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The Role of Histone H2av Variant Replacement and Histone H4 Acetylation in the Establishment of Drosophila Heterochromatin
The role of histone H2Av variant replacement and histone H4 acetylation in the establishment of Drosophila heterochromatin Jyothishmathi Swaminathan, Ellen M. Baxter, and Victor G. Corces1 Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA Activation and repression of transcription in eukaryotes involve changes in the chromatin fiber that can be accomplished by covalent modification of the histone tails or the replacement of the canonical histones with other variants. Here we show that the histone H2A variant of Drosophila melanogaster, H2Av, localizes to the centromeric heterochromatin, and it is recruited to an ectopic heterochromatin site formed by a transgene array. His2Av behaves genetically as a PcG gene and mutations in His2Av suppress position effect variegation (PEV), suggesting that this histone variant is required for euchromatic silencing and heterochromatin formation. His2Av mutants show reduced acetylation of histone H4 at Lys 12, decreased methylation of histone H3 at Lys 9, and a reduction in HP1 recruitment to the centromeric region. H2Av accumulation or histone H4 Lys 12 acetylation is not affected by mutations in Su(var)3-9 or Su(var)2-5. The results suggest an ordered cascade of events leading to the establishment of heterochromatin and requiring the recruitment of the histone H2Av variant followed by H4 Lys 12 acetylation as necessary steps before H3 Lys 9 methylation and HP1 recruitment can take place. [Keywords: Chromatin; silencing; transcription; histone; nucleus] Received September 8, 2004; revised version accepted November 4, 2004. The basic unit of chromatin is the nucleosome, which is guchi et al. 2004). The role of histone variants, and spe- made up of 146 bp of DNA wrapped around a histone cially those of H3 and H2A, in various nuclear processes octamer composed of two molecules each of the histones has been long appreciated (Wolffe and Pruss 1996; Ah- H2A, H2B, H3, and H4. -
Masondentinger Umn 0130E 1
The Nature of Defense: Coevolutionary Studies, Ecological Interaction, and the Evolution of 'Natural Insecticides,' 1959-1983 A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA BY Rachel Natalie Mason Dentinger IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY Mark Borrello December 2009 © Rachel Natalie Mason Dentinger 2009 Acknowledgements My first thanks must go to my advisor, Mark Borrello. Mark was hired during my first year of graduate school, and it has been my pleasure and privilege to be his first graduate student. He long granted me a measure of credit and respect that has helped me to develop confidence in myself as a scholar, while, at the same time, providing incisive criticism and invaluable suggestions that improved the quality of my work and helped me to greatly expand its scope. My committee members, Sally Gregory Kohlstedt, Susan Jones, Ken Waters, and George Weiblen all provided valuable insights into my dissertation, which will help me to further develop my own work in the future. Susan has given me useful advice on teaching and grant applications at pivotal points in my graduate career. Sally served as my advisor when I first entered graduate school and has continued as my mentor, reading nearly as much of my work as my own advisor. She never fails to be responsive, thoughtful, and generous with her attention and assistance. My fellow graduate students at Minnesota, both past and present, have been a huge source of encouragement, academic support, and fun. Even after I moved away from Minneapolis, I continued to feel a part of this lively and cohesive group of colleagues. -
TALE-Light Imaging Reveals Maternally Guided, H3k9me2/3-Independent Emergence of Functional Heterochromatin in Drosophila Embryos
Downloaded from genesdev.cshlp.org on September 29, 2021 - Published by Cold Spring Harbor Laboratory Press TALE-light imaging reveals maternally guided, H3K9me2/3-independent emergence of functional heterochromatin in Drosophila embryos Kai Yuan and Patrick H. O’Farrell Department of Biochemistry, University of California at San Francisco, San Francisco, California 94158, USA Metazoans start embryogenesis with a relatively naïve genome. The transcriptionally inert, late-replicating het- erochromatic regions, including the constitutive heterochromatin on repetitive sequences near centromeres and telomeres, need to be re-established during development. To explore the events initiating heterochromatin forma- tion and examine their temporal control, sequence specificity, and immediate regulatory consequence, we estab- lished a live imaging approach that enabled visualization of steps in heterochromatin emergence on specific satellite sequences during the mid-blastula transition (MBT) in Drosophila. Unexpectedly, only a subset of satellite se- quences, including the 359-base-pair (bp) repeat sequence, recruited HP1a at the MBT. The recruitment of HP1a to the 359-bp repeat was dependent on HP1a’s chromoshadow domain but not its chromodomain and was guided by maternally provided signals. HP1a recruitment to the 359-bp repeat was required for its programmed shift to later replication, and ectopic recruitment of HP1a was sufficient to delay replication timing of a different repeat. Our results reveal that emergence of constitutive heterochromatin follows a stereotyped developmental program in which different repetitive sequences use distinct interactions and independent pathways to arrive at a heterochro- matic state. This differential emergence of heterochromatin on various repetitive sequences changes their replica- tion order and remodels the DNA replication schedule during embryonic development. -
Drosophila Ribosomal Proteins Are Associated with Linker Histone H1 and Suppress Gene Transcription
Downloaded from genesdev.cshlp.org on October 2, 2021 - Published by Cold Spring Harbor Laboratory Press Drosophila ribosomal proteins are associated with linker histone H1 and suppress gene transcription Jian-Quan Ni,1,3 Lu-Ping Liu,1,3 Daniel Hess,1 Jens Rietdorf,1 and Fang-Lin Sun1,2,4 1Friedrich Miescher Institute for Biomedical Research, Basel CH-4058, Switzerland; 2Institute of Epigenetics and Cancer Research, School of Medicine, Tsinghua University, Beijing 100080, China The dynamics and function of ribosomal proteins in the cell nucleus remain enigmatic. Here we provide evidence that specific components of Drosophila melanogaster ribosomes copurify with linker histone H1. Using various experimental approaches, we demonstrate that this association of nuclear ribosomal proteins with histone H1 is specific, and that colocalization occurs on condensed chromatin in vivo. Chromatin immunoprecipitation analysis confirmed that specific ribosomal proteins are associated with chromatin in a histone H1-dependent manner. Overexpression of either histone H1 or ribosomal protein L22 in Drosophila cells resulted in global suppression of the same set of genes, while depletion of H1 and L22 caused up-regulation of tested genes, suggesting that H1 and ribosomal proteins are essential for transcriptional gene repression. Overall, this study provides evidence for a previously undefined link between ribosomal proteins and chromatin, and suggests a role for this association in transcriptional regulation in higher eukaryotes. [Keywords: Ribosomal protein; L22; histone H1; chromatin; transcription] Supplemental material is available at http://www.genesdev.org. Received September 25, 2005; revised version accepted May 8, 2006. Transcription and translation in eukaryotes are generally discrete nuclear sites was sensitive to inhibitors of both believed to take place within two spatially separated cel- transcription and translation, arguing that the two pro- lular compartments. -
Introduction to the Genomics Education Partnership and Collaborative Genomics Research in Drosophila
Tested Studies for Laboratory Teaching Proceedings of the Association for Biology Laboratory Education Vol. 34, 135-165, 2013 Introduction to the Genomics Education Partnership and Collaborative Genomics Research in Drosophila Julia A. Emerson1, S. Catherine Silver Key2, Consuelo J. Alvarez3, Stephanie Mel4, Gerard P. McNeil5, Kenneth J. Saville6, Wilson Leung7, Christopher D. Shaffer7 and Sarah C. R. Elgin7 1Amherst College, Department of Biology, P.O. Box 5000, Amherst MA 01002 USA 2North Carolina Central University, Department of Biology, 2246 MTSB, Durham NC 27701 USA 3Longwood University, Department of Biological and Environmental Sciences, 201 High St., Farmville VA 23909 USA 4University of California San Diego, Division of Biological Sciences, 9500 Gilman Drive 0355, La Jolla CA 92093 USA 5York College/CUNY, Department of Biology, 94-20 Guy R. Brewer Blvd., Jamaica NY 11451 USA 6 Albion College, Biology Department, 611 E. Porter St., Albion MI 49224 USA 7Washington University, Department of Biology, Campus Box 1137, One Brookings Dr., St. Louis MO 3130 USA ([email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]; [email protected]) The GEP, a group of faculty from over 90 primarily undergraduate institutions, is using comparative genomics to engage students in research within regular courses. Using a versatile curriculum, GEP undergraduates undertake projects to improve draft genomic sequences and/or participate in the annotation of these improved sequences. An additional goal of the annotation curriculum is for students to gain a sophisticated understanding of eukaryotic gene structure. Students do so by carefully mapping the protein-coding regions of putative genes from recently- sequenced Drosophila species. -
Workshop Notebook
GCAT WORKSHOPS 2009 NSF SUPPORTED DNA MICROARRAY WORKSHOPS FOR HISTORICALLY BLACK COLLEGES AND UNIVERSITIES, HISPANIC-SERVING INSTITUTIONS AND TRIBAL COLLEGES FACULTY JULY 5 - July 11, 2009 HOST INSTITUTION: MOREHOUSE COLLEGE BIOLOGY DEPARTMENT; ATLANTA, GA INSTRUCTORS Consuelo Alvarez, Malcolm Campbell, Todd Eckdahl, Edison Fowlks, Charles Hauser, Laurie Heyer, and Anne Rosenwald Genome Consortium for Active Teaching (GCAT) NSF GRANT DBI-0520908 Awarded to Hampton University PI: Edison R. Fowlks; Co-PIs: Mary Lee Ledbetter and Anne Rosenwald and NSF GRANT DBI-0520908 Awarded to Davidson College PI: Malcolm Campbell; Co-PIs: Laurie Heyer and Todd Eckdahl By the DIRECTORATE FOR BIOLOGICAL SCIENCES NATIONAL SCIENCE FOUNDATION DR. SALLY O’CONNOR, MANAGERING PROGRAM OFFICER NSF-SPONSORED GCAT DNA MICROARRAY SUMMER WORKSHOPS FOR UNDERGRADUATE HBCU, HSI AND TRIBAL COLLEGE FACULTY TAB I. Origin of this NSF Workshop and History of GCAT 1 II. Workshop Participants and Instructors 2 III. Workshop Schedule of Dry and Wet Lab Activities 3 IV. Assessment Material 4 A. Pre-Test B. Post-Test V. Wet Lab Activities 6 A. Culturing Yeast B. Isolating RNA C. 3DNA Protocol VI. Dry Lab Activities 7 A. Magic Tool User Guide B. Magic Tool: Exploring Diauxic Shift Microarray Data C. Exploring Correlations VII. Sampling of Microarray Articles 7 VIII. Notes, Special Instructions & Directions 8 ORIGIN OF THIS NSF WORKSHOP At a curriculum gathering during summer of 2004, Drs. Fowlks and Campbell presented their perspectives on the undergraduate educational implications of the NIH Roadmap. Fowlks addressed curricular changes in undergraduate biology, as well as recruitment and training for underrepresented populations. Campbell provided an overview of activities by GCAT, a non-profit educational consortium, to bring functional genomics methods into undergraduate courses and independent student research. -
Thank You to Our 2016 Donors
THANK YOU TO OUR 2016 DONORS Lifetime Giving Society Rush Holt and Celeste M. Rohlfing Roger and Terry Beachy Mary E. Clutter The Lifetime Giving Margaret Lancefield Robert L. Smith Jr. Cynthia M. Beall Morrel H. Cohen Society recognizes Alice S. Huang and Daniel Vapnek Gary and Fay Beauchamp Donald G. Comb individuals who have David Baltimore contributed a cumulative Raymond G. Beausoleil Jeffrey A. Cooper total of $100,000 or more $2,500-$4,999 $25,000- $49,999 Nicholas A. Begovich Jonathan C. Coopersmith during the course of their Anonymous, in memory Kenneth A. Cowin involvement of Myrtle Ray Zeiber, Jerry A. Bell and Vincent D’Aco with AAAS. Benjamin C. Hammett Jill Sharon Sheridon, Mary Ann Stepp William H. Danforth Tucker Hake Alan and Agnes Leshner May R. Berenbaum Peter B. Danzig Kathleen S. Berger Edwin J. Adlerman Lawrence H. Linden Margaret M. Betchart Vincent Davisson Stephen and Janelle Ersen Arseven Fodor David E. Shaw and James Bielenberg David H. de Weese Beth Kobliner Shaw David R. Atkinson Richard M. Forester † Dennis M. Bier Jeffrey S. Dean Drs. Larry and Jan Allison Bigbee Sibyl R. Golden and $10,000- $24,999 Baldwin John and Mary Deane the Golden Family Thomas R. and Johanna Amy Blackwell Helena L. Chum George E. DeBoer Rush Holt and K. Baruch Peter D. Blair Hans G. Dehmelt Margaret Lancefield Jonathan Bellack Rita R. and Jack H. Colwell C. John Blankley Charles W. Dewitt Alan and Agnes Leshner Floyd E. Bloom Troy E. Daniels Carla Blumberg Ruth A. Douglas Lawrence H. Linden Fred A. -
Claire Barrett, Greg Creacy, Charles Hauser
Charles R. Hauser Associate Professor of Bioinformatics St. Edward’s University Voice: (512) 233.1671 Bioinformatics Program Fax. (512) 448.8764 Austin TX 78704 e-mail: [email protected] Professional Preparation University of Texas, Austin, TX 1972-1977 Botany University of Houston, TX 1984-1989 PhD. Biochemistry and Biophysics Duke University 1989-1995 Post-doctoral fellowship Appointments 2008 - Associate Professor Bioinformatics, St. Edward’s University 2004 - 2008 Assistant Professor Bioinformatics, St. Edward’s University 2000 - 2004 Research Scientist: Duke University, Durham NC 1995 - 2000 Research Associate: Duke University, Durham, NC 1989 - 1995 Postdoctoral Associate: Duke University, Durham, NC 1984 - 1989 Graduate Student/Researcher: University of Houston Awards and Honors 2016 St. Edward’s School of Natural Sciences Distinguished Research Award, 2015-16. 1990 NIH Postdoctoral Fellowship. Department of Botany, Duke University, Durham, NC. 1989 Hargitt Fellowship. Department of Zoology, Duke University, Durham, NC. Grants 2016 Howard Hughes Medical Institute (USE), Inclusive Excellence Grants 2017 Pre-proposal. Research L Kopec (PI), Charles R Hauser (collaborator) 2016 NSF, IUSE, “Integrating Bioinformatics into the Life Sciences—Phase 3” Mark Pauley (U. Nebraska, Omaha), Vince Buonaccorsi (Juniata College), Anya Goodman (California Polytechnic State University), Anne Rosenwald (Georgetown University) and Bill Tapprich (University of Nebraska at Omaha) Co-PIs. Charles Hauser (Advisory Committee Member). 2015 USDA, The Agricultural-STEM Pipeline: Progressive Experiential Learning Linking Three HSI Academic Tiers (Ag-STEM), 3 year ($275,000), Drs. O’Leary (PI), Quinn, Hauser, Deaton (co-PIs) 2015 NIH, “A Genome Browser On Ramp to Engage Biologists with Big Data”, Dr. Sarah Elgin, Washington University St. Louis (PI), Hauser (collaborator). -
Contents Trade Offerings
CONTENTS TRADE OFFERINGS The Secret Life of the Brain 2 Richard Restak, M.D. Eclipse 4 Duncan Steel In Search of the Lost Cord 6 Luba Vikhanski The Genomic Revolution 8 Rob DeSalle and Michael Yudell How Students Learn 10 National Research Council A Case of Chronic Neglect 11 Felicia Cohn, Marla Salmon, and John Stobo Previously Announced Books and New and Recently Published Books Adding It Up 13 Jeremy Kilpatrick, Jane Swafford, and Bradford Findell Educating Children with Autism 14 Catherine Lord and James P.McGee Knowing What Students Know 15 James Pellegrino, Robert Glaser, and Naomi Chudowsky Speaking of Health 16 Institute of Medicine Backlist Offerings 30 General Information 34 October General Interest Science ISBN 0-309-07435-5 $35.00 8 x 10, 224 pages, index Cloth with jacket Color photographs and illustrations A Joseph Henry Press book Rights: World MARKETING • Concurrent publicity with airing of PBS series in early 2002 • Full-color blads • National review attention • National print advertising campaign • National media attention: radio and television • Co-op available 2 THE SECRET LIFE OF THE BRAIN Richard Restak, M.D. with a foreword by David Grubin Companion to the five-part television series brought to PBS by award- winning producer David Grubin, The Secret Life of the Brain takes readers on a tour of the human brain. Lavishly illustrated and beautifully presented, the many mysteries of the brain are explored from infancy to old age. en years ago a presidential proclamation ushered in the “Decade of the Brain.”We have Dr. Richard Restak since realized enormous benefits from this decade of discovery. -
21St Annual Meeting of the ISCE 23-27 July, 2005
21st Annual Meeting of the ISCE 23-27 July, 2005 1 21st Annual Meeting of the ISCE 23-27 July, 2005 Table of Contents Organizers, Officers & Sponsors ........................................................................................ 3 Conference at a Glance ....................................................................................................... 4 Hotel Map ........................................................................................................................... 5 Program............................................................................................................................... 6 Saturday, 23rd afternoon.................................................................................................. 6 Sunday, 24th morning...................................................................................................... 6 Sunday, 24th afternoon .................................................................................................... 7 Sunday, 24th evening....................................................................................................... 8 Monday, 25th morning..................................................................................................... 8 Monday, 25th afternoon................................................................................................... 9 Tuesday, 26th morning .................................................................................................. 11 Tuesday, 26th morning-afternoon................................................................................. -
SWEET-DISSERTATION-2018.Pdf
UNTANGLING THE COEVOLUTIONARY HISTORY BETWEEN DOVES AND THEIR PARASITIC LICE BY ANDREW DONALD SWEET DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Ecology, Evolution, and Conservation Biology in the Graduate College of the University of Illinois at Urbana-Champaign, 2018 Urbana, Illinois Doctoral Committee: Dr. Kevin Johnson, Chair, Director of Research Professor May Berenbaum Professor James Whitfield Associate Professor Brian Allan Assistant Professor Julian Catchen ABSTRACT In host-parasite systems, any given host species can be associated with multiple types of parasites, each of which can have a unique ecological relationship with the host. However, it remains unclear how these ecological differences link to evolutionary patterns. What shapes the dynamics of a host-parasite interaction over evolutionary time? An ideal approach for addressing this question is to compare multiple lineages of similar parasites that are associated with the same group of hosts but have distinct ecological differences – or “ecological replicates.” For my dissertation, I applied this strategy by focusing on the wing and body lice of doves. These two “ecomorphs” of lice are not closely related yet exclusively parasitize the same group of hosts. Notably, wing lice have a greater capability for dispersal than body lice. Dispersal is an important ecological component of host-parasite interactions and speciation in general. The first part of my dissertation examined broad cophylogenetic patterns across the dove-louse system. I found that wing and body lice did not have correlated patterns, and body lice showed more cospeciation with their hosts. This pattern agreed with previous studies, the results of which suggested that the increased cospeciation in body lice was due to differences in dispersal ability. -
Finding Genes in a New Fly Genome: Teaching About Genes/Genomes Via Bioinformatics Research
Finding Genes in a New Fly Genome: Teaching about Genes/Genomes via Bioinformatics Research Sarah Elgin, Anya Goodman, Wilson Leung Eric Tsoi, Charlene Emerson, David Carranza January 2012 Workshop Goals • Introduce Genomics Education Partnership • Hands-on practice with genome annotation • Discussion of curriculum options 3-week module ( ~10 hr: 1 lecture, 3X3 lab) 5-week – add a more difficult project 10-week - real research! • Scientific background on Drosophila genome • http://gep.wustl.edu [email protected] • Next workshops: June 24-26, August 19-22 (HHMI supported) Genomics Education Partnership (GEP) Goal: to engage students in a genomics research project, via a research-oriented AY lab course. Work organized through the GEP website. Our GEP research goal: Use comparative genomics to learn more about heterochromatic domains, analyzing the dot chromosomes and a control euchromatic region of Drosophila genomes Status Reference Completed Annotation Sequence Improvement New Project FlyBase: http://flybase.org I hear and I forget. I see and I remember. I do and I understand Confucius The scientific method allows ordinary people to do extraordinary things. Francis Bacon Genomics provides terrific opportunities to engage undergraduates in research! Strategy: divide and conquer! The D. mojavensis dot chromosome • Students completed 68 projects covering 1.7 Mb closing 26/28 gaps, adding ~15,000 bp and improving ~5000 bp. • Each project finished and annotated (all isoforms) twice; reconciliation for quality control done at Wash U Fosmid