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BIO-IMAGing in research INnovation and Education

Final Report Summary - BIO-IMAGINE (BIO-IMAGing in research INnovation and Education)

Executive Summary:
Scientific ideas develop effectively only in favorable, creative and open atmosphere, which guarantees free transfer of knowledge between the world’s most prominent experts, and research unfettered with infrastructural constraints. Setting up optimal conditions for creative scientific activity was the main task of the FP7 Project BIO-IMAGINE, carried out by the Nencki Institute of Experimental Biology of the Polish Academy of Sciences in Warsaw. The original aim of the Project was to significantly strengthen the Nencki Institute’s research capacity as a national center of excellence in the field of bio-imaging, and to improve its image in Europe and worldwide. The task was achieved perfectly. Within the framework of BIO-IMAGINE twinning activities the researchers from the Nencki Institute had a chance to deepen their knowledge in a number of issues in the field of neuroscience and bio-imaging. The Institute developed or strengthened cooperation with scientific institutions from several countries, including such well-known centres as the German Max-Planck-Institut für Genetik und Molekulare Zellbiologie, the French Centre National de la Recherche Scientifique, or the British University of Cambridge. Significant support to the scientific potential of the Nencki Institute, achieved thanks to BIO-IMAGINE, was the attraction of 14 high-class specialists are at an early stage of their career development. After the completion of the project and verification of the merits, 9 of them found employment at the Institute. Good personnel decisions allowed the Institute to expand existing research topics and scientific cooperation with other research centers. A great example is the construction of a high resolution optical microscope, carried out in collaboration with the group of prof. Maciej Wojtkowski from the Nicolaus Copernicus University in Torun. Within the frame of the Project three major international conferences with the Nobel Prize winners as the speakers were organized, as well as a number of symposia and workshops. Tens to hundreds of scientists from Poland and all over the world participated in each of these events. During the project dozens of domestic and foreign experts conducted workshops and seminars for scientists running companies, or intending to do so in the nearest future. Cooperation with six companies was inaugurated during the Project lifetime. It included projects related to the production of innovative cosmetics, antibacterial and anti-cancer therapy. Although BIO-IMAGINE was not a research project, purchase of modern scientific equipment (a modern Zeiss / Yokogawa confocal spinning disc microscope and a Guava easyCyte 8HT flow cytometer) constituted its major part. The equipment purchased and installed as part of the BIO-IMAGINE Project has been extensively used for many months for the study of brain plasticity, long-term memory, Alzheimer's and Parkinson diseases, as well as the search for cancer therapy and diagnosis of diseases of the endothelium by the Nencki Institute researchers and groups from other centers and to external stakeholders. The EU financial contribution to the BIO-IMAGINE project facilitated involvement in a number of activities related to the promotion of science. The Nencki Institute brand name was created and popularized. Well-known popular scientific events, such as the Brain Awareness Week, the Scientific Picnic of the Polish Radio and the Copernicus Science Centre or the Warsaw Festival of Science were coorganized by the Nencki Institute. The total number of participants in these events amounted to almost 20 thousand. The efforts to popularize science were recognized by the Polish Press Agency, which in 2013 honored the Nencki Institute with the title of the Science Populariser.

Project Context and Objectives:
BIO-IMAGINE Project was designed to stimulate development of new bio-imaging techniques at the Nencki Institute by fostering interactions with a number of leading research partners from across Europe as well as by making new cutting-edge technologies and methods accessible to researchers from other institutions in Poland and beyond. Providing access to these new technologies and research tools was planned to position the Nencki Institute as a regional bio-imaging centre of competence.
BIO-IMAGINE aimed at fostering the Nencki interactions with leading research partners in Europe; expanding the scope of technologies used at the Institute and broadening its know-how; strengthening the competence of the Institute and increasing its attractiveness to researchers from other institutions and countries; and improving the Institute’s position as a regional competence centre and an important node of the Euro-BioImaging (European Biomedical Imaging Infrastructure) initiative in Europe.

EU funds available through this FP7 Capacities call for proposals provided an outstanding opportunity for the Nencki Institute to fully capitalize on the investments financed previously from ERDF and to achieve the desired synergy between the measures set out in this action plan and the activities of the National Reference Framework (for Cohesion and Structural Funds). The action plan lead to achieving the following specific project objectives:
1) To improve the Institute’s human potential and intellectual capacity by recruiting thirteen experienced researchers – eleven at the post-doctoral level, one as a new group leader and one as imaging core facility manager;
2) To initiate, reinforce and/or consolidate the cooperation, transfer of know-how and research methods between fourteen (14) Nencki research groups and their partners from prominent research institutions in Europe;
3) To stimulate innovation through implementation of a policy for management of intellectual property and knowledge transfer, through activities and support mechanisms by partnering with and transferring know-how and best practice from European leaders in this area;
4) To upgrade the highly specialized equipment base by acquiring a confocal system based on the spinning (or Nipkow) disk technology and a Guava easyCyte 8HT Flow Cytometry System, a “desk top” solution. Both systems will be used in joint research by the recruited researchers, in education and training as well as for technology transfer and innovation-type activities;
5) To promote knowledge exchange and the Institute’s research at the European level by i) organizing six (6) workshops allowing for hands-on demonstration and training in the bio-imaging core competencies at the Institute, three (3) international conferences and two (2) satellite sessions to larger meetings as well as ii) supporting attendance at international conferences (18) and workshops (6) for Nencki researchers;
6) To increase the recognition of the Nencki Institute brand name, to disseminate knowledge and improve awareness of the results of its scientific research among various stakeholder groups through organization of 18 promotional and open education events and use of other promotion channels;
7) To improve and update the management procedures and the organizational structure of the Institute through effective project management and recommendations from an 11-member Steering Committee comprised of several prominent European Scientists and science managers among other stakeholder representatives;
8) To evaluate the achieved project results and their long term sustainability by an external group of Commission experts working closely with the Steering Committee and the project management team.

In order to achieve the main goal of the Project, which is to enhance the potential of the Nencki Institute to participate actively in international research in experimental biology (cell biology, neurobiology, biochemistry) that uses cutting edge biological imaging techniques, seven interrelated Work Packages had been planned, each consisting of several tasks. The proposed activities to be carried out by the Institute over three years (with an additional 6 month evaluation phase – WP8) were a logical continuation of a strategic plan to position the Institute as a leading regional competence centre in bio-imaging techniques applied primarily in neurobiological research. This process had started at the very beginning of the 21st century with the successful submission of the FP5 Centre of Excellence in Neurobiology BRAINS in September of 2001, the first stepping stone in strengthening Nencki’s cooperation with several leading research entities in Europe. Half-way through the Project a 6 month extension was requested by the Project Coordinator and approved by the European Commission.

The whole Project duration was divided in 2 reporting periods: Jan 1, 2011 – Dec 31, 2012 and Jan 1, 2013 – Dec 31, 2014.

The flagship work package of the project and its most critical component was WP1 (Increasing Human Potential). The recruitment process was carried out in the first reporting period. In the second reporting period research activities of the experienced researchers recruited within the Project were supervised and evaluated.

Work Package 2 (Sharing of Know-How and Technologies through Networking) facilitated scientific exchange with twenty nine (originally fourteen) outstanding research groups at leading research organizations in Europe. WP2 assured transfer of know-how in research methods involving imaging techniques at all levels (from molecular to the whole organism). Outcome of this work package involved joint publications and research grants applications.

Work Package 3 was designed to stimulate Innovation and Technology Transfer, an area of weakness not only at the Institute but also on the Ochota Research Campus and Poland in general. While before 2011 the Nencki and other leading Polish scientific institutions located on this Campus had received significant investment funding from ERDF, their innovation potential has remained largely untapped. WP3 was realized in partnership with EMBLEM, an SME representing a commercial arm of the European Molecular Biology Laboratory (EMBL) and in consultation with the Technology Transfer department of the Weizmann Institute. Results of this WP enable designing a TT model suitable for implementation for the entire Ochota Research Campus and the Centre for Preclinical Research and Technology (CePT) consortium, as a model case study for Poland in the Life Sciences sector.

Purchases of research tools and equipment planned within WP4 (Improvement of Research Capacity) filled in a small but significant gap in the scheme of investments funded from ERDF. They were critical to successful completion of WPs 1, 2, 5 and 6, as they have been extensively used for research, training and education purposes, while providing the base for development of innovating methods and diagnostic technologies subject to activities within the Project.

Within WP5 (Conferences and Workshops) a number of workshops, small-to-medium size conferences and satellite symposia to larger meetings were organized, all within the general thematic scope of WP1 and 2. Workshops and conferences addressed topics relevant to the research conducted at the Nencki Institute under the common theme of “Bio-imaging” which was in agreement with the strategic goals of the Institute, and in line with the Nencki’s participation in scientific networks of European Light Microscopy Initiative (ELMI).

WP6 (Promotional Activities and Dissemination of Knowledge) greatly helped to increase the awareness and appreciation of the significance of scientific results and discoveries generated by the Institute researchers among various stakeholder groups (decision makers, funding agencies, students at high school and university levels and the general public).

Work Package 7 (Project Management) facilitated efficient and effective execution of all other project activities and provided guidance for the Institute to sustain project results and build on its positive impact to fulfil its long-term mission.

The Institute achievements in the BIO-IMAGINE Project have recently been evaluated by a team of independent experts in WP8 after the completion of all other activities.

14 leading research groups at the Institute were involved in BIO-IMAGINE. The project was managed within the existing Institute structure and in accordance with its internal rules and regulations, compliant and consistent with EC guidelines for FP7 projects.

Although the Institute’s Scientific Council as a part of the overall activities of the Institute played an advisory role to the Project Coordinator, a dedicated project International Advisory Board was formed in order to ensure high impact and sustainability of the Project results and to strengthen its European components. The following internationally renowned scientists and representatives of other stakeholder groups accepted the invitation and constituted the BIO-IMAGINE IAB:
1. Prof. Richard Frackowiak, Universite de Lausanne, Switzerland
2. Prof. Benjamin Geiger, Weizmann Institute of Science, Rehovot, Israel
3. Prof. Daniel Choquet, CNRS-Universite de Bordeaux 2, Bordeaux, France
4. Prof. Daniela Corda, National Research Council, Italy
5. Prof. Paolo Pinton, University of Ferrara, Italy
6. Dr. Stefan Diez, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
7. Dr. Rainer Pepperkok, EMBL Heidelberg, Germany
8. Dr. Gabor Lamm, EMBLEM GmBH, Heidelberg, Germany
9. Prof. Jacek Kuźnicki, International Institute of Molecular and Cell Biology, Poland
10. Anna Wisniewska, National Contact Point, Warsaw, Poland
11. Prof. Jerzy Duszynski, Nencki Institute, Warsaw, Poland

Throughout the Project lifetime an impressive number of the Nencki employees were somehow involved in the BIO-IMAGINE activities, either working directly in the project and receiving remuneration (75 members of staff), participating in the events organized within the Project (more than 100 people) or receiving Project financial support to attend scientific events outside the Institute (85 researchers).

6 Milestones and 23 Deliverables were to be achieved in the Project. All they were achieved in time, or with minor delays. Total estimated staff effort for the Project was 509 person-months. Actual staff effort was recorded at 549,5 person-months.

Project Results:
During the lifetime of the BIO-IMAGINE Project all of its major objectives and technical goals were achieved.

Work Package 1

The recruitment process for the Project was carried out and completed by the end of 2012, i.e. in the BIO-IMAGINE first reporting period. The second reporting period was a period of active involvement of the newly recruited researchers in the Nencki Institute research and other activities.

A detailed list of the employed researchers is provided in Attachment 1.

The performance of the recruited researchers is quite impressive.
The total number of publications published by the Post-docs and Core Facility Leaders since joining the Institute is: 29 full papers and 17 scientific communications.
The full list of the BIO-IMAGINE publications has been reported to the EC in Deliverable 7.3.

External Grants obtained by PostDocs:
1. Functions of posttranslational modifications of selected tubulins in a ciliate Tetrahymena thermophila and in mammalian cell lines. Ministry of Science and Higher Education Grant nr. N N303 817840 (2011-2014) (E. Joachimiak, PI)
2. Mechanisms of osteopontin dependent microglia activation in brain tumors. Ministry of Science and Higher Education Iuventus Plus 2012 grant (P. Gajdanowicz, PI)
3. Optogenetic model for studying synaptic plasticity. National Science Centre SONATA3 grant (2013-2018) (Tomasz Jaworski, PI)
4. Characterization of colon cancer cells resistant to chemotherapy-induced senescence. Ministry of Science and Higher Education Iuventus Plus (2013-2015) (Halina Was, PI)
5. Can senescence and autophagy lead do cancer cell division? Analysis of microscopic images as a tool for predication of fate of cancer cells treated with chemotherapeutics. Foundation for Polish Science INTER 2014 grant. (Halina Was, PI)
6. Role of the interneuronal electrical synapses of the neocortex in learning. National Science Centre SONATA grant (2013-2016) (Anna Posluszny, PI)

External Grants obtained by MRI Core Facility:
7. “Histological and behavioral correlates of abnormal magnetic resonance markers of the brain in rats of high fat diet”, PI: Dr. Stefan Gazdzinski, National Science Centre, UMO-2011/03/B/NZ4/03771.
8. „The influence of emotion on long-term memory - simultaneous EEG-fMRI study”, PI: Dr. Artur Marchewka, National Science Centre, SONATA, 2012-2015
9. "Perception of dynamic emotional expression - study using functional magnetic resonance imaging (fMRI) and facial electromyography (EMG)”, PI: Dr. Wojciech Dragan, co-PI: Dr. Artur Marchewka.
10. "How fearfulness influences attention - EEG-fMRI study." PI Dr Jarosław Michałowski, co-PI: Dr. Artur Marchewka.
11. “Program running versus problem solving: Two modes of information processing”. National Science Centre, OPUS, 2013-2016 (PI: Prof. Tytus Sosnowski, Faculty of Psychology, University of Warsaw; Co-PI: Dr. Artur Marchewka)
12. “The relationship between the level of trait fear and visual stimulus processing: A combined ERP and fMRI study”. National Science Centre, SONATA, 2012-2015 (PI: Dr. Jaroslaw Michalowski, Faculty of Psychology, University of Warsaw; Co-PI: Dr. Artur Marchewka)
13. “Analysis of neuronal and hormonal correlates of temperamental endophenotypes of anxiety disorders in groups differing in the CRFR1gene variability and early childhood adversities”. National Science Centre, OPUS, 2011-2014. (PI: Dr. Wojciech Dragan, Faculty of Psychology, University of Warsaw; Co-PI: Dr. Artur Marchewka)
14. “Long-term memory of emotionally charged verbal material. Behavioral and functional magnetic resonance study”. National Science Centre, OPUS, 2013-2016 (PI: Prof. Anna Grabowska; Co-PI: Dr. Artur Marchewka)
15. “Decoding dyslexia - functional organization of letter-speech sound association in children at risk of developmental dyslexia”. National Science Centre, SONATA, 2012-2016 (PI: Dr. Katarzyna Jednorog; Dr. Artur Marchewka)
16. “Brain correlates of dimension of emotions - fMRI study”. Ministry of Science and Higher Education. IUVENTUS PLUS, 2013-2015 (PI: Dr. Artur Marchewka)
17. “Influence of emotion on attention and memory”. Ministry of Science and Higher Education. IUVENTUS PLUS, 2012-2014 (PI: Dr. Artur Marchewka)

External Grants obtained by Core Microscopy Facility:
18. 3D superresolution microscopy for investigation of chromatin architecture changes of neuronal nuclei in epileptic stress, NCN Sonata Bis grant (2012-2016) PI: Tytus Bernas.

Work Package 2

WP2 concentrated on scientific exchange of the Nencki Institute researchers with outstanding research groups at leading research organizations in Europe invited to participate in the twinning activities. 29 European top-class research centres hosted the Nencki researchers or came to visit our facilities and shared their knowledge and know-how. Planned outcome of this Work Package: 1 publication per Task and 5 research grants applications was achieved in full.

Transferring and implementing the best research standards, new research methods and techniques from the EU institutions collaborating with the Nencki Institute was planned via:
a) 31 incoming visits (17 senior, 14 junior) of the foreign Partners’ representatives to the Nencki Institute (54 weeks in total);
b) 52 outgoing missions (27 senior, 25 junior) of the Nencki staff to the foreign laboratories Institute (121 weeks in total).

Detailed description of the WP2 performance is to be found in Attachment 2.

Work Package 3

The following tasks were executed under BIO-IMAGINE Work Package 3:

Task 3.1: Evaluation of TT development at the Nencki and within the CePT consortium.
• Deliverable 3.1: Analysis and improvement strategy of TT processes at the Nencki Institute and Ochota Research Campus was submitted to the EC in December 2011
• Deliverable 3.2: Extended report with the analysis of various successful TT models was submitted to the EC in December 2011.

One short-term visit of EMBLEM expert was planned and carried out by Dr. Gabor Lamm in parallel with the delivery of seminars and the meeting of BIO-IMAHINE International Advisory Board (June 1-3, 2011).

Task 3.2: Organization of seminars and training sessions
Task 3.2a: Organization of training sessions on intellectual property management
• A training session entitled “Introduction to Intellectual Property Rights and Technology Transfer” organized on June 2, 2011 at the Nencki Institute was delivered by Dr. Birget Kerber – Business Development Manager at EMBLEM GmbH.
• A seminar entitled “Function defines Structure: how to set-up a successful Tech Transfer Office” organized on June 2, 2011 at the Nencki Institute was delivered by Dr. Gábor M. Lamm, Ph.D - Managing Director EMBLEM Technology Transfer GmbH.
• A seminar “Science, Research and Patents” was organized with the help of Dr. Nigel Clarke from European Patent Office on October 8-9, 2012

Task 3.2b: Organization of seminars for researchers
• A workshop entitled “Add value to knowledge” was organized on May 31, 2011 at the Nencki Institute. The workshop presented examples of how to add value to existing research programs and inventions of research institutions using the technology transfer toolbox.
• Practical workshop on searching in patent databases provided by specialist from European Patent Office, Dr. Nigel Clarke. The workshop topics covered information on the background to patent information and patent searching. Ca. 30 attendees from the Nencki Institute and Ochota Campus.
• Workshop “Life Sciences Start-up companies – how to start?”, April 18-19, 2013 Lecturer: Roland Kozlowski, PhD, ca. 20 attendees from the Nencki Institute and Ochota Campus.
• Seminar on “Drug discovery and development - opportunities for collaboration between companies and research institutes in Poland and worldwide”, April 25, 2013, speaker: Stanislaw Pikul, PhD, ca. 20 attendees from the Nencki Institute and Ochota Campus.
• May 21, 2013. “Trusted to Lead”. Trainer: Robert Porter Lynch, ca. 20 attendees. The Workshop was organized for the CePT consortium member institutions Management. During the Workshop attendees discussed the issues of trust in cooperation and effective academic institutions development.
• May 23, 2013, “Trusted to Innovate”. Trainer: Robert Porter Lynch, ca. 15 attendees. The workshop revealed how best practices produce dramatic improvements in innovation.
• May 24, 2013. “Trusted to Negotiate”. Trainer: Robert Porter Lynch, ca. 15 attendees. Workshop agenda consisted of: Three negotiation options, basic process flow, art of listening and inquiry, building trust, selecting right negotiating teams.
• October 24, 2013. “Workshop on research projects evaluation based on their commercial potential – quick look methodology”. Trainer: Andrzej Bialkowski-Miler, ca. 20 attendees.

Task 3.3: Organization of and participation in training missions and exchange of know-how of TT procedures
• Attending ACES “Academic Enterprise Awards Europe 2011” in Zurich – The awards give public recognition to those researchers, engineers, professors, students and government officials in Europe who have done the most in 2010 to foster a culture of enterprise on campus.
• Attending the eHealth Conference in Oslo “Disarming the ageing population time bomb: local challenges, global solutions” – the conference was attended by representatives of bio-clusters, techno-parks and technology transfer specialists from Baltic Sea Region countries.
• Study mission in Heidelberg – visiting EMBLEM GmbH and BioRN Cluster
• Attending ISLI – BioMed Coonference in Tel Aviv, Israeal as well as visiting Yeda Research and Development Company Ltd. - the Technology Transfer Company of the Weizmann Institute of Science.
• Attending CEITEC opening conference in Brno, Czech Republic. CEITEC - Central European Institute of Technology is a project focused on the establishment of a European centre of excellence in the area of life sciences and advanced materials and technologies.
• Attending Stratified Medicine Conference in London, Great Britain – organized by London Genetics.
• Attending the Innovation Union Convention in Brussels.
• Attending Biobusiness workshop in Gdynia, Poland.
• Attending BioRN conference in Heidelberg, Germany organized by Biotech Cluster in Rein – Neckar Region. Establishing network and exchanging best practice with representatives from academia and pharma-industry sector.
• Taking part in two month mission to Stanford and Silicon Valley for a study mission on innovation management and technology transfer.
• On site visit in VIB (Flanders Institute of Biotechnology), Flanders, Belgium. Visit held in order to add more details to Deliverable 3.3 “Technology Transfer model” which is based mainly on the VIB case study. Two representatives of Nincki Institute (Marcin Szumowski and Pawel Nowicki) and two from Polish Science Fundation took part in the visit.

Task 3.4: Organization of the regional CePT conference
Under this task the Nencki Institute organized an international conference on innovation management:
Managing Innovation 2013 international conference
The event took place on January 17-18, 2013 in Foksal Press Centre in Warsaw, addressing the general topic on When and How to create & finance Life Science start-ups.
The conference was organized under the auspices of prof. dr. hab. Barbara Kudrycka, the Minister of Science and Higher Education of Poland. Among organizing partners of the conference there were such institutions as the Medical University of Warsaw and the BioTechMed Mazovia Cluster.
The conference featured case studies and success stories relayed both by Polish and international entrepreneurs and scientists. Best practice examples from abroad and practical solutions for the Polish legal and financial environment were presented along with possible solutions to eliminate the main bottlenecks and limitations in the Polish system. Along with the successful researcher / entrepreneur perspective the conference provided a Venture Capital/Investor view on success factors in securing investment and building company value.
The invited speakers and panelists featured CEOs, CTOs and founders of successful high-tech companies, scientists, inventors, and entrepreneurs, investors, venture capitalists and life science consultants, university and funding agency leaders, such as the Ministry of Science and Higher Education, the National Center for Research and Development (NCBR) and the Mazovia Region (MJWPU).
Report summarizing the conference was provided in Deliverable 3.4 submitted to the EU in year 3.

Task 3.5: EMBELEM expert’s evaluation of new technologies at the Campus
Deliverable 3.5 Evaluation of technologies was submitted to the EU in February 2014. Three technologies from the Nencki Institute had been evaluated:
1. Novel Antibacterial High Throughput Screen (Financed by NCBR; PCT pending). The project is based on a unique design of a high throughput test created to search the combinatorial chemical library: a combination of a target based and a whole cell screening. We have identified an untested novel target. If successful, this approach would be the first example of finding a new broad-spectrum antibiotic with a novel mechanism of action in about 40 years. The Nencki Institute has a patent in international (PCT) phase pending for the HTS technology invented by the project team.
2. New molecular targets for brain cancer treatment (applying for financing; US provisional). The aim of this project is to develop active compounds for complex and highly specific glioblastoma therapy – the most frequent primary brain tumor. Effectiveness of the proposed solution will be verified in an animal model of glioblastoma, accepted by the American Food and Drug Administration (FDA) for preclinical tests.
The commercial value of the project will be established based on ground breaking basic research results obtained at the Nencki Institute.
3. Microscopy: A. Spine Magick - A computational tool for accurate detection and morphometric measurement of dendritic spines (patent pending – PCT phase); B. Segmentation Magick - A tool to solving problems of accurate segmentation and morphometric measurements of cellular nuclei (patent pending – PCT phase) Interest from several entities including Weizmann Institute.

Execution of the BIO-IMAGINE WP3 at the Nencki Institute results in significant increase in patent applications, which is shown on the picture in Attachment 3.

Work Package 4

WP4 consisted of two main tasks:

Task 4.1: Acquisition of a spinning disc confocal microscope
As previously reported, the disc was installed on 31st January 2013. After training led by specialists from Zeiss (Germany) for the staff of Laboratory of Imaging Tissue Structure and Function, the microscope had been tested till April 2013. Since then it has had a record of 1.230 working hours, which makes approximately 135 working hours per month.
Occasionally the system is used for long-term experiments: overnight and 3-days experiments.
Researchers from the Nencki Institute use the microscope for recording fast processes in living cells and for imaging cells or slices.
The material mostly studied with the use of the microscope:
- slices from rodents brain
- tissue cells
- dendritic spines
- ciliates.

Trainings for members of the Laboratory of Imaging Tissue Structure and Function: 5.02.2013 – Training for the laboratory staff organized by Zeiss.
Workshops and trainings for other users (the infrastructure is also accessible to the users from other institutions):
- 8.05.2013 – 10 hours workshop for PhD students from the University of Technology, Wroclaw.
- 18-19.06.2013 – workshop: “Confocal Microscopy – Live imagine: Practical course”, focused on advanced microscopy techniques /in vivo/. The practical part of the workshop included studies of intracellular processes using the Spinning Disc Microscope.
- 18.06.2013 – Spinning Disc Microscope practical course during Life Science Imaging – Workshop on Visualization of Molecules, Interactions and Biological Processes.
- 15-16.11.2013 – during the Bio-Imaging Poland First Annual Conference Laboratory of Imaging Tissue Structure and Function presented a practical course on „Fast imagine using Zeiss Spinning Disc Confocal Microscope”
- 3-5.06.2014 – „VIII Meeting of Confocal Microscopes Users”. Lecture “Spinning disc confocal microscope – the tool for the live visualizations”, and practical course “Application of Spinning Disc Confocal Microscope” – dr Wojciech Brutkowski.
- 16.06.2014 Summer school of Studies of Molecular Medicine – Presentation of Spinning Disc Microscope.

Individual practical courses for users upon a request.

Current studies:
- Tracking of mitochondria movement in living cells using Spinning Disc Confocal microscopy.
- In vivo analysis of the dynamics of proteins involved replication process during the S phase of the cell cycle.

Task 4.2: Acquisition of a Guava easyCyte 8HT Flow Cytometry System (Millipore)
The equipment was delivered and installed in October 2012.

Trainings for members of the Laboratory of Cytometry:
- 31.10.2012 – Instalation of the Guava System and the first basic technical – Michal Konieczny i Philippe Durbiano (Area Manager Merck Millipore)
- 12-13.02.2013 – Advanced training covering the use of the System and software – Dr. Sebastian Seth (Instrument Field Application Specialist, Flow Cytometry Bioscience Division)

Seminars and trainings for other users:
1. Sending of agenda to all researchers at the Nencki Institute with the presentation of the Guava System and possible applications
2. 23.04.2013 – BIO-IMAGINE practical workshop: FLOW CYTOMETRY WORKSHOP: "Apoptosis and cell signaling" - training for participants – studies of apoptosis and viability
3. Summer school of Studies of Molecular Medicine - 18-19. 06.2013 – presentation of the Guava System
4. Presentation for PhD students at the Nencki Institute – June 2013
5. Constantly - individual trainings dependently on needs.

Currently, researchers from different groups at the Nencki Institute and Neurobiology Centre at the Nencki Institute use the System. It is available for the non-assisted use after the training provided by the members of Laboratory of Cytometry and used mostly for analysis of different parameters of cytotoxicity, viability and apoptosis as well as calculations of IC50 parameter in the cytotoxicity study.

Data presentation at the conferences:
1. Bugajski L, Podszywalow-Bartnicka P, Dudka-Ruszkowska W, Piwocka K. Utility of the Millipore Guava easyCyte microcapillary system to analyze cell death parameters in the cytotoxicity studies. Poznan Days of Cytometry and Immunopathology, 16-17.05.2013 Poznan, abstract book: P1-6
2. Piwocka K, Podszywalow-Bartnicka P, Brewinska-Olchowik M, Bugajski L, Kusio-Kobialka M. Simultaneous tracking of cell type, viability, proliferation and expression of intracellular proteins in co-cultures of leukemia and HS-5 stroma cells using multiparameter flow cytometry. XXVIII Congress of the International Society for Advancement of Cytometry Cyto2013, 19-22.05.2013 San Diego, USA; ABSTR. 277/B156, abstract book p. 198.
3. Podszywalwo-Bartnicka P, Bugajski L, Cmoch A, Tkaczyk M, Dadlez M, Piwocka K. Modification of protein and microRNA profile in extracellular microvesicles by pro-survival pathways in CML cells. ISEV 2014 Conference, 30.04-3.05.2014 Rotterdam, The Netherlands (submitted).

Work Package 5

The goals of organization of conferences within the frame of WP5 were to promote the exchange of ideas and the results of scientific work between researchers of the Nencki Institute and their colleagues form Europe and beyond.
Workshops were addressed especially to Polish researchers, giving them an opportunity to acquire the knowledge of the state of the art techniques of bio-visualization. An added value of the organized conferences and workshops was the attendance of researchers from the countries of Middle and Eastern Europe, thus giving them the exceptional opportunity to meet the first-class specialists in the field and build new relations with Polish scientists.

In the frame of BIO-IMAGINE six workshops, three conferences and three symposia were organized.

Task 5.1: Organization of Workshops
1. “Molecular morphology techniques in neurobiology”, 2011, associated with 10th International Congress of Polish Neuroscience Society, organized by the Nencki Institute by Grzegorz Wilczynski.
2. “Imaging neural activity in sensory systems: experimental and modeling approach”, 2011, associated with 10th International Congress of Polish Neuroscience Society, organized at the Nencki Institute by Wioletta Waleszczyk.
3. “3D imaging and mapping of elements by X-ray microanalysis in electron microscopy”, 2012, organized at the Nencki Institute by prof. Elżbieta Wyroba and the Laboratory of Electron Microscopy form the Nencki Institute.
4. “Confocal Microscopy – Advanced Techniques for Modern Biology”. The event took place on 11-12th April, 2013 at the Nencki Institute. It was organized by Prof. Wanda Klopocka, the head of the Laboratory of Confocal Microscopy.
5. “Confocal Microscopy – Live Imaging: Practical Courses”. The workshop was held on June 18-19th, 2013 at the Nencki Institute in Warsaw. It was organized by Prof. Wanda Klopocka, the head of the Laboratory of Confocal Microscopy.
6. “Flow Cytometry Worshop: Apoptosis and Cell Signaling”. The workshop took place on 22-23th April, 2013 at the Nencki Institute in Warsaw. It was organized by Dr. Katarzyna Piwocka, the head of the Laboratory of Cytometry.

Task 5.2: Organization of conferences
1. The VIII Parnas Conference, 2011, Warsaw
This large five-day international conference co-organized by Prof. Leszek Kaczmarek and Prof. Jacek Kuznicki along with the Polish Biochemical Society, gathering above 280 scientist form Poland, Ukraine and Israel, was held on August 27-31, 2011 in Warsaw.
2. Visualizing senescent cells in vitro and in vivo, 2012, Warsaw
The conference took place on 15-16 December 2012 in Warsaw and was organized by prof. Ewa Sikora from the Nencki Institute. The meeting was in the frame of the “Biogerontological Meetings at the Nencki Institute organized since 2005. There were more than 150
3. „Inhibitory Control of Brain Plasticity – Bio-imaging Methods Reveal Brain Plasticity”, 2012, Cracow
The conference took place on September 5-7, 2012, at the Jagiellonian University in Cracow. It was organized by prof. Malgorzata Kossut from the Nencki Institute and prof. Jerzy Mozrzymas from the Wroclaw Medical University.

Task 5.3: Organization of satellite symposia
1. “Brain Tumors 2012 - from biology to therapy”, Warsaw.
The symposium was organized by Prof. Bozena Kaminska-Kaczmarek from the Nencki Institute, and held on May 28-30th 2012 in Warsaw.

2. “Images of the Spinal Cord: from Functionally Identified Neurons to Functional Recovery” 2013, Warsaw.
The Symposium took place on November 25th, 2013 at the Nencki Institute in Warsaw. It was organized by prof. Urszula Slawinska and dr. Anna Cabaj from the Nencki Institute, and prof. Larry Jordan form the University of Manitoba, Canada.

3. “1st Nencki Symposium on: Jerzy Konorski contribution to modern neuroscience” 2013, Warsaw
The Symposium was held on September 19th, 2013 at the Nencki Institute in Warsaw. It was organized by prof. Andrzej Wrobel, prof. Malgorzata Skup and prof. Ewelina Knapska from the Nencki Institute. The symposium commemorated the outstanding achievements of Jerzy Konorski and marked the 40th anniversary of his death. Jerzy Konorski discovered secondary conditioned reflexes and carried out intensive research on this topic. His scientific achievements had worldwide impact on the concepts of fundamental brain functions.
Organization of this meeting was not originally planned within the BIO-IMAGINE framework. However, taking into account the importance of Konorski’s work and his strong impact on contemporary neurobiology, and keeping in mind the recommendation of the BIO-IMAGINE External Advisory Board to create regular Nencki-specific meeting/workshop series to increase even further its visibility in the imaging community (brand-marking), the symposium – the first edition in a series – was included in the list of events supported by the BIO-IMAGINE Project.

Written reports from the organized events were posted at the BIO-IMAGINE website.

Task 5.4: Participation of Institute’s staff in international conferences and short term training events
Within the frame of Work Package 5, financial support was provided to c.a. 85 the Nencki’s employees to facilitate their participation in international conferences and workshops. This provided a great possibility for the Nencki Institute employees to get in touch with most advanced and newest achievements in biology, to present and discuss their data and to establish new research contacts.
Conferences held in Europe were the most desired destinations of the employees of the Nencki Institute. However, 13 of 85 trips were outside Europe. All the requests for the support to the participation in the events outside Europe was approved by the BIO-IMAGINE Project Officer. Some conferences were attended by more than one person form the Nencki Institute.
All participants supported from the BIO-IMAGINE project either presented posters or provided lectures.

Work Package 6

Dissemination of the project results implies active web site, preparing reports, publishing of informative articles and educational material, and involving policy and decision makers.

The following goals were achieved within BIO-IMAGINE WP6:
- The design of the project "image" in terms of the logo and the associated colours to be used on the entire project outputs (2011)
- Creation and maintenance of the BIO-IMAGINE webpage
- A Polish / English BIO-IMAGINE web page was created and published on January 25, 2011 ( The site presented important information about the project, its scope and implementation. It served as one the channels of communication among the Nencki employees involved in the Project activities, but also as hub for offering information to general public and other stakeholders. The content of the site were updated periodically. Information about the events, seminars, workshops, lectures, conferences and training sessions were continuously posted on the website. The recruitment process within Bio-IMAGINE WP1 as well as other announcements concerning available positions related to the Project scope were run using an interactive module of the website. The BIO-IMAGINE webpage was (and still is) accessible to the scientists of the Institute, the Ochota Campus and to the Internet users from all over the world.
- Production and presentation of the BIO-IMAGINE promotional products
The following promotional products were produced for BIO-IMAGINE:
i) 4 roll-ups in Polish and English
ii) informational posters in Polish
iii) project flyers
iv) promotional products with the Project and/or the Nencki logo (e.g. pens, pencils, notebooks, T-shirts, balloons, mugs, bags).

In M1-42 the Project promotional products were distributed during all the events supported by the Project and organized in or by the Nencki Institute. In consideration of the huge interest in promotional products they were gradually re-ordered and distributed.
In line with the 95th anniversary of the Nencki Institute of Experimental Biology establishment at 1918, the ‘Microscopy and Imaging’ book edited by Prof. Leszek Kuznicki and Prof. Jerzy Sikora was published. The book is a collection of pictures, images and descriptions of methods used at the Nencki Institute, from the very early to the contemporary, elucidating biological imaging techniques to wide audience.
2nd, 3rd and 4th edition of the biannual Nencki Newsletter was published with the support of BIO-IMAGINE funds. This electronic publication appearing twice a year summarizes in a condensed and colourful format the most important news and events of the last six months.
2013 calendar containing a selection of the best scientific microphotographs presented in articles and reviews published by the Institute’s staff with full description (in Polish and English) was also co-financed by BIO-IMAGINE.

Organization of hands-on events
A great number of extremely successful events were organized or co-organized by the Nencki Institute with the support of the BIO-IMAGINE funds. The most important include:
• 2011, 2012, 2013, 2014 BRAIN AWARENESS WEEK IN WARSAW
• 2011, 2012, 2013, 2014 OPEN DAYS FOR PhD STUDIES CANDIDATES
• 2011, 2012, 2013, 2014 OPEN DAYS FOR PUPILS organized by the Nencki PhD students
• 2011, 2012, 2013, 2014 SCIENCE FESTIVAL IN WARSAW
• Videocast about the Center of Neurobiogy in Nencki Institute, Warsaw (2013)
• 1st Nencki Institute PhD Student Conference - International PhD Program in Neurobiology, (2013)
Workshops and hands-on events differ from conferences in that they are targeted at smaller groups of participants and involve a much higher and more active level of engagement. The value of the workshops and hands-on events organized within BIO-IMAGINE WP6 was to provide an opportunity for pupils, students or teachers to meet and discuss the issues raised by experimental work at the Nencki Institute with colleagues. We took care to organize such workshops as often as possible to ensure that the opportunity to attend is made available to as many people as possible. Overall, the total number of participants in the events amounted to almost 20,000 people (including the visitors to the Scientific Picnics or Science Festivals). The efforts to popularize science were recognized by the Polish Press Agency, which in 2013 honored the Nencki Institute with the title of the Science Populariser.

Work Package 7

Administrative and financial management and reporting
Although BIO-IMAGINE was a single partner project, to ensure the overall coordination of the project, several EU partners were supporting the Nencki Institute to strengthen its research capacity building. By consequence, the management structure of the project was based on the Project Management Committee (Project Coordinator + Project Manager + Project Support Team + Work Packages Leaders), but working in close cooperation with the International Advisory Board. Project Management Committee (PMC) was responsible for the technical and financial coordination and implementation of foreseen activities. The main activities of the PMC members were:

Project Coordinator (PC):
• Leading and supporting scientific and managerial coordination of the whole project

Project Manager (PM)
• Overall day-to-day management of BIO-IMAGINE
• Administering the EC financial contribution regarding its allocation between activities, in accordance with the GA
• Keeping contact with the European Commission on technical and financial issues
• Communicating with external contacts on behalf of the project
• Ensuring quality control of work and deliverables
• Leading the establishment and maintenance of the project web sites (including portal)
• Assisting and supporting work package leaders on managerial issues

Work Package leaders (WPL):
• Coordinating the activities within the work package on a managerial and scientific level
• Overseeing the progress in the respective WPs
• Monitoring and reporting on the progress of the work package and deliverables achieved to the PC.

PM was also responsible to organize project meetings, and the proper framework for communications with the Advisory Board members, External Evaluators and Stakeholders Group. An important tool for communication between PMT and external groups (Advisory Board, Stakeholders Group, EC) was the project's web site. Therefore, it was the special task of the WP6 leader to ensure rapid and clear dissemination of important information via the web portal.
Each WPL was given by the PM a list of milestones and deliverables to be fulfilled, the corresponding schedule and budget. Consultative meetings were organized by the PC and PM with WPL in order to:
• report on each WP's activities: results obtained, problems occurred, solutions foreseen
• discuss on administrative and financial issues such as: expenditure control, tender /delivery delays, reallocations of resources (human and materials) between activities
• discuss on the following milestones and deliverables, agree on actions and schedule.

During the project, the Coordinator was in close contact with Project Manager. Effective communication channels between different members of the Project Management Committee, the European Commission and the Project Steering Committee were also maintained.

The project website ( has been maintained and updated regularly.

Administrative support for tasks of all the Work Packages was provided by the Project Support Team upon request.

Organizing and coordination of Project Meetings
1st Project Management Committee Meeting M1 January 27, 2011
2nd Project Management Committee Meeting M4 April 11, 2011
3rd Project Management Committee Meeting M5 May 13, 2011
1st Project International Advisory Board Meeting M6 June 2-4, 2011
BIO-IMAGINE recruitment committee meetings M4, M5, M7, M9, M10, M35, M36
4th Project Management Committee Meeting M16 April 18, 2012
2nd Project International Advisory Board Meeting M22 October 8-9, 2012
5th Project Management Committee Meeting M25 January 9, 2013
6th Project Management Committee Meeting M26 February 21, 2013
7th Project Management Committee Meeting M33 September 20, 2013
8th Project Management Committee Meeting M35 November 22, 2013
9th Project Management Committee Meeting M37 January 9, 2014
1st Project Review Meeting M25 January 15-17, 2013
2nd Project Review Meeting M37 January 23-25, 2014
10th Project Management Committee Meeting M41 May 13, 2014
11th Project Management Committee Meeting M45 September 17, 2014
12th Project Management Committee Meeting M46 October 17, 2014
3rd Project Review Meeting M46 October 20-22, 2014
3rd Project International Advisory Board Meeting M46 October 20-22, 2014

Twelve Project Management Committee meetings were held during the Project lifetime.
All organizational and administrative issues of the project management were analyzed and discussed in the meetings. Some of the meetings included briefings before other important Project events, such as International Advisory Board meetings or Project Review Meetings.
In the second half of 2013 a special Committee was created by the Project Coordinator to analyze the requests of 9 Laboratory Leaders of the Nencki Institute to extend the contracts with the Post-doctoral fellows employed by the Nencki Institute within BIO-IMAGINE WP1.
The Committee consisted of 4 Nencki senior scientists with no conflict of interest (leaders of the research groups with no BIO-IMAGINE post-doc) and Prof. Adam Szewczyk – BIO-IMAGINE Coordinator, as the chairman of the Committee.

The following criteria were taken into account in the process of evaluation:
- scientific activity – papers published or submitted, grants obtained;
- innovation – introduction of any new method or expertise to the Nencki Institute, innovative topics, etc.;
- activity in the dissemination of science – papers presented or lectures delivered at international conferences, received awards, media activity;
- level of expertise of the lab - a place in the rank of the Institute’s laboratories (over the last 5 years);
- feedback from the lab leader / supervisor;
- duration of employment at the Nencki Institute.
All the 9 requests submitted by the post-docs’ supervisors were positively evaluated and the contracts with the researchers were extended (in result, all the 9 post-docs will be employed by the Nencki Institute at least for 24 months). For details, please see the table on page 3 of this report.

Preparing reports (scientific and financial)
BIO-IMAGINE lifetime (36 months + a 6-month period of evaluation) was originally divided in two reporting periods (M1-24 and 25-42). In May 2013 the Project Coordinator submitted to the Project Officer a letter of request to extend the duration of the BIO-IMAGINE project by 6 months. The request was motivated with delays in some work packages and would allow the Nencki Institute to successfully complete all tasks foreseen in Annex I and maximize the anticipated impact of the project. The Project Officer accepted the justification and a proper request for amendment was forwarded to the EC. In result, in June 2013 by a decision of the European Commission the Project duration was extended by 6 months. The end date of the Project was postponed to 30 June 2014 for WP1-6 and 31 December 2014 for WP7 and 8.
Apart from periodic reporting 23 Deliverables (reports) were to be submitted to the EC and 6 Milestones to be achieved.
In general, reporting fell mainly under the responsibility of the Project Coordinator and Project Manager, but was supported by WP leaders and other participants. Any issue occurred was dealt professionally and solved accordingly.
All the 6 Project Milestones were achieved. All the 23 Deliverables were completed and submitted to the EC, some with minor delays.

Financial aspects
In October 2012 during the 2nd meeting of the BIO-IMAGINE International Advisory Board the Project Coordinator raised a concern during the presentations and discussions on the Project’s current status. The concern was that the twinning groups in WP2 were unable to meet the planned number of visits and missions, which posed a significant risk of not utilizing the allocated budget of WP2 by the end of the project. At the same time the Nencki Institute experienced a significant shortage of funds in WP5 (outgoing missions and travel costs of invited participants to workshops and conferences organized by the Institute as well as other meeting organization costs). In result, a recommendation was made by the IAB members to formulate re-allocation of funds from WP2 (twinning) to WP2 (conferences and workshops), with the mission to organize targeted workshops/meetings to build the brand of the Nencki Institute.
The Project Coordinator wrote to the BIO-IMAGINE Project Officer at the EC a request to approve the reallocation of funds without going through the formal contract amendment process. The request was to move 40% of WP2 total budget (of which 103.200 EUR represents the EC contribution) to cover the activities within WP5. This transfer would not affect the main objectives or deliverables of the project and will largely remain in the same cost categories (“travel” and “other”). The request was approved by Ms. Anna Remond-Niewiarowska, the BIO-IMAGINE Project Officer, and the re-allocation of funds was proceeded accordingly.

Work Package 8

BIO-IMAGINE evaluation by external experts was planned in order to evaluate the impact which the Project had on facilitation and execution of research at the Nencki Institute. The External Evaluators Panel was expected to provide recommendations for short-term and long-term strategic activities aimed at preserving and enhancing the Nencki Institute in its key competence areas to improve its contribution to the European research community and regional development.
In M20 (August 2012) the names of the three experts who accepted the EC invitation to perform the ex-post evaluation of the Project under WP8 were presented to the BIO-IMAGINE Coordinator. The Project Manager and the WP8 Leader contacted the experts and provided them with all the necessary information about the Project. A draft date and agenda of the 1st Project Review Meeting was suggested.
In November 2012 one of the experts cancelled her participation in the evaluation for the reason of a serious disease and was replaced by another expert. Then, the final date of the first Project Review Meeting was finally set for January 15-17, 2013. The WP8 Leader with the assistance of the Project Manager set off to arrange the details of the meeting.
The first 3-day BIO-IMAGINE Project Review Meeting was organized at the premises of the Nencki Institute on January 15-17, 2013. The WP8 Leader with the assistance of the Project Manager arranged the details of the meeting. The Agenda included a welcome by Prof. Adam Szewczyk, Director of the Nencki Institute and BIO-IMAGINE Coordinator, presentations by BIO-IMAGINE WP Leaders, Nencki Institute site visit and a closed door meeting of the evaluators followed by the closing remarks from the evaluators to the Project Coordinator.
On the final day of the meeting the Project Evaluators participated in the 2013 Managing Innovation Conference organized by the Nencki Institute within the BIO-IMAGINE Project Work Package 3.

The second Project Review Meeting was held on January 23-35, 2014. The agenda of the meeting included presentations by BIO-IMAGINE WP Leaders, presentations of experienced researchers recruited within WP1, a closed door meeting of the External Evaluation panel, closing remarks from the Evaluators and the Evaluators internal meeting to work on a preliminary version of the Evaluation Report.
The Final BIO-IMAGINE Project Meeting including the 3rd BIO-IMAGINE International Advisory Board (“the IAB”) meeting and the 3rd Project Review (“RV3”) meeting was held on October 21-23, 2014. The agenda of the joint event included reports on BIO-IMAGINE activities by the Work Package Leaders and a round table meeting during which a discussion on the results of BIO-IMAGINE was held, and a statement of the BIO-IMAGINE International Advisory Board and a statement of the BIO-IMAGINE External Evaluators were presented. The final item on the agenda was a discussion about the best ways and methods to preserve Nencki Institute’s scientific excellence and increase its contribution to the economic and social sustainable development of the region.
In December 2014 the External Evaluators presented their report from evaluation which constitutes the BIO-IMAGINE Deliverable 8.1 already submitted to the EC.

Potential Impact:
The Nencki Institute is already one of the leading scientific centres in neurobiological research in this part of Europe. BIO-IMAGINE aimed to enable the Nencki Institute to further develop its research capacities and truly unlock its potential in by the end of this decade. We believe its success allowed the Nencki Institute achieving all of the expected impacts listed in the work programme and strengthen the attractiveness and competitiveness of the Institute itself, but also of the region and Poland as a country. The Project increased the Nencki Institute contribution to regional economic and social development. It also increased the potential of the Institute research groups to participate in Horizon 2020 and future EU Framework Programmes.

Partnerships with European Molecular Biology Laboratory and its commercial arm EMBLEM as well as twinning with research groups from 29 prominent European research laboratories without any doubt helped the Nencki Institute better integrate in the European Research Area. BIO-IMAGINE networking stimulated innovation driven research in future collaborative projects.
The project certainly improved the quality of research performed at the Institute by upgrading its RTD capacity, both in terms of human potential and cutting edge research equipment. This improvement has already been triggered by new talented researchers and research professionals, recruited within WP1 for the posts of new lab leaders with experience in imaging technologies as a primary tool of research, leaders of two new biological imaging (advanced light microscopy) and brain imaging (magnetic resonance) core facility laboratories as well as post-doctoral fellows working with the leading research groups at the Institute.
The capacity and capability has been further increased by acquisition of specialized modern imaging equipment within WP4.
The impact of the BIO-IMAGINE Project has been recognized and well perceived by the Project twinning partners, the International Advisory Board members and the WP8 External Evaluators, proving that BIO-IMAGINE represents an important element that contributed to shaping the ERA in the area of biological and biomedical imaging. 

Project Coordinator
Prof. Adam Szewczyk
+48 22 589 22 07

Project Manager
Marta Rucińska
+48 22 589 23 30