BioASP Newsletter
Volume 2, Edition 6
May 19, 2004



Research news

FEI Company joins EU Interaction Proteome project

FEI Company announced that they will join the EU-funded Interaction Proteome project formed to enable Europe to become an international scientific leader in functional Proteomics.


The project, coordinated by the Max Planck Institute for Biochemisty in Germany, brings together the scientific excellence of eleven leading European research institutions and companies. The project will receive euro 12 million over five years within the 6th Framework Program of the European Commission to develop new technologies for Proteomics research.


Interaction Proteome will provide direct interaction between technology developers and structural biologists in the consortium, shortening the time required to bring new knowledge through the application stage. It will permit development of new technologies, including a high-end mass spectrometer, high-density peptide arrays and enhanced visualization technology for light

and electron microscopy. 


FEI is a leader in advanced electron microscopy with offices in the US, the Netherlands, Canada and India. The collaboration with the Max Planck Institute of

Biochemistry will stimulate the development of a new gene ration of instruments with improved sensitivity suited to the analysis of protein complexes within the cell.


Extensive bioinformatics support is a key element in the project to cope with the massive increase in experimental data on protein interactions obtained using new technologies. In particular, efficient integration of data sets represents a key challenge in proteomics and functional genomics.

(Source: PR Newswire, 26-04-2004)

Magnetic tweezers help to understand DNA

How DNA unfolds itself during the reading of the genetic code, is still a riddle. Magnetic tweezers reveal a piece of the puzzle.


DNA is able to transform like an accordion, but also to be stiff as a stick. Scientists discovered this the last few years by simply pulling the molecule. “It is very good that you can find out a lot with relatively simple techniques”, says John van Noort, researcher at the Huygens Laboratory and one of the first users of magnetic tweezers in the Netherlands.


John van Noort and the student Sander Verbrugge together looked at how the knot of DNA stored in the bacteria Escheruchia coli unfolds. It seems that the HU-protein stretches the DNA, perhaps to create space for the molecules that should read out the DNA.


New physical instruments offer indeed sight at the individual molecule. Magnetic tweezers are able to track movement, in contrast with established techniques at which the molecules need to be fixated. In magnetic tweezers, DNA is able to twist enthusiastically. When the molecule is dipped in liquid, proteins are able to fulfil the same role as in the plasma within the wall of a living cell.


During the research on the HU-protein, Van Noort has been working in the research group Molecular Biophysics at the TU in Delft. He recently changed over to Leiden and formed his own research group.

(Source: NRC, 25-04-2004)

Plasterk: The decay of European Science?

In the “David de Wied-lezing 2004” Ronald Plasterk wonders if European science will be ruined in the near future.


Ronald Plasterk is Professor of Developmental Genetics at the University of Utrecht and director of the Hubrecht Laboratory. Plasterk identifies that the important scientific successes are booked in America and England, while the European continent stays behind more often. Examples enough, also in developmental biology, Plasterk’s specialism. He thinks that it is not so much a matter of money, however more of outdated structures within universities, insufficient opportunities for young talent and minimal mobility of scientists.


The way in which Europe stimulates science, offers little hope for the future according to Plasterk. In his speech he describes the picture of Europe as the new Atlantis.


The foundation “David de Wied-lezing”, established by the Utrecht University and CenE Bankiers NV, organizes a lecture by a prominent scientist every year.

(Source: Utrechts Nieuwsblad, 28-04-2004)

Genomics and society

Genomics and society is a very important subject. In time, the applications of genomics will become a part of our daily lives.


Society has been an integral element of NGI’s strategy right from the start, according to Peter Folstar – director of the NGI. This has lead to an all round approach to the interaction between genomics and society. The Centres of Excellence have incorporated research and communication activities on the societal side of their research into their work programmes.


The research programme The Social Component of Genomics Research has resulted in a broad range of research projects. Various questions are addressed from a philosophical, ethical, legal and/or psychological standpoint to generate a firm academic basis.


Finally, the Centre for Society and Genomics is off the ground, with researchers from various backgrounds and an innovative research programme. This centre will play an important role on both national and international level.

(Source:, 04-2004)

Proposals boost project funding

Following the first call for proposals under the Sixth Framework Programme’s ‘Life Sciences, Genomics and Biotechnology for Health’ thematic priority (25 March 2003), 32 projects were selected in the field of fundamental genomics.


These projects build upon the excellence of the strong fundamental genomics community which already exists in Europe in both public and private sectors. The high quality of proposals submitted led the European Commission to increase the budget available for fundamental genomics from €134 million to €166 million. Of this, 80% will fund the so-called ‘new instruments’ in FP6 – Integrated Projects (IP) and Networks of Excellence (NoE) – which aim to structure and give critical mass to research across the EU.


The 32 projects were selected from 116 proposals after a rigorous evaluation procedure involving experts from academia, public and private research organisations and industry. Five key areas in fundamental genomics are covered by the selection:


Gene expression and proteomics

Structural genomics

Comparative genomics and population genetics


Multidisciplinary functional genomics approaches to basic biological processes



(Source: EU Genomic News, 01-04-2004)

Permanent school of bioinformatics

BioSapiens is an EC sponsored collaboration of 26 prominent European Bioinformatics groups. This consortium aims, in a FP6 sponsored collaboration, at improving sequence annotation technology and facilities.


BioSapiens organizes a `permanent school of bioinformatics`. I.e., each six months there will be a high quality bioinformatics course open to European bioscientists. The courses are highly sponsored by BioSapiens. The permanent school will organize courses and not conference/workshop-style events. The main aim is teaching students to do things themselves, which means many hands-on practical sessions.


The first course takes place in two weeks in Verona. The second course will be held in January 2005 at the CMBI in Nijmegen, one of the official partners in the BioSapiens consortium.

(Source: BioASP)

QIAGEN launches human siRNA library sets

QIAGEN announced that it has launched a series of off-the-shelf human library siRNA sets. All siRNA designs were accomplished using the HiPerformance siRNA design algorithm that QIAGEN licensed from Novartis Pharma AG.


Along with the introduction of these library siRNA sets, QIAGEN also announced the launch of Custom siRNA sets where researchers provide their targeted genes of interest and QIAGEN provide siRNA design using the same Novartis algorithm.


RNAi is a powerful discovery tool of biomedical research using siRNA segments to turn off or silence a specific gene to study gene expression patterns as well as the impact of specific expression profiles directly on a cell or an entire organism.


QIAGEN N.V. is a provider of innovative enabling technologies and products for the separation, purification and handling of nucleic acids. The company has developed and marketed a broad range of proprietary products for academic and industrial markets, including life science research, genomics, gene-based drug discovery, nucleic acid-based molecular diagnostics, genetic vaccination, and gene therapy markets.

(Source: PR Newswire, 03-05-2004)

Matching of research subsidies


The current financing system of scientific research leads to exploitation of the system of universities and research institutions. The obligation for universities to undertake matching of research subsidies, causes this.This is the conclusion of the report ‘The price of success. Matching research subsidies in knowledge institutions’ from the Advisory Council for Science and Technology Policy (AWT).


Universities have to put their administrative systems in order, as there is no insight in the real costs of research. According to Joop Sistermans, chairman of the AWT, they should break through the culture in which it is obvious not to pay the integral costs. “Research groups have to match more and more money and are collapsing by their own success”, says Sistermans. In the last few years, the share in the second and third flow of funds within the total of research financing has increased significantly. This has lead to the sharpening of matching from the first flow of funds.


The AWT advises the Ministry of Education, Culture and Science (OCW) to settle agreements with all financiers of research on when matching is allowable. Besides that, the AWT advises the universities to manage better. There have to be distinct criteria for matching. At last, better administrative systems are needed to gain more insight in the actual costs of research.


OCW has asked the Netherlands’ Bureau for Economic Policy Analysis to examine the number based foundation of the AWT-advice. This unusual step indicates that the Ministry has doubts about the research.


According to Joke van den Bandt, secretary technology policy at VNO-NCW (Confederation of Netherlands Industry and Employers), matching is not the problem, but a lack of a distinct strategy of the universities. “Universities should not want to do research that will not contribute to their strategy, unless they are able to gain profit on behalf of other projects.”


NWO (Netherlands Organisation for Scientific Research) concludes from the advice that her policy can be continued. AWT mentions the open programs of the NWO as an example of the exception to the rule that external financiers have to pay for the integral costs. The NWO-programs are focused on strengthening the quality of research.


The VSNU (Association of Universities in the Netherlands) has welcomed the advice as a support in the debate on matching. Universities have to pass changes in Dutch and European subsidy programs as there is no money to match the granted subsidy. The organisation insists on a quick solution.

(Source: Onderzoek Nederland/AWT, 22-04-2004)

Work programme `Life Sciences, genomics and biotechnology for health`

On 30 April 2004 the Programme Commitee members approved the work programme for the priority `Life Sciences, genomics and biotechnology for health`. The European Commission was afraid that the work programme would not gain enough votes with the ongoing discussion on embryo stem cells.


With the programme approved, the European Commision is able to publish the third call without any delay in June. The budget for this call will be 540 million euro. The expected closing date is halfway November.


From the first calls comes true that the objective of the European Commission to grant 15% of the budget to the SMEs in the priority `Life Sciences, genomics and biotechnology for health` will not be obtained. The European Commission will consult the Commitee members  and Expert Groups about this and take measures to still obtain this objective.

(Source: EG Liaison, 05-2004)

Research institutes Wageningen focus on the international market

The research institutes of Wageningen UR will focus their life sciences research more on the international market. The plan, Focus 2006, has been approved by the supervisory board.


Knowledge that will not lead to added value on the market, will be finished in favour of new research. Besides that, cost control will be sharpened. Four hundred tasks will expire.


The speed of the orientation of the research institutes is a consequence of the slumping national market. Companies delay their investments and the government puts less research out to tender.


The plan is not applicable to the research of Wageningen University.
(Source: Onderzoek Nederland, 07-05-2004 )


BioASP news

Genome Quest, release 1.2

From April 27th a new version of Gene-its, Genome Quest 1.2, has been put online. With this new version, Gene-It made again a step forward to greater stability of Genome Quest. Running sequence comparisons has been made more stable. In this version a user guide has been included, which users can consult to find more about the application features. The filtering of results and sequences has been improved, which enables users to filter on date and numbers, or to select a with list of keywords or sequence IDs. Also, users can update their personal information, like password and e-mail address.

BioASP has a flyer about the Genome Quest service available. Are you interested? Please do not hesitate to contact us at:


(Source: BioASP)

BioASP: Commandline service – from one of our users

The BioASP Roadshow visited Plant Research International recently. Among the services that were presented, was the possibility to obtain commandline access to the `teras` computer. Little did BioASP know what they let themselves in for!

CPU hungry as always and despite the fact that we have an (rather heavily used) in house linux cluster I decided to give it a go. In the course of my research on micro-RNA genes (small non-coding regulatory RNA elements digested from a hairpin) I ran several hundred of thousands RNA structure analyses (RNAfold) and, as a desert, a couple of thousand Interpro`s. Everything ran to my full satisfaction and was finished in a fraction of the time it would have taken in the old constellation. As usually  is the case in such circumstances: I came up with many more calculations which are still running (try `qstat`). Apparently the sysadmins have altered the queueing system somewhat, so that I cannot any  longer `hog` the system…


Remark BioASP: Do you want to become an (inter)active user from BioASP infrastructure and services? Please let us know and get your personal account ASAP!


(Source: BioASP)

Text mining tools for Micro Array analysis

Users Forum meeting, June 17th afternoon


What are the text mining principles, which tools have been developed by members from the BioASP community and what is the usability and applicability of these tools for micro array analysis?

These questions are topics for presentation, demonstation and discussion in the upcoming event organised by the BioASP Users Forum. Please set the date of this event (June 17th, afternoon) in your agenda or register for participation right away by sending an e-mail to: The programme of this event will be published online shortly.

(Source: BioASP)

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