International Cooperation

Max Planck Society, Germany
First cooperation programme
• Laboratory of Structural Biology MPG/PAS in Warsaw, headed by Matthias Bochtler
• Laboratory of Cell Cortex Mechanics MPG/PAS in Dresden, headed by Ewa Paluch

     The cooperation started in 2001 as an initiative of the Max Planck Society (MPG) and Polish Academy of Sciences (PAS). According to the agreement, the Junior Research Group, with Dr. Matthias Bochtler as Lab Leader, selected in an open international competition run jointly by MPG and PAS, was funded by MPG and hosted at IIMCB. Dr. Bochtler’s laboratory was provided with the modern protein crystallography equipment. The lab has been active in the structural biology of peptidases, proteases and protein degradation. The group has also been first to publish the structures of several new peptidase clans, and, in studies on the staphopain system, has discovered a novel cysteine peptidase inhibitor mechanism.
     The Laboratory of Cell Cortex Mechanics MPG/PAS, headed by Dr. Ewa Paluch as a twin laboratory of Matthias Bochtler’s MPG/PAS laboratory, was established in February 2006. The equipment and running costs of the laboratory, including personnel, were covered by Polish funds, but the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden (MPI-CBG; a host for this laboratory) was responsible for local operational costs, maintenance, and administrative support. Dr. Paluch's group focused on the biochemical and physical mechanisms of cell shape and deformations. The research was funded mainly by the Polish Ministry of Science and Higher Education and concentrated on movements of the actomyosin cortex and, in particular, the involvement of spontaneous cortical ruptures and flows in cell division. The group’s most spectacular achievements to date include a paper published in Nature and a ERC grant. In 2013, Dr. Paluch relocated her research activities to University College London under an arrangement whereby she formally remained an IIMCB employee on a leave of absence for the duration of the ERC project and retained the use of part of our research equipment, which allowed her research at the new location to commence without undue delay. She completed her employment at IIMCB, at the end of 2015.

Second cooperation programme – established 2 Max Planck/IIMCB research groups:
• Laboratory of Angiogenesis and Metabolism, Max Planck/IIMCB Research Group in Bad Nauheim, headed by Michael Potente
• Laboratory of Zebrafish Developmental Genomics, Max Planck/IIMCB Research Group in Warsaw, headed by Cecilia Winata

     In March 2012, a new cooperation agreement was signed between IIMCB and MPG. The agreement concerned the establishment of two Max Planck/IIMCB Research Groups, one at IIMCB and the other at the Max-Planck Institute of Heart and Lung Research (MPI-HLR) in Bad Nauheim. Each of the parties finances a research group with its own budget. The lab leader position at Bad Nauheim was filled by Dr. Michael Potente who started MaxPlanck/IIMCB Angiogenesis and Metabolism Laboratory, which constitutes the Independent Research Group at MPI-HLR. Dr. Potente research program is devoted to the molecular analysis of transcriptional regulatory circuits that govern the growth, maintenance and regression of blood vessels. He has focused on the analysis of Notch signaling and FOXO transcription factors, two pivotal transcriptional regulators of vascular growth and homeostasis, as well as their regulation by reversible acetylation. He explores specifically the function of sirtuins, which are NAD+ – dependent deacetylases, for the dynamic regulation and adaptation of endothelial cell responses. Using conditional mouse mutants and in vivo models of vessels formation, combined with high resolution imaging and state-of-the-art proteomics and genomics, his research aims to delineate novel regulatory pathways and mechanisms that control vascular growth and function in development, physiology and disease. Dr. Potente is a coauthor of many important papers e.g. in Nature, Annu Rev Physiol, Cell, J Clin Invest, PNAS, Dev Cell, J Biol Chem.

   The mirror position in Warsaw has been filled by Dr. Cecilia L. Winata, who runs the Laboratory of Zebrafish Developmental Genomics, which is dedicated to the study of developmental processes of the heart by applying genomics methods in combination with experimental embryology and biochemistry. Winata’s group focuses on the transcriptional regulatory network of heart development and on epigenome profile of heart development. The group bases mainly on genomics approach. This is the first research laboratory in Poland which, together with an extensive experience of the Zebrafish Core Facility, displays top expertise in experimental studies on zebrafish model. The group is also affiliated with MPI-HLR in Bad Nauheim, our strategic partner for the creation and development of the FishMed Centre. The laboratory has full access to MPI-HLR equipment, animal facilities, and genetic modification techniques for zebrafish and mice.

RegPot Project FishMed
The FishMed Center was a consortium of eight groups from IIMCB and six European institutions, including the Max Planck Institute for Heart and Lung Research (MPI-HLR) as a strategic partner. The twinning partners were chosen based on their expertise in research using zebrafish models, excellent publication records, and compatibility with the scientific interests of the FishMed Center groups at IIMCB. The aim of the project was to establish IIMCB as the first in Poland research center where zebrafish is widely used as a model for studies on human diseases (see page 58).

Collaborative Project EPISTOP
The aim of the project is to better understand the mechanisms of epilepsy in patients with tuberous sclerosis complex (TSC). This is a multicenter study, involving 14 hospitals and laboratories from Europe and the United States, at IIMCB coordinated by Prof. Jacek Jaworski.

Collaborative Project BESTCILIA
This multi-partner project concentrated on observational studies to characterize the clinical course and improve the diagnosis and treatment of primary ciliary dyskinesia (PCD) a genetic disease caused by mutations in genes involved in ciliary structure and function.

Domestic Cooperation

Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University (IBMIB-AMU), Poznań http://www.labbit.eu
The aim of the agreement is to establish a new research group in the field of bioinformatics affiliated with both AMU and IIMCB. The lab leader position was filled by Dr. Jan Brezovsky who created the Laboratory of Biomolecular Interactions and Transport UAM/IIMCB located in Poznań.
The laboratory focuses on solving fundamental questions concerning roles of ligand transport pathways in proteins for the proper functioning of the living cell. The aim of the research is to understand the transport-related pathologies by investigating of interactions of small molecules with amino acid residues forming such pathways. The group develops new computational protocols and tools to apply them to the analysis of biomedically and biotechnologically relevant proteins. Ultimately the obtained results will help to develop potential treatments of transport-related pathologies.

Intercollegiate Faculty of Biotechnology (IFB UG-MUG), Gdańsk
The partnership is based on a consortium agreement with the IFB UG-MUG of Gdańsk our strategic Polish Road Map Partner and one of the best academic biotechnology units in Poland. The agreement to establish a new joint laboratory has been signed. This cooperation is very promising in the field of medical biology and molecular diagnostics.

Museum and Institute of Zoology PAS (MIZ), Warsaw
The formal consortial agreement was signed to set up a joint sequencing platform (Seq4All) between IIMCB and Museum and Institute of Zoology PAS. The successful grant application to the Polish Ministry of Science and Higher Education resulted in funds of about 5 mln PLN for a purchase of two next generation sequencers: Illumina NextSeq 500 and MiSeq sequencers.

In January 2008, the scientific activities of the Biocentrum Ochota Consortium of the Polish Academy of Sciences were launched as the initiative of six research institutes that operate at the Ochota Campus in Warsaw. The basic principle behind Biocentrum Ochota is that the considerable scientific potential, represented by the combined group of experts who work in these six institutes, should be pooled and used for the development of large-scale research projects that go beyond the capabilities of individual units.