BSCB Magazine BRITISH SOCIETY for CELL BIOLOGY
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Dynamical Gene Regulatory Networks Are Tuned by Transcriptional Autoregulation with Microrna Feedback Thomas G
www.nature.com/scientificreports OPEN Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback Thomas G. Minchington1, Sam Grifths‑Jones2* & Nancy Papalopulu1* Concepts from dynamical systems theory, including multi‑stability, oscillations, robustness and stochasticity, are critical for understanding gene regulation during cell fate decisions, infammation and stem cell heterogeneity. However, the prevalence of the structures within gene networks that drive these dynamical behaviours, such as autoregulation or feedback by microRNAs, is unknown. We integrate transcription factor binding site (TFBS) and microRNA target data to generate a gene interaction network across 28 human tissues. This network was analysed for motifs capable of driving dynamical gene expression, including oscillations. Identifed autoregulatory motifs involve 56% of transcription factors (TFs) studied. TFs that autoregulate have more interactions with microRNAs than non‑autoregulatory genes and 89% of autoregulatory TFs were found in dual feedback motifs with a microRNA. Both autoregulatory and dual feedback motifs were enriched in the network. TFs that autoregulate were highly conserved between tissues. Dual feedback motifs with microRNAs were also conserved between tissues, but less so, and TFs regulate diferent combinations of microRNAs in a tissue‑dependent manner. The study of these motifs highlights ever more genes that have complex regulatory dynamics. These data provide a resource for the identifcation of TFs which regulate the dynamical properties of human gene expression. Cell fate changes are a key feature of development, regeneration and cancer, and are ofen thought of as a “land- scape” that cells move through1,2. Cell fate changes are driven by changes in gene expression: turning genes on or of, or changing their levels above or below a threshold where a cell fate change occurs. -
SM08 Programme
SATELLITE MEETING Regulation of gene expression from a distance: exploring mechanisms The Royal Society at Chicheley Hall, home of the Kavli Royal Society International Centre Organised by Professor Wendy Bickmore and Professor Veronica van Heyningen FRS Wednesday 24 – Thursday 25 October 2012 DAY 1 DAY 2 SESSION 1 SESSION 2 SESSION 3 SESSION 4 Enhancer assays Quantitative and dynamic analysis Quantitative & dynamic analysis of Defining enhancers and their mechanisms – transgenes, genetics, and interactomes of transcription protein binding at regulatory of action Chair: Professor Nick Hastie CBE FRS Chair: elements Chair: Dr Duncan Odom Welcome by RS & lead 09.00 Professor Anne Ferguson-Smith Chair: Professor Constance Bonifer organiser The evolution of global Dynamic use of enhancers in Design rules for bacterial Massively parallel functional 09.05 enhancers 13.30 development 09.00 enhancers 13.15 dissection of mammalian enhancers Professor Denis Duboule Professor Mike Levine Dr Roee Amit Dr Rupali Patwardhan 09.30 Discussion 14.00 Discussion 09.30 Discussion 13.45 Discussion Complex protein dynamics at HERC2 rs12913832 modulates The pluripotent 3D genome Gene expression genomics eukaryotic regulatory human pigmentation by attenuating 09.45 14.15 09.45 Professor Wouter de Laat Dr Sarah Teichmann elements chromatin-loop formation between a 14.00 Dr Gordon Hager long-range enhancer and the OCA2 promoter 10.15 Discussion 14.45 Discussion 10.15 Discussion Dr Robert-Jan Palstra 10.30 Coffee 15.00 Tea 10.30 Coffee 14.15 Tea Maps of open chromatin -
ZMYND10 Functions in a Chaperone Relay During Axonemal Dynein Assembly
bioRxiv preprint doi: https://doi.org/10.1101/233718; this version posted December 13, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 ZMYND10 functions in a chaperone relay during axonemal dynein assembly. 2 3 Girish R Mali1,9 , Patricia Yeyati1, Seiya Mizuno2, Margaret A Keighren1, Petra zur Lage3, Amaya 4 Garcia-Munoz4, Atsuko Shimada5, Hiroyuki Takeda5, Frank Edlich6, Satoru Takahashi2,7, Alex von 5 Kreigsheim4,8, Andrew Jarman3 and Pleasantine Mill1,*. 6 7 1. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of 8 Edinburgh, Edinburgh, UK, EH4 2XU 9 2. Laboratory Animal Resource Centre, University of Tsukuba, Tsukuba, Japan, 305-8575 10 3. Centre for Integrative Physiology, University of Edinburgh, Edinburgh, UK, EH8 9XD 11 4. Systems Biology Ireland, University College Dublin, Dublin, Ireland 12 5. Department of Biological Sciences, University of Tokyo, Tokyo, Japan, 113-0033 13 6. Institute for Biochemistry and Molecular Biology, University of Freiburg, Freiburg, Germany, 14 79104 15 7. Department of Anatomy and Embryology, Faculty of Medicine, University of Tsukuba, Tsukuba, 16 Japan, 305-8575 17 8. Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University 18 of Edinburgh, Edinburgh, UK, EH4 2XU 19 9. Current address: MRC Laboratory of Molecular Biology, Cambridge, UK, CB2 0QH 20 * Corresponding author: [email protected] 21 22 23 24 25 26 27 28 29 30 31 1 bioRxiv preprint doi: https://doi.org/10.1101/233718; this version posted December 13, 2017. -
Mothers in Science
The aim of this book is to illustrate, graphically, that it is perfectly possible to combine a successful and fulfilling career in research science with motherhood, and that there are no rules about how to do this. On each page you will find a timeline showing on one side, the career path of a research group leader in academic science, and on the other side, important events in her family life. Each contributor has also provided a brief text about their research and about how they have combined their career and family commitments. This project was funded by a Rosalind Franklin Award from the Royal Society 1 Foreword It is well known that women are under-represented in careers in These rules are part of a much wider mythology among scientists of science. In academia, considerable attention has been focused on the both genders at the PhD and post-doctoral stages in their careers. paucity of women at lecturer level, and the even more lamentable The myths bubble up from the combination of two aspects of the state of affairs at more senior levels. The academic career path has academic science environment. First, a quick look at the numbers a long apprenticeship. Typically there is an undergraduate degree, immediately shows that there are far fewer lectureship positions followed by a PhD, then some post-doctoral research contracts and than qualified candidates to fill them. Second, the mentors of early research fellowships, and then finally a more stable lectureship or career researchers are academic scientists who have successfully permanent research leader position, with promotion on up the made the transition to lectureships and beyond. -
BSCB Newsletter 2017D
2017 BSCB Newsletter BRITISH SOCIETY FOR CELL BIOLOGY Meet the new BSCB President Royal Opening of the Crick Meeting reports 2017 CONTENTS BSCB Newsletter News 2 Book reviews 7 Features 8 Meeting Reports 24 Summer students 30 Society Business 33 Editorial Welcome to the 2017 BSCB newsletter. After several meeting hosted several well received events for our Front cover: years of excellent service, Kate Nobes has stepped PhD and Postdoc members, which we discuss on The head of a Drosophila pupa. The developing down and handed the reins over to me. I’ve enjoyed page 5. Our PhD and Postdoc reps are working hard compound eye (green) is putting together this years’ newsletter. It’s been great to make the event bigger and better for next year! The composed of several hundred simple units called ommatidia to hear what our members have been up to, and I social events were well attended including the now arranged in an extremely hope you will enjoy reading it. infamous annual “Pub Quiz” and disco after the regular array. The giant conference dinner. Members will be relieved to know polyploidy cells of the fat body (red), the fly equivalent of the The 2016 BSCB/DB spring meeting, organised by our we aren’t including any photos from that here. mammalian liver and adipose committee members Buzz Baum (UCL), Silke tissue, occupy a big area of the Robatzek and Steve Royle, had a particular focus on In this issue, we highlight the great work the BSCB head. Cells and Tissue Architecture, Growth & Cell Division, has been doing to engage young scientists. -
Ventral Hindgut and Bladder Development
Ventral Hindgut and Bladder Development by Wei CHENG A thesis submitted in conformity with the requirements For the degree of PhD Graduate Department of Institute of Medical Science University of Toronto © Copyright by Wei Cheng, 2008 Library and Bibliotheque et 1*1 Archives Canada Archives Canada Published Heritage Direction du Branch Patrimoine de I'edition 395 Wellington Street 395, rue Wellington Ottawa ON K1A0N4 Ottawa ON K1A0N4 Canada Canada Your file Votre reference ISBN: 978-0-494-40009-8 Our file Notre reference ISBN: 978-0-494-40009-8 NOTICE: AVIS: The author has granted a non L'auteur a accorde une licence non exclusive exclusive license allowing Library permettant a la Bibliotheque et Archives and Archives Canada to reproduce, Canada de reproduire, publier, archiver, publish, archive, preserve, conserve, sauvegarder, conserver, transmettre au public communicate to the public by par telecommunication ou par Plntemet, prefer, telecommunication or on the Internet, distribuer et vendre des theses partout dans loan, distribute and sell theses le monde, a des fins commerciales ou autres, worldwide, for commercial or non sur support microforme, papier, electronique commercial purposes, in microform, et/ou autres formats. paper, electronic and/or any other formats. The author retains copyright L'auteur conserve la propriete du droit d'auteur ownership and moral rights in et des droits moraux qui protege cette these. this thesis. Neither the thesis Ni la these ni des extraits substantiels de nor substantial extracts from it celle-ci ne doivent etre imprimes ou autrement may be printed or otherwise reproduits sans son autorisation. reproduced without the author's permission. -
Gene Expression Studies: from Case-Control to Multiple-Population-Based Studies
From the Institute of Human Genetics, Helmholtz Zentrum Munchen,¨ Deutsches Forschungszentrum fur¨ Gesundheit und Umwelt (GmbH) Head: Prof. Dr. Thomas Meitinger Gene expression studies: From case-control to multiple-population-based studies Thesis Submitted for a Doctoral Degree in Natural Sciences at the Faculty of Medicine, Ludwig-Maximilians-Universitat¨ Munchen¨ Katharina Schramm Dachau, Germany 2016 With approval of the Faculty of Medicine Ludwig-Maximilians-Universit¨atM ¨unchen Supervisor/Examiner: Prof. Dr. Thomas Illig Co-Examiners: Prof. Dr. Roland Kappler Dean: Prof. Dr. med. dent. Reinhard Hickel Date of oral examination: 22.12.2016 II Dedicated to my family. III Abstract Recent technological developments allow genome-wide scans of gene expression levels. The reduction of costs and increasing parallelization of processing enable the quantification of 47,000 transcripts in up to twelve samples on a single microarray. Thereby the data collec- tion of large population-based studies was improved. During my PhD, I first developed a workflow for the statistical analyses of case-control stu- dies of up to 50 samples. With large population-based data sets generated I established a pipeline for quality control, data preprocessing and correction for confounders, which re- sulted in substantially improved data. In total, I processed more than 3,000 genome-wide expression profiles using the generated pipeline. With 993 whole blood samples from the population-based KORA (Cooperative Health Research in the Region of Augsburg) study we established one of the largest population-based resource. Using this data set we contributed to a number of transcriptome-wide association studies within national (MetaXpress) and international (CHARGE) consortia. -
Translational Activity of the Splicing Factor SRSF1 Is Required for Development and Cilia Function
bioRxiv preprint doi: https://doi.org/10.1101/2020.09.04.263251; this version posted September 4, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Haward, Maslon, Yeyati et al. Translational activity of the splicing factor SRSF1 is required for development and cilia function Fiona Haward,1,5,6 Magdalena M. Maslon,1,6 Patricia L. Yeyati,1,6 Nicolas Bellora,2 Jan N. Hansen,3 Stuart Aitken,1 Jennifer Lawson,1 Alex von Kriegsheim,4 Dagmar Wachten,3 Pleasantine Mill,1,* Ian R. Adams1,* and Javier F. Cáceres1,7,* 1MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK 2IPATEC, ConseJo Nacional de Investigaciones, Científicas y Técnicas (CONICET)- Universidad Nacional del Comahue, 8400, Bariloche, Argentina. 3Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, Bonn, Germany 4Edinburgh Cancer Research UK Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road South, Edinburgh EH4 2XU, UK 5Present address: Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK 6These authors contributed equally to this work 7Lead contact *Correspondence: [email protected]; [email protected]; [email protected] Running title: Nucleo-cytoplasmic shuttling of SR proteins [Key Words: SR proteins; SRSF1; alternative splicing; mRNA translation; cilia] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.09.04.263251; this version posted September 4, 2020. -
Former Fellows Biographical Index Part
Former Fellows of The Royal Society of Edinburgh 1783 – 2002 Biographical Index Part Two ISBN 0 902198 84 X Published July 2006 © The Royal Society of Edinburgh 22-26 George Street, Edinburgh, EH2 2PQ BIOGRAPHICAL INDEX OF FORMER FELLOWS OF THE ROYAL SOCIETY OF EDINBURGH 1783 – 2002 PART II K-Z C D Waterston and A Macmillan Shearer This is a print-out of the biographical index of over 4000 former Fellows of the Royal Society of Edinburgh as held on the Society’s computer system in October 2005. It lists former Fellows from the foundation of the Society in 1783 to October 2002. Most are deceased Fellows up to and including the list given in the RSE Directory 2003 (Session 2002-3) but some former Fellows who left the Society by resignation or were removed from the roll are still living. HISTORY OF THE PROJECT Information on the Fellowship has been kept by the Society in many ways – unpublished sources include Council and Committee Minutes, Card Indices, and correspondence; published sources such as Transactions, Proceedings, Year Books, Billets, Candidates Lists, etc. All have been examined by the compilers, who have found the Minutes, particularly Committee Minutes, to be of variable quality, and it is to be regretted that the Society’s holdings of published billets and candidates lists are incomplete. The late Professor Neil Campbell prepared from these sources a loose-leaf list of some 1500 Ordinary Fellows elected during the Society’s first hundred years. He listed name and forenames, title where applicable and national honours, profession or discipline, position held, some information on membership of the other societies, dates of birth, election to the Society and death or resignation from the Society and reference to a printed biography. -
EMBC Annual Report 2007
EMBO | EMBC annual report 2007 EUROPEAN MOLECULAR BIOLOGY ORGANIZATION | EUROPEAN MOLECULAR BIOLOGY CONFERENCE EMBO | EMBC table of contents introduction preface by Hermann Bujard, EMBO 4 preface by Tim Hunt and Christiane Nüsslein-Volhard, EMBO Council 6 preface by Marja Makarow and Isabella Beretta, EMBC 7 past & present timeline 10 brief history 11 EMBO | EMBC | EMBL aims 12 EMBO actions 2007 15 EMBC actions 2007 17 EMBO & EMBC programmes and activities fellowship programme 20 courses & workshops programme 21 young investigator programme 22 installation grants 23 science & society programme 24 electronic information programme 25 EMBO activities The EMBO Journal 28 EMBO reports 29 Molecular Systems Biology 30 journal subject categories 31 national science reviews 32 women in science 33 gold medal 34 award for communication in the life sciences 35 plenary lectures 36 communications 37 European Life Sciences Forum (ELSF) 38 ➔ 2 table of contents appendix EMBC delegates and advisers 42 EMBC scale of contributions 49 EMBO council members 2007 50 EMBO committee members & auditors 2007 51 EMBO council members 2008 52 EMBO committee members & auditors 2008 53 EMBO members elected in 2007 54 advisory editorial boards & senior editors 2007 64 long-term fellowship awards 2007 66 long-term fellowships: statistics 82 long-term fellowships 2007: geographical distribution 84 short-term fellowship awards 2007 86 short-term fellowships: statistics 104 short-term fellowships 2007: geographical distribution 106 young investigators 2007 108 installation -
Feedback Interactions Between Cell–Cell Adherens Junctions and Cytoskeletal Dynamics in Newt Lung Epithelial Cells□V Clare M
Molecular Biology of the Cell Vol. 11, 2471–2483, July 2000 Feedback Interactions between Cell–Cell Adherens Junctions and Cytoskeletal Dynamics in Newt Lung Epithelial Cells□V Clare M. Waterman-Storer,*†‡ Wendy C. Salmon,†‡ and E.D. Salmon‡ *Department of Cell Biology and Institute for Childhood and Neglected Diseases, The Scripps Research Institute, La Jolla, California 92037; and ‡Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599 Submitted February 3, 2000; Revised April 20, 2000; Accepted May 11, 2000 Monitoring Editor: Jennifer Lippincott-Schwartz To test how cell–cell contacts regulate microtubule (MT) and actin cytoskeletal dynamics, we examined dynamics in cells that were contacted on all sides with neighboring cells in an epithelial cell sheet that was undergoing migration as a wound-healing response. Dynamics were recorded using time-lapse digital fluorescence microscopy of microinjected, labeled tubulin and actin. In fully contacted cells, most MT plus ends were quiescent; exhibiting only brief excursions of growth and shortening and spending 87.4% of their time in pause. This contrasts MTs in the lamella of migrating cells at the noncontacted leading edge of the sheet in which MTs exhibit dynamic instability. In the contacted rear and side edges of these migrating cells, a majority of MTs were also quiescent, indicating that cell–cell contacts may locally regulate MT dynamics. Using photoactivation of fluorescence techniques to mark MTs, we found that MTs in fully contacted cells did not undergo retrograde flow toward the cell center, such as occurs at the leading edge of motile cells. Time-lapse fluorescent speckle microscopy of fluorescently labeled actin in fully contacted cells revealed that actin did not flow rearward as occurs in the leading edge lamella of migrating cells. -
Reflections on the Historiography of Molecular Biology
Reflections on the Historiography of Molecular Biology HORACE FREELAND JUDSON SURELY the time has come to stop applying the word revolution to the rise of new scientific research programmes. Our century has seen many upheavals in scientific ideas--so many and so varied that the notion of scientific revolution has been stretched out of shape and can no longer be made to cover the processes of change characteristic of most sciences these past hundred years. By general consent, two great research pro- grammes arising in this century stand om from the others. The first, of course, was the one in physics that began at the turn of the century with quantum theory and relativity and ran through the working out, by about 1930, of quantum mechanics in its relativistic form. The trans- formation in physics appears to be thoroughly documented. Memoirs and biographies of the physicists have been written. Interviewswith survivors have been recorded and transcribed. The history has been told at every level of detail and difficulty. The second great programme is the one in biology that had its origins in the mid-1930s and that by 1970 had reached, if not a conclusion, a kind of cadence--a pause to regroup. This is the transformation that created molecular biology and latter-day biochemistry. The writing of its history has only recently started and is beset with problems. Accounting for the rise of molecular biology began with brief, partial, fugitive essays by participants. Biographies have been written of two, of the less understood figures in the science, who died even as the field was ripening, Oswald Avery and Rosalind Franklin; other scientists have wri:tten their memoirs.