The BIOXHIT TID centres
Training activities are considered cornerstones of the BIOXHIT project. Training of new users from the structural biology community represents a challenge that would be impossible to meet by the synchrotron radiation core-facilities alone. Four Training, Implementation and Dissemination (TID) centres have been created outside the participating laboratories to disseminate the BIOXHIT developments. The first two centres, selected in autumn 2004, are located in Oulu (Finland) and Poznan (Poland), whilst the centres in Oeiras (Portugal) and Heraklion (Greece) have been selected in spring 2006. Together with core-facilities for hardware and software development the TID-centres will be responsible for the majority of technology transfer that will be possible after the first 18 months of the project.
The TID-Committee within the BIOXHIT project has been established for practical aspects of training, implementation and dissemination activities. The committee consists of Andrew Thompson (Partner 13 - Synchrotron SOLEIL, St. Aubin, France), Paul Tucker (Partner 1A - EMBL, Hamburg, Germany), and is chaired by Sine Larsen (Partner 16 - University of Copenhagen, Denmark). Each TID Centre is associated with a member of the Committee who will give practical advice on the Centre's development. The BIOXHIT TID-committee coordinates the preparation of the necessary documentation and training material provided by the Partners. The TID-committee ensures proper testing and the smooth transfer of this information to the core facilities and TID centres responsible for the training. It will also conduct annual evaluation of the activities in the TID centres.
Oulu
Poznan
Heraklion
Oeiras
The TID Centre in Oulu
TID Centre's website
The TID Centre in Oulu, Finland has been selected in autumn 2004 after the first call for TID centres. It is located at the Department of Biochemistry, University of Oulu. The TID Centre runs under the supervision of Prof. Rik Wierenga who is supported by Dr. Tuomo Glumoff and Prof. Jari Ylänne. The centre is a joint effort of the approx. 20 researchers involved in protein crystallographic research.
The TID Centre in Oulu is equipped with:
protein crystallisation laboratory with +4/+20 rooms, crystallisation robot, DLS
rotating anode X-ray diffractometer with cryo cooling and fine focus mirrors
ca. 20 graphics computers with stereo setups
frequent beamtime available in European synchrotrons
Persons interested may contact the TID Centre to arrange for a visit and introduction to DNA, BEST, MOSFLM and SCALA. Such visits can be financially subsidised by BIOXHIT.
Workshops:
1st Oulu BIOXHIT workshop on protein crystallography
Oulu, 2nd - 4th May 2006
The workshop programme
Tutorial on the application of on the application of DNA/ BEST/ MOSFLM/ SCALA
Oulu, 18th - 19th October 2006
The tutorial programme
2nd Oulu BIOXHIT workshop on the application of DNA/ BEST/ MOSFLM/ SCALA and SHARP/ BUSTER-TNT
Oulu, 7th - 11th May 2007
The workshop programme and more details will be published in due time.
Poster
Contact details:
Department of Biochemistry
University of Oulu
PO Box 3000
FIN-90014 University of Oulu
Finland
Tel. +358-(0)8-553-1199
Fax +358-(0)8-553-1141
Email: Rik.Wierenga@oulu.fi
Web: http://www.biochem.oulu.fi/BIOXHITWEB/index.html
The TID Centre in Poznan
TID Centre's website
One of the first two TID centres selected in autumn 2004 is the centre in Poznan, Poland. The co-ordinator of the TID Centre is Prof. Mariusz Jaskolski who is mainly assisted by Dr. Wojtek Rypniewski. The TID Centre is located at the Centre for Biocrystallographic Research in Poznan, which is affiliated with the Institute of Bioorganic Chemistry, Polish Academy of Sciences. It is the first protein crystallography laboratory in Poland and the second in central-Eastern Europe. The center is fully equipped with modern facilities for crystallization, X-ray data collection and processing, and has excellent computer facilities networked to the new Poznan Metropolitan Supercomputer Center and it constitutes a center of integration for the Polish and central-European structural biology community.
Workshops:
1st TID workshop on Biocrystallography with Synchrotron Radiation,
Poznan, 28th November - 2nd December 2005
The workshop programme
List of participants
2nd TID workshop on Biocrystallography with Synchrotron Radiation,
Poznan, 5th - 9th December 2005
The workshop programme
List of participants
3rd TID workshop on Structural Biology with Synchrotron Radiation,
Poznan, 28th November - 2nd December 2006
The workshop programme
Press
The Poznan TID centre workshop - article
Contact details:
Mariusz Jaskolski
Centre for Biocrystallographic Research
Insitute of Bioorganic Research
Polish Academy of Sciences
Noskowskiego 12/14
61-704 Poznan
Poland
Tel: +48-(61)-829-1274
Fax: +48-(61)-852-0532
Email: mariuszj@amu.edu.pl
Web: http://tid.ibch.poznan.pl/
The TID Centre in Heraklion
TID Centre's website
Index
The Institute of Molecular Biology & Biotechnology at the Foundation for Research & Technology Hellas (IMBB-FORTH) is located in Heraklion, Greece, and is directed by Dr. Kyriacos Petratos. He will be supported by the scientific groups of Prof. Michael Kokkinidis, IMBB-FORTH and Biology Department, University of Crete and Dr. Nikos G. Oikonomakos, Structural & Chemical Biology Group (SCBG), Director of Institute of Organic and Pharmaceutical Chemistry, National Hellenic Research Foundation (NHRF). It has been selected in spring 2006.
Proposed training activities:
The primary aim of the Greek centre will be to strengthen the interactions between the crystallographers in Greece and the researchers at the central facilities for structural research in Europe involved with the current development of hardware and software. This way the local scientific communities and in particular young investigators will become acquainted with the progress made in today's biological crystallography.
The means the TID Centre Heraklion is going to apply for achieving the best possible training are:
To promote travelling and the stay of selected scientists at central laboratories, e.g. synchrotron site, for the direct exchange of information on the state-of-the-art developments.
To organise formal presentations by researchers who visited a central laboratory for the distribution to other local scientists and students. The seminars will be posted in due time on the TID Centre’s website and the BIOXHIT website.
Organise a workshop with invited speakers who are directly involved in the development of novel methods and techniques within the BIOXHIT project. This way the best possible dissipation will be achieved of the advancements in current structural biology research.
Establishment and maintenance of an up-to-date website containing the description of all relevant activities and news of the TID Centre, e.g. scientific contents provided by the speakers, workshop abstracts, seminars of individuals, and appropriate links.
The infrastructure for Macromolecular Structure at IMBB-FORTH:
Equipment for protein crystallography of IMBB includes: Rotating anode generator (Rigaku/MSC, RU-3HR), imaging plate detector system (MARresearch-MAR300), cryo‑crystallography instrumentation (provided by the University of Crete), a CAD4 X-ray diffractometer (Nonius), SGI workstations, a fermentor of 30 liter capacity (Bioengineering), incubators for bacterial cell growth, two Fast Protein Liquid Chromatography systems, sonicators, centrifuges and a crystallization room. Circular Dichroism and Mass-Spectrometry facilities are available at the University of Crete.
The infrastructure of SCBG-NHRF:
Multinuclear NMR (Bruker, 300 MHz for liquid samples and 400 MHz for solids), MS (Finnigan MAT TSQ 7000), GC (Varian Star 3400 CX), GC/MS/MS (Varian Saturn 2000), FT-IR (Nicolet Impact 420), elemental analyzer (Perkin-Elmer PE 2400 II), DSC, HPLC. Facilities for cloning, expression and purification of protein targets (PCR thermocyclers). Constant-temperature (20 °C) room, 2nd generation crystallization robot and a number of bench top controlled temperature incubators for protein crystallisation. X-ray facilities for macromolecular crystallography (Rigaku RU‑H3RHB), equipped with an R-AXIS IV image plate detector and an Oxford cryo-system. Among other computers, two Silicon Graphics O2 (R10000 and R12000) workstations, one Hewlett Packard Visualise B2000, one Fujitsu-Siemens Celsius K330 workstation, one Linux cluster based on eight AMD processors ATHLON 1.4 GHz (Octathlon).
The above-mentioned groups are currently working on various projects:
Projects at IMBB-FORTH:
Copper-containing redox proteins, the SecA-preprotein translocase from E. coli, a psychrophilic Alcohol dehydrogenase from the psychrophile Moraxella sp. TAE123, the ribosome inactivating protein (RIP) Charybdin from the local plant Charybdis maritima agg. (K. Petratos).
Studies of bacterial type III secretion systems, enzymes for DNA modification: biomedical applications, protein folding: the case of the 4-α-helical bundle, enzyme structure and mechanisms: carbohydrate esterase family 4, chloramphenicol acetyltransferase (CAT) (M. Kokkinidis).
Projects at SCBG-NHRF:
Proteins involved in the control of glycogen metabolism, RNases, calcium/calmodulin regulated kinases, nicotinic acetylcholine receptor-control of neuromuscular transmission, lectins involved in cell-cell interactions, human TAF9 protein isoforms involved in nucleus organization, RNA processing and DNA transcription, phosphoenolpyruvate carboxykinase, pancreatic glucokinase, alkaline xylanases F/10 and F/11 and Type A and Type B feruloyl esterases.
Contact details:
Kyriacos Petratos
Protein Structure Macromolecular Crystallography IMBB-FORTH
P.O.Box 1385
Vassilika Vouton
71110 Heraklion
Greece
Tel: +30-2810-394353
Fax : +30-2810-394408
Email: petratos@imbb.forth.gr
Web: http://www.imbb.forth.gr/people/petratos/index.html
Index: http://www.imbb.forth.gr/people/petratos/bioxhit/index.html
The TID Centre in Oeiras
TID Centre's website
This TID Centre has been selected in spring 2006 and is located at the Macromolecular Crystallography (MX) laboratory of the "Instituto de Tecnologia
Quimica e Biologica" in Oeiras, Portugal under the direction of. The MX laboratory, coordinated by Maria Arménia Carrondo, includes three
internal groups dedicated to Macromolecules with Industrial and Medical Application, Crystallographic Structure-Function Relationship and Membrane Proteins.
ITQB MX laboratory in the past years has been fully involved in training activity: BioCrys course "Fundamentals of Modern Methods in
Biocrystallography" has been organized in 2002, 2004 and 2006), while in 2005 the course "Membrane Protein the rocky road from gene to structure" was
also organised. To assist BIOXHIT consolidating the dissemination of knowledge, a further edition of BIOCRYS is planned in 2008. As TID center a more
specific workshop will be held from 3th to 6th October 2007, "S-SAD diffraction data phasing of macromolecule single crystals from home and
Synchrotron X-ray sources" and will teach state of the art methods and protocols in the collection, processing, scaling and phasing of S-SAD
diffraction data from crystals of macromolecules aimed at obtaining the best possible interpretable map prior to model building.
Information about the course can be found on the TID center web page http://tid.itqb.unl.pt/activities.html.
BioCrys course on "Fundamentals of Modern Methods in Biocrystallography"
Oeiras, 6th - 13th October 2006
Poster programme
Report and Statistics
Contact details:
Maria Armenia Carrondo
ITQB- Instituto Tecnologia Quimica e Biologica
Av. de Republica, E.A.N.
2748 - 505
Oeiras
Portugal
Tel: +351-21-4469-657
Fax : +351-21-441-12-77
Email: carrondo@itqb.unl.pt
Web: http://tid.itqb.unl.pt/
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