 25, 2011, Technische Universität München, Germany.
    Simulation of nucleic acid and peptide dynamics using advanced sampling.
  • Prof. Joanna Trylska, March 9 – 11, 2011, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Poland.
    Understanding aminoglycoside association and binding with the ribosomal RNA.
  • RNDr. Vladimir Pevala, March 28 – April 1, 2011 , Slovak Academy of Sciences, Slovakia.
    Analysis of DNA binding of Mgm101 protein.
  • Igor Tvaroška, Ph.D, DSc., April 5 - May 29, 2011, Slovak Academy of Sciences, Slovakia.
    Carbohydrate processing inhibitors – rational design of transition state analogue inhibitors for glycosyltransferases.
  • Dr. Anton Meinhart, April 13 – 17, 2011, Max Planck Institute for Medical Research, Heidelberg, Germany.
    Networks for RNA tailoring.
  • Mgr. Joanna Panecka, April 11 – 22, 2011, Centre for Mathematical and Computational Modelling - University of Warsaw, Poland.
    Study of A-site in the decoding ribosomal centre using molecular dynamics.
  • Dr. Anne Imberty, May 1 – 6, 2011, CERMAV-CNRS , Domaine Universitaire de Grenoble , France.
    Protein cristallization of lectins.
  • Prof. Serge Perez, May 1 – 6, 2011, CERMAV-CNRS, Domaine Universitaire de Grenoble, France.
    Partnership in Structural Biology.
  • Prof. Johannes Clevers, May 12 – 13, 2011, Hubrecht Institute, Netheerlands.
    Wnt signaling, Lgr5 stem cells and cancer.
  • Dr. Vladimir Rogov, May 22 – June 3, 2011, Goethe University, Germany.
    The rcs phosphorelay in Enterobacteria: structural views and perspectives.
  • Dr. Vladimir Saudek, May 23 – June 3, 2011, Sanofi-Aventi, Recherche et Développement, Toulouse, France.
    In search of function of FTO, a gene strongly implicated in obesity.
  • Prof. Jeffrey Errington, May 23 – 29, 2011, Newcastle University, UK.
    L-form bacteria and the origins of life.
  • Ms.C. Fedor Nikulenkov, June 3 – 9, 2011, Karolinska Institute, Sweden.
    Reactivation of p53 and induction of tumor cell apoptosis.
  • Dr. Peter Burkovics Ph.D., June 13 – July 8, 2011, Hungarian Academy of Sciences , Hungary.
    Characterization of human HLF translocaze and its ability to form a D-loop.
  • Igor Tvaroška, Ph.D., DSc., June 15 – 30, 2011, Slovak Academy of Sciences, Slovakia.
    Carbohydrate processing inhibitors – based on the catalytic mechanism of carbohydrate processing enzymes.
  • Dr. Andrzej Dziembowski, June 26 – 28, 2011, Warsaw University, Poland.
    Analysis of the macromolecular assemblies involved in RNA metabolism in eukaryotes.
  • Dr. Gernot Walko, June 27 – July 1, 2011, University of Vienna, Austria.
    Building (tissues) on firm ground: novel insights into hemidesmosome homeostasis.
  • RNDr. Vladimir Pevala, July 4 – 8, 2011, Slovak Academy of Sciences, Slovakia.
    Analysis of DNA binding of Mgm101 protein.
  • Igor Tvaroška, Ph.D., DSc., July 11 – August 22, 2011, Slovak Academy of Sciences, Slovakia.
    Carbohydrate processing inhibitors – based on the catalytic mechanism of carbohydrate processing enzymes.
  • Dr. Peter Lukavský, August 17 - 19, 2011, Laboratory of Molecular Biology Medical research council, Cambridge, UK.
    A´- form RNA helices drive microtubule – based mRNA transport in Drosophila.

WP6 - Workshops (start month 10)

Objective:

  • To organize three workshops in order to enhance practical research skills of MU (NCBR) scientists by transfer of knowledge of most advanced techniques of biomolecular interactions research.

Activities:

  1. We will organize three workshops (one per year) focused on practical aspects of individual techniques involved in biomolecular interactions. Each workshop will consist of about seven speakers that are experts in individual fields.
    Three different topics will be covered:
    • Workshop 1: Biomolecular interactions in a view of structural methods.
    • Workshop 2: Structural and thermodynamical aspects of biomolecular interactions: in-silico methods.
    • Workshop 3: Thermodynamics and kinetics of biomolecular interactions by experimental methods.
    These workshops will be held in parallel with PhD Courses (see WP3). We expect that each workshop will be attended by 40 participants.

Current progress:

  • The workshop on Biomolecular Interactions by Computational Chemistry Tools was held on November 5, 2008. The workshop was attended by approximately 83 participants.
    More info: www.ncbr.chemi.muni.cz/interactions08
  • The workshop on Biomolecular Interactions by Experimental Methods was held in November 4, 2009. The workshop was attended by approximately 80 participants.
    More info: www.ncbr.chemi.muni.cz/interactions09
  • The workshop on Frontiers in Structural Biology was held in October 6, 2010. The workshop was attended by approximately 80 participants.
    More info: www.ncbr.chemi.muni.cz/interactions10

WP7 - Stay and training at foreign institutes (start month 1)

Objective:

  • To facilitate knowledge transfer from the best European laboratories to scientists from MU (NCBR) through their stay and trainings at foreign institutes.

Activities:

  1. We will send people for stays and trainee-ships abroad. Based on our main three Research Topics RT1, RT2, RT3 a nubmer of foreign institutes has been selected.

Current progress:

  1. Past stays:
    • Prof. Jaroslav Koča, April 26 - May 11, 2008, Grenoble, France, CERMAV.
      Conformation analysis of oligosacharides.
    • Doc. Michaela Wimmerová, April 6 - May 11, 2008, Grenoble, France, CERMAV.
      Protein crystalography.
    • Doc. Michaela Wimmerová, June 17 - 20, 2008, Amsterdam, The Nederlands.
      Protein Crystallography Europe Conference and exhibition.
    • Doc. Štěpánka Vaňáčová, July 24 - 26, 2008, Basel, Switzerland.
      Biozentrum der Universitat Basel.
    • Mgr. Grabicová Lenka, August 3 - 8, 2008, Il Ciocco, Italy.
      NMR Course.
    • Prof. Jaroslav Koča, November 8 - 19, 2008, Grenoble, France, CERMAV.
      Conformation analysis of oligosacharides.
    • Doc. Michaela Wimmerová, November 8 - 19, 2008, Grenoble, France, CERMAV.
      Protein crystallography.
    • Mgr. Marek Šebesta, November 30 – December 6, 2008, Paris, France.
      Institut Curie DNA metabolism workshop.
    • Mgr. Jan Vrbský, January 25 - 30, 2009, Saariselka, Finland.
      Winter School held by ESTOOLS - stem cells research.
    • Mgr. Josef Houser, February 27 - April 5, 2009, Grenoble, France, CERMAV.
      Study of lectin AFL from Aspergillus fumigatus.
    • Mgr. Josef Houser, April 19 - May 31, 2009, Grenoble, France, CERMAV.
      Study of lectin AFL from Aspergillus fumigatus.
    • Mgr. Jana Laláková, May 15 - 30, 2009, Barcelona, Spain, Centre for Genomic Regulation.
      Technics of yeast extracts prepartion and splicing reactions.
    • Mgr. Jan Vrbský, May 24 - 27, 2009, Rome, Italy.
      Conference ESTOOLS - stem cells cultivation, differentiation and application in medicine.
    • Prof. Jaroslav Koča, May 16 - 25, 2009, Grenoble, France, CERMAV.
      Discussions on POSTBIOMIN project topics.
    • Doc. Michaela Wimmerová, May 16 - 25, 2009, Grenoble, France, CERMAV.
      Discussions on POSTBIOMIN project topics.
    • Mgr. Veronika Altmannová, August 29 - September 1, 2009, Amsterdam, Netherlands.
      Conference EMBO.
    • Prof. Jaroslav Koča, October 21 - 29, 2009, London, U.K.
      Stay at Imperial College London and University College London.
    • Doc. Michaela Wimmerová October 21 - 29, 2009, London, U.K.
      Stay at Imperial College London and University College London.
    • Doc. Michaela Wimmerová December 11 - 16, 2009, Grenoble, France.
      Discussions on POSTBIOMIN project topics.
    • Prof. Jaroslav Koča, December 11 - 16, 2009, Grenoble, France.
      Discussions on POSTBIOMIN project topics.
    • Ondřej Šulák, PhD, December 11 - 16, 2009, Grenoble, France.
      Discussions on POSTBIOMIN project topics.
    • Ondřej Šulák, PhD, January 4 - February 28, 2010, Grenoble, France.
      Research stay at CERMAV.
    • Ondřej Šulák, PhD, March 1 - April 30, 2010, Grenoble, France.
      Research stay at CERMAV.
    • Lumír Krejčí, PhD, March 10 - 11, 2010, Copenhagen, Denmark.
      Discussions of project topics at Univerisy of Copenhagen.
    • Mário Špírek, PhD, April 12 - 16, 2010, Budapest, Hungary.
      Research stay at laboratory of Dr. Mihál Kovács.
    • Prof. Jaroslav Koča, May 1 - 5, 2010, Grenoble, France.
      Discussions of POSTBIOMIN project topics.
    • Doc. Michaela Wimmerová, May 1 - 5, 2010, Grenoble, France.
      Discussions of POSTBIOMIN project topics.
    • Dmitro Ustianenko, May 6 - June 6, 2010, Basel, Switzerland.
      Research stay at Laboratory of Computational Systems Biology, University of Basel.
    • Veronika Bačíková, June 13 - 26, 2010, Zurich, Switzerland.
      Research stay at Institute of Molecular Biology and Biophysics.
    • Radka Svobodobá Vařeková, July 30 - August 29, 2010, Dublin, Ireland.
      Research stay at institute Royal College of Surgeons in Ireland.
    • Sushil Kumar Mishra, August 1 - September 30, 2010, Upsala, Sweden.
      Research stay at group of Prof. Aqvist in the Department of Cell and Molecular Biology at Uppsala University.
    • Mário Špírek, August 30 - September 3, 2010, Budapest, Hungary.
      Research stay at the laboratory of dr. Mihály Kovács.
    • Petr Bystrický, September 1 - 3, 2010, Zurich, Switzerland.
      Participation at 10th NCCR Symposia on New Trends in Structural Biology.
    • Kristýna Hrazdilová, September 3 - November 30, 2010, Aarhus, Denmark.
      Research stay in the group of Dr. Torben Heick Jensen at Department of Molecular Biology, Aarhus University.
    • Lumír Krejčí, September 10, 2010, Vienna, Austria.
      Meeting with Dr. Karel Říha (Gregor Mendel Institute of Molecular Planr Biology GmbH) - consultation of reasearch topics in the field of telomeres and DNA repair..
    • Veronika Altmanová, September 23 - 26, 2010, Madrid, Spain.
      Participation at conference EMBO DNA Repair Meeting organized by institute CNIO.
    • Lumír Krejčí, September 23 - 26, 2010, Madrid, Spain.
      Participation at conference EMBO DNA Repair Meeting organized by institute CNIO.
    • Marek Šebesta, September 23 - 26, 2010, Madrid, Spain.
      Participation at conference EMBO DNA Repair Meeting organized by institute CNIO.
    • Štěpánka Vaňáčová, September 30 - October 2, 2010, Paris, France.
      Research stay at laboratory of Dr. Domenico Libri and Dr. Torbena Jensena in the Centre de Génétique Moléculaire .
    • Dominika Hroššová, September 30 - October 2, 2010, Paris, France.
      Research stay at laboratory of Dr. Domenico Libri and Dr. Torbena Jensena in the Centre de Génétique Moléculaire .
    • Peter Holub, September 30 - October 2, 2010, Paris, France.
      Research stay at laboratory of Dr. Domenico Libri and Dr. Torbena Jensena in the Centre de Génétique Moléculaire .
    • Fruzsina Hobor, September 30 - October 2, 2010, Paris, France.
      Research stay at laboratory of Dr. Domenico Libri and Dr. Torbena Jensena in the Centre de Génétique Moléculaire .
    • Zora Střelcová, October 4 - November 27, 2010, Jülich, Germany.
      Research stay at group of Prof. Paolo Carloni (German Research School for Simulation Sciences GmbH).
    • Jakub Štěpán, October 4 - November 27, 2010, Jülich, Germany.
      Research stay at group of Prof. Paolo Carloni (German Research School for Simulation Sciences GmbH).
    • Stanislav Kozmon, October 25 - 27, 2010, Bratislava, Slovakia.
      Research stay at Chemical Institute SAV - consultation of molecular interactions calculations.
    • Stanislav Kozmon, November 8 - 10, 2010, Bratislava, Slovakia.
      Participation at conference GCCP 2010.
    • Petr Kulhánek, November 8 - 10, 2010, Bratislava, Slovakia.
      Participation at conference GCCP 2010.
    • Jaroslav Koča, November 13 - 16, 2010, Athens, Greek.
      Stay at Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Athens.
    • Michaela Wimmerová, November 13 - 16, 2010, Athens, Greek.
      Stay at Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Athens.
    • Jaroslav Koča, November 25 - December 6, 2010, Jerusalem, Israel.
      Stay at Hebrew University in Jerusalem.
    • Michaela Wimmerová, November 25 - December 6, 2010, Jerusalem, Israel.
      Stay at Hebrew University in Jerusalem.
    • Lenka Malinovská, December 1 - 6, 2010, Grenoble, France.
      Measurement of difraction data of crystals of protein BclA at CERMAV.
    • Josef Houser, December 1 - 6, 2010, Grenoble, France.
      Measurement of difraction data of crystals of protein BclA at CERMAV.
    • Štěpánka Vaňáčová, December 8 - 10, 2010, Basel, Switzerland.
      Research stay at laboratories of Pharmacentre and Biozentre of Basel University.
    • Stanislav Kozmon, February 23 - 25, 2011, Bratislava, Slovakia.
      Research stay at Chemical Institute SAV - consultation of molecular interactions calculations.

WP8 - Improvement of Technology Transfer in the sector of biomolecular research (start month 4)

Objective:

  • To create conditions for successful transfer of research results produced by MU (NCBR) into economic practice within the Brno region and more widely.

Activities:

  1. Recruitment of experienced technology transfer manager from EU-15
    He will assist with improving the system of technology transfer at Masaryk University as a whole and NCBR - National Center for Biomolecular Research in particular. His main tasks will be analysis of technology transfer potential of NCBR and associated laboratories, management of concrete cases of technology transfer as well as knowledge dissemination and training of colleagues.
  2. Training courses in technology transfer
    Specialised training courses in technology transfer will be organised within the project. These will be targeted especially at young scientists and specialists from MU (NCBR), other regional universities, spin-off companies, innovation and research centers, regional SMEs, clusters and other institutions. International trainers will be focusing on the following topics:
    • General rules and aspects of TT procedures
    • Legal and financial aspects of TT
    • Specificity of TT within biotechnologies
    • Specific problems linked with TT in health sector

Current progress:

  • Starting from July 2008 the Technology Transfer Office (TTO) team was enriched with the arrival of Bernd Thomas, technology transfer and R&D commercialization expert with 25+ years of experience. he is closely involved in the acitivies of TTO and with his help and advice we should improve the services which are offered to scientists at Masaryk University.
    Bernd Thomas was exchanged with Jan Pavlovi.
  • First round of TT trainings was held in January and February 2009.
  • Second round of TT trainings was held in May and June 2009.

This work package is managed by Technology Transfer Office of Masaryk University in close collaboration with NCBR.
 

WP9 - Project Management

This work package will comprise of the following activities which will support successful project execution:

  • Administration and logistics
  • Quality management
  • Diffusion of the project results
  • Dissemination and exploitation management
  • Technical and financial reports
  • Communication with EC

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The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 205872.


 

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