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Uniprot at EMBL-EBI's Role in CTTV
Barbara P. Palka, Daniel Gonzalez, Edd Turner, Xavier Watkins, Maria J. Martin, Claire O’Donovan European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK UniProt at EMBL-EBI’s role in CTTV: contributing to improved disease knowledge Introduction The mission of UniProt is to provide the scientific community with a The Centre for Therapeutic Target Validation (CTTV) comprehensive, high quality and freely accessible resource of launched in Dec 2015 a new web platform for life- protein sequence and functional information. science researchers that helps them identify The UniProt Knowledgebase (UniProtKB) is the central hub for the collection of therapeutic targets for new and repurposed medicines. functional information on proteins, with accurate, consistent and rich CTTV is a public-private initiative to generate evidence on the annotation. As much annotation information as possible is added to each validity of therapeutic targets based on genome-scale experiments UniProtKB record and this includes widely accepted biological ontologies, and analysis. CTTV is working to create an R&D framework that classifications and cross-references, and clear indications of the quality of applies to a wide range of human diseases, and is committed to annotation in the form of evidence attribution of experimental and sharing its data openly with the scientific community. CTTV brings computational data. together expertise from four complementary institutions: GSK, Biogen, EMBL-EBI and Wellcome Trust Sanger Institute. UniProt’s disease expert curation Q5VWK5 (IL23R_HUMAN) This section provides information on the disease(s) associated with genetic variations in a given protein. The information is extracted from the scientific literature and diseases that are also described in the OMIM database are represented with a controlled vocabulary. -
Gabriel Dover)
Dear Mr Darwin (Gabriel Dover) Home | Intro | About | Feedback | Prev | Next | Search Steele: Lamarck's Was Signature Darwin Wrong? Molecular Drive: the Third Force in evolution Geneticist Gabriel Dover claims that there is a third force in evolution: 'Molecular Drive' beside natural selection and neutral drift. Molecular drive is operationally distinct from natural selection and neutral drift. According to Dover it explains biological phenomena, such as the 700 copies of a ribosomal RNA gene and the origin of the 173 legs of the centipede, which natural selection and neutral drift alone cannot explain. by Gert Korthof version 1.3 24 Mar 2001 Were Darwin and Mendel both wrong? Molecular Drive is, according to Dover, an important factor in evolution, because it shapes the genomes and forms of organisms. Therefore Neo-Darwinism is incomplete without Molecular Drive. It is no wonder that the spread of novel genes was ascribed to natural selection, because it was the only known process that could promote the spread of novel genes. Dover doesn't reject the existence of natural selection but points out cases where natural selection clearly fails as a mechanism. Molecular drive is a non-Darwinian mechanism because it is independent of selection. We certainly need forces in evolution, since natural selection itself is not a force. It is the passive outcome of other processes. It is not an active process, notwithstanding its name. Natural selection as an explanation is too powerful for its own good. Molecular drive is non-Mendelian because some DNA segments are multiplied disproportional. In Mendelian genetics genes are present in just two copies (one on the maternal and one on the paternal chromosome). -
Download Program Guide
2011 C. elegans Meeting Organizing Committee Co-chairs: Oliver Hobert Columbia University Meera Sundaram University of Pennsylvania Organizing Committee: Raffi Aroian University of California, San Diego Ikue Mori Nagoya University Jean-Louis Bessereau INSERM Benjamin Podbilewicz Technion Israel Institute of Keith Blackwell Harvard Medical School Technology Andrew Chisholm University of California, San Diego Valerie Reinke Yale University Barbara Conradt Dartmouth Medical School Janet Richmond University of Illinois, Chicago Marie Anne Felix CNRS-Institut Jacques Monod Ann Rougvie University of Minnesota David Greenstein University of Minnesota Shai Shaham Rockefeller University Alla Grishok Columbia University Ahna Skop University of Wisconsin, Madison Craig Hunter Harvard University Ralf Sommer Max-Planck Institute for Bill Kelly Emory University Developmental Biology, Tuebingen Ed Kipreos University of Georgia Asako Sugimoto RIKEN, Kobe Todd Lamitina University of Pennsylvania Heidi Tissenbaum University of Massachusetts Chris Li City College of New York Medical School Sponsored by The Genetics Society of America 9650 Rockville Pike, Bethesda, MD 20814-3998 telephone: (301) 634-7300 fax: (301) 634-7079 e-mail: [email protected] Web site: http:/www.genetics-gsa.org Front cover design courtesy of Ahna Skop 1 Table of Contents Schedule of All Events.....................................................................................................................4 Maps University of California, Los Angeles, Campus .....................................................................7 -
Completed Thesis
THE UNIVERSITY OF WINCHESTER Faculty of Humanities and Social Sciences Human Uniqueness: Twenty-First Century Perspectives from Theology, Science and Archaeology Josephine Kiddle Bsc (Biology) MA (Religion) Thesis for the degree of Doctor of Philosophy February 2013 This Thesis has been completed as a requirement for a postgraduate research degree of the University of Winchester. The word count is: 89350 THE UNIVERSITY OF WINCHESTER ABSTRACT FOR THESIS Human Uniqueness: Twenty-First Century Perspectives from Theology, Science and Archaeology A project aiming to establish, through the three disciplines, the value of human uniqueness as an integrating factor for science with theology Josephine Kiddle Bsc (Biology) MA (Religion) Faculty of Humanities and Social Sciences Doctor of Philosophy February 2013 The theme that underlies the thesis is the challenge presented by science, as it developed from the time of the Enlightenment through the centuries until the present day, to Christian theology. The consequent conflict of ideas is traced in respect of biological science and the traditions of Protestant Christian doctrine, together with the advances of the developing discipline of prehistoric archaeology since the early nineteenth century. The common ground from which disagreement stemmed was the existence of human beings and the uniqueness of the human species as a group amongst all other creatures. With the conflict arising from this challenge, centring on the origin and history of human uniqueness, a rift became established between the disciplines which widened as they progressed through to the twentieth century. It is this separation that the thesis takes up and endeavours to analyse in the light of the influence of advancing science on the blending of philosophical scientific ideas with the elements of Christian faith of former centuries. -
Caenorhabditis Microbiota: Worm Guts Get Populated Laura C
Clark and Hodgkin BMC Biology (2016) 14:37 DOI 10.1186/s12915-016-0260-7 COMMENTARY Open Access Caenorhabditis microbiota: worm guts get populated Laura C. Clark and Jonathan Hodgkin* Please see related Research article: The native microbiome of the nematode Caenorhabditis elegans: Gateway to a new host-microbiome model, http://dx.doi.org/10.1186/s12915-016-0258-1 effects on the life history of the worm are often profound Abstract [2]. It has been increasingly recognized that the worm Until recently, almost nothing has been known about microbiota is an important consideration in achieving a the natural microbiota of the model nematode naturalistic experimental model in which to study, for Caenorhabditis elegans. Reporting their research in instance, host–pathogen interactions or worm behavior. BMC Biology, Dirksen and colleagues describe the first Dirksen et al [3] present the first step towards under- sequencing effort to characterize the gut microbiota standing understanding the complex interactions of the of environmentally isolated C. elegans and the related natural worm microbiota by reporting a 16S rDNA-based taxa Caenorhabditis briggsae and Caenorhabditis “head count” of the bacterial population present in wild remanei In contrast to the monoxenic, microbiota-free nematode isolates (Fig. 1). Interestingly, it appears that cultures that are studied in hundreds of laboratories, it nematodes isolated from diverse natural environment- appears that natural populations of Caenorhabditis s—and even those that have been maintained for a short harbor distinct microbiotas. time on E. coli following isolation—share a “core” host- defined microbiota. This finding is in agreement with work by Berg et al. -
From the President's Desk
JAN/FEB 2006 From the President’s desk: 2006, the 75th anniversary of the Genetics Society of America, will be marked by a number of initiatives to reinvigorate the Society’s mission of promoting research and education in genetics. A highlight was the recently held GSA sponsored conference, “Genetic Analysis: From Model Organisms to Human Biology” in San Diego from January 5-7. This conference emphasized the importance of model organism research by illustrating the crucial contributions to human biology resulting from discoveries in these organisms. The National Institutes of Health (NIH) supported this conference both financially and by participation of key NIH administrators, including Jeremy M. Berg, director of the National Institute of General Medical Sciences. In addition to the superb science talks by international leaders the MOHB conference showcased other important and new GSA initiatives including education, public policy advocacy, graduate student support and recognition of outstanding model organism geneticists. Robin Wright, Education Committee chair, led a round table discussion on undergraduate education and the Joint Steering Committee for Public Policy and the Congressional Liaison Committee sponsored a session on science advocacy and public policy. There was a mentor lunch to support graduate students and postdocs in the next steps of their careers, and the three GSA medals were presented during the banquet, with Victor Ambros receiving the GSA Medal, Fred Sherman the Beadle Award, and Masatoshi Nei the Morgan Award. (For research highlights at the meeting, see pages 6 and 7 of this issue.) The 75th anniversary will also usher in changes to our society’s journal, GENETICS. -
Genetics Society News
July 2008 . ISSUE 59 GENETICS SOCIETY NEWS www.genetics.org.uk IN THIS ISSUE Genetics Society News is edited by Steve Russell. Items for future issues should be sent to Steve Russell, preferably by email to • Genetics Society Epigenetics Meeting [email protected], or hard copy to Department of Genetics, • Genetics Society Sponsored Meetings University of Cambridge, Downing Street, Cambridge CB2 3EH. The Newsletter is published twice a year, with copy dates of 1st June and • Travel, Fieldwork and Studentship Reports 26th November. • John Evans: an Appreciation Cocoons of the parasitoid wasp Cotesia vestalis on cabbage leaf in Taiwan. From the • Twelve Galton Lectures fieldwork report by Jetske G. de Boer on page 36. • My Favourite Paper A WORD FROM THE EDITOR A word from the editor ow soon until the $1000 based on the results of tests we genome is actually with barely understand! Here in the Hus and individual UK there is currently a sequencing is widespread? The moratorium, adhered to by publication of increasing most insurers, on the use of numbers of individual human genetic testing information for genome sequences suggests assessing life insurance that we should start to consider applications. It is important some of the implications that this remains in place and associated with the availability its effectiveness is reviewed of personal genetic well before the current information. In this issue we moratorium expires in 2011. present two articles reflecting The Human Genetics on his issue: a report from a Commission Genetics Society sponsored (http://www.hgc.gov.uk) meeting recently held in monitor issues relating to Cambridge organised by The genetic discrimination in the Triple Helix, an international UK and are a point of contact undergraduate organisation, as for those with any concerns in the Millennium Technology Prize. -
Dissecting Dispensability
NEWS AND VIEWS Dissecting dispensability Laurence D Hurst & Csaba Pál Like most organisms, yeast has relatively few genes that are necessary for viability. The presence of a duplicate gene elsewhere in the genome underpins many cases of dispensability. A new study suggests that the backup mechanism is more complex than previously assumed and requires feedback loops that ensure transcriptional upregulation of the duplicate. Four-fifths of yeast’s genes are not essential there is no relationship between the degree of The idea that the process involves active for viability1. This preponderance of dis- coexpression and the likelihood that a gene will reprogramming of transcription might lead pensable genes is observed in eukaryotes2,3 be dispensible11. Kafri et al. show that, in yeast, some to suggest that the process might be the and prokaryotes4,5, with only one known most duplicate-associated backup involves product of selection for dispensability. But this exception to date (the intracellular parasite genes that, on average, are not strongly coex- would be too hasty a conclusion. Isozymes are Mycoplasma genitalium)6. Many examples of pressed, do not share many similar 5′ motifs not maintained for key reactions in the meta- apparent dispensability may depend on the (that bind particular transcription factors) bolic network, suggesting that their retention specific conditions under which some genes and diverged from each other a long time ago. is not due to selection7. are required (conditions not normally seen in How can such genes be redundant but not the laboratory)7, but this explanation cannot coexpressed? Feedback loops and upregulation account for all cases. -
PDF of Connecting Science's 2017
Connecting Science Wellcome Genome Campus Hinxton, Cambridgeshire CB10 1RQ wellcomegenomecampus.org/connectingscience Annual Review 2017/18 2 02 Contents DIRECTO R’S INTRODUCTION Connecting Science in twelve months 04 – 05 Global ambitions Have you had your say on your DNA? 10 – 1 1 Increasing global impact by tailoring training needs 12 – 13 Worm hunting in Colombia 14 – 16 Catalysing collaboration Bringing together scientific partners 20 – 21 First global event for genetic counsellors 22 – 23 Decoding genomes together 24 – 26 Snapshot: May 2017 to April 2018 27 – 32 Democratising genomics CONNECTING SCIENCE Blood, sweat and success – Implementing a gender balance policy 36 – 37 2017/18 ANNUAL REVIEW Science communication: remembering to listen 38 – 39 Exploring our world in the Genome Gallery 40 – 41 The mission of Connecting Science is simple: to enable team, the commitment and support of our many partners and everyone to explore genomic science and its impact on collaborators, and the financial support and encouragement research, health and society. Behind those simple words is of Wellcome. I am personally very thankful for all of those Wellcome Genome Campus: considerable complexity. The science itself is complex and things, and know that this support and energy often translates ever-changing, with new technologies being continually into life- or career-changing experiences for the tens of A hub of knowledge, learning, developed and put into practice in both research and thousands of people we engage with directly every year. healthcare. The work that we do is also deceptively and engagement complex, reaching audiences from primary schools to I hope that some of the stories highlighted in this Annual research scientists, NHS staff to patients and their families; Review give you a sense of the excitement we have in all Creating spaces for thinking 46 – 47 it spans the globe, and everything we do involves constant that we do. -
The Role of Causal Processes in the Neutral and Nearly Neutral Theories
Dartmouth College Dartmouth Digital Commons Dartmouth Scholarship Faculty Work 12-2008 The Role of Causal Processes in the Neutral and Nearly Neutral Theories Michael R. Dietrich Dartmouth College Roberta L. Millstein University of California, Davis Follow this and additional works at: https://digitalcommons.dartmouth.edu/facoa Part of the Biology Commons, Evolution Commons, and the Philosophy of Science Commons Dartmouth Digital Commons Citation Dietrich, Michael R. and Millstein, Roberta L., "The Role of Causal Processes in the Neutral and Nearly Neutral Theories" (2008). Dartmouth Scholarship. 1906. https://digitalcommons.dartmouth.edu/facoa/1906 This Article is brought to you for free and open access by the Faculty Work at Dartmouth Digital Commons. It has been accepted for inclusion in Dartmouth Scholarship by an authorized administrator of Dartmouth Digital Commons. For more information, please contact [email protected]. The Role of Causal Processes in the Neutral and Nearly Neutral Theories Michael R. Dietrich and Roberta L. Millstein† The neutral and nearly neutral theories of molecular evolution are sometimes char- acterized as theories about drift alone, where drift is described solely as an outcome, rather than a process. We argue, however, that both selection and drift, as causal processes, are integral parts of both theories. However, the nearly neutral theory ex- plicitly recognizes alleles and/or molecular substitutions that, while engaging in weakly selected causal processes, exhibit outcomes thought to be characteristic of random drift. A narrow focus on outcomes obscures the significant role of weakly selected causal processes in the nearly neutral theory. 1. Introduction. Gabriel Dover once complained that being nearly neutral is like being “just a little bit pregnant” (Dover 1997, 91). -
Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications
University of Pennsylvania ScholarlyCommons Publicly Accessible Penn Dissertations 2015 Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications Yang Ding University of Pennsylvania, [email protected] Follow this and additional works at: https://repository.upenn.edu/edissertations Part of the Bioinformatics Commons, Biology Commons, and the Evolution Commons Recommended Citation Ding, Yang, "Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications" (2015). Publicly Accessible Penn Dissertations. 1687. https://repository.upenn.edu/edissertations/1687 This paper is posted at ScholarlyCommons. https://repository.upenn.edu/edissertations/1687 For more information, please contact [email protected]. Detecting Selection on Noncoding Nucleotide Variation: Methods and Applications Abstract There has been a long tradition in molecular evolution to study selective pressures operating at the amino-acid level. But protein-coding variation is not the only level on which molecular adaptations occur, and it is not clear what roles non-coding variation has played in evolutionary history, since they have not yet been systematically explored. In this dissertation I systematically explore several aspects of selective pressures of noncoding nucleotide variation: The first project (Chapter 2) describes research on the determinants of eukaryotic translation dynamics, which include selection on non-coding aspects of DNA variation. Deep sequencing of ribosome-protected mRNA fragments and polysome gradients in various eukaryotic organisms have revealed an intriguing pattern: shorter mRNAs tend to have a greater overall density of ribosomes than longer mRNAs. There is debate about the cause of this trend. To resolve this open question, I systematically analysed 5’ mRNA structure and codon usage patterns in short versus long genes across 100 sequenced eukaryotic genomes. -
Issue 84 of the Genetics Society Newsletter
JANUARY 2021 | ISSUE 84 GENETICS SOCIETY NEWS In this issue The Genetics Society News is edited by • Non-canonical Careers: Thinking Outside the Box of Academia and Industry Margherita Colucci and items for future • Celebrating the 35th anniversary of DNA fingerprinting issues can be sent to the editor by email • Genetics Society Summer Studentship Workshop 2020 to [email protected]. • 2020 Heredity best student-led paper prize winners The Newsletter is published twice a year, • Industrious Science: interview with Dr Paul Lavin with copy dates of July and January. Celebrating students’ achievements: 2020 Genetics Society Summer Studentship Workshop, 2020 Heredity best student-led paper prize. Page 30 A WORD FROM THE EDITOR A word from the editor Welcome to Issue 84 elcome to the latest issue of the Thinking Outside the Box of WGenetics Society Newsletter! Academia and Industry”. This little This issue is packed with great news vade mecum for careers in genetics of achievements and good science. The collects inspiring interviews led first Genetics Society virtual workshop by our very own Postgraduate for the 2020 Summer studentship saw Representative, Emily Baker. In exceptional contributions from the Emily’s words, these experiences attending students. You can read more “demonstrate how a PhD in genetics about participants’ experiences in the can be a platform for a career in just interviews with the talk’s winners in about anything. Pursuing a career the Feature section. in academia, industry, publishing or science communication could be for Many more prizes were awarded: you, but so could many others. Why Heredity journal announced the not take a career path less travelled 2020 Heredity best student-led paper by, it might make all the difference?” winners, and James Burgon’s Heredity podcast dedicated an episode to the Enjoy! first prize winner, with insights from Best wishes, Heredity Editor-in-Chief, Barbara Margherita Colucci Mable.