|FEI Company joins EU Interaction Proteome
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
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
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,
|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
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
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
|Plasterk: The decay of European
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
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
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,
|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.
|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
Gene expression and proteomics
Comparative genomics and population
Multidisciplinary functional genomics
approaches to basic biological processes
|(Source: EU Genomic News,
|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
|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.
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,
|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
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
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
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
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,
|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
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
and Expert Groups about this and take measures to
still obtain this objective.
|(Source: EG Liaison,
|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.
plan is not applicable to the research of Wageningen
|(Source: Onderzoek Nederland,
Quest, release 1.2|
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
has a flyer about the Genome Quest service available.
Are you interested? Please do not hesitate to contact us
Commandline service – from one of our
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!
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
Do you want to become an (inter)active user from BioASP
infrastructure and services? Please let us know and get
your personal account ASAP!
mining tools for Micro Array
Forum meeting, June 17th
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?
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: firstname.lastname@example.org. The
programme of this event will be published online