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Section B2

Objectives

  Coordinator: Prof. Richard Villems 
E-mail:    rvillems@ebc.ee
Project duration: 01.02.03-01.02.06
EU funding: nearly 300 000 EUR

Estonian Biocentre has participated in the call for centres of excellence within the INCO 2 package of FP5. Our proposal, titled as Geneticists for the Next Millennium (Genemill), was placed 3-5 during the evaluation and we have received financing. While we now discussed among ourselves whether to participate in a somewhat similar call, we first hesitated: the named project is still ongoing and we have not yet exhausted its possibilities. Probably, we thought, a repeated competition may be seen as an attempt to become a sort of permanent salesman of the same bag, wherever and whenever there is a market. Yet we have decided to participate. Why did we change our mind?

First and foremost, the previous application was prepared more than 2 years ago. Then, not much was known about the next FP and the European Research Area initiative was in its embryonic stage. And although the very final documents about the rules for the FP6 are not approved yet by the EP and by the Council, many and probably the most essential aspects of it have became clear. Directly relevant here is a turn from the financing of limited in scale joint research projects, to networks of excellence and to integrated projects. Bearing that in mind, we asked our international advisory board, together with us (i.e. the local steering committee), to look over the goals an aims ('workpackages") in our ongoing project, as well as other developments during the last two years, in order to make recommendations. The recommendation was to participate in this competition. More specifically, it was pointed out by the board that while the instruments of the ongoing project are, so to say, overwhelmingly self-centred and in a way fragmented, the challenges ahead need more clearly, say, even more narrowly, targeted actions. In other words - to cover less different general activities, but to make a clear stress to the networking with the excellence in the field of life sciences and technologies. Primarily with the excellence in Europe, but also keeping a close eye to the best in US and, possibly, elsewhere. As the Advisory Board concluded: carry on as you have done so far - look to excellence in abroad and in directions where you have reached a real working collaboration on equal footing, your own work is very likely excellent as well. You will see that in the field of basic science and, sometimes even more clearly, where you attract industrial partnership and private resources in general. This, likely, will be your way into the ERA.

These recommendations of the Board led us to the understanding that there is in fact not much use in copying the instruments of the previous proposal: there is a need for new concepts. Furthermore, it was now possible to capitalize from a significantly wider and deeper long-term collaboration with different research centres and industrial partners than 2-3 years ago. Notably, thanks to joint research projects of FP5 we are involved in (or plan shortly to join), but not at all only. The ongoing INCO 2 excellence centres project opened additional possibilities, whereas rapid growth of our spin-offs has opened altogether different directions and dimensions.

The third argument (or, rather, several such arguments) for the participation can be seen as "local", but we have considered it equally seriously. "Seriously" is a right word here because all relatively large-scale projects like that, addressed to not-so-prosperous conditions, rise a legitimate question - what happens when the project is over? Say - you use your money to attract lots of nice fellows, good lecturers etc. and, when it is over after 3 years or so, they pack up and leave - probably with the best among your grad students. Let us here limit with a statement that although we understand this sort of fears, our now already almost 10-year experience makes us rather immune against them; we return to this issue in more depth below (see also B4 and, in particular, subsection C4).

Here, however, we briefly try to explain a relevant, but a more general "Estonian-centred" point, why we believe that the R&D activities of the Estonian Biocentre, and of this proposal, are in a focus of the strategic vision of Estonia for the future of R&D in this country and an additional guarantee for a sustainable development. Namely, in December, 2001, Estonian Parliament approved the presented by the Government "white book on R&D" for Estonia for the next 4 year period (electronic version in English is available at the www site of the Estonian R&D Council at the Prime Minister: www.tan.ee). It is the first such level R&D document for our country: former versions have been governmental position papers, not legally binding to any new administration. Only three "key areas" in the field of R&D are now defined for Estonia, one of them being biotechnology and, in its more detailed description, with a stress on genomics and on molecular medicine in general - for healthcare and industrial innovation. Its explanatory chapter includes also gene technologies to be used to improve the quality of the environment. This rather complex document foresees organisational and financial means to be used by the administration to achieve the named goals. We mention it here in order to demonstrate that: (i) the current project fulfils, in the most direct sense, one of the criteria for the current call: relevance for the economy and/or the society of NAS, listed under section C8 and (ii) also because strategic decisions made in Estonia give an additional "insurance" for sustainability of undertakings in the field of biomedical R&D in this country.

It is worthwhile to add that the same document is now used as a blueprint for relevant chapters in a new version of the Estonian National Development Plan (referred now as Single Planning Document), currently under preparation and to be presented to, and get approved by, the EU, as a basis to distribute the Structural Funds of the EU in future.

Finally, we trust that the overall spirit and the key positions of our proposal are in a good conformity with the discussed earlier in length and approved by the European Commission on 23.01.2002 a comprehensive plan for the development of life sciences and biotechnology in Europe.

All these diverse components, taken together, convinced us to submit the current proposal. From the Genemill proposal, we kept a central introductory principle, defined as: this proposal is not to carry out any particular scientific enquiry, neither developmental work directly, because we have adequate means for that from different sources.

Here we add: This proposal is to extend and to make more efficient a platform for a successful entering of the Estonian Biocentre into the European Research Area - in our particular field. This is the objective of the proposal, further explained as follows.

This single general objective covers different components. Instruments for it (work packages) are outlined elsewhere in the proposal (section B4). Although one may think about a long list of aspects indirectly influencing successful participation of the Estonian Biocentre in the ERA, many of them are beyond our effective control, there are several, what we can affect and out of them we selected those where an additional temporarily available resources can make a significant difference.

Under "a platform" we keep in mind a variety of components, depending primarily from us, like attractive research themes, good equipment and premises and an adequate research support, efficient electronic network and access to literature, friendly atmosphere etc.

While seeking support under current call, our strategy to make this platform more efficient, foresees many undertakings outside this support scheme. In a way, they can be viewed as matching costs above the usual research and teaching support, either national or international. They include, in Summer 2002, a profound reconstruction of premises for bioinformatics (planned 0.6 MEUR for construction works and 0.2 MEUR for additional network equipment). It also includes final planning of the third stage of the lab complex, possibly also the beginning of its construction (about 3500 sq.m) within the next 3 years. An additional 1 MUSD recently received for sending our postdocs abroad may be also viewed as "building a platform".

Thus, our sub-objectives are:

  1. to build twinning relations with (a limited list of) scientific institutions of recognized European and world level excellence in research;
  2. to open research themes and positions in EBC for an international competition and to internationalise our graduate school.
  3. to gather recognition as being among the leaders in the field by organizing a continuous system of international/regional seminars, hands-on training courses and workshops.

There seems to be a strong political will in the European Union that quite a few associated countries will receive a call to join the EU soon. Current political decisions of the member states suggest that it should happen so that citizens of these countries may participate in EP elections in 2004. In this sense it is seems that non of the listed objectives would likely face setbacks for reasons outside our control.

What, then, may be seen as problematic? Indeed, here is a question about the objective. The ERA does not exist, so one cannot enter it. At least not yet. Therefore, it would be more proper to say that the proposal is an element, albeit a very small one, of the creating of the ERA. Nevertheless, we can speak about FP6 and our success in participation in its main instruments, as about a verifiable indicator, but here the time horizon appears to be wider than the duration of this call. On the other hand, the sub-objectives, reflecting the content of work packages, are individually verifiable and, together with many other necessary components would hopefully create a synergistic effect expected. In particular, we view the proposed twinning scheme as a beginning of organizing networking of excellence under common research programme.

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Section B3

Innovation

The European Research Area is itself a new innovative concept and its development an evolutionary process, needing also quite a few small revolutions in the attitude of not only of the member state governments, but their research councils as well, since they, by and large, represent fairly well scientists of the countries. It would be a long way to go. But it starts now, with FP6. Yet it would be a gross overestimation to say that because of the innovative nature of the ERA, our particular approach here is ipse facto automatically innovative. The first (sub)objective - twinning with known centres of excellence, is innovative in our concrete context but not necessarily in principle - good labs do collaborate extensively anyway, including across borders. So do we as well, and not only through FPs.

However, usually this sort of collaboration is project-based and short-living. If to take a careful look to the new Finnish centres of excellence, launched this January for a 6 year period, then there, one may perhaps see arrangements, more close to the "twinning": different research units from different universities agreed to collaborate on the basis of relatively long programs, not just projects. There may be examples like that elsewhere. In this sense our twinning schemes may be considered innovative, though not original.

There is nothing innovative in our proposal to achieve opening of research positions, including top positions, to international competition - just a common practice in many EU countries, though not in all. Yet it is quite innovative in Estonian conditions - if not necessarily in words, then certainly so in practice. It should be done, but per se it is but a remote prerequisite for the ERA. The same concerns opening grad studies and postdocs positions (and here we have already some positive experience): funds available for mobility can be considered here as a vital component.

More innovative would be to test approaches for the opening of long-term national research themes internationally. We are well aware that this issue is currently debated quite extensively (e.g in a recent issue of Science by G. Radda from MRC, EL. Winnaker from DFG and H. Wigzell from Karolinska) and we are quite willing to test it, e.g., at the level of the Estonian Gene Heritage program. Possibly in some other close-to-industry projects as well - limiting it here to the margin of pre-competitive applied biomedical research, e.g. in DNA vaccines. Of course, the present proposal can only be seen as a small-scale pilot in this direction.

In sum, a benevolent reader may hopefully see certain innovative aspects in this proposal. Here, we keep in mind the instruments to be applied, not science itself. There, we trust, an innovative nature of our research and developmental work is less foggy.

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Section B4

Work plan

Introduction

The current work plan consists of 4 work packages and is structured along the main activities of the proposed project. Those activities will be carried out by targeted measures. The proposed 4 work packages will help the centre to achieve the objectives of the proposal, described above. The total funding and time effort of all work packages is indicated in the cost summary.

Part of the main rationale of the work packages can be described as "to see as well as to be seen": they address using different instruments, our capacity to function efficiently as a partner in the European Research Area. All four work packages serve the same objective in different ways.

The first of them is the most traditional, opening new possibilities for learning and serious intellectual contacts. European genetics is not any longer what it was 30 years ago: the number of excellent groups has increased very significantly and new innovative methods of analysis are now coming from many centres of different countries. This is why WP1 identifies of certain methods of a specific value for the Estonian Biocentre and lists European centres of advanced knowledge in the corresponding specific problems. Again - neither of the lists should be taken as closed: the field is very dynamic and new knowledge generated in a large number of labs.

WP2 is quite different: its implementation may seem business as usual for many advanced centres where all positions are open for international competition, but it would be a big change in a CEEC environment. However, this change in policy is not "abstract" - its real aim is to facilitate opening of our long-term research and development programs for European researchers. We bear in mind Estonian Gene Heritage project, as well as our long-term projects in other directions. The other idea behind this WP is to create means for opening new directions much faster, by recruiting specialists, active and experienced in a particular profile. They, in turn, will have local young researchers and grad students growing under his/her guidance. Junior positions are meant, in classical way, for postdoc level applicants, who, also working as a part of a research team, will have his/her own research plan and freedom within it. Senior positions are planned for a particular field where the Centre seeks for experts in a certain field of research/developmental area, where such an expertise is needed for strengthening the position of the Centre, its general R&D directions. In addition to finances available from the project, the Centre will take a commitment to guarantee, both for junior and senior positions, adequate means for successful scientific work. Senior positions are maximum for two years under this project, but the contract with the Centre can be extended after this period using already different financial sources.

WP3 - the twinning scheme - differs from both WP1 and 2 in a sense that it does not address any longer any special know-how, method or project and does not rely that much on a concrete person as such. Instead, it is aimed to build up long-lasting collaboration with centres of excellence in research in areas, overlapping with our strategic interests and where, as we believe, our own knowledge is on the level what may make us partners for advancing an important for European life sciences direction. Thus, it seeks not for projects but for common programs where the partnership would allow a much more powerful approach. It is also clear that such partnerships cannot be build up from zero level within a period of a few years. Therefore, this partnership is selected bearing in mind two criteria: twinning partners must be top quality research centres and there should have been real positive collaboration experience already. Scientific reputation of the Sanger Centre, Cambridge University, DKFZ and the two Italian centres of excellence in genetics hopefully do not need advertising. Some of the listed twinning partners (Sanger Centre, DKFZ) are large or very large research establishments with diverse research programs. It should be understood that in this case "twinning" covers only a subset of such large centres. One may be a bit surprised seeing in this list an archaeological institute (U. of Cambridge), but it happens to be so that this institute became, within the last decade, one of the leaders in Europe in the understanding of genetic history of modern humans (calling it "archaeogenetics"): it turned now out that approaches developed there (though not only there of course) turned out to be of specific value also in the search for gene combinations behind disease phenotypes.

WP4 may seem again more traditional and in a way it is indeed. However, note that a significant part of it is covered by hands-on training courses/seminars: the aim of them is to combine here an advanced international lecture course with training in advanced methods, where the elements of the latter have been developed "in situ" - i.e locally. Hence, in rather direct way such courses serve as an advert for our know-how and would, hopefully, facilitate export capacity of our emerging biotech. Larger conferences are well in the fields of general interest and there is little doubt that they will be attended enthusiastically all over Europe and from elsewhere. In fact, there is already certain pressure on us to organize such meetings -e.g. to prolong successful GeneForum series: this proposal would greatly help their organisation. And there is a specifically valuable for us long-term strategy aspect in it - bringing together genetics, ethics and entrepreneurship at its best and opening such forums to a wide local audience as well. It continues our ongoing effort to rise public awareness and help them to formulate an informed consent in modern genetics, where we have hold and continue to organise (co-organise and co-finance with Estonian TV) TV debates, issue "Gene News" as a free add to a major daily, publish books, including those for children from the age of 7 - 10 years, etc. And we must admit that here, the Estonian Government, Ministry of Social Affairs in particular, has been very understanding and supportive. This traditional activity of the EBC, also "bolstered" by applying, within the FP5, to joint grants in the field of bioethics, will continue. It may be added here that WP4 is not exhausting bi- and multilateral seminars/workshops activity of the Centre: many such events have been, are, and will be organised in coming years, often in quite informal basis, at the level of workgroups, gathering together interested specialists.

Above (in B2), we have used a term "an efficient platform" to enter the European Research Area. We are quite convinced that fulfilment of the planned activities would indeed make such a platform more efficient. Furthermore, we are also sure that the change generated would be sustainable: Estonian academic and applied research in molecular medicine is in a fast growth phase, both public and private resources have increased significantly and this tendency continues. Ideas what seemed beyond reasonable five years ago, are at present in a phase of execution or at least advanced planning. These ideas cover not just technologies but also rapid growth in intellectual capacity. And we do not keep all eggs in one basket - several parallel activities increase chances for a continuous progress. The "platform building" has many aspects and developments in different directions, beyond those covered by the instruments proposed in this project.

Summing up, the following work packages are proposed:

· WP1 - Capacity building through know-how transfer and mobility
· WP2 - Opening Centre for European Research Area
· WP3 - Building Twinning Relations for the Networking of
_______Excellence
· WP4 - Thematic conference and workshops

All measures proposed in this work plan will help to:
Increase our networking with leading European research ___centres
Increase focusing our activities in terms of thematic and ___regional coverage
Increase our human capacity, with particular attention on ___young researchers
Increase our links and joint initiatives with social and economic ___spheres of Estonia
Increase our participation in the forthcoming 6th Framework ___programme

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Work Packages

Work package number and title WP1:
Capacity building through know-how transfer and mobility

Type of activity : VR, CO
Relative start month: 0
Timetable: 36 months (0-36)

Objectives:

This work package aims at strengthening the human potential and research capacity of the Centre through relevant know-how transfer and outward short and medium term mobility of young and experienced researchers from the Centre. In particular, we would like to facilitate the training of our post-doctoral and PhD students at leading European Research institutions.

Description of the contents, the workplan, the steps, the approach or the methodology:

This work package includes measures related to short and medium term outward mobility of our researchers. Researchers from the centre will visit leading European research institutions for a minimum period of 1 week and up to 1 year. The principle approach would be that the more senior is the rank of researcher the shorter is his/her stay at a given European research centre and thus more junior researcher will stay abroad for a longer period. We however consider that staying away for more than 1 year might already lead to potential brain drain rather than expected know-how transfer. Based on development objectives and thematic priorities of the Centre, the following thematic fields are of particular interest for know-how transfer and outward mobility:

  • development of algorithms to handle very large data sets in genome-wide STR analysis; defining disease-associated haplogroups and haplotypes
  • development of relational d-bases, bringing together phenotypes, genotypes, "expressotypes" etc.
  • executing large-scale epidemiological studies
  • new approaches in establishing networks of protein interactions in a living cell
  • pico- and atomol scale analytical methods in genomics and proteomics
  • complex transgenic phenotypes
  • stem cell research
  • modelling of phylogenetic/population history scenarios in time and space
  • dynamics of host-pathogen interaction.

Partners Involved

Besides and above possibilities, available in/through several twinning partnerships, a much wider choice is kept in mind. The following examples do not close the list:

  • BMC, Uppsala University
  • Rudbeck Centre, Uppsala University
  • Karolinska Institutet, Stockholm
  • Viiki Centre of Helsinki University
  • Medical Genetics, Rotterdam University
  • EMBL, Heidelberg
  • MRC Laboratory of Molecular Biology, Cambridge
  • Genethon, Paris
  • KTH, Stockholm
  • International Agency for Cancer Research, Lyon
  • Dept. Medical Biometry, Bonn- European Bioinformatics Institute, Hinxton
  • Danish Centre for Human Genome Resarch, Aarhus
  • Genzentrum, Ludwig
  • Maximilians University, Munich

Deliverables, expected results, milestone for the overall package:

  • Young researchers from the centre will visit European research centres for total of 14 man months (D1)
  • Experienced researchers will visit European research centres for total 3 man months (D2)
  • Increased scientific know-how and enhanced research capacity

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Work package number and title WP2:
Opening Centre for European Research Area

Type of activity : V1, V2, V3, V4
Relative start month: 0
Timetable: 36 months (0-36)

Objectives:

This work package aims at opening all research positions within the centre to the European academic community.

Description of the contents, the workplan, the steps, the approach or the methodology:

We intend to use a package of measure to allow European researchers to apply for available research position within the Centre. Those measures range from advertising the positions in international academic journals to specific grants for elected European researchers to partially cover their opportunity and transition costs. A steering committee, including several members of the International Advisory Board (or appointed by), will screen applications. In case of junior positions, the leader of the corresponding field will of course be consulted and an exact research plan agreed already between a successful applicant and the centre. Senior researchers will provide their own research agenda, including suggestions on short lecture/seminar courses for MSc and PhD students. They will also supervise grad students and guide young researchers.The contract will be from 12 month, up to 2 years stay, at our Centre. In case of senior positions, further extension will be made possible and negotiable from the very beginning, but not under this project. The full package will contain appropriate support for research, financed by the Centre. Provided calculation is based on one-year period, the following positions will be announced during the coming three years:

  • 2 junior researchers in the field of genome diversity analysis
  • 1 senior position in bioinformatics
  • 1 senior position in cancer genomics

The time frame for filling these positions is planned from the very beginning and bearing in mind that it would be optimal if two senior positions - in bioinformatics and in cancer genomics were filled as soon as possible. Junior research positions in genome diversity will be announced in year 2 and 3.

Partners Involved

There are no specific fixed partners for this workplan, though pro-active approach (e.g. partnerships to be organised via twinning) will be of course used in addition to open advertising.

Deliverables, expected results, milestone for the overall package:

  • 2 junior positions for European scientists (D3)
  • 2 senior positions for European scientists (D4)
  • Increased internationalisation of the centre

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Work package number and title WP3:
Building Twinning Relations for the Networking of Excellence

Type of activity : VR, CO
Relative start month: 0
Timetable: 36 months (0-36)

Objectives:

We intend to introduce several twinning actions with selected leading research institutions in Europe in order to meet the specific needs of the Centre.

Description of the contents, the workplan, the steps, the approach or the methodology:

Twinning arrangements are planned in the following fields:

  • High-density, high-throughput genome analysis for multifactorial diseases
  • Vector systems for DNA vaccination and gene therapy; vaccine development and clinical trials
  • European and worldwide studies in human genetic variation
  • Cell cycle regulatory networks, in particular in cancer research

Twinning a subject of bi- and multilateral agreements, defining workplan aims, timetables and delivery of tasks between partners. Because the planned partnerships will be built up from already existing professional contacts and collaboration, the implementation of the twinning arrangements is expected to be a relatively fast procedure. Twinning scheme will be based, first and foremost, on a long-term common interests in one or other scientific or/and applied research direction, i.e., it will be program- , rather than project-based. The corresponding fields are listed above. Twinning will be implemented by working out a common research agenda for a list of problems to be addressed jointly. The main aspect here is to address a class of problems (scope, depth), which would not likely be addressed separately. Two-way study visits, joint colloquia and seminars will be used at the initial stage for building up efficient "everyday" contacts at all level of researchers. We consider this "human aspect" in the twinning schemes most important: contacts at the top level are necessary but not sufficient.

Partners Involved

  • The Wellcome Trust Sanger Institute, Hinxton, UK
  • DKFZ (German Cancer Research Institute) in Heidelberg
  • Institute of Medical Technology, University of Tampere, together with Finnish Immunotechnology plc, Tampere, Finland
  • Department of Biochemistry and McDonald Institute of Archaeological Research, Cambridge University, UK
  • Department of genetics, University of Pavia together with Department of Genetics and Molecular Biology, University of Roma "La Sapienza"

Deliverables, expected results, milestone for the overall package:

  • 7 Study visits (D5)
  • 1 Brainstorm meeting (D6)
  • Published research works, performed in tight co-operation with the twinning partners (D7)

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Work package number and title WP4:
Thematic Conferences and Seminars

Type of activity : CF, WS
Relative start month: 4
Timetable: 36 months (0-36)

Objectives:

This work package aims to organise several thematic conferences and seminars during the project in order to increase the overall visibility and international attraction of the centre.

Description of the contents, the workplan, the steps, the approach or the methodology:

We intend to use this work package for organising seminars and conference on selected topics, which are both relevant to our research priorities and will be of broader interest to European Research Community. For all planned conference we will establish international steering committee. This work package also includes covering costs related to inviting keynote speakers as well as limited amount of travel grants for young researchers from European research organisations. We intend to organise seminars and conferences in the following thematic fields:

  • Yearly GeneForum conferences bringing together scientists, entrepreneurs and bioethics specialist from Europe and elsewhere, to present new knowledge and new ideas in a field of genomics and postgenomics;
  • 3 combined hands-on practical courses/seminars in genome analysis
  • 3 combined hands-on practical courses/seminars in postgenomic tools

Partners Involved

  • ESF, NORFA, HUGO, FEBS, EMBO, NIH, Estonian Technology Agency, Estonian Genome Foundation

Deliverables, expected results, milestone for the overall package:

  • 6 international practical courses/seminars will be organised (D8)
  • 3 international conferences will be organised (D9)
 

 

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