Sixth ANNUAL NIH GRADUATE STUDENT RESEARCH SYMPOSIUM the Faces of Tomorrow’S Science
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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). -
Curriculum Vitae
Kamhawi S., 1 CURRICULUM VITAE NAME: Shaden Kamhawi, Ph.D. h index 2014, 29 ADDRESS Vector Molecular Biology Section Laboratory of Malaria and Vector Research National Institute of Allergy and Infectious Diseases National Institutes of Health 12735 Twinbrook Parkway Room 2E-32D Rockville, MD, 20852 Phone: 301-594-5547 Fax: 301-594-5373 Email: [email protected] PROFESSIONAL EXPERIENCE 2014-Present, Associate Scientist, Core, Laboratory of Malaria and Vector Research (LMVR), NIAID, NIH 2006-2014, Staff Scientist, Core, Laboratory of Malaria and Vector Research (LMVR), NIAID, NIH 2001- 2006, Staff Scientist, Laboratory of Parasitic Diseases (LPD), NIAID, NIH. 1997- 2001, Visiting associate, LPD, NIAID, NIH. 1996- 2000, Associate professor, Department of Biological Sciences, Yarmouk University, Irbid, Jordan. 1990-1996, Assistant professor, Department of Biological Sciences, Yarmouk University, Irbid, Jordan. EDUCATION 1990, Ph.D. in Medical Entomology, Salford Univeristy, Salford, England. 1985, B.Sc. in Biological & Biochemical Sciences, Salford University, Salford, England. AREA OF EXPERTISE Vector Biology; Vector-Parasite-Host molecular interactions; Host immune response to transmission of Leishmania by sand fly bite; Development of vector-based vaccines; Field-oriented investigations of epidemiology of leishmaniases and transmission patterns. CURRENT DUTIES: Dr. Kamhawi plays an essential role in sand fly-related research at NIAID. She brings a unique set of skills including extensive field expertise in leishmaniasis epidemiology and Kamhawi S., 2 a proficiency in experimental techniques covering various fields including entomology, parasitology, immunology and molecular biology. Current duties of Dr. Kamhawi include: The sand fly Unit: Dr. Kamhawi is a world expert on phlebotomine sand flies, vectors of the neglected tropical disease leishmaniasis. -
The Next Generation of Biomedical and Behavioral Sciences Researchers: Breaking Through
THE NATIONAL ACADEMIES PRESS This PDF is available at http://nap.edu/25008 SHARE The Next Generation of Biomedical and Behavioral Sciences Researchers: Breaking Through DETAILS 162 pages | 6 x 9 | PAPERBACK ISBN 978-0-309-47137-4 | DOI 10.17226/25008 CONTRIBUTORS GET THIS BOOK Committee on the Next Generation Initiative; Board on Higher Education and Workforce; Policy and Global Affairs; National Academies of Sciences, Engineering, and Medicine FIND RELATED TITLES Visit the National Academies Press at NAP.edu and login or register to get: – Access to free PDF downloads of thousands of scientific reports – 10% off the price of print titles – Email or social media notifications of new titles related to your interests – Special offers and discounts Distribution, posting, or copying of this PDF is strictly prohibited without written permission of the National Academies Press. (Request Permission) Unless otherwise indicated, all materials in this PDF are copyrighted by the National Academy of Sciences. Copyright © National Academy of Sciences. All rights reserved. The Next Generation of Biomedical and Behavioral Sciences Researchers: Breaking Through THE NEXT GENERATION OF BIOMEDICAL AND BEHAVIORAL SCIENCES RESEARCHERS: BREAKING THROUGH Committee on the Next Generation Initiative Board on Higher Education and Workforce Policy and Global Affairs A Consensus Study Report of PREPUBLICATION COPY—UNEDITED PROOFS Copyright National Academy of Sciences. All rights reserved. The Next Generation of Biomedical and Behavioral Sciences Researchers: Breaking Through THE NATIONAL ACADEMIES PRESS 500 Fifth Street, NW Washington, DC 20001 This activity was supported by contracts between the National Academy of Sciences and The National Institutes of Health (#HHSN263201200074I, Order No. -
Deptbiochemistry00ruttrich.Pdf
'Berkeley University o'f California Regional Oral History Office UCSF Oral History Program The Bancroft Library Department of the History of Health Sciences University of California, Berkeley University of California, San Francisco The UCSF Oral History Program and The Program in the History of the Biological Sciences and Biotechnology William J. Rutter, Ph.D. THE DEPARTMENT OF BIOCHEMISTRY AND THE MOLECULAR APPROACH TO BIOMEDICINE AT THE UNIVERSITY OF CALIFORNIA, SAN FRANCISCO VOLUME I With an Introduction by Lloyd H. Smith, Jr., M.D. Interviews by Sally Smith Hughes, Ph.D. in 1992 Copyright O 1998 by the Regents of the University of California Since 1954 the Regional Oral History Office has been interviewing leading participants in or well-placed witnesses to major events in the development of Northern California, the West, and the Nation. Oral history is a method of collecting historical information through tape-recorded interviews between a narrator with firsthand knowledge of historically significant events and a well- informed interviewer, with the goal of preserving substantive additions to the historical record. The tape recording is transcribed, lightly edited for continuity and clarity, and reviewed by the interviewee. The corrected manuscript is indexed, bound with photographs and illustrative materials, and placed in The Bancroft Library at the University of California, Berkeley, and in other research collections for scholarly use. Because it is primary material, oral history is not intended to present the final, verified, or complete narrative of events. It is a spoken account, offered by the interviewee in response to questioning, and as such it is reflective, partisan, deeply involved, and irreplaceable. -
Regional Oral History Office University of California the Bancroft Library Berkeley, California
Regional Oral History Office University of California The Bancroft Library Berkeley, California Daniel Koshland, Jr. Retrospective Oral History Project: Bruce Alberts Interviews conducted by Sally Smith Hughes in 2012 Copyright © 2014 by The Regents of the University of California ii Since 1954 the Regional Oral History Office has been interviewing leading participants in or well-placed witnesses to major events in the development of Northern California, the West, and the nation. Oral History is a method of collecting historical information through tape-recorded interviews between a narrator with firsthand knowledge of historically significant events and a well-informed interviewer, with the goal of preserving substantive additions to the historical record. The tape recording is transcribed, lightly edited for continuity and clarity, and reviewed by the interviewee. The corrected manuscript is bound with photographs and illustrative materials and placed in The Bancroft Library at the University of California, Berkeley, and in other research collections for scholarly use. Because it is primary material, oral history is not intended to present the final, verified, or complete narrative of events. It is a spoken account, offered by the interviewee in response to questioning, and as such it is reflective, partisan, deeply involved, and irreplaceable. ********************************* All uses of this manuscript are covered by a legal agreement between The Regents of the University of California and Bruce Alberts on March 21, 2014. The manuscript is thereby made available for research purposes. All literary rights in the manuscript, including the right to publish, are reserved to The Bancroft Library of the University of California, Berkeley. Excerpts up to 1000 words from this interview may be quoted for publication without seeking permission as long as the use is non-commercial and properly cited. -
Massive Turnover of Functional Sequence in Human and Other Mammalian Genomes
Downloaded from genome.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Research Massive turnover of functional sequence in human and other mammalian genomes Stephen Meader,1 Chris P. Ponting,1,3 and Gerton Lunter1,2,3 1MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, United Kingdom; 2The Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, United Kingdom Despite the availability of dozens of animal genome sequences, two key questions remain unanswered: First, what fraction of any species’ genome confers biological function, and second, are apparent differences in organismal complexity reflected in an objective measure of genomic complexity? Here, we address both questions by applying, across the mammalian phylogeny, an evolutionary model that estimates the amount of functional DNA that is shared between two species’ genomes. Our main findings are, first, that as the divergence between mammalian species increases, the predicted amount of pairwise shared functional sequence drops off dramatically. We show by simulations that this is not an artifact of the method, but rather indicates that functional (and mostly noncoding) sequence is turning over at a very high rate. We estimate that between 200 and 300 Mb (;6.5%–10%) of the human genome is under functional constraint, which includes five to eight times as many constrained noncoding bases than bases that code for protein. In contrast, in D. melanogaster we estimate only 56–66 Mb to be constrained, implying a ratio of noncoding to coding constrained bases of about 2. This suggests that, rather than genome size or protein-coding gene complement, it is the number of functional bases that might best mirror our naı¨ve preconceptions of organismal complexity. -
X CRG Annual Symposium
X CRG SYMPOSIUM 10-11 November 2011 COMPUTATIONAL BIOLOGY OF MOLECULAR SEQUENCES Organizers: R.Guigó, C.Notredame, T.Gabaldón, F.Kondrashov, G.G.Tartaglia Thursday 10 November 08:00 – 09:00 Registration 09:00 – 09:05 Welcome by Luis Serrano 09:05 – 09:15 Introduction by Roderic Guigó Session 1: Protein Analysis Chair: Gian Gaetano Tartaglia 09:15 – 10:00 Temple F. SMITH Department of Biomedical Engineering, Boston University, Boston US “A Unique Mammalian Apoptosis Regulatory Gene, Lfg5, and a Homo sapiens Neanderthal Mystery” 10:00 – 10:45 Michele VENDRUSCOLO Department of Chemistry, University of Cambridge, Cambridge UK “Life on the edge: Proteins are close to their solubility limits” 10:45 – 11:30 Amos BAIROCH Swiss Institute of Bioinformatics, and Department of Structural Biology and Bioinformatics, Faculty of Medicine, University of Geneva, Geneva CH “Organising human protein-centric knowledge: the challenge of neXtProt” 11:30 – 12:00 Coffee break Session 2: Genome Evolution Chair: Fyodor Kondrashov 12:00 – 12:45 Eugene V. KOONIN National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda (MD) USA “Are there laws in evolutionary genomics?” 12:45 – 13:30 Nick GOLDMAN EMBL - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton UK “Adventures in Evolutionary Alignment” 13:30 – 15:00 Lunch 15:00 – 15:45 Mathieu BLANCHETTE School of Computer Science, McGill University, Montreal CA “Ancestral Mammalian Genome Reconstruction and its Uses toward Annotating the Human -
Novel Protein Domains and Repeats in Drosophila Melanogaster: Insights Into Structure, Function, and Evolution
Downloaded from genome.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press Article Novel Protein Domains and Repeats in Drosophila melanogaster: Insights into Structure, Function, and Evolution Chris P. Ponting,1,4 Richard Mott,2 Peer Bork,3 and Richard R. Copley3 1MRC Functional Genetics Unit, Department of Human Anatomy and Genetics, University of Oxford, Oxford OX1 3QX, UK; 2Wellcome Trust Centre for Human Genetics, Oxford OX37BN, UK; 3European Molecular Biology Laboratory, 69012 Heidelberg, Germany Sequence database searching methods such as BLAST, are invaluable for predicting molecular function on the basis of sequence similarities among single regions of proteins. Searches of whole databases however, are not optimized to detect multiple homologous regions within a single polypeptide. Here we have used the prospero algorithm to perform self-comparisons of all predicted Drosophila melanogaster gene products. Predicted repeats, and their homologs from all species, were analyzed further to detect hitherto unappreciated evolutionary relationships. Results included the identification of novel tandem repeats in the human X-linked retinitis pigmentosa type-2 gene product, repeated segments in cystinosin, associated with a defect in cystine transport, and ‘nested’ homologous domains in dysferlin, whose gene is mutated in limb girdle muscular dystrophy. Novel signaling domain families were found that may regulate the microtubule-based cytoskeleton and ubiquitin-mediated proteolysis, respectively. Two families of glycosyl hydrolases were shown to contain internal repetitions that hint at their evolution via a piecemeal, modular approach. In addition, three examples of fruit fly genes were detected with tandem exons that appear to have arisen via internal duplication. -
Mechanisms to the Human in Life Body
FROM DEFENSE BACTERIA MECHANISMS TO THE HUMAN IN LIFE BODY FOURTEENTH ANNUAL LSI SYMPOSIUM MAY 21, 2015 Images courtesy of Katherine D. Walton, research investigator, and Deborah Gumucio, professor, Department of Cell and Developmental Biology, U-M Medical School SCHEDULE FORUM HALL, PALMER COMMONS (OVERFLOW SEATING AVAILABLE IN GREAT LAKES NORTH) 8:30 A.M. 1:15 P.M. WELCOME | Alan Saltiel, Ph.D. ROLE OF THE MICROBIOTA IN INFECTION CONTROL Mary Sue Coleman Director of the Life Sciences Institute AND SEQUELAE | Yasmine Belkaid, Ph.D. Chief of Mucosal Immunology Section, Laboratory of 8:35 A.M. Parasitic Diseases, National Institutes of Health, National INTRODUCTION OF THE MARY SUE AND KENNETH Institute of Allergy and Infectious Diseases COLEMAN LIFE SCIENCES LECTURER | Mary Sue Coleman, Ph.D. 1:55 P.M. President Emerita IMMUNE REGULATION OF INTESTINAL HEALTH AND DISEASE | Gregory F. Sonnenberg, Ph.D. 8:50 A.M. Assistant Professor of Microbiology and Immunology in MARY SUE AND KENNETH COLEMAN LIFE SCIENCES Medicine, Weill Cornell Medical College LECTURE: HOMEOSTASIS, INFLAMMATION AND DISEASE | Ruslan Medzhitov, Ph.D. AFTERNOON BREAK David W. Wallace Professor of Immunobiology, Yale School of Medicine; Investigator, Howard Hughes 3:15 P.M. Medical Institute TISSUE CONTROL OF MACROPHAGE HOMEOSTASIS AND FUNCTION | Miriam Merad, M.D., Ph.D. MORNING BREAK Professor of Oncological Science and Medicine; Mount Sinai Chair in Cancer Immunology; Director of Human 10:30 A.M. Immune Monitoring Center, Tisch Cancer Institute, Icahn GENERATION OF A MEMORY OF INFECTION DURING School of Medicine at Mount Sinai CRISPR-CAS IMMUNITY | Luciano Marraffini, Ph.D. Assistant Professor, head of the Laboratory of 3:55 P.M. -
Big Knowledge from Big Data in Functional Genomics
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Edinburgh Research Explorer Edinburgh Research Explorer Big knowledge from big data in functional genomics Citation for published version: Ponting, C 2017, 'Big knowledge from big data in functional genomics' Emerging Topics in Life Sciences . DOI: 10.1042/ETLS20170129 Digital Object Identifier (DOI): 10.1042/ETLS20170129 Link: Link to publication record in Edinburgh Research Explorer Document Version: Publisher's PDF, also known as Version of record Published In: Emerging Topics in Life Sciences Publisher Rights Statement: This is an open access article published by Portland Press Limited on behalf of the Biochemical Society and the Royal Society of Biology and distributed under the Creative Commons Attribution License 4.0 (CC BY). General rights Copyright for the publications made accessible via the Edinburgh Research Explorer is retained by the author(s) and / or other copyright owners and it is a condition of accessing these publications that users recognise and abide by the legal requirements associated with these rights. Take down policy The University of Edinburgh has made every reasonable effort to ensure that Edinburgh Research Explorer content complies with UK legislation. If you believe that the public display of this file breaches copyright please contact [email protected] providing details, and we will remove access to the work immediately and investigate your claim. Download date: 05. Apr. 2019 Emerging Topics in Life Sciences (2017) 1 245–248 https://doi.org/10.1042/ETLS20170129 Commentary Big knowledge from big data in functional genomics Chris P. -
18Th Annual Upstate New York Immunology Conference
20152015 18th Annual Upstate New York Immunology Conference Major Corporate Sponsors: BD Biosciences BioLegend, Inc. Taconic Bioscience Keynote Speakers: Supported by Yasmine Belkaid, Ph.D. NIH/NIAID Kristin A. Hogquist, Ph.D. Grant Funding Workshop Presentation by: Yasmine Belkaid, Ph.D. Jacob Schumacher, AAI AAI Young Investigator Awards eBioscience/affymetrix Trainee Travel Awards Welcome to The Sagamore Resort and Conference Center Bolton Landing, NY October 25-28, 2015 2. UPSTATE NEW YORK IMM UNOLOGY CONFERENCE ( NYIC) We’ve come a long way from Garnet Hill! This meeting started in 1997 as a small retreat to facilitate interactions among young scientists, institutions, and renowned experts in the field of Immunology. In just a few short years, the number of attendees grew and a larger venue was needed to meet the future needs of the Conference. We are happy to announce the American Association of Immu- nologists (AAI) is once again providing 10 Young Investigator Awards. eBioscience is also proving 10 Trainee Travel Awards. All award winners will give Oral Poster Presentations. There will also be two Workshops. Keynote speakers are Dr. Yasmine Belkaid (NIH/NIAID) and Dr. Kristin A. Hogquist (University of Minnesota). As part of our leisure activities, there will be a cruise on Lake George, as well as a recreational night including miniature golf, Wii, X-box, whiffle ball, and movies! Mr. Brown’s Pub will be open Tuesday night for informal discussions. Trainees will also have an opportunity to win an iPad during one of two drawings. You must be present at the drawing to win! While all these elements lend to the atmosphere, one simple principle goal of this Conference re- mains. -
Pinpointing Pathogens Technologies to Track Infections from the Skies and on the Ground
JULY 2015 | WWW.THE-SCIENTIST.COM PINPOINTING PATHOGENS TECHNOLOGIES TO TRACK INFECTIONS FROM THE SKIES AND ON THE GROUND ERADICATING POLIO AND GUINEA WORM DISEASE THE CONSEQUENCES OF AN INCOMPLETE MICROBIOME MAKING CLINICAL STUDIES MORE DIVERSE PLUS STAYING ACTIVE AFTER RETIREMENT THE NO-WASH ELISA ALTERNATIVE THAT TRANSFORMS YOUR LAB is a registered trademark of PerkinElmer, Inc. All other trademarks are the property their respective owners. ® © 2015 PerkinElmer, Inc. 400334_02 All rights reserved. PerkinElmer Copyright The perfect combination of convenience and results. Drug development and disease prevention are a race against time – so researchers need the confidence in their biology to enable quick go-to-market decisions. AlphaLISA® technology delivers a fast, cost-effective, no-wash ELISA alternative that reduces user error, prevents washing away weak interactions, and makes walkaway, overnight immunoassays possible. All with wider dynamic range, better sensitivity – and more confidence in your findings, especially when used with the EnVision® multimode plate reader. AlphaLISA technology: The no-wash ELISA alternative that fits your research perfectly. Find out more at www.perkinelmer.com/alphalisa High Performance Solution for Your Clinical Research Reliability PRECISION IN YOUR CLINICAL RESEARCH ® VIP Series CytoGROW -86ºC Freezer Optimal Series - CO2 Incubator Rethink High Performance Look to Panasonic’s VIP® freezers for >99% reliability rate, more energy efficiency, and superior temperature uniformity. Match this freezer with our CytoGROW Optimal CO2 incubator, with precise temperature control and contamination resistance, for a high performance solution. Learn more at us.panasonic-healthcare.com Celebrating 40 Years of Passion in Science The 2015-16 NEB Catalog & Technical Reference New England Biolabs introduces the latest edition of its award- winning Catalog & Technical Reference, featuring over 50 new products, up-to-date selection charts, protocols and troubleshooting tips.