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The for Report 07-08 THE CENTER FOR INTEGRATIVE GENOMICS REPORT 07-08 www.unil.ch/cig Table of Contents INTRODUCTION 2 The CIG at a glance 2 The CIG Scientific Advisory Committee 3 Message from the Director 4 RESEARCH 6 Richard Benton Chemosensory perception in Drosophila: from genes to behaviour 8 Béatrice Desvergne Networking activity of PPARs during development and in adult metabolic homeostasis 10 Christian Fankhauser The effects of light on plant growth and development 12 Paul Franken Genetics and energetics of sleep homeostasis and circadian rhythms 14 Nouria Hernandez Mechanisms of basal and regulated RNA polymerase II and III transcription of ncRNA in mammalian cells 16 Winship Herr Regulation of cell proliferation 18 Henrik Kaessmann Mammalian evolutionary genomics 20 Sophie Martin Molecular mechanisms of cell polarization 22 Liliane Michalik Transcriptional control of tissue repair and angiogenesis 24 Alexandre Reymond Genome structure and expression 26 Andrzej Stasiak Functional transitions of DNA structure 28 Mehdi Tafti Genetics of sleep and the sleep EEG 30 Bernard Thorens Molecular and physiological analysis of energy homeostasis in health and disease 32 Walter Wahli The multifaceted roles of PPARs 34 Other groups at the Génopode 37 CORE FACILITIES 40 Lausanne DNA Array Facility (DAFL) 42 Protein Analysis Facility (PAF) 44 Core facilities associated with the CIG 46 EDUCATION 48 Courses and lectures given by CIG members 50 Doing a PhD at the CIG 52 Seminars and symposia 54 The CIG annual retreat 62 The CIG and the public 63 Artist in residence at the CIG 63 PEOPLE 64 1 Introduction The Center for IntegratiVE Genomics (CIG) at A glance The Center for Integrative Genomics (CIG) is the newest depart- ment of the Faculty of Biology and Medicine of the University of Lausanne (UNIL). Its establishment was made possible as a result of the program “Sciences, Vie, Société”, a tri-institutional program linking the Universities of Geneva and Lausanne and the Federal Institute of Technology in Lausanne (Ecole polytechnique fédérale de Lausanne – EPFL), which aimed to develop the life sciences as well as the humanities and social sciences in the Lémanic region. The CIG has three main missions: • The pursuit of a first rate research program in the biological sciences • The development of an outstanding teaching program • The development and support of core facilities offering cutting-edge technologies to the Lémanic research com- munity and beyond The research at the CIG centers on genome structure and function in a number of different experimental systems and relies on a large number of different techniques. It is performed by an international community of scientists, yet the character of the CIG is one of an integrated research center, where interactions among groups are numerous both in formal and informal settings. 2 CIG 2007/2008 Scientific Advisory Committee members The Scientific ADVisorY Prof. Robert EISENMAN Prof. Jacques SAMARUT* Committee (SAC) (President of the SAC) Director of the The CIG Scientific Advisory Committee (SAC) is a consultative com- Fred Hutchinson Cancer Ecole Normale Supérieure mission of external experts widely recognized for their contribution Research Center de Lyon, in the fields of activity of the CIG. Its principal responsibilities are : University of Washington Lyon, France School of Medicine, Seattle, USA • To advise on scientific objectives and priorities *until January 2009 • To evaluate the outcomes Prof. Steve BROWN* • To propose means of improving outcomes and visibility Director of the MRC Mammalian Prof. Ueli SCHIBLER • To propose the acquisition of new technologies or the Dpt of Molecular Biology and Genetics Unit Harwell development of new research and educational activities or NCCR Frontiers in Genetics Harwell, UK services University of Geneva *since January 2009 Geneva, Switzerland The members of the SAC visited the CIG in June 2007 and in June 2008. During these visits, they had discussions with the CIG Direc- tor, with each group leader, with the CIG students and postdoc- Dr Laurent DURET Prof. Ivan STAMENKOVIC toral fellows, and with members of the administrative and techni- Biometry and Evolutionary Director of the Dpt of cal staff. They also met with the Dean of the Faculty of Biology and Biology laboratory, CNRS Experimental Pathology Medicine. Université Claude Bernard Lyon I University of Lausanne (UNIL) Villeurbanne, France Lausanne, Switzerland Their conclusions and recommendations, which were each time summarized in a report, led to considerable improvements for the CIG in aspects as diverse as policies for promotion proposals or the Prof. Susan GASSER Prof. Markus STOFFEL establishment of a cozy “coffee corner” on the CIG main floor. Director of the Friedrich Miescher Institute of Molecular Their next visit is scheduled for 2010. Institute for Biomedical Research Systems Biology (FMI), Swiss Federal Institute of Basel, Switzerland Technology Zurich (ETHZ) Zurich, Switzerland Prof. Ueli GROSSNIKLAUS Institute of Plant Biology Prof. Gisou VAN DER GOOT University of Zurich Global Health Institute Zurich, Switzerland Ecole Polytechnique Fédérale de Lausanne (EPFL) Lausanne, Switzerland 3 Introduction Message from the Director The Center for Integrative Genomics was started in 2002 with the speed. We can determine which genes are active when, when and appointment of its founding Director, Walter Wahli. This was fol- where specific proteins are bound to the genome, how these pro- lowed by a period of faculty recruitment as well as, starting in the teins are modified, all of this on a genomic scale. Progress in the pro- Fall of 2004, the extensive remodeling of the building now known teomics field allows the analysis of large mixture of proteins, indeed as the Génopode. These efforts culminated with the inauguration of of the entire proteome of a cell under various circumstances. With the CIG in October 2005. Thus, the CIG will enter its fourth year as such developments we can test the generality of mechanisms stud- a fully functional department in its own quarters in the Fall of 2009. ied until now in only a few model systems. We can also use these In the last two years, it has grown from thirteen to sixteen faculty large-scale data as a discovery tool, for example to compare the members and is now at full steam! Together with this growth in genomic landscapes of cells in different states. These developments the number of faculty members, the CIG has seen a steep increase also mean that an increasing number of large datasets produced for in its research activities as measured, for example, by the amounts a specific published study are accessible to other researchers who of external funds that have been raised. We have gone from about can then use the same data to answer another question. This activ- 35% of our UNIL budget in 2006 to close to 60% of this budget in ity of data mining will become more and more important for the 2008, and this number is likely to increase further in the next few advancement of any research project as the number of searchable years. Thus, the CIG is doing very well indeed and is well on its way datasets increases. to fulfilling its promise as a flagship research department of the We are indeed fortunate enough The new biology, the “omics” biology has important implications University of Lausanne (UNIL). to be biologists in a time of for the teaching of biology, as it demands skills from researchers remarkable advances in our field, Why put so much emphasis on research in universities, whose main that were dispensable in the days of “good old” molecular biology. function is, after all, the education of students? In fact, at the uni- Indeed, whereas the human brain can easily deal with a few data the time of “omics”. versity level, research is intimately linked to teaching and vice-versa. points, it is another story when an experiment produces from thou- On the one hand, the research carried out in our laboratories feeds sands to millions of data points. Thus, the composition of research Nouria Hernandez, CIG Director directly into our courses and allows us to teach at the cutting-edge groups involved in large scale experiments is, ideally, a mix of “wet of current knowledge. On the other hand, in an academic environ- lab” researchers, who deal with real molecules, cells, tissues, or organ- ment a large part of the research is conducted by people in training; isms, and the “dry lab” researchers, who deal with virtual molecules, master- and graduate students, postdoctoral fellows, and even tech- datafiles and databanks, scripts, and algorithms. In this ideal situation nician trainees! Without them, there would be little research indeed again, researchers are familiar with both the “wet” and “dry” aspects in universities! Teaching, and attracting the brightest students, is of the research and capable of carrying out both, even if each special- thus of paramount importance to maintain a high level of research, izes more in one aspect. The reality, however, is quite different. Most and vice-versa. The various CIG faculty members are now contrib- students studying molecular biology or biochemistry have little or no uting to teaching at the Bachelor, Master, and PhD levels, but our training in computational biology, even today. As a result, they lack next goal is the establishment of a flagship course or program that the proficiency to analyze their own large-scale experiments as well could be identified with the CIG. In thinking about such a program, as to take full advantage of published large datasets. In general, there it seems obvious that the role of the Center for Integrative Genomics is a lack of computational biologists in Switzerland, which will only should be to teach aspects of functional genomics, thus transmitting become more severe in the next few years. to the students the excitement of a biology revolution we are in the This is where I believe the CIG could make a unique contribution to midst of experiencing.
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