Sequence Analysis Allows Functional Annotation of Tyrosine Recombinases in Prokaryotic Genomes
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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. -
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 Metagenomic Data Life-Cycle: Standards and Best Practices Petra Ten Hoopen1, Robert D
GigaScience, 6, 2017, 1–11 doi: 10.1093/gigascience/gix047 Advance Access Publication Date: 16 June 2017 Review REVIEW Downloaded from https://academic.oup.com/gigascience/article-abstract/6/8/gix047/3869082 by guest on 01 October 2019 The metagenomic data life-cycle: standards and best practices Petra ten Hoopen1, Robert D. Finn1, Lars Ailo Bongo2, Erwan Corre3, Bruno Fosso4, Folker Meyer5, Alex Mitchell1, Eric Pelletier6,7,8, Graziano Pesole4,9, Monica Santamaria4, Nils Peder Willassen2 and Guy Cochrane1,∗ 1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom, 2UiT The Arctic University of Norway, Tromsø N-9037, Norway, 3CNRS-UPMC, FR 2424, Station Biologique, Roscoff 29680, France, 4Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, CNR, Bari 70126, Italy, 5Argonne National Laboratory, Argonne IL 60439, USA, 6Genoscope, CEA, Evry´ 91000, France, 7CNRS/UMR-8030, Evry´ 91000, France, 8Universite´ Evry´ val d’Essonne, Evry´ 91000, France and 9Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari “A. Moro,” Bari 70126, Italy ∗Correspondence address. Guy Cochrane, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK. Tel: +44(0)1223-494444; E-mail: [email protected] Abstract Metagenomics data analyses from independent studies can only be compared if the analysis workflows are described ina harmonized way. In this overview, we have mapped the landscape of data standards available for the description of essential steps in metagenomics: (i) material sampling, (ii) material sequencing, (iii) data analysis, and (iv) data archiving and publishing. Taking examples from marine research, we summarize essential variables used to describe material sampling processes and sequencing procedures in a metagenomics experiment. -
Microbial Community Structure in Rice, Crops, and Pastures Rotation Systems with Different Intensification Levels in the Temperate Region of Uruguay
Supplementary Material Microbial community structure in rice, crops, and pastures rotation systems with different intensification levels in the temperate region of Uruguay Sebastián Martínez Table S1. Relative abundance of the 20 most abundant bacterial taxa of classified sequences. Relative Taxa Phylum abundance 4,90 _Bacillus Firmicutes 3,21 _Bacillus aryabhattai Firmicutes 2,76 _uncultured Prosthecobacter sp. Verrucomicrobia 2,75 _uncultured Conexibacteraceae bacterium Actinobacteria 2,64 _uncultured Conexibacter sp. Actinobacteria 2,14 _Nocardioides sp. Actinobacteria 2,13 _Acidothermus Actinobacteria 1,50 _Bradyrhizobium Proteobacteria 1,23 _Bacillus Firmicutes 1,10 _Pseudolabrys_uncultured bacterium Proteobacteria 1,03 _Bacillus Firmicutes 1,02 _Nocardioidaceae Actinobacteria 0,99 _Candidatus Solibacter Acidobacteria 0,97 _uncultured Sphingomonadaceae bacterium Proteobacteria 0,94 _Streptomyces Actinobacteria 0,91 _Terrabacter_uncultured bacterium Actinobacteria 0,81 _Mycobacterium Actinobacteria 0,81 _uncultured Rubrobacteria Actinobacteria 0,77 _Xanthobacteraceae_uncultured forest soil bacterium Proteobacteria 0,76 _Streptomyces Actinobacteria Table S2. Relative abundance of the 20 most abundant fungal taxa of classified sequences. Relative Taxa Orden abundance. 20,99 _Fusarium oxysporum Ascomycota 11,97 _Aspergillaceae Ascomycota 11,14 _Chaetomium globosum Ascomycota 10,03 _Fungi 5,40 _Cucurbitariaceae; uncultured fungus Ascomycota 5,29 _Talaromyces purpureogenus Ascomycota 3,87 _Neophaeosphaeria; uncultured fungus Ascomycota -
5 February 2020 Draft Programme
Genomic Practice for Genetic Counsellors Wellcome Genome Campus Hinxton, Cambridge, UK 3 - 5 February 2020 Draft Programme Monday 3 February 11:00 – 11:00 Registration with coffee 11:30 – 12:00 Welcome and introduction to the course 12:00 – 13:45 Session 1: The role of genomics in healthcare The role in the NHS Nicki Taverner Cardiff University and All Wales Medical Genetic Service, UK Catherine Houghton Liverpool Women's NHS Foundation Trust, UK Outside the NHS Gemma Chandratilake University of Cambridge, UK An international perspective – Melbourne Genomics Health Alliance Lyndon Gallacher Victorian Clinicial Genetics Service, Australia Q&A with speakers 13:45 – 14:45 Lunch 14:45 – 16:00 Session 2: Variant interpretation Introduction to a genome browser Gemma Chandratillake University of Cambridge, UK Variant interpretation: going from millions to one of interest that could be the answer Helen Firth Cambridge University Hospitals, UK 16:00 – 16:20 Afternoon tea 16:20 – 18.20 Workshop: Variant interpretation using DECIPHER {and other approaches} Julia Foreman WSI, UK + Gemma Chandratillake University of Cambridge, UK 18:29 – 19:00 Consolidating learning for Day 1, Q+A Led by programme committee 19:00 Dinner Tuesday 4 February 09:00 – 10:00 Session 3: Cancer genomics Cancer Genomics: bridging from the tumour to the germline in variant interpretation Clare Turnbull The Institute of Cancer Research, UK 10:00 – 12:00 Workshop: Cancer variant interpretation Heather Pierce Cambridge University Hospitals, UK 12:00 – 13:00 Functional studies -
Compile.Xlsx
Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge; -
Rfam 14: Expanded Coverage of Metagenomic, Viral and Microrna Families Ioanna Kalvari, Eric P
Rfam 14: expanded coverage of metagenomic, viral and microRNA families Ioanna Kalvari, Eric P. Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska, Kevin Lamkiewicz, Manja Marz, Sam Griffiths-Jones, Claire Toffano-Nioche, Daniel Gautheret, Zasha Weinberg, et al. To cite this version: Ioanna Kalvari, Eric P. Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska, Kevin Lamkiewicz, et al.. Rfam 14: expanded coverage of metagenomic, viral and microRNA families. Nucleic Acids Research, 2020, 10.1093/nar/gkaa1047. hal-03031715 HAL Id: hal-03031715 https://hal.archives-ouvertes.fr/hal-03031715 Submitted on 14 Dec 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. This article has been accepted for publication in Nucleic Acid Research Published by Oxford University Press : • DOI : 10.1093/nar/gkaa1047 • PUBMED : 33211869 Nucleic Acids Research, 2020 1 doi: 10.1093/nar/gkaa1047 Rfam 14: expanded coverage of metagenomic, viral and microRNA families Ioanna Kalvari 1,EricP.Nawrocki 2, Nancy Ontiveros-Palacios 1, Joanna Argasinska 1, Kevin Lamkiewicz 3,4, Manja Marz 3,4, Sam Griffiths-Jones 5, Claire Toffano-Nioche 6, Daniel Gautheret 6, Zasha Weinberg 7, Elena Rivas 8, Sean R. Eddy 8,9,10, Downloaded from https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaa1047/5992291 by guest on 14 December 2020 Robert D. -
S41467-018-05712-5.Pdf
ARTICLE DOI: 10.1038/s41467-018-05712-5 OPEN Biology and genome of a newly discovered sibling species of Caenorhabditis elegans Natsumi Kanzaki 1,8, Isheng J. Tsai 2, Ryusei Tanaka3, Vicky L. Hunt3, Dang Liu 2, Kenji Tsuyama 4, Yasunobu Maeda3, Satoshi Namai4, Ryohei Kumagai4, Alan Tracey5, Nancy Holroyd5, Stephen R. Doyle 5, Gavin C. Woodruff1,9, Kazunori Murase3, Hiromi Kitazume3, Cynthia Chai6, Allison Akagi6, Oishika Panda 7, Huei-Mien Ke2, Frank C. Schroeder7, John Wang2, Matthew Berriman 5, Paul W. Sternberg 6, Asako Sugimoto 4 & Taisei Kikuchi 3 1234567890():,; A ‘sibling’ species of the model organism Caenorhabditis elegans has long been sought for use in comparative analyses that would enable deep evolutionary interpretations of biological phenomena. Here, we describe the first sibling species of C. elegans, C. inopinata n. sp., isolated from fig syconia in Okinawa, Japan. We investigate the morphology, developmental processes and behaviour of C. inopinata, which differ significantly from those of C. elegans. The 123-Mb C. inopinata genome was sequenced and assembled into six nuclear chromo- somes, allowing delineation of Caenorhabditis genome evolution and revealing unique char- acteristics, such as highly expanded transposable elements that might have contributed to the genome evolution of C. inopinata. In addition, C. inopinata exhibits massive gene losses in chemoreceptor gene families, which could be correlated with its limited habitat area. We have developed genetic and molecular techniques for C. inopinata; thus C. inopinata provides an exciting new platform for comparative evolutionary studies. 1 Forestry and Forest Products Research Institute, Tsukuba 305-8687, Japan. 2 Biodiversity Research Center, Academia Sinica, Taipei city 11529, Taiwan. -
Management Training Scheme Introduction from Mike Stratton
Management Training Scheme Introduction from Mike Stratton It’s an exciting time to join us as we continue to build an international centre for scientific, business, cultural and educational activities emanating from Genomes and BioData. With a significant expansion of our Wellcome Genome Campus on the horizon, we are now able to shift our horizons to ask and answer even bolder questions. Our mission is “to maximise the societal benefit of knowledge obtained from genome sequences”. The ambition of Genome Research Limited, with our Campus partners, is to progressively strengthen its well-established foundations in scientific research and discovery, and to build on them, developing the Wellcome Genome Campus over the forthcoming 25 years. Genomic research is still in the foothills of extracting and using the knowledge buried in the 6 billion letters of code in the human genome. The ever increasing numbers of human genomes sequenced for research or clinical diagnosis will reveal patterns and motifs that will shape health and disease research for decades to come. When we also consider the rest of the genomes on Earth the potential is vast and the Wellcome Sanger Institute will be in the vanguard of this revolution in science and society. Professor Sir Mike Stratton, FMedSci FRS Director of the Wellcome Sanger Institute and Chief Executive Officer of the Wellcome Genome Campus About Wellcome Sanger Institute Our Mission Our Benefits To maximise the societal benefit of knowledge obtained Our employees have access to a comprehensive range of from genome sequences. benefits and facilities including: Delivery of this mission will have three elements: • 25 days annual leave (extra 1 day to a maximum of 30 • Research: advancing understanding of biology using days for every year you work) genome sequences and other types of large-scale • Auto-enrolment into a generous Group Defined biological data. -
RNA Promotes Phase Separation of Glycolysis Enzymes Into
RESEARCH ARTICLE RNA promotes phase separation of glycolysis enzymes into yeast G bodies in hypoxia Gregory G Fuller1, Ting Han2, Mallory A Freeberg1†, James J Moresco3‡, Amirhossein Ghanbari Niaki4, Nathan P Roach1, John R Yates III3, Sua Myong4, John K Kim1* 1Department of Biology, Johns Hopkins University, Baltimore, United States; 2National Institute of Biological Sciences, Beijing, China; 3Department of Chemical Physiology, The Scripps Research Institute, La Jolla, United States; 4Department of Biophysics, Johns Hopkins University, Baltimore, United States Abstract In hypoxic stress conditions, glycolysis enzymes assemble into singular cytoplasmic granules called glycolytic (G) bodies. G body formation in yeast correlates with increased glucose consumption and cell survival. However, the physical properties and organizing principles that define G body formation are unclear. We demonstrate that glycolysis enzymes are non-canonical RNA binding proteins, sharing many common mRNA substrates that are also integral constituents of G bodies. Targeting nonspecific endoribonucleases to G bodies reveals that RNA nucleates G body formation and maintains its structural integrity. Consistent with a phase separation *For correspondence: [email protected] mechanism of biogenesis, recruitment of glycolysis enzymes to G bodies relies on multivalent homotypic and heterotypic interactions. Furthermore, G bodies fuse in vivo and are largely † Present address: EMBL-EBI, insensitive to 1,6-hexanediol, consistent with a hydrogel-like composition. Taken together, -
Chemosynthetic and Photosynthetic Bacteria Contribute Differentially to Primary Production Across a Steep Desert Aridity Gradient
The ISME Journal https://doi.org/10.1038/s41396-021-01001-0 ARTICLE Chemosynthetic and photosynthetic bacteria contribute differentially to primary production across a steep desert aridity gradient 1,2 3,4 5 6 2 Sean K. Bay ● David W. Waite ● Xiyang Dong ● Osnat Gillor ● Steven L. Chown ● 3 1,2 Philip Hugenholtz ● Chris Greening Received: 23 November 2020 / Revised: 16 April 2021 / Accepted: 28 April 2021 © The Author(s) 2021. This article is published with open access Abstract Desert soils harbour diverse communities of aerobic bacteria despite lacking substantial organic carbon inputs from vegetation. A major question is therefore how these communities maintain their biodiversity and biomass in these resource-limiting ecosystems. Here, we investigated desert topsoils and biological soil crusts collected along an aridity gradient traversing four climatic regions (sub-humid, semi-arid, arid, and hyper-arid). Metagenomic analysis indicated these communities vary in their capacity to use sunlight, organic compounds, and inorganic compounds as energy sources. Thermoleophilia, Actinobacteria, and Acidimicrobiia 1234567890();,: 1234567890();,: were the most abundant and prevalent bacterial classes across the aridity gradient in both topsoils and biocrusts. Contrary to the classical view that these taxa are obligate organoheterotrophs, genome-resolved analysis suggested they are metabolically flexible, withthecapacitytoalsouseatmosphericH2 to support aerobic respiration and often carbon fixation. In contrast, Cyanobacteria were patchily distributed and only abundant in certain biocrusts. Activity measurements profiled how aerobic H2 oxidation, chemosynthetic CO2 fixation, and photosynthesis varied with aridity. Cell-specific rates of atmospheric H2 consumption increased 143-fold along the aridity gradient, correlating with increased abundance of high-affinity hydrogenases. Photosynthetic and chemosynthetic primary production co-occurred throughout the gradient, with photosynthesis dominant in biocrusts and chemosynthesis dominant in arid and hyper-arid soils. -
Genomic Analysis of Uncultured Microbes in Marine Sediments
University of Tennessee, Knoxville TRACE: Tennessee Research and Creative Exchange Doctoral Dissertations Graduate School 12-2017 Singled Out: Genomic analysis of uncultured microbes in marine sediments Jordan Toby Bird University of Tennessee, [email protected] Follow this and additional works at: https://trace.tennessee.edu/utk_graddiss Recommended Citation Bird, Jordan Toby, "Singled Out: Genomic analysis of uncultured microbes in marine sediments. " PhD diss., University of Tennessee, 2017. https://trace.tennessee.edu/utk_graddiss/4829 This Dissertation is brought to you for free and open access by the Graduate School at TRACE: Tennessee Research and Creative Exchange. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of TRACE: Tennessee Research and Creative Exchange. For more information, please contact [email protected]. To the Graduate Council: I am submitting herewith a dissertation written by Jordan Toby Bird entitled "Singled Out: Genomic analysis of uncultured microbes in marine sediments." I have examined the final electronic copy of this dissertation for form and content and recommend that it be accepted in partial fulfillment of the equirr ements for the degree of Doctor of Philosophy, with a major in Microbiology. Karen G. Lloyd, Major Professor We have read this dissertation and recommend its acceptance: Mircea Podar, Andrew D. Steen, Erik R. Zinser Accepted for the Council: Dixie L. Thompson Vice Provost and Dean of the Graduate School (Original signatures are on file with official studentecor r ds.) Singled Out: Genomic analysis of uncultured microbes in marine sediments A Dissertation Presented for the Doctor of Philosophy Degree The University of Tennessee, Knoxville Jordan Toby Bird December 2017 Copyright © 2017 by Jordan Bird All rights reserved.