SGM Meeting Abstracts
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A Historical Analysis of Herpes Simplex Virus Promoter Activation in Vivo Reveals Distinct Populations of Latently Infected Neurones
Journal of General Virology (2008), 89, 2965–2974 DOI 10.1099/vir.0.2008/005066-0 A historical analysis of herpes simplex virus promoter activation in vivo reveals distinct populations of latently infected neurones Joa˜o T. Proenc¸a,1 Heather M. Coleman,1 Viv Connor,1 Douglas J. Winton2 and Stacey Efstathiou1 Correspondence 1Division of Virology, Department of Pathology, University of Cambridge, Tennis Court Road, S. Efstathiou Cambridge CB2 1QP, UK [email protected] 2Cancer Research UK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK Herpes simplex virus type 1 (HSV-1) has the capacity to establish a life-long latent infection in sensory neurones and also to periodically reactivate from these cells. Since mutant viruses defective for immediate-early (IE) expression retain the capacity for latency establishment it is widely assumed that latency is the consequence of a block in IE gene expression. However, it is not clear whether viral gene expression can precede latency establishment following wild-type virus infection. In order to address this question we have utilized a reporter mouse model system to facilitate a historical analysis of viral promoter activation in vivo. This system utilizes recombinant viruses expressing Cre recombinase under the control of different viral promoters and the Cre reporter mouse strain ROSA26R. In this model, viral promoter-driven Cre recombinase mediates a permanent genetic change, resulting in reporter gene activation and permanent marking of latently infected cells. The analyses of HSV-1 recombinants containing human cytomegalovirus major immediate-early, ICP0, gC or latency-associated transcript Received 20 June 2008 promoters linked to Cre recombinase in this system have revealed the existence of a population of Accepted 4 September 2008 neurones that have experienced IE promoter activation prior to the establishment of latency. -
Extensive Microbial Diversity Within the Chicken Gut Microbiome Revealed by Metagenomics and Culture
Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture Rachel Gilroy1, Anuradha Ravi1, Maria Getino2, Isabella Pursley2, Daniel L. Horton2, Nabil-Fareed Alikhan1, Dave Baker1, Karim Gharbi3, Neil Hall3,4, Mick Watson5, Evelien M. Adriaenssens1, Ebenezer Foster-Nyarko1, Sheikh Jarju6, Arss Secka7, Martin Antonio6, Aharon Oren8, Roy R. Chaudhuri9, Roberto La Ragione2, Falk Hildebrand1,3 and Mark J. Pallen1,2,4 1 Quadram Institute Bioscience, Norwich, UK 2 School of Veterinary Medicine, University of Surrey, Guildford, UK 3 Earlham Institute, Norwich Research Park, Norwich, UK 4 University of East Anglia, Norwich, UK 5 Roslin Institute, University of Edinburgh, Edinburgh, UK 6 Medical Research Council Unit The Gambia at the London School of Hygiene and Tropical Medicine, Atlantic Boulevard, Banjul, The Gambia 7 West Africa Livestock Innovation Centre, Banjul, The Gambia 8 Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Edmond J. Safra Campus, Hebrew University of Jerusalem, Jerusalem, Israel 9 Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK ABSTRACT Background: The chicken is the most abundant food animal in the world. However, despite its importance, the chicken gut microbiome remains largely undefined. Here, we exploit culture-independent and culture-dependent approaches to reveal extensive taxonomic diversity within this complex microbial community. Results: We performed metagenomic sequencing of fifty chicken faecal samples from Submitted 4 December 2020 two breeds and analysed these, alongside all (n = 582) relevant publicly available Accepted 22 January 2021 chicken metagenomes, to cluster over 20 million non-redundant genes and to Published 6 April 2021 construct over 5,500 metagenome-assembled bacterial genomes. -
1985517720.Pdf
JOURNAL OF BACTERIOLOGY, Jan. 2009, p. 347–354 Vol. 191, No. 1 0021-9193/09/$08.00ϩ0 doi:10.1128/JB.01238-08 Copyright © 2009, American Society for Microbiology. All Rights Reserved. Complete Genome Sequence and Comparative Genome Analysis of Enteropathogenic Escherichia coli O127:H6 Strain E2348/69ᰔ† Atsushi Iguchi,1 Nicholas R. Thomson,2 Yoshitoshi Ogura,1,3 David Saunders,2 Tadasuke Ooka,3 Ian R. Henderson,4 David Harris,2 M. Asadulghani,1 Ken Kurokawa,5 Paul Dean,6 Brendan Kenny,6 Michael A. Quail,2 Scott Thurston,2 Gordon Dougan,2 Tetsuya Hayashi,1,3 Julian Parkhill,2 and Gad Frankel7* Division of Bioenvironmental Science, Frontier Science Research Center,1 and Division of Microbiology, Department of Infectious Diseases, Faculty of Medicine,3 University of Miyazaki, Miyazaki, Japan; Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom2; School of Immunity and Infection, University of Downloaded from Birmingham, Birmingham, United Kingdom4; Department of Biological Information, School and Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Kanagawa, Japan5; Institute of Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, United Kingdom6; and Centre for Molecular Microbiology and Infection, Division of Cell and Molecular Biology, Imperial College London, London, United Kingdom7 Received 5 September 2008/Accepted 15 October 2008 Enteropathogenic Escherichia coli (EPEC) was the first pathovar of E. coli to be implicated in human disease; however, no EPEC strain has been fully sequenced until now. Strain E2348/69 (serotype O127:H6 belonging to E. http://jb.asm.org/ coli phylogroup B2) has been used worldwide as a prototype strain to study EPEC biology, genetics, and virulence. -
Quadram Institute Newsletter
Autumn 2019 Welcome to the newsle�er of the Quadram Ins�tute. This issue highlights recent research breakthroughs at the We con�nue to build our team and are pleased to welcome Quadram Ins�tute (QI) that could have posi�ve impacts on Professor Cynthia Whitchurch to the QI. Cynthia is se�ng public health. Working with clinicians our researchers have up a research group inves�ga�ng bacterial lifestyles, and shown how the latest sequencing technologies can aid in how these make them more infec�ous or resistant to diagnos�cs and surveillance. Coupling these techniques an�microbials. Cynthia joins us from the ithree ins�tute at with ‘Big Data’ analy�cal approaches will be vital to the University of Technology Sydney. Her research led to addressing 21st century popula�on health challenges, and the discovery that extracellular DNA is required for biofilm the QI aims to be a leader in this area. development. Big Data in the NHS was the topic of a roundtable We con�nue to welcome visitors to our new building to discussion I a�ended with Patricia Hart at the policy share our vision to understand how food and microbes development think tank Reform. This roundtable was interact to promote health and prevent disease. In June, we sponsored by QI and explored how universi�es and industry had the honour of hos�ng His Excellency Simon Smits, can work with government to realise poten�al applica�ons Ambassador of the Netherlands to the UK. The Ambassador of Big Data. The event was chaired by Baroness Blackwood, visited the Norwich Research Park as part of an Parliamentary Under-Secretary of State, Department of interna�onal trade delega�on to East Anglia to learn about Health and Social Care (DHSC) and included senior the region’s world-leading life sciences research and trade policy-makers, public service prac��oners, academics and opportuni�es. -
Curriculum Vitae Professor Mark John Pallen
Curriculum Vitae Professor Mark John Pallen MA (Hons) Cantab, MBBS, MD, PhD January 2014 Mark Pallen — Curriculum vitae Personal Details Name Mark John Pallen Date of Birth 6 July 1960 Nationality British Address 17 Lodge Drive, Malvern Worcestershire, WR14 4LS E-mail address [email protected] Telephone 01684 567710 (home); 07824 086946 (mobile) Web Page: http://tinyurl.com/ncul2p3 Twitter: http://twitter.com/mjpallen YouTube Channel: http://www.youtube.com/user/pallenm/ Education and Qualifications PhD 1998 Imperial College, London An investigation into the links between stationary phase and virulence in Salmonella enterica enterica serovar Typhimurium MD 1993 St Bartholomew's Hospital Medical College Detection and characterisation of diphtheria toxin genes and insertion sequences MRCPath by examination in Medical Microbiology 1991 (upgraded to FRCPath 2005) MB BS 1981-84 London Hospital Medical College Undergraduate Prizes: LEPRA National Essay Prize, 1982 Turnbull Prize in Pathology, 1983, 1984 Sutton Prize in Pathology, 1983 BA (Hons) in Medical Sciences 1978-81 University of Cambridge Fitzwilliam College (Lower Second, converted to MA, 1985) Page 1 Mark Pallen — Curriculum vitae Employment Professor of Microbial Genomics Head of Division of Microbiology and Infection Apr 2013-now Warwick Medical School, University of Warwick Professor of Microbial Genomics 2001-2013 University of Birmingham Professor and Head of Department 1999-2001 Department of Microbiology and Immunobiology Queen’s University, Belfast Senior Lecturer (Honorary Consultant) 1992–99 Department of Medical Microbiology St Bartholomew's and the Royal London School of Medicine and Dentistry (Queen Mary Westfield College) Visiting Research Fellow 1994–97 Department of Biochemistry Imperial College of Science, Technology and Medicine (on a Wellcome Trust Research Leave Fellowship, working at Imperial, while still employed by Barts) Lecturer (Hon. -
Journal of Virology
JOURNAL OF VIROLOGY Volume 68 November 1994 No. 11 MINIREVIEW Molecular Biology of the Human Immunodeficiency Virus Ramu A. Subbramanian and Eric 6831-6835 Accessory Proteins A. Cohen ANIMAL VIRUSES Monoclonal Antibodies against Influenza Virus PB2 and NP J. Baircena, M. Ochoa, S. de la 6900-6909 Polypeptides Interfere with the Initiation Step of Viral Luna, J. A. Melero, A. Nieto, J. mRNA Synthesis In Vitro Ortin, and A. Portela Low-Affinity E2-Binding Site Mediates Downmodulation of Frank Stubenrauch and Herbert 6959-6966 E2 Transactivation of the Human Papillomavirus Type 8 Pfister Late Promoter Template-Dependent, In Vitro Replication of Rotavirus RNA Dayue Chen, Carl Q.-Y. Zeng, 7030-7039 Melissa J. Wentz, Mario Gorziglia, Mary K. Estes, and Robert F. Ramig Improved Self-Inactivating Retroviral Vectors Derived from Paul Olson, Susan Nelson, and 7060-7066 Spleen Necrosis Virus Ralph Dornburg Isolation of a New Foamy Retrovirus from Orangutans Myra 0. McClure, Paul D. 7124-7130 Bieniasz, Thomas F. Schulz, Ian L. Chrystie, Guy Simpson, Adriano Aguzzi, Julian G. Hoad, Andrew Cunningham, James Kirkwood, and Robin A. Weiss Cell Lines Inducibly Expressing the Adeno-Associated Virus Christina Holscher, Markus Horer, 7169-7177 (AAV) rep Gene: Requirements for Productive Replication Jurgen A. Kleinschmidt, of rep-Negative AAV Mutants Hanswalter Zentgraf, Alexander Burkle, and Regine Heilbronn Role of Flanking E Box Motifs in Human Immunodeficiency S.-H. Ignatius Ou, Leon F. 7188-7199 Virus Type 1 TATA Element Function Garcia-Martinez, Eyvind J. Paulssen, and Richard B. Gaynor Characterization and Molecular Basis of Heterogeneity of Fernando Rodriguez, Carlos 7244-7252 the African Swine Fever Virus Envelope Protein p54 Alcaraz, Adolfo Eiras, Rafael J. -
Monoclonal Antibodies to Herpes Simplex Virus Type 2
INIS-mf—8650 MONOCLONAL ANTIBODIES TO HERPES SIMPLEX VIRUS TYPE 2 C.S.McLean-Piaper .-.- i Promotor: dr. A. van Kannen hoogleraar in de moleculaire biologie Co-promotor: dr. A.C. Minson hoogleraar in de virologie aan de University of Cambridge, Cambridge, Engeland C.S. McLean-Pieper MONOCLONAL ANTIBODIES TO HERPES SIMPLEX VIRUS TYPE 2 Proefschrift ter verkrijging van de graad van doctor in de landbouwwetenschappen, op gezag van de rector magnificus, dr. C.C. Oosterlee, hoogleraar in de veeteeltwetenschap in het openbaar te verdedigen op vrijdag 3 september 1982 des namiddags te vier uur in de aula van de landbouwhogeschool te Wageningen. ACKNOWLEDGEMENTS. I would like to thank the following people for their help during the various stages of the work described in this thesis. Without them it would never have been written. First of all, Tony Minson, whose support and encouragement as my supervisor have been invaluable. He was always available to give advice and practical help when problems, arose. I have learned much form his critical supervision, both in the practical work and in the writing of this thesis. Ab van Kammen, especially for his help and comments during the writing. Tony Nash, for his invaluable help with the animal experiments, and for his discussion and comments on many aspects of the work. David Hancock, for his excellent technical assistance during the later stages of the project. Anne Buckmaster, who provided the data involving the antibodies AP7 and AP12, and was always available for friendly discussion. Professor P. Wildy, who made it possible for me to work in the department of pathology. -
ICP8 Self Interactions Are Essential for HSV-1 Replication Compartment Formation Anthar Darwish University of Connecticut - Storrs, [email protected]
University of Connecticut OpenCommons@UConn Doctoral Dissertations University of Connecticut Graduate School 8-9-2018 ICP8 Self Interactions are Essential for HSV-1 Replication Compartment Formation Anthar Darwish University of Connecticut - Storrs, [email protected] Follow this and additional works at: https://opencommons.uconn.edu/dissertations Recommended Citation Darwish, Anthar, "ICP8 Self Interactions are Essential for HSV-1 Replication Compartment Formation" (2018). Doctoral Dissertations. 1940. https://opencommons.uconn.edu/dissertations/1940 ICP8 Self Interactions are Essential for HSV-1 Replication Compartment Formation Anthar S. Darwish, PhD University of Connecticut, 2018 ABSTRACT The objective of this thesis was to understand the ICP8 protein interactions involved during the formation of HSV-1 replication compartments. We focused our efforts on mapping the ICP8-ICP8 self-interactions that are involved in the formation of DNA independent filaments. We report here that the FNF motif (F1142, N1143 and F1144) and the FW motif (F843 and W844) are essential for ICP8 filament formation. Furthermore we observed a positive correlation between ICP8 filamentation and the formation of replication compartments. Mammalian expression plasmids bearing mutations in these motifs (FNF and FW) were unable to complement an ICP8 null virus for growth and replication compartment formation. We propose that filaments or other higher order structures of ICP8 may provide a scaffold onto which other proteins are recruited to form prereplicative sites and replication compartments. In an attempt to broaden our understanding of ICP8 self-interactions and its interactions with other essential viral proteins we searched for potential protein interaction sites on the surface of ICP8. Using the structural information of ICP8 and sequence comparison with homologous proteins, we identified conserved residues in the shoulder region (R262, H266, D270, E271, E274, Q706 and F707) of ICP8 that might function as protein interaction sites. -
Clinical Metagenomics
Clinical metagenomics Nick Loman Jonathan Eisen Mick Watson 16S vs metagenomics • Cheap • Expensive • Targets single marker • In theory can detect gene anything • Limited to bacteria • Harder to analyse • Relatively easy to analyse • Fewer biases (?) • Lots of known biases • Taxonomic assignment at • Function information species level problematic directly accessible • Function can only be • Strain-level inferred, not detected information • Goes deeper • Shallower Definition of a metagenome • The collection of genomes and genes from the members of a microbiota • Microbiota: The assemblage of microorganisms present in a defined environment. • Microbiome: This term refers to the entire habitat, including the microorganisms, their genomes (i.e., genes) and the surrounding environmental conditions. http://www.allthingsgenomics.com/blog/2013/1/11/the-vocabulary-used-to-describe- microbial-communities-microbiome-metagenome-microbiota Metagenomics – Your questions • What are the best ways to address getting representation of bacteria, viruses, fungi and others? Techniques for doing so? – Thoughts on the use of physical enrichment techniques to isolate microbe of interest rather than traditional metagenomic sequencing? • What are the best bioinformatic software packages and pipelines for functional analysis? – What are the best analysis pipelines for full viral sequencing to detect whether mutations are true or not? Comparing closely related taxa? • As an initial approach, should one try 16s sequencing prior to shotgun sequencing if interested -
Genetically Modified Plants for Food Use
September 1998 Ref: 1/98 (summary) 2/98 (full report) GENETICALLY MODIFIED PLANTS FOR FOOD USE Contents Page Summary 1 Introduction 4 Outline 4 1. What is genetic modification? 5 2. Is genetic modification regulated? 6 3. Will genes transfer from GM plants? 7 3.1 Transfer of genes from GM crop plants to wild plant species 7 3.2 Transfer of genes from GM crops to non-GM crops 8 3.3 Ways to minimise or prevent gene transfer 9 3.4 Uptake of genes via the food chain 10 3.5 Antibiotic resistance genes in GM food 11 4. Will GM crops harm the environment? 12 4.1 Insect tolerant crops 12 4.1.1 Effects on non-target species 12 4.1.2 Pest resistance to insect tolerant GM crops 13 4.2 Herbicide tolerant crops 14 4.2.1 Transfer of genes to wild relatives 14 4.2.2 Transfer of genes to non-GM crops 15 4.2.3 Will use of the herbicide affect other plants and animals?16 4.3 Virus resistant crops 16 5. Specific issues related to GM plants for food use 17 5.1 Labelling and segregation 17 5.2 Toxic and allergenic effects as a result of the inserted gene 18 5.3 GM crops containing non-food genes 19 5.4 Phenotypic/genotypic stability of GM crops 19 5.5 Pleiotropic effects of genes 20 Summary of recommendations 20 Annex I - Historical developments of plant breeding Annex II - Membership of Advisory Committee on Genetic Modification Annex III - Membership of Advisory Committee on Releases to the Environment Annex IV - Membership of Advisory Committee on Novel Foods and Processes Annex V - Membership of Food Advisory Committee Annex VI - Segregation and Labelling Summary 1. -
Genome-Wide Engineering of an Infectious Clone of Herpes Simplex
Genome-wide engineering of an infectious clone of PNAS PLUS herpes simplex virus type 1 using synthetic genomics assembly methods Lauren M. Oldfielda,1, Peter Grzesikb,1, Alexander A. Voorhiesc, Nina Alperovicha, Derek MacMathb, Claudia D. Najeraa, Diya Sabrina Chandrab, Sanjana Prasadb, Vladimir N. Noskova, Michael G. Montaguea,2, Robert M. Friedmand, Prashant J. Desaib,3, and Sanjay Vasheea,3 aDepartment of Synthetic Biology and Bioenergy, J. Craig Venter Institute, Rockville, MD 20850; bDepartment of Oncology, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, The Johns Hopkins University, Baltimore, MD 21231; cDepartment of Infectious Diseases, J. Craig Venter Institute, Rockville, MD 20850; and dPolicy Center, J. Craig Venter Institute, La Jolla, CA 92037 Edited by Jef D. Boeke, New York University Langone Medical Center, New York, NY, and approved August 25, 2017 (received for review January 11, 2017) Here, we present a transformational approach to genome engineer- single modification with the BAC-based system takes weeks to ing of herpes simplex virus type 1 (HSV-1), which has a large DNA complete. If multiple changes in the genome are desired, each genome, using synthetic genomics tools. We believe this method will must be made sequentially, greatly increasing the timeframe of enable more rapid and complex modifications of HSV-1 and other making mutant viruses. large DNA viruses than previous technologies, facilitating many The synthetic genomics assembly method described herein has useful applications. Yeast transformation-associated recombination many potential advantages over the BAC-based system (9). It is an was used to clone 11 fragments comprising the HSV-1 strain KOS application of existing tools to engineer large virus genomes and 152 kb genome. -
2011 to 2018 Lister Annual Report and Accounts
The L ister Institute of Preventive Medicine PO Box 1083, Bushey, Hertfordshire WD23 9AG 3 ANNUAL REPORT AND FINANCIAL STATEMENTS for the year ended 3 1 December 2011 O o The Lister Institute of Preventive Medicine is a company limited by guarantee (England 34479) and a registered charity (206271) The Institute was founded in 1891 and for the next 80 years played a vital role in the development of the laboratory aspects of preventive medicine as an independent research institute in the UK. Financial pressures in the 1970s led to the closure of the research and production facilities and the conversion of the Lister Institute into a highly successful trust awarding prestigious Research Fellowships from 1982 which in 2003, again because of financial pressures, were revised to become Prize Fellowships. The cover portrait of Lord Lister reproduced by courtesy of the Royal Veterinary College THE LISTER INSTITUTE OF PREVENTIVE MEDICINE LEGAL AND ADMINISTRATIVE INFORMATION for the year ended 3 1 December 2 0 1 I THE GOVERNING BODY Dame Bridget M Ogilvie, DBE, AC, ScD, FMedSci, FRS, Chairman (Retired 9 September 2011) Professor Sir Alex Markham, DSc, FRCP, FRCPath, FMedSci, Chairman (From 9 September 2011) Mr Michael French, BSc(Eng), FCA, Hon Treasurer Professor Janet Darbyshire, CBE, FRCP, FFPH, FMedSci (Appointed I December 2011) Professor Dame Kay Davies, CBE, DBE, MA, DPhil, FMedSci, FRCP (Hon), FRCPath, FRS, (Appointed I December 2011) Hon Rory M B Guinness Professor Douglas Higgs, MB, BS, MRCP, MRCPath, DSc, FRCP, FRCPath (Appointed 9 September