2020 Online Session Descriptions
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Distinctive Regulatory Architectures of Germline-Active and Somatic Genes in C
Downloaded from genome.cshlp.org on October 7, 2021 - Published by Cold Spring Harbor Laboratory Press Research Distinctive regulatory architectures of germline-active and somatic genes in C. elegans Jacques Serizay, Yan Dong, Jürgen Jänes, Michael Chesney, Chiara Cerrato, and Julie Ahringer The Gurdon Institute and Department of Genetics, University of Cambridge, CB2 1QN Cambridge, United Kingdom RNA profiling has provided increasingly detailed knowledge of gene expression patterns, yet the different regulatory ar- chitectures that drive them are not well understood. To address this, we profiled and compared transcriptional and regu- latory element activities across five tissues of Caenorhabditis elegans, covering ∼90% of cells. We find that the majority of promoters and enhancers have tissue-specific accessibility, and we discover regulatory grammars associated with ubiquitous, germline, and somatic tissue–specific gene expression patterns. In addition, we find that germline-active and soma-specific promoters have distinct features. Germline-active promoters have well-positioned +1 and −1 nucleosomes associated with a periodic 10-bp WW signal (W = A/T). Somatic tissue–specific promoters lack positioned nucleosomes and this signal, have wide nucleosome-depleted regions, and are more enriched for core promoter elements, which largely differ between tissues. We observe the 10-bp periodic WW signal at ubiquitous promoters in other animals, suggesting it is an ancient conserved signal. Our results show fundamental differences in regulatory architectures of germline and somatic tissue–specific genes, uncover regulatory rules for generating diverse gene expression patterns, and provide a tissue-specific resource for future studies. [Supplemental material is available for this article.] Cell type–specific transcription regulation underlies production tissues are achieved and whether expression is governed by dis- of the myriad of different cells generated during development. -
Springer A++ Viewer
PublisherInfo PublisherName : BioMed Central PublisherLocation : London PublisherImprintName : BioMed Central Ira Herskowitz dies ArticleInfo ArticleID : 4766 ArticleDOI : 10.1186/gb-spotlight-20030506-01 ArticleCitationID : spotlight-20030506-01 ArticleSequenceNumber : 118 ArticleCategory : Research news ArticleFirstPage : 1 ArticleLastPage : 4 RegistrationDate : 2003–5–6 ArticleHistory : OnlineDate : 2003–5–6 ArticleCopyright : BioMed Central Ltd2003 ArticleGrants : ArticleContext : 130594411 Brendan Maher Email: [email protected] Ira Herskowitz, professor of genetics at the University of California, San Francisco (UCSF), died at home on April 28 of pancreatic cancer. He was 56. Remembered for clarity of mind, exceptional science, enthusiastic teaching, and a love of music, his death sent a shock throughout the yeast community this week, where Herskowitz made many great contributions and friends. "It's a great loss to us all," said Paul Nurse, Nobel Laureate and new president of The Rockefeller University. "Ira Herskowitz had a huge influence on the yeast field and on me personally." Laureate Leland Hartwell, president of Fred Hutchinson Cancer Research Center told us in an e-mail, "I'll bet there are few scientists in genetics, molecular and cell biology who were not personally affected by him." Born in Brooklyn, NY, Herskowitz moved with his family about the country as father Irwin, a Drosophilageneticist, took various academic positions. Herskowitz received a bachelor's degree in science from the California Institute of Technology in 1967 and a PhD in microbiology from the Massachusetts Institute of Technology (MIT) in 1971. After a short postdoctoral stint there, he assumed an assistant professor position at the University of Oregon. Moving in 1982 to UCSF, he immediately revamped the genetics program there, chaired the department of biochemistry and biophysics from 1990 to 1995, and co-directed the program in human genetics from 1997. -
Gurdon Institute 20122011 PROSPECTUS / ANNUAL REPORT 20112010
The Wellcome Trust/Cancer Research UK Gurdon Institute 20122011 PROSPECTUS / ANNUAL REPORT 20112010 Gurdon I N S T I T U T E PROSPECTUS 2012 ANNUAL REPORT 2011 http://www.gurdon.cam.ac.uk CONTENTS THE INSTITUTE IN 2011 INTRODUCTION........................................................................................................................................3 HISTORICAL BACKGROUND..........................................................................................................4 CENTRAL SUPPORT SERVICES....................................................................................................5 FUNDING.........................................................................................................................................................5 RETREAT............................................................................................................................................................5 RESEARCH GROUPS.........................................................................................................6 MEMBERS OF THE INSTITUTE................................................................................44 CATEGORIES OF APPOINTMENT..............................................................................44 POSTGRADUATE OPPORTUNITIES..........................................................................44 SENIOR GROUP LEADERS.............................................................................................44 GROUP LEADERS.......................................................................................................................48 -
Transcriptomic Description of an Endogenous Female State in C
bioRxiv preprint first posted online Oct. 27, 2016; doi: http://dx.doi.org/10.1101/083113. The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license. Transcriptomic Description of an Endogenous Female State in C. elegans David Angeles-Albores1,y Daniel H.W. Leighton2,y Tiffany Tsou1 Tiffany H. Khaw1 Igor Antoshechkin3 Paul W. Sternberg1,* October 29, 2016 y These authors contributed equally to this work 1 Department of Biology and Biological Engineering, and Howard Hughes Medical Institute, Caltech, Pasadena, CA, 91125, USA 2 Department of Human Genetics, Department of Biological Chemistry, and Howard Hughes Medical Insti- tute, University of California, Los Angeles, Los Angeles, CA 90095, USA 3 Department of Biology and Biological Engineering, Caltech, Pasadena, CA, 91125, USA * Corresponding author. Contact:[email protected] Abstract Understanding genome and gene function in a whole organism requires us to fully compre- hend the life cycle and the physiology of the organism in question. Although C. elegans is traditionally though of as a hermaphrodite, XX animals exhaust their sperm and become (en- dogenous) females after 3 days of egg-laying. The molecular physiology of this state has not been studied as intensely as other parts of the life cycle, in spite of documented changes in behavior and metabolism that occur at this stage. To study the female state of C. elegans, we designed an experiment to measure the transcriptomes of 1st day adult females; endoge- nous, 6th day adult females; and at the same time points, mutant feminized worms. -
Curriculum Vitae Jasper Rine Address: Work Home Department of Molecular and Cellular Biology 400 Western Drive Division of Genet
Curriculum Vitae Jasper Rine Address: Work Home Department of Molecular and Cellular Biology 400 Western Drive Division of Genetics Richmond, California 94801 California Institute for Quantitative Biosciences 374A Stanley Hall 510-232-4293 University of California Birth Date: October 16, 1953 Berkeley, CA 94720-3202 Tel: 510-642-7047 Fax: 510-666-2768 Higher Education Post-doctoral Fellow 1980-1982 Stanford University School of Medicine Advisor: Ronald W. Davis University of Oregon, Ph.D. 1975-1979 Molecular Genetics Advisor: Ira Herskowitz State University of New York at Albany 1971-1975 B.S. Biological Sciences, Magna Cum Laude Professional Experience Professor of Genetics Division of Genetics, Genomics and Development Department of Molecular and Cell Biology University of California, Berkeley 1990-Present Director, Human Genome Center Lawrence Berkeley Labs Berkeley, California 1991-1994 Associate Professor of Genetics Division of Genetics Department of Molecular and Cell Biology University of California, Berkeley 1989-1990 Assistant Professor of Biochemistry Department of Biochemistry University of California, Berkeley 1982-1988 Honors/Awards N.I.H. Postdoctoral Fellowship 1980-1982 The Camille and Henry Dreyfus Teacher Scholar Award 1986 Miller Research Professor, UC Berkeley 1993 Philips Distinguished Lecturer, Haverford College 1993 American Academy of Microbiology – Fellow Election 1993 Streisinger Lecturer, University of Oregon 1993 UCB Distinguished Teaching Award 1997 Richard & Rhoda Goldman Distinguished Professor of Biology -
2020 Program Book
PROGRAM BOOK Note that TAGC was cancelled and held online with a different schedule and program. This document serves as a record of the original program designed for the in-person meeting. April 22–26, 2020 Gaylord National Resort & Convention Center Metro Washington, DC TABLE OF CONTENTS About the GSA ........................................................................................................................................................ 3 Conference Organizers ...........................................................................................................................................4 General Information ...............................................................................................................................................7 Mobile App ....................................................................................................................................................7 Registration, Badges, and Pre-ordered T-shirts .............................................................................................7 Oral Presenters: Speaker Ready Room - Camellia 4.......................................................................................7 Poster Sessions and Exhibits - Prince George’s Exhibition Hall ......................................................................7 GSA Central - Booth 520 ................................................................................................................................8 Internet Access ..............................................................................................................................................8 -
Fall 2016 Is Available in the Laboratory of Dr
RNA Society Newsletter Aug 2016 From the Desk of the President, Sarah Woodson Greetings to all! I always enjoy attending the annual meetings of the RNA Society, but this year’s meeting in Kyoto was a standout in my opinion. This marked the second time that the RNA meeting has been held in Kyoto as a joint meeting with the RNA Society of Japan. (The first time was in 2011). Particular thanks go to the local organizers Mikiko Siomi and Tom Suzuki who took care of many logistical details, and to all of the organizers, Mikiko, Tom, Utz Fischer, Wendy Gilbert, David Lilley and Erik Sontheimer, for putting together a truly exciting and stimulating scientific program. Of course, the real excitement in the annual RNA meetings comes from all of you who give the talks and present the posters. I always enjoy meeting old friends and colleagues, but the many new participants in this year’s meeting particularly encouraged me. (Continued on p2) In this issue : Desk of the President, Sarah Woodson 1 Highlights of RNA 2016 : Kyoto Japan 4 Annual Society Award Winners 4 Jr Scientist activities 9 Mentor Mentee Lunch 10 New initiatives 12 Desk of our CEO, James McSwiggen 15 New Volunteer Opportunities 16 Chair, Meetings Committee, Benoit Chabot 17 Desk of the Membership Chair, Kristian Baker 18 Thank you Volunteers! 20 Meeting Reports: RNA Sponsored Meetings 22 Upcoming Meetings of Interest 27 Employment 31 1 Although the graceful city of Kyoto and its cultural months. First, in May 2016, the RNA journal treasures beckoned from just beyond the convention instituted a uniform price for manuscript publication hall, the meeting itself held more than enough (see p 12) that simplifies the calculation of author excitement to keep ones attention! Both the quality fees and facilitates the use of color figures to and the “polish” of the scientific presentations were convey scientific information. -
Real-Time Egg Laying Dynamics in Caenorhabditis Elegans
UNIVERSITY OF CALIFORNIA, IRVINE Real-time egg laying dynamics in Caenorhabditis elegans DISSERTATION submitted in partial satisfaction of the requirements for the degree of DOCTOR OF PHILOSOPHY in Biomedical Engineering by Philip Vijay Thomas Dissertation Committee: Professor Elliot Hui, Chair Professor Olivier Cinquin Professor Abraham Lee 2015 c 2015 Philip Vijay Thomas TABLE OF CONTENTS Page LIST OF FIGURES iv ACKNOWLEDGMENTS v CURRICULUM VITAE vi ABSTRACT OF THE DISSERTATION viii 1 Introduction and motivation 1 1.1 The impact of C. elegans in aging and lifespan studies along with current limitations . 1 1.2 Starvation and its effect on worms . 4 1.3 Microfabricated systems for C. elegans biology . 5 2 Real-time C. elegans embryo cytometry to study reproductive aging 7 2.1 High capacity low-weight passive bubble trap . 8 2.2 Microfluidic device layout . 10 2.3 Tuning habitat exit sizes to flush out embryos while retaining worms . 11 2.4 Equal flow resistance to make identical habitats . 12 2.5 Video enumeration of eggs . 13 2.6 Switching between discrete and continuously varying media concentrations . 15 3 Optimizing worm health in C. elegans microfluidics 17 3.1 E. coli densities of 1010 cells/mL maintain egg-laying in liquid worm culture 18 3.2 E. coli biofilms in devices . 19 3.3 Amino acid addition to S-media, γ irradiation of bacteria, and elevated syringe temperatures are ineffective in reducing biofilms in devices . 20 3.4 Use of a curli major subunit deletion strain significantly reduces biofilm in S-media . 23 4 Conclusions and future directions 26 Bibliography 30 ii A Appendix Title 41 A.1 Methods . -
COMPASS Mediates Transgenerational Epigenetic Inheritance in Caenorhabditis Elegans
COMPASS Mediates Transgenerational Epigenetic Inheritance in Caenorhabditis elegans By: Rosamund Clifford A thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy The University of Leeds Faculty of Biological Sciences School of Biology Submission Date February 2021 Acknowledgements There are a great many people who have contributed to the development of this thesis, who I would like to thank here. Professor Ian Hope, who took on the role of my primary supervisor midway through my PhD and guided me through to the end with constant support and advice during the bulk of the experiments and entire writing process. My first PhD supervisor, Dr Ron Chen, whose ideas and support in the first two years gave me a solid foundation on which to build this thesis. Professor Mark Dickman and the Dickman group at the University of Sheffield, in particular Dr Eleanor Hanson, Dr Joby Cole and Dr Caroline Evans, for their technical expertise in LC-MS/MS and support with performing the experiments described here. Professor Julie Ahringer and the Ahringer group at the University of Cambridge, for their support with the immunofluorescence microscopy experiments, which I learned to do under the supervision of Yan Dong on a visit to the Ahringer lab. Thanks also to the imaging team at the Gurdon Institute, particularly Dr Nicola Lawrence, for training me to use a confocal microscope, and Dr Richard Butler, for writing the code that enabled analysis of the images. At the University of Leeds, my thanks go to Dr Ruth Hughes at the Bio-imaging facility for her advice on image analysis, and Dr Brittany Graham for helping me settle into the Hope lab. -
UNIVERSITY of CALIFORNIA Los Angeles Linking Human
UNIVERSITY OF CALIFORNIA Los Angeles Linking Human Evolutionary History to Phenotypic Variation A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Human Genetics by Arun Kumar Durvasula 2021 c Copyright by Arun Kumar Durvasula 2021 ABSTRACT OF THE DISSERTATION Linking Human Evolutionary History to Phenotypic Variation by Arun Kumar Durvasula Doctor of Philosophy in Human Genetics University of California, Los Angeles, 2021 Professor Kirk Edward Lohmueller, Co-chair Professor Sriram Sankararaman, Co-chair A central question in genetics asks how genetic variation influences phenotypic variation. The distribution of genetic variation in a population is reflective of the evolutionary forces that shape and maintain genetic diversity such as mutation, natural selection, and genetic drift. In turn, this genetic variation affects molecular phenotypes like gene expression and eventually leads to variation in complex traits. In my dissertation, I develop statistical methods and apply computational approaches to understand these dynamics in human populations. In the first chapter, I describe a statistical model for detecting the presence of archaic haplotypes in modern human populations without having access to a reference archaic genome. I apply this method to the genomes of individuals from Europe and find that I can recover segments of DNA inherited from Neanderthals as a result of archaic admixture. In the second chapter, I apply this method to the genomes of individuals from several African populations and find that approximately 7% of the genomes are inherited from an archaic species. Modeling of the site frequency spectrum suggests that the presence of these haplotypes is best explained by admixture with an unknown archaic hominin species. -
From Controlling Elements to Transposons: Barbara Mcclintock and the Nobel Prize Nathaniel C
454 Forum TRENDS in Biochemical Sciences Vol.26 No.7 July 2001 Historical Perspective From controlling elements to transposons: Barbara McClintock and the Nobel Prize Nathaniel C. Comfort Why did it take so long for Barbara correspondence. From these and other to prevent her controlling elements from McClintock (Fig. 1) to win the Nobel Prize? materials, we can reconstruct the events moving because their effects were difficult In the mid-1940s, McClintock discovered leading up to the 1983 prize*. to study when they jumped around. She genetic transposition in maize. She What today are known as transposable never had any inclination to pursue the published her results over several years elements, McClintock called ‘controlling biochemistry of transposition. and, in 1951, gave a famous presentation elements’. During the years 1945–1946, at Current understanding of how gene at the Cold Spring Harbor Symposium, the Carnegie Dept of Genetics, Cold activity is regulated, of course, springs yet it took until 1983 for her to win a Nobel Spring Harbor, McClintock discovered a from the operon, François Jacob and Prize. The delay is widely attributed to a pair of genetic loci in maize that seemed to Jacques Monod’s 1960 model of a block of combination of gender bias and gendered trigger spontaneous and reversible structural genes under the control of an science. McClintock’s results were not mutations in what had been ordinary, adjacent set of regulatory genes (Fig. 2). accepted, the story goes, because women stable alleles. In the term of the day, they Though subsequent studies revealed in science are marginalized, because the made stable alleles into ‘mutable’ ones. -
The University of Chicago Leveraging Haplotype
THE UNIVERSITY OF CHICAGO LEVERAGING HAPLOTYPE-BASED INFERENCE TO DESCRIBE ADAPTATION AND SPECIATION A DISSERTATION SUBMITTED TO THE FACULTY OF THE DIVISION OF THE BIOLOGICAL SCIENCES AND THE PRITZKER SCHOOL OF MEDICINE IN CANDIDACY FOR THE DEGREE OF DOCTOR OF PHILOSOPHY DEPARTMENT OF ECOLOGY AND EVOLUTION BY JOEL HAVILAND SMITH CHICAGO, ILLINOIS JUNE 2018 TABLE OF CONTENTS LIST OF FIGURES . iv LIST OF TABLES . ix ACKNOWLEDGMENTS . xi ABSTRACT . xii 1 INTRODUCTION . 1 2 ESTIMATING TIME TO THE COMMON ANCESTOR FOR A BENEFI- CIAL ALLELE . 8 2.1 Abstract . .8 2.2 Introduction . .9 2.3 Model Description . 15 2.4 Inference . 21 2.5 Results . 23 2.5.1 Recombination Versus Mutation as a Source of Information . 27 2.5.2 Application to 1000 Genomes Data . 29 2.6 Discussion . 35 2.7 Materials and Methods . 43 3 ESTIMATING THE TIMING OF ADAPTIVE INTROGRESSION . 47 3.1 Abstract . 47 3.2 Introduction . 48 3.3 Coat Color Adaptation in North American Wolves . 50 3.4 High Altitude Adaptation in Tibetans . 55 3.5 Discussion . 58 4 EXPECTED PATTERNS OF LOCAL ANCESTRY IN A HYBRID ZONE 63 4.1 Abstract . 63 4.2 Introduction . 64 4.2.1 Two-Locus Genetic Incompatibilities . 68 4.3 Model Description . 71 4.3.1 Tract Length Distributions Under Neutral Admixture . 71 4.3.2 A Locus-Specific Tract Length Distribution With Selection . 73 4.4 Discussion . 95 ii 5 DO HELICONIUS BUTTERFLY SPECIES EXCHANGE MIMICRY ALLE- LES? . 99 5.1 Abstract . 99 5.2 Introduction . 100 5.3 Materials and Methods . 104 5.4 Results .