Gurdon Institute 20122011 PROSPECTUS / ANNUAL REPORT 20112010
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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. -
President's Message
Winter Issue 2013–2014 SOT News President’s Message I’m starting this President’s message with a quiz!!! It’s just one question, but it’s important that everyone knows the answer. The question is: What do prenatal programming and toxicity, perfluorinalkyl acids ,and human relevance of hemangiosarcomas in rodents have in common? [the answer appears at the end of this message]. While you ponder the answer to that question, I want to reflect on events of this fall and focus on several activities of the Society during recent times of uncertainty. The shutdown of the US government had some effect on nearly all of us. Important meetings, study sections, and day-to- day professional discussion and dialog were all furloughed during this time. However, the most significant impact was on our members who are government employees, and we can only hope that these matters are completely behind us. Unfortunately, there were significant deadlines for SOT matters scheduled during this time, particularly for abstract submissions and award President nominations. Lois D. Lehman- McKeeman I want to specifically acknowledge the work of the Scientific Program and Awards Committees for showing remarkable flexibility in modifying deadlines to accommodate member needs. As a quick review, the Awards committee moved deadlines for nominations to the last possible minute—giving them only about 1 week to review all nominations prior to meeting to select award winners. The prestigious Society awards are central to celebrating member accomplishments, and the work of this committee, against their own time limitations, underscores their commitment to this important activity. -
Society for Developmental Biology 64Th Annual Meeting
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Developmental Biology 283 (2005) 537 – 574 www.elsevier.com/locate/ydbio Society for Developmental Biology 64th Annual Meeting Hyatt Regency, San Francisco, CA July 27–August 1, 2005 Organizing Committee: Judith Kimble (Chair, SDB President), Kathy Barton, Minx Fuller, Nipam Patel, Didier Stainier, Xin Sun, Bill Wood Local Organizers: Didier Stainier, Ida Chow Numbers in italics are program abstract numbers and names in bold are speakers. Poster assignments are listed at the end of the meeting program. Program Wednesday, July 27 9 am–5 pm Satellite Symposia (not organized by SDB) Segmentation Seacliff AB Co-organizers: Kenro Kusumi and Olivier Pourquie´ Molecular Biology of Plant Development Seacliff CD Organizer: Kathy Barton 12–7 pm Meeting Registration Grand Foyer Poster Session I and Exhibits Set-up Pacific Concourse See poster assignments at the end of the program 7–9 pm President’s Symposium Grand Ballroom Fundamental Problems of Developmental Biology Chair: Judith Kimble, University of Wisconsin-Madison and HHMI, Madison, WI 7:00 The soma-germline dichotomy. G. Seydoux. Johns Hopkins University, Baltimore, MD 1 7:40 MicroRNAs and their regulatory roles in plants and animals. D.P. Bartel. MIT and Whitehead Institute for Biomedical Research, Cambridge, MA 8:20 The genetics and genomics of evolving new traits in vertebrates. D. Kingsley. Stanford University and HHMI, Stanford, CA 9–11 pm Opening Reception in Honor of Eric Olson, Pacific Concourse Developmental Biology Editor-in-Chief, for invaluable service to the community Poster Session I and Exhibits Pacific Concourse See poster assignments at the end of the program YDBIO-02007; No. -
The Role of Model Organisms in the History of Mitosis Research
Downloaded from http://cshperspectives.cshlp.org/ on September 30, 2021 - Published by Cold Spring Harbor Laboratory Press The Role of Model Organisms in the History of Mitosis Research Mitsuhiro Yanagida Okinawa Institute of Science and Technology Graduate University, Okinawa 904-0495, Japan Correspondence: [email protected] Mitosis is a cell-cycle stage during which condensed chromosomes migrate to the middle of the cell and segregate into two daughter nuclei before cytokinesis (cell division) with the aid of a dynamic mitotic spindle. The history of mitosis research is quite long, commencing well before the discovery of DNA as the repository of genetic information. However, great and rapid progress has been made since the introduction of recombinant DNA technology and discovery of universal cell-cycle control. A large number of conserved eukaryotic genes required for the progression from early to late mitotic stages have been discovered, confirm- ing that DNA replication and mitosis are the two main events in the cell-division cycle. In this article, a historical overview of mitosis is given, emphasizing the importance of diverse model organisms that have been used to solve fundamental questions about mitosis. Onko Chisin—An attempt to discover new truths by checkpoint [SAC]), then metaphase (in which studying the past through scrutiny of the old. the chromosomes are aligned in the middle of cell), anaphase A (in which identical sister chro- matids comprising individual chromosomes LARGE SALAMANDER CHROMOSOMES separate and move toward opposite poles of ENABLED THE FIRST DESCRIPTION the cell), anaphase B (in which the spindle elon- OF MITOSIS gates as the chromosomes approach the poles), itosis means “thread” in Greek. -
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. -
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. -
FOI Ref 6871 Response Sent 17 March Can You Please Provide The
FOI Ref 6871 Response sent 17 March Can you please provide the following details from the most recent records which you hold under The Licensing Act 2003: On-trade alcohol licensed premises, including: Premises Licence Number Date Issued Premises Licence Status (active, expired etc.) Premises Name Premises Address Premises Postcode Premises Telephone Number Premises on-trade Category (e.g. Cafe, Bar, Theatre, Nightclub etc.) Premises Licence Holder Name Premises Licence Holder Address Premises Licence Holder Postcode Designated Premises Supervisor Name Designated Premises Supervisor Address Designated Premises Supervisor Postcode The information you have requested is held and in the attached. However the personal information relating to Designated Premises Supervisors you have requested is refused under the exemption to disclosure at Section 40(2) of the Act Further queries on this matter should be directed to [email protected] Full address Telephone number Licence type Status Date issued Licence holder 1 and 1 Rougamo Ltd, 84 Regent Street, Cambridge, 07730029914 Premises Licence Current Licence 10/03/2020 Yao Qin Cambridgeshire, CB2 1DP 2648 Cambridge, 14A Trinity Street, Cambridge, 01223 506090 Premises Licence Current Registration 03/10/2005 The New Vaults Limited Cambridgeshire, CB2 1TB 2nd View Cafe - Waterstones, 20-22 Sidney Street, Premises Licence Current Registration 17/09/2010 Waterstones Booksellers Ltd Cambridge, Cambridgeshire, CB2 3HG ADC Theatre, Park Street, Cambridge, Cambridgeshire, CB5 01223 359547 Premises Licence -
Ordered Proteolysis in Anaphase Inactivates Plk1 To
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by PubMed Central JCBArticle Ordered proteolysis in anaphase inactivates Plk1 to contribute to proper mitotic exit in human cells Catherine Lindon and Jonathon Pines Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Zoology, University of Cambridge, Cambridge CB2 1QR, England, UK e have found that key mitotic regulators show identified a putative destruction box in Plk1 that is required distinct patterns of degradation during exit from for degradation of Plk1 in anaphase, and have examined W mitosis in human cells. Using a live-cell assay for the effect of nondegradable Plk1 on mitotic exit. Our results proteolysis, we show that two of these regulators, polo-like show that Plk1 proteolysis contributes to the inactivation of kinase 1 (Plk1) and Aurora A, are degraded at different Plk1 in anaphase, and that this is required for the proper times after the anaphase-promoting complex/cyclosome control of mitotic exit and cytokinesis. Our experiments (APC/C) switches from binding Cdc20 to Cdh1. Therefore, reveal a role for APC/C-mediated proteolysis in exit from events in addition to the switch from Cdc20 to Cdh1 control mitosis in human cells. the proteolysis of APC/CCdh1 substrates in vivo. We have Introduction In animal cells, the regulated proteolysis of cyclin A, cyclin APC/C switches from its Cdc20- to Cdh1-activated form, or B1, and securin during mitosis are all essential for the proper whether they are degraded at distinct times, perhaps to coor- timing of events leading up to separation of sister chromatids dinate exit from mitosis. -
Gurdon Institute 2010 PROSPECTUS / ANNUAL REPORT 2009
The Wellcome Trust/Cancer Research UK Gurdon Institute 2010 PROSPECTUS / ANNUAL REPORT 2009 Gurdon I N S T I T U T E PROSPECTUS 2010 ANNUAL REPORT 2009 http://www.gurdon.cam.ac.uk THE GURDON INSTITUTE 1 CONTENTS THE INSTITUTE IN 2009 INTRODUCTION....................................................................................................................3 HISTORICAL BACKGROUND..........................................................................................................4 CENTRAL SUPPORT SERVICES....................................................................................................4 FUNDING...........................................................................................................................................4 RETREAT.................................................................................................................................................5 RESEARCH GROUPS.........................................................................................................6 MEMBERS OF THE INSTITUTE................................................................................38 CATEGORIES OF APPOINTMENT..............................................................................38 POSTGRADUATE OPPORTUNITIES..........................................................................38 SENIOR GROUP LEADERS.............................................................................................38 GROUP LEADERS.......................................................................................................................45 -
Anatomically and Functionally Distinct Lung Mesenchymal Populations Marked by Lgr5 and Lgr6
Anatomically and Functionally Distinct Lung Mesenchymal Populations Marked by Lgr5 and Lgr6 The MIT Faculty has made this article openly available. Please share how this access benefits you. Your story matters. Citation Lee, Joo-Hyeon et al. “Anatomically and Functionally Distinct Lung Mesenchymal Populations Marked by Lgr5 and Lgr6.” Cell 170, 6 (September 2017): 1149–1163 © 2017 The Authors As Published http://dx.doi.org/10.1016/J.CELL.2017.07.028 Publisher Elsevier BV Version Final published version Citable link http://hdl.handle.net/1721.1/116555 Terms of Use Creative Commons Attribution 4.0 International License Detailed Terms http://creativecommons.org/licenses/by/4.0/ Article Anatomically and Functionally Distinct Lung Mesenchymal Populations Marked by Lgr5 and Lgr6 Graphical Abstract Authors Joo-Hyeon Lee, Tuomas Tammela, Matan Hofree, ..., Tyler Jacks, Aviv Regev, Carla F. Kim Correspondence [email protected] (J.-H.L.), [email protected] (C.F.K.) In Brief Heterogeneous mesenchymal cell populations in the lung play a central role in epithelial maintenance and alveolar differentiation. Highlights d Lgr5 and Lgr6 mark mesenchymal cells in adult lungs d Single-cell transcriptome analysis defines mesenchymal heterogeneity d Distinct mesenchymal niches drive airway and alveolar differentiation d Wnt activity affects epithelial differentiation specified by mesenchymal cells Lee et al., 2017, Cell 170, 1149–1163 September 7, 2017 ª 2017 The Authors. Published by Elsevier Inc. http://dx.doi.org/10.1016/j.cell.2017.07.028 Article Anatomically and Functionally Distinct Lung Mesenchymal Populations Marked by Lgr5 and Lgr6 Joo-Hyeon Lee,1,2,3,4,5,* Tuomas Tammela,6 Matan Hofree,7 Jinwook Choi,4 Nemanja Despot Marjanovic,6 Seungmin Han,4,8 David Canner,6 Katherine Wu,6 Margherita Paschini,1,2,3 Dong Ha Bhang,9 Tyler Jacks,6,10 Aviv Regev,6,7,10 and Carla F.