FEBS- Sysbio Course Office: Anneke (J.G.) Koster
Amsterdam
Systems Biology Institute
Charlie
Parkerstraat 25
NL-1066 GV Amsterdam, EU
Phone: +31-20-6143163
FAX: +31-20-6143163
e‑mail: hweste@bio.vu.nl
wweb: http://www.febssysbio.net
At the Venue in Gosau: Anneke (J.G.) Koster
Sport
und Erlebnis Hotel**** Gosau
A-4824
Gosau am Dachstein 713, Austria
Phone: +43-6136-8811-390
Mobile: +43 676 572 4348
FAX: +43-6136-8811-352
e‑mail: hweste@bio.vu.nl
wwweb: http://www.febssysbio.net
FEBS-SysBio2005 Hotlines: +43
676 572 4348 and +43 676 572 4349
FEBS-SysBio2005 received generous financial
support from
FEBS [The
Federation of the European Biochemical Societies]
BMBF [German Bundesministerium für Bildung und Forschung]
NWO-ALW [Netherlands Organization for Scientific Research, NL]
DKFZ [Deutsche Krebsforschungszentrum]
AstraZeneca
NovoNordisk
Teranode
BioCentrum Amsterdam
EMBL [European Molecular Biology Laboratories]
ESF [European Science Foundation] 
BioSim NoE-EU
The Systems Biology Institute
DSM 
EUSYSBIO-EU
FEBS Journal 
Purac
Amsterdam Systems Biology Institute
EML (European Media Laboratory)
GENome Research in AUstria
Merck A.G.
Unilever
Table of Contents
Organizers. 1
Teacher-Members of the Scientific Advisory Board. 2
Technical Support & Registration &
Course Office. 2
FEBS-SysBio2005
received generous financial support from.. 3
Additional donations and contributions came from.. 4
Willkommen
in Gosau, Welkom in Gosau, Welcome to Gosau! 6
Scientific Program - its principles. 9
Symposia. 9
Morning: Plenary Lectures - Discussion of the
Issues. 9
Break for Lunch, Physical Activities, Tea. 9
Black-Board Teaching. 9
Workshop (W) & Short Talks (S) 10
Late Afternoon Discussion. 10
Poster Presentations, Poster Committees,
Analyses, Discussions. 10
Power Poster Presentations (PoPs) 10
Participant Task List: Contribution of each
Participant and its Timing. 11
Course Book - its Principles. 15
Abstracts. 15
Course (Abstract) Book - Paper 15
Course Book - Electronic. 15
Systems Biology Young Investigator Awards. 15
Web Site. 16
Technical Local Information. 16
Connections You and the World. 16
Departure. 16
FEBS Evaluation Form.. 16
FEBS-SysBio2005
Course Office. 16
Help. 17
Message Board. 17
Meals, Beverages & Lunch Packages. 17
Payments. 17
Presentations. 17
Skiing and Outdoor Leasure. 18
Social Program.. 18
Sport & Erlebnis Hotel Facilities. 19
Scientific Program.. 21
Speaker abstracts. 35
Abstracts of Posters & Power Posters. 105
Principles. 106
Tools and Methods. 124
Unicellular Organisms. 142
Multicellular/mammalian. 159
Address list 177
Author and Subject Index. 186
In this snowy environment, we warmly welcome you to
the first European Advanced Course on Systems Biology. Around the turn of the previous century,
Biology was revolutionized: the
sequence of complete genomes became available.
Almost immediately many high-throughput, genome-wide analyses sprung up, which will soon enable us
also to measure the expression levels of all genes at most levels of the
cellular hierarchy. Perhaps never
before, there has been such a sense of urgency. Never before did we seem to be so close to knowing how Life
functions in terms of the properties of its molecules. Never before could we begin to think of the
rational engineering of drugs targeting pathophysiology rather than individual
molecules. Yet, when confronted with
massive data sets about the molecules of living cells, one tends to get
confused rather than illuminated; the function of living cells cannot easily be
read from what happens to the molecules.
Much of functioning depends on many molecules simultaneously, which
engage in complex interactions.
In parallel,
biochemistry and biophysics focused more and more on the experimental
assessment of molecular interactions.
Together with mathematical biochemistry, these disciplines generated new
paradigms for understanding how functional properties arise in interactions. These paradigms remained limited however,
because not all components of the cellular systems were considered in the
analyses, and because most components could not be accessed experimentally.
In 2005 much
excitement lies in the synergy of the two above developments: functional genomics gleans from biochemistry,
biophysics and mathematical biology how new function arises in nonlinear
interactions, whereas the latter three may engage in functional genomics in
order to measure all components that are important for the living cell. In fact all these paradigms are now merging
into what one might call Integrative Systems Biology. Integrative Systems Biology is here defined as the science
investigating how much of the functioning of living organisms comes about in
the nonlinear interactions of all their molecules.
From this
definition, from the large size of even the smallest genomes, and from the
multitude and diversity of nonlinear interactions in Biology, it is readily
understood that the challenge that Integrative Systems Biology poses is
enormous. This young Science will
require so much expertise in both experimental molecular biology and
mathematics, in a highly interactive mode, that the way of doing Biology is
being revolutionized. As Physics was in
the 1950s, Biology is now becoming Big Science, i.e. Systems Biology. A
new generation of scientists is needed.
These scientists should be at ease with both experimental molecular
biology and complex mathematics, and with almost anything that is in
between. They should also be able to
interact strongly and productively with each other, in large teams. This Course is meant to catalyze the
formation of this new generation of scientists, from very young Ph D students,
but also from established researchers.
In this way the course should contribute to the development of science,
also for the sake of humanity.
The need for
training in Systems Biology was well recognized by our main sponsor, i.e.
the Federation of European Biochemical Societies (FEBS). We
appreciate the strong support through the FEBS Advanced Course Committee, in
particular its previous chairman Karel
Wirtz.
The need for
training is also recognized by the national European organizations that fund
modern biological and medical research.
Indeed, the German Ministry for Education and Research (BMBF) and the Dutch Organization for Scientific Research,
in particular its section on Earth and Life Sciences (NWO-ALW), have generously supported the course largely
through student registration waivers.
The European
Science Foundation (ESF), which aims to make the activities of the National
European Science Funding Organizations synergize, has likewise given strong
support. The ESF engages in a Forward
Look study on Systems Biology, which will prepare its final report during the
two days following this course, also in Gosau.
The 6th
Framework Program of the European Union has funded a similar reconnaissance
study on Systems Biology, through a Specific Support Action EUSYSBIO. EUSysBio also supports this course, as it will help define the
Systems Biology field. A network of
Excellence recently funded by the EU and partly directed at Systems Biology, i.e. BioSim coordinated by
Erik Mosekhilde, has immediately
assimilated this Course into its program of furthering excellent Systems
Biology in Europe.
The number of new
drugs that reach the market, and the number that thereafter survive, is
diminishing. The cost of developing the
drugs is becoming astronomical, largely because it is too difficult to choose
between the large numbers of promising drug leads at an
early stage. The ones that are plagued
by side effects and will not interact optimally with their target in the
context of the living organism, are identified so late in the process that they
absorb most of the budget. The critical
issues here are again Systems Biology issues, and modern pharmaceutical
companies are engaging strongly in this new field. Two of these, i.e., AstraZeneca and NovoNordisk, enthusiastically support this meeting, both in terms
of its lectures and AstraZeneca also
in terms of the USB-sticks provided to all participants. Of course, various Software companies engage
strongly in Systems Biology, not the least in interaction with these companies
and the top Systems Biology Centers (see below). Of these, Teranode co-supports
the USB sticks and their formatting.
It is unbelievable
how ill-defined some of the food is that we enjoy on a daily basis. Both in terms of food safety, and in terms
of improvements in their contribution to health, food production methodology is
a field that may also be revolved by Systems Biology developments. After all, the production of food by living
organisms and its use by human beings, abounds of interacting molecules in the
context of living cells. DSM and Purac are supporting
this Course.
The European
Journal of Biochemistry (EJB) has been a pillar under Biochemistry in more than
one way. First, it has always published
scientific articles of high quality and significance. Second, it has always earned much of the money that is used to
subsidize FEBS courses. At present, the journal is even more
relevant to the emerging field of Systems Biology: (i) it is one of the earliest journals that highlighted the
topic, such as through the direct link to the siliconcell model-base (www.siliconcell.net ), and (ii) it has just undergone a facelift,
becoming the FEBS Journal and orienting itself more towards quantitative cell
biology and systems biology. To
celebrate this, the journal offers us drinks at the Welcome Mixer.
Europe already has
a number of Centers for Systems Biology.
Of these, the BioCentrum
Amsterdam, the Deutsche
Krebsforschungszentrum, the European
Molecular Biology Laboratory, and the European Media Laboratory, support
this course financially. We expect that
many Systems Biologist of the future will have been nurtured at these
institutions. Likewise Japan has very
important institutes, one of which has been world-leading for systems biology,
including activities in California. We
are pleased that The Systems Biology Institute is generously
sponsoring this course.
Of course, the home institutions of the organizers have contributed
rather importantly to the organization, i.e.
the BioCentrum Amsterdam, the DKFZ and the
Max F. Perutz Laboratories of the Vienna Biocenter. We also thank the Institute of Molecular Pathology (IMP)
and the Vienna Veterinary University
for providing poster walls,
and the Institute for Molecular Cell
Biology, Amsterdam for lending some of the additional equipment. Likewise the Teachers of the course (i.e.
the Lecturers and the members of the
Scientific Advisory Board: Drs.
Aebershold, Alberghina, Alon, Boone, Cascante, Doyle, Eichelbaum, Goldbeter, Goryanin, Heinrich, Hohmann, Kell, Kholodenko, Kitano, Klingmüller, Klipp, Kummer, LeNovere, Noble, Reuss, Sauer, Schuster, Snoep, Stelling, Tomita, Van
Driel, Wanner, and Wodak) have spent quite some time in order to
optimize their teaching at this course; their institutes have thereby also
contributed.
A course is a
matter of human beings, much more than of institutions. This course is possible thanks to the
enthusiasm of the many people involved in the actual organization. Jacky
L. Snoep has
provided us with much of the artwork for the abstract book. We thank Maria Bausback for secretarial assistance during the course, Walter
Glaser for helping with the
adaptation of the web page, and Hannes Davidek of helping with graphic design.
Of course the local organizing committee is quite important: we thank Karen van Eunen, Frank
Bruggeman, Richard
Notebaart, and all others for their contribution to the
dynamics of the course. The director
and staff of the Sport und Erlebnis
Hotel Gosau are thanked for the professional way they arrange for
infrastructure and food. And we thank Emilia, for her patience.
But of course, we should not forget the all-but-silent majority, i.e. the participants and their
supporters (institutions and mentors), who contributed much effort and
inspiration. Reading the abstracts we
found that a great many innovative ideas were going to be contributed by the
participants in spe. This course was the first of its kind in
Systems Biology. Because of the novelty
of the field we had applied to FEBS for a course
of 120 students. When the number of
registrants exceeded 200, we were pleased because it demonstrated great
interest and enthusiasm, but saddened because we had to deny many high quality
applicants participation. Because
quality and potential of most abstracts was high, we also had to select on the
basis of more technical parameters, e.g.
we limited the number of students coming from any same institution. We hope that the students we could not admit
will come to a next course. Likewise,
we have to admit that although our speakers/teachers are excellent Systems
Biologists, we have not been able to attract all excellent Systems Biologist to
the course: we had too few speaker slots.
What is next? An exciting course here in Gosau with lots
of excellent teaching. The teaching
program is special in that it hosts a number of unconventional teaching
elements. The latter include the systematic
discussion of each poster contribution
by a number of senior scientists, black-board teaching, power-poster presentations, discussion sessions formulating
key questions and subsequent sessions trying to address them. Equally importantly, new and more
established Systems Biologists from various science directions will meet and
discuss science intensively. We expect
that Gosau will be the cradle of a network of excellent Systems Biologists who
will know to find each other in the future for advice and collaboration. Thus, the interdisciplinary activities that
are so important for Systems Biology, take off and make excellent new
Science.
The organizers,
and
her troika (i.e.., Roland Eils , Karl
Kuchler , and Hans
V. Westerhoff)
The course has been
organized in terms of 4 Symposia,
dedicated to areas within Systems Biology, i.e.
Principles, Tools and Methodology, Unicellular
Organisms and (Cells from) Multicellular
Organisms. Each symposium has its dedicated day. On that day the symposium is kicked off with
a number of plenary lectures in the morning.
Discussions, Workshop talks by invited Principal Investigators, Short
talks by invited poster presenters, and a Discussion
follow. The posters and power posters corresponding to the
symposium are have been grouped together, and will be presented in sequel on
the three poster evenings (Sunday, Monday and Wednesday).
Tuesday morning has two
extra lectures for symposium T and three extra for symposium
U, before the cultural break.
Each symposium is kicked off with four plenary
lectures in the morning. The lecturer
presents an oral presentation for 35 minutes, with a subsequent 10 minutes
discussion period. This oral
presentation should spend 5 minutes to introduce the field/topic, 15 minutes to
teach a few important principles relevant to that topics, and then 15 minutes
to report on recent work in which the principles are used in generating some
excellent Systems Biology. It is
important to realize that it is better to teach little well, than all not at
all!
This is followed by a
discussion session in which the most cogent Systems Biology questions related
to the symposium topic are formulated.
Lunch will be in the hotel
restaurant. Course teachers are requested
not to seat together. They should rather sit at their own table
and be joined by students. Similarly,
students are kindly requested not to
sit together with other students from their own institute, but with Teachers,
or with students and principal investigators of other institutes.
After lunch there is a break
for physical activities, such as ski-ing, rock climbing, chess, or hang gliding. Be back for tea (coffee if you wish) at 16h00 to engage in the
afternoon session that begins at 16h30.
On Sunday and on Monday,
Blackboard teaching sessions will be held after the physical activity break and
tea. These are optimized for
interactive teaching. Key concepts for
Systems Biology will be explained, in interactive mode, using blackboard and chalk, or equivalent. 4 Blackboard presentations will be held in
parallel, such that each should be expected to host some 30 students. As a
rule, each Blackboard teacher (-couple) presents his Blackboard presentation
twice, i.e. on Sunday and then again
on Monday. Each student is expected to
be present at 2 out of 4 Black-board talks.
The following topics have
been agreed to:
ˇ
Motifs
and networks (Alon)
ˇ
Stability
and flux mode analysis (Heinrich, & Schuster)
ˇ
Control
analysis and silicon cells (Snoep & Westerhoff)
ˇ
Robustness
(Stelling & Bruggeman)
The topics of workshop
presentations and short talks during the afternoon sessions, fall within the
area of the main symposium of that particular day (or, in
the case of M, of the day thereafter). These talks are usually delivered by
principal investigators (W) and students (S), respectively. These speakers have
been invited on the basis of their poster abstracts.
During the late-afternoon
discussion, the questions raised during the morning discussion session will be
addressed by the Lecturers and other Teachers of that symposium. This will be followed by a
general discussion. The results of the
discussion will be noted down and reported to FEBS, ESF and EUSYSBIO.
The posters are up
throughout the meeting; they should be mounted Sunday evening and removed
Thursday evening.
Each poster will be presented for at least
an hour by its prime author. Poster
numbers n-2 will be
presented/analyzed/discussed Sunday evening from 21h00 for at least an
hour. Numbers 3n-1 will be presented/analyzed/discussed Monday evening. Numbers 3n-3
will be presented/analyzed/discussed Wednesday evening. Also the presenters of short talks are
requested to present their poster, on the day of their short talk.
Authors presenting posters
are asked to indicate on their poster additional times when they will
be available at their poster for discussion.
Every student will get to
speak the teachers in her/his symposium: each symposium has a
corresponding Poster Committee, which consists of all lecturers at that
symposium plus:
Symposium Principles: Alberghina (chair), Westerhoff plus P lecturers
Symposium Tools: Cascante (chair), Goryanin plus T lecturers
Symposium Unicellular organisms: Hohmann (chair), Kuchler plus U lecturers
Symposium Mammalian systems: Van Driel (chair), Kitano plus M lecturers.
During the first 45 minutes
of each of the three poster sessions, this committee will
inspect the one third of the posters belonging to their symposium that is being presented by
their author that evening (i.e. up to
ten posters). At the end of the poster
session, i.e. from 22h30 23h00), i.e. in the poster round table
discussion, the poster committee will discuss in a session with all poster
presenters of their symposium all the posters they have seen that evening (i.e. this will be a non-plenary session
with approximately 6 committee members and 10 poster presenters).
Principal investigators who
have not been asked to give an oral presentation as Lecture or Workshop Talk,
are requested to give a so-called PowerPoster Presentation (PoP). This is a 5 minutes
powerpoint presentation on one of five computers available in the poster halls. They will be asked to run this presentation
repeatedly for any PoP viewer interested during the time slot allotted to the
PoP presenter. PoPs occur in parallel
to the poster presentation by students.
(westerhoffgosau3corr998.doc)
