Lectures and Seminars, Michaelmas Term 2016
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Genetic and Epigenetic Mechanisms of the Regulation of Mouse Embryonic Stem Cells Self-Renewal by the Pluripotency Transcription Factor Nanog
Genetic and epigenetic mechanisms of the regulation of mouse embryonic stem cells self-renewal by the pluripotency transcription factor Nanog Victor HEURTIER Thèse de doctorat de Biologie Dirigée par Pablo NAVARRO GIL Laboratoire Epigénétique des cellules souches – Institut Pasteur Sorbonne Université Ecole doctorale Complexité du Vivant (ED 515) Présentée et soutenue publiquement le 18/09/2018 Devant un jury composé de : Président : Pr MOUCHEL-VIELH Emmanuèle, Professeur Rapporteur : Dr SAVATIER Pierre, Directeur de Recherche Rapporteur : Dr RADA-IGLESIAS Alvaro, Chef d’équipe Examinateur : Dr AZUARA Veronique, Maître de conférences Examinateur : Dr PINSKAYA Marina, Maître de conférences Directeur de thèse : Dr NAVARRO GIL Pablo, Chef d’équipe Abstract Mouse embryonic stem (ES) cells are derived from the pre-implantation blastocyst and are able to maintain their pluripotent state through virtually limitless cell divisions in vitro. The study of the mechanisms regulating the specific features of ES cells led to the discovery of the transcription factors (TFs) governing their unique transcriptome. Among those TFs, Nanog plays a central role in the gene regulatory network that supports ES cells self-renewal. However, the molecular mechanisms by which Nanog exerts its functions are not fully elucidated. We adapted an inducible CRISPR activation (CRISPRa) system in mouse ES cells and demonstrated its functionality to stimulate transcription at endogenous loci. We then accurately determined the list of Nanog responsive genes using gain (CRISPRa cell line) and loss of function experiments and total RNA sequencing. Moreover, the DNA binding profiles of distinct pluripotency TFs were assessed genome-wide by chromatin immunoprecipitation (ChIP) and sequencing upon Nanog depletion and revealed the importance of the latter in the regulation of the pluripotency network activity at thousands of loci. -
Full Programme
Full Programme www.bristol.ac.uk/ehbea2014 1 Contents Welcome 3 Key Events 5 Schedule at a Glance 6 Plenary Abstracts 9 Talk Abstracts 15 Poster Abstracts 61 2 Welcome Welcome to the 9th Annual Conference of the European Human Behaviour and Evolution Association! We are delighted to welcome you to Bristol, a unique and bustling city in South West England. The conference venue At-Bristol is located in the central area, by the historic harbourside. Most of the attractions are within walking distance: Bristol Aquarium, Brunel’s ss Great Britain, M Shed (museum of Bristol’s history), Bristol Cathedral, Bristol Shopping Quarter, Bristol Museum and Art Gallery, and University of Bristol. The Bristol Zoo Gardens and the world- famous Clifton Suspension Bridge are a 40-minute walk (or a short bus ride) from the centre. There are also many green spaces nearby: College Green, Queen Square, Brandon Hill, and Castle Park. For the conference, we are delighted to welcome our plenary speakers Russell Gray, Martie Haselton, Daniel Hruschka, Annette Karmiloff-Smith, and Samir Okasha. We are also excited to have as our sixth plenary speaker, the 2014 New Investigator Award winner Willem Frankenhuis. In addition, we have 46 talks and 104 posters spanning a wide range of topics and approaches from researchers around the world. On Monday morning, Prof Nick Lieven (Pro Vice-Chancellor, University of Bristol) will open the conference, which will be followed by the first plenary. The Poster Session will take place on Monday evening, but we invite the presenters to have their posters displayed for the duration of the conference starting Sunday evening. -
Cultural Group Selection Plays an Essential Role in Explaining Human Cooperation: a Sketch of the Evidence
BEHAVIORAL AND BRAIN SCIENCES (2016), Page 1 of 68 doi:10.1017/S0140525X1400106X, e30 Cultural group selection plays an essential role in explaining human cooperation: A sketch of the evidence Peter Richerson Emily K. Newton Department of Environmental Science and Policy, University of California– Department of Psychology, Dominican University of California, San Rafael, CA Davis, Davis, CA 95616 94901 [email protected] [email protected] http://emilyknewton.weebly.com/ www.des.ucdavis.edu/faculty/richerson/richerson.htm Nicole Naar Ryan Baldini Department of Anthropology, University of California–Davis, Graduate Group in Ecology, University of California–Davis, Davis, CA 95616 Davis, CA 95616 [email protected] https://sites.google.com/site/ryanbaldini/ [email protected] Adrian V. Bell Lesley Newson Department of Anthropology, University of Utah, Salt Lake City, UT 84112 Department of Environmental Science and Policy, University of California– [email protected] http://adrianbell.wordpress.com/ Davis, Davis, CA 95616 [email protected] [email protected] Kathryn Demps https://www.researchgate.net/profile/Lesley_Newson/ Department of Anthropology, Boise State University, Boise, ID 83725 [email protected] Cody Ross http://sspa.boisestate.edu/anthropology/faculty-and-staff/kathryn- Santa Fe Institute, Santa Fe, NM 87501 demps/ [email protected] http://scholar.google.com/citations?user=xSugEskAAAAJ Karl Frost Graduate Group in Ecology, University of California–Davis, Davis, CA 95616 Paul E. Smaldino [email protected] https://sites.google.com/site/karljosephfrost/ Department of Anthropology, University of California–Davis, Davis, CA 95616 [email protected] http://www.smaldino.com/ Vicken Hillis Department of Environmental Science and Policy, University of California– Timothy M. -
Biological Basics and the Economics of the Family Author(S): Donald Cox Reviewed Work(S): Source: the Journal of Economic Perspectives, Vol
American Economic Association Biological Basics and the Economics of the Family Author(s): Donald Cox Reviewed work(s): Source: The Journal of Economic Perspectives, Vol. 21, No. 2 (Spring, 2007), pp. 91-108 Published by: American Economic Association Stable URL: http://www.jstor.org/stable/30033719 . Accessed: 31/08/2012 19:26 Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at . http://www.jstor.org/page/info/about/policies/terms.jsp . JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. American Economic Association is collaborating with JSTOR to digitize, preserve and extend access to The Journal of Economic Perspectives. http://www.jstor.org Journal of EconomicPerspectives-Volume 21, Number2-Spring 2007-Pages 91-108 Biological Basics and the Economics of the Family Donald Cox any economic models of the family are based on a generic "person one/person two" household or "parent-child" family, rather than their anatomicallyanatomically correct counterparts: sons and daughters, fathers and mothers, and grandfathers and grandmothers. These economic models can offer powerful insights into family behavior, but also can leave certain patterns unex- plained and neglect potentially important crosscurrents. Melding biological in- sights with family economics can cast new light on existing knowledge and open up novel paths for research. For example, study after study has found that putting family income in the hands of mothers, rather than fathers, tends to increase the consumption of children, as noted in this journal in Lundberg and Pollak (1996). -
Towards a Unified Science of Cultural Evolution
BEHAVIORAL AND BRAIN SCIENCES (2006) 29, 329–383 Printed in the United States of America Towards a unified science of cultural evolution Alex Mesoudi Centre for Social Learning and Cognitive Evolution and School of Psychology, University of St. Andrews, St. Andrews, Fife KY16 9JP, Scotland, United Kingdom; and Department of Anthropology, University of Missouri – Columbia, Columbia, MO 65211; and W. Maurice Young Centre for Applied Ethics, University of British Columbia, Vancouver, British Columbia V6T 1Z2, Canada. [email protected] www.missouri.edu/mesoudia/ Andrew Whiten Centre for Social Learning and Cognitive Evolution and School of Psychology, University of St. Andrews, St. Andrews, Fife KY16 9JP, Scotland, United Kingdom. [email protected] www.st-and.ac.uk/aw2/ Kevin N. Laland Centre for Social Learning and Cognitive Evolution and School of Biology, University of St. Andrews, St. Andrews, Fife KY16 9TS, Scotland, United Kingdom. [email protected] www.st-andrews.ac.uk/seal Abstract: We suggest that human culture exhibits key Darwinian evolutionary properties, and argue that the structure of a science of cultural evolution should share fundamental features with the structure of the science of biological evolution. This latter claim is tested by outlining the methods and approaches employed by the principal subdisciplines of evolutionary biology and assessing whether there is an existing or potential corresponding approach to the study of cultural evolution. Existing approaches within anthropology and archaeology demonstrate a good match with the macroevolutionary methods of systematics, paleobiology, and biogeography, whereas mathematical models derived from population genetics have been successfully developed to study cultural microevolution. -
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SUBMISSION TO THE INTERNATIONAL DEVELOPMENT SELECT COMMITTEE INQUIRY INTO THE PHILOSOPHY AND CULTURE OF AID Summary and recommendation 1. We recommend that as part of your ‘philosophy and culture of aid’ inquiry that you consider prioritizing the topic of cuts to ODA-funded research. All organisations and actors within the international development sector in the UK and internationally – INGOs, academics, research programmes, diaspora – are extremely concerned about the harm caused by these cuts. 2. An inquiry would be an opportunity to assess the likely impact on both UK organisations but also our partners in the Global South, and to argue that the decision should be reconsidered. We anticipate that witnesses would raise philosophical questions about (a) the precautionary principle; for example, should international agencies commit to the prevention of severe harm in their aid and development policies? (b) the importance of UK’s aid programme to our reputation, (c) the UK’s partnerships across the world and what responsibilities these entail, (d) the importance and hierarchies of knowledge in international development, (e) what kind of policy-making creates risk in our investments (also of interest to the Public Accounts Committee). 3. We recommend that you call this inquiry – ‘Cuts to partnership, knowledge and the prevention of harm’ and ask UK universities and INGOs to encourage submissions from across the Global South. We are aware that the IDSC has been diversifying witnesses, including encouraging practitioners and researchers in countries overseas to submit evidence, as a result of your 2019 global conference co-hosted with UKRI and GCRF. We would encourage every development studies department in the UK to encourage colleagues in the Global South to submit evidence. -
Conference Report: the Generalized Theory of Evolution, Duesseldorf Center for Logic and Philosophy of Science, January 31 – February 3, 2018
Conference Report: The Generalized Theory of Evolution, Duesseldorf Center for Logic and Philosophy of Science, January 31 { February 3, 2018 Gregor P. Greslehner According to Theodosius Dobzhansky's famous dictum, \nothing in bi- ology makes sense except in the light of evolution" [3]. On the other hand, philosophers like Ludwig Wittgenstein used to be rather skeptical concerning the relevance of evolutionary thinking to philosophy: \The Darwinian theory has no more to do with philosophy than has any other hypothesis of natural science" [6, 4.1122]. In the last decades, however, { in particular since Richard Dawkins coined the term `meme' for the cultural counterpart of the gene [2]{ the application of evolutionary principles has been successfully pursued in areas other than biology. The central principles are reproduction, variation, and selection [4]. Based on these principles, several models, methods, and theories of a wide range of phenomena have been developed { not confined to the realm of biology. More generally, philosophy of science, social sciences, psychology, economics, and many other areas show a growing interest in a generalized theory of evolution. Like in many disciplines and areas of research, the publication of an introductory textbook indicates a certain stage of maturity. Such a textbook has been provided (in German) by Gerhard Schurz [5]. An updated English version is currently in preparation. Being one of the first big conferences in this area, \The Generalized Theory of Evolution" brought together international researchers, schol- ars, and an interested audience to discuss the current state and trends of the interdisciplinary field of a generalized theory of evolution. -
Toward a New Comparative Musicology
Analytical Approaches To World Music 2.2 (2013) 148-197 Toward a New Comparative Musicology Patrick E. Savage1 and Steven Brown2 1Department of Musicology, Tokyo University of the Arts 2Department of Psychology, Neuroscience & Behaviour, McMaster University We propose a return to the forgotten agenda of comparative musicology, one that is updated with the paradigms of modern evolutionary theory and scientific methodology. Ever since the field of comparative musicology became redefined as ethnomusicology in the mid-20th century, its original research agenda has been all but abandoned by musicologists, not least the overarching goal of cross-cultural musical comparison. We outline here five major themes that underlie the re-establishment of comparative musicology: (1) classification, (2) cultural evolution, (3) human history, (4) universals, and (5) biological evolution. Throughout the article, we clarify key ideological, methodological and terminological objections that have been levied against musical comparison. Ultimately, we argue for an inclusive, constructive, and multidisciplinary field that analyzes the world’s musical diversity, from the broadest of generalities to the most culture-specific particulars, with the aim of synthesizing the full range of theoretical perspectives and research methodologies available. Keywords: music, comparative musicology, ethnomusicology, classification, cultural evolution, human history, universals, biological evolution This is a single-spaced version of the article. The official version with page numbers 148-197 can be viewed at http://aawmjournal.com/articles/2013b/Savage_Brown_AAWM_Vol_2_2.pdf. omparative musicology is the academic comparative musicology and its modern-day discipline devoted to the comparative study successor, ethnomusicology, is too complex to of music. It looks at music (broadly defined) review here. -
Emotions in the Field: the Psychology and Anthropology of Fieldwork
Emotions in the Field Emotions in the Field The Psychology and Anthropology of Fieldwork Experience Edited by James Davies and Dimitrina Spencer Stanford University Press Stanford, California Stanford University Press Stanford, California ©2010 by the Board of Trustees of the Leland Stanford Junior University. All rights reserved. No part of this book may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying and recording, or in any information storage or retrieval system without the prior written permission of Stanford University Press. Printed in the United States of America on acid-free, archival-quality paper Library of Congress Cataloging-in-Publication Data Emotions in the field : the psychology and anthropology of fieldwork experience / edited by James Davies and Dimitrina Spencer. p. cm. Includes bibliographical references and index. ISBN 978-0-8047-6939-6 (cloth : alk. paper) -- ISBN 978-0-8047-6940-2 (pbk. : alk. paper) 1. Ethnology--Fieldwork--Psychological aspects. 2. Emotions--Anthropological aspects. I. Davies, James (James Peter) II. Spencer, Dimitrina. GN346.E46 2010 305.8'00723--dc22 2009046034 Typeset by Bruce Lundquist in 10/14 Minion Contents Acknowledgments vii Contributors ix Introduction: Emotions in the Field 1 James Davies Part I Psychology of Field Experience 1 From Anxiety to Method in Anthropological Fieldwork: An Appraisal of George Devereux’s Enduring Ideas 35 Michael Jackson 2 “At the Heart of the Discipline”: Critical Reflections on Fieldwork 55 Vincent -
Attenuated Spread of X-Inactivation in an X;Autosome Translocation
Attenuated spread of X-inactivation in an X;autosome translocation Bilyana C. Popova*, Takashi Tada†, Nobuo Takagi‡, Neil Brockdorff*§, and Tatyana B. Nesterova* *Developmental Epigenetics, Medical Research Council Clinical Sciences Center, Imperial College Faculty of Medicine, Hammersmith Hospital, DuCane Road, London W12 ONN, United Kingdom; †Stem Cell Engineering, Stem Cell Research Center, Institute for Frontier Medical Sciences, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto 606-8507, Japan; and ‡Hokusei Gakuen University, Atsubetsu-ku, Sapporo 004-8631, Japan Communicated by Mary F. Lyon, Medical Research Council, Didcot, United Kingdom, March 14, 2006 (received for review January 20, 2006) X inactivation in female mammals involves transcriptional silencing autosomal material is attenuated in early development, soon after of an entire chromosome in response to a cis-acting noncoding the onset of random X inactivation. RNA, the X inactive-specific transcript (Xist). Xist can also inactivate To account for increased efficiency of silencing on the X chro- autosomal sequences, for example, in X;autosome translocations; mosome relative to autosomes, Gartler and Riggs (15) proposed the but here, silencing appears to be relatively inefficient. This varia- idea of ‘‘way stations’’ or ‘‘booster elements’’ that facilitate spread- tion has been attributed to either attenuated spreading of Xist RNA ing (and͞or maintenance) of X inactivation. These elements are at the onset of X inactivation or inefficient maintenance of auto- predicted to be unique to, or at least more prevalent on, the X somal silencing. Evidence to date has favored the latter. Here, we chromosome. More recently, Lyon (16) suggested that LINE-1 (L1) demonstrate attenuated spreading of Xist RNA at the onset of X repetitive elements, which are present at a relatively high density on inactivation in the T(X;4)37H X;autosome translocation. -
Local Tandem Repeat Expansion in Xist RNA As a Model for the Functionalisation of Ncrna
non-coding RNA Review Local Tandem Repeat Expansion in Xist RNA as a Model for the Functionalisation of ncRNA Neil Brockdorff Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK; [email protected] Received: 19 September 2018; Accepted: 16 October 2018; Published: 19 October 2018 Abstract: Xist, the master regulator of the X chromosome inactivation in mammals, is a 17 kb lncRNA that acts in cis to silence the majority of genes along the chromosome from which it is transcribed. The two key processes required for Xist RNA function, localisation in cis and recruitment of silencing factors, are genetically separable, at least in part. Recent studies have identified Xist RNA sequences and associated RNA-binding proteins (RBPs) that are important for these processes. Notably, several of the key Xist RNA elements correspond to local tandem repeats. In this review, I use examples to illustrate different modes whereby tandem repeat amplification has been exploited to allow orthodox RBPs to confer new functions for Xist-mediated chromosome inactivation. I further discuss the potential generality of tandem repeat expansion in the evolution of functional long non-coding RNAs (lncRNAs). Keywords: X inactivation; Xist; lncRNA; tandem repeat 1. Introduction The long non-coding RNA (lncRNA) Xist mediates X chromosome inactivation (X inactivation), the process that, in mammals, equalises levels of X-linked gene expression in XX female relative to XY male cells [1–5]. Xist RNA is expressed from the inactive chromosome-elect at the onset of X inactivation during early embryogenesis and then localises to a subnuclear domain corresponding to the X chromosome nuclear territory [4,6]. -
Features RNA Illuminating Xist
Features RNA Illuminating Xist Heather Coker, Benoit Moindrot, Greta Pintacuda and Neil Brockdorff (University of Oxford, UK) The Central Dogma proposed that RNA, encoded by DNA in the genome, acts as the template used by cells for protein production. The simplicity of RNA as a discrete mediator of information has subsequently been challenged by the discovery of non-protein-coding RNAs. Understanding Downloaded from http://portlandpress.com/biochemist/article-pdf/37/2/24/5434/bio037020024.pdf by guest on 30 September 2021 of this intricate new field has been fuelled by the development of new research techniques. In this article, we consider how recent advances in microscopy have added to our current understanding of the non-coding RNA Xist (X-inactive specific transcript). In female placental mammals, the process RNA cloud that can be visualized using fluorescent in of X-inactivation results in the permanent situ hybridization (FISH). This technique, in which silencing of one of the two X-chromosomes. The fluorescent probes are directed against Xist RNA inactive X-chromosome (Xi) is embedded into a (RNA-FISH), has been of particular use in visualizing repressive heterochromatic region known as the the effect of genetic changes upon the structure and Barr body, a DNA-dense region in the nucleus formation of the Xist domain (Figure 1). of XX somatic cells visible by light microscopy. Xist has been identified in all placental mammals, Xist is regarded as the ‘master regulator’ of this and shown to be composed of six broadly conserved6 complex process, which corrects the genetic segments of short repeats, named A to F (Figure imbalance of close to a thousand X-linked genes 2).