by Andrzej Rabczenko

The Institute of Biochemistry and Biophysics (IBB) of the Polish Academy of Sciences was founded in 1957. It is formally associated with the Department of Biology, Warsaw University.

IBB is managed by the Director Prof. Wlodzimierz Zagorski-Ostoja, supported by a Board of Directors, the Scientific Council and the Trustee Council, consisting of former IBB staff members currently working abroad.

Several associated research and educational organizations are located in IBB quarters: the Polish-French Center for Plant Biotechnology, the IBB Polish National Node of European Molecular Biology Network (EMBNet), the Regional Node of the International Center for Cooperation in Bioinformatics under the auspices of UNESCO and also the Interdisciplinary Center for Advanced Computer Modelling, Warsaw University (equipped with the most advanced Cray computers), the Institute of Experimental Plant Biology and the Department of Genetics, Warsaw University.

In the 2000 IBB was accepted as EU Center of Excellence in Molecular Biotechnology in the 5th EU Framework Program on the base of an international competition. Project financing by EU and KBN has allowed to increase mobility of IBB researchers as well as has allowed to invite the best European specialists to Poland.

Special interests
The scientific interests of the Institute have evolved over the years from classical biochemistry, biophysics and physiological chemistry towards up-to-date molecular biology. The topics of special concentration are: yeast molecular genetics; mutagenesis and DNA repair; plant molecular biology; structural biology and bioinformatics.

Microbial genetics is focusing on the areas of sulphate metabolism in Enterobacteriaceae, sugar metabolism in Lactococci and mechanisms of stable plasmid maintenance.

Yeast functional genomics. Our previous participation in the European yeast genome sequencing effort is followed today by functional analysis of 26 new ORFs, identified by Institute teams. This research is conducted within the EURO-FAN program.

Plant molecular biology. Plant pathogen genome expression is studied in vivo and in vitro, appropriate virus-resistant plants have been constructed and patented, and went through field trials under the control of the Ministry of Agriculture (first such tests in Poland).

Plant transformation. Signal transduction is studied with appropriate transformants (Arabidopsis, potato, tobacco, carrot, lettuce, maize); the protein kinases involved are identified and isolated in work carried out within EU consortia. A NATO-funded program on oral plant vaccines has been initiated and got support from US Department of Agriculture.

Advanced nucleoside and nucleotide chemistry. Synthesis of prospective anti-HIV and anti HCV compounds and potent specific kinase inhibitors has recently been achieved.

The fidelity of DNA repair and mechanisms of mutagenesis induced by chemicals and environmental stresses in bacteria, yeast and plants are the subject of work of our internationally recognized teams of molecular biologists. Recently, these teams have been shifting their interest to human genes that control mutagenesis and the mechanisms of oncogenesis and ageing.

Gene engineering programs receive support from groups with expertise in the overexpression of proteins in E. coli, S. cerevisiae, Pichia pastoris and Baculovirus systems.

Bioinformatics provide the IBB network accessible nation-wide through the Internet. Over 800 molecular biology database users are registered at the Institute mainframe.

International strategy
IBB is strongly embedded into the international network of science. Research has always been treated, not on the local, but the world level. As a result, active IBB researchers are firmly connected with the best laboratories from Europe and the USA. This cooperative activity is supported by over hundred former employees of IBB who are working outside Poland. Some of them are active in a Trustee Board which supports IBB activity.

The international contacts are especially good with French laboratories. There was organized the Polish-French Center of Plant Biotechnology which supports exchange of researchers and stimulated common project. In the last ten years over 200 scientists have visited French or IBB labs resulting in 125 joint publications and over 120 joint communications.

Educational program
Of special importance are PhD studies in IBB. More than 90 PhD students attend the Warsaw School of Molecular Biology affiliated with IBB. The students join particular IBB research teams and also participate in the rich educational program led by IBB and Warsaw University staff.

A recent improvement in the PhD studies program is the co-directed study in which students spend part of their time in a sister laboratory abroad (mainly in France) with additional tutors. This activity has led to over 30 PhD degrees being awarded to Polish and French students.

The Marie Curie Training Site - Education and Research in Molecular Biology supported by the EU, allows young EU researchers to visit IBB for 3 to 12 months of PhD studies in their parental laboratories. This, very efficient system create direct links between laboratories in different EU countries, practically creating the European Research Area. The program is active since 1.5 years and already six persons have participated in the project.

Fundamental platforms of IBB research
IBB has highly specialized, state-of -the art laboratories for the following disciplines:
Bioinformatics including protein modeling (homology and threading); design of protein sequences fitting to a target structure; protein-protein interactions including macromolecular crowding phenomena; modeling of metabolic pathways; and analysis of genome sequence data (particularly in the context of phylogenetic analysis).

DNA sequencing lab which took part in the European Yeast Genome Project and now is in the Polish-French-German Paramecium Genome Project (recently the first chromosome somatic was fully sequenced and annulated). The lab is also providing DNA sequencing for researchers from other IBB labs as well outside customers.

Proteomic lab with two modern mass spectrometers and another on the way. The laboratory concentrates on protein structure studies with such achievements as identification of protein fragments through advanced methods of mass spectrometry; identification of postranslational modification of proteins; proteomics of human plasma and studies on the structure of specific markers of Alzheimer disease.

Biological NMR concentrating on protein-ligand interactions. With 400 and 500 MHz instruments they are studying the structure of calcium binding protein in solution; nuclear relaxation studies of backbone protein dynamics; conformational analysis of cyclic peptides; NMR monitoring of safety and efficiency of CDP-choline treatment in brain injured patients and chiral recognition by cyclodextrines.

GMO Reference Laboratory. Having a deep expertise in mutation research, IBB obtained the rights to organize one of three in Poland such a laboratory. The GMO lab will start soon and will specialize in detection of DNA modifications in microorganisms. The lab is working tightly with EU Joint Research Institute in Ispra (Italy).

The Bank of Biological Materials collects different constructs of plasmids, bacteria and yeast. At the moment it has more than 7,000 samples in the collection that is informatized and available for outside researchers.

The Institute's aim is to apply its facilities and the talents of its staff in implementing new programs where synergy between theory and application are achieving the highest scientific standards while also solving specific problems indicated by end-users active in bio-medicine, food production and environment protection. We believe that in biology, there is no sharp distinction between basic and applied research and the commercialization of the scientific results is important.

Contact
Professor Andrzej Rabczenko
The Institute of Biochemistry and Biophysics, Center of Excellence in Molecular Biotechnology, Polish Academic of Siences, 5a Pawinski St., Warsaw, Poland
tel. (+48-22) 823 71 89
e-mail: ara@ibb.waw.pl
www.ibb.waw.pl

Recent achievements
- Created a nation wide system for potato virus detection by molecular hybridisation. This cost-effective system, relying on a series of specific DNA and RNA probes, effectively supplements the Polish phytosanitary system. The successful pilot program, started in the eighties with over 2000 potato test plants, resulted in standard safe testing systems. Today the implemented system covers the whole country, with over 120 thousand samples, received during last ten years from phytosanitary services and potato seed producers and tested in the IBB dedicated laboratory.

- Constructed over 300 novel potato transformants, selecting several lines as prospective new cultivars resistant to local PLRV and PVY variants. These new variants underwent field tests and were supplied to the state potato seed producing agency (Institute of Plant Breeding and Acclimatization). These new cultivars are awaiting production, depending on the decision of the appropriate authorities regarding GMO policy.

- Developed a unique collection of the lactic acid bacteria (400 strains) derived from local small diaries. The collection contributes to the preservation of bio-diversity in this important branch of food production. The Institute is negotiating purchase of the collection by the Danone - affiliated company.

- Perform diagnostic DNA sequencing on order for several clinics. The identification in the Polish population of novel mutations that cause anemia in humans has led to improved diagnostic procedures.

Current works
- Molecular diagnosis of myopathies linked with mitochondrial dysfunctions in collaboration with clinics.

- An oral plant vaccine against Helicobacter pylori in collaboration with the Thomas Jefferson University, Philadelphia.