SIFTS: Updated Structure Integration with Function, Taxonomy and Sequences Resource Allows 40-Fold Increase in Coverage of Struc
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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. -
Annual Conference Abstracts
ANNUAL CONFERENCE 14-17 April 2014 Arena and Convention Centre, Liverpool ABSTRACTS SGM ANNUAL CONFERENCE APRIL 2014 ABSTRACTS (LI00Mo1210) – SGM Prize Medal Lecture (LI00Tu1210) – Marjory Stephenson Climate Change, Oceans, and Infectious Disease Prize Lecture Dr. Rita R. Colwell Understanding the basis of antibiotic resistance University of Maryland, College Park, MD, USA as a platform for early drug discovery During the mid-1980s, satellite sensors were developed to monitor Laura JV Piddock land and oceans for purposes of understanding climate, weather, School of Immunity & Infection and Institute of Microbiology and and vegetation distribution and seasonal variations. Subsequently Infection, University of Birmingham, UK inter-relationships of the environment and infectious diseases Antibiotic resistant bacteria are one of the greatest threats to human were investigated, both qualitatively and quantitatively, with health. Resistance can be mediated by numerous mechanisms documentation of the seasonality of diseases, notably malaria including mutations conferring changes to the genes encoding the and cholera by epidemiologists. The new research revealed a very target proteins as well as RND efflux pumps, which confer innate close interaction of the environment and many other infectious multi-drug resistance (MDR) to bacteria. The production of efflux diseases. With satellite sensors, these relationships were pumps can be increased, usually due to mutations in regulatory quantified and comparatively analyzed. More recent studies of genes, and this confers resistance to antibiotics that are often used epidemic diseases have provided models, both retrospective and to treat infections by Gram negative bacteria. RND MDR efflux prospective, for understanding and predicting disease epidemics, systems not only confer antibiotic resistance, but altered expression notably vector borne diseases. -
2016 Joint Meeting Program
April 15 – 17, 2016 Fairmont Chicago Millennium Park • Chicago, Illinois The AAP/ASCI/APSA conference is jointly provided by Boston University School of Medicine and AAP/ASCI/APSA. Meeting Program and Abstracts www.jointmeeting.org www.jointmeeting.org Special Events at the 2016 AAP/ASCI/APSA Joint Meeting Friday, April 15 Saturday, April 16 ASCI President’s Reception ASCI Food and Science Evening 6:15 – 7:15 p.m. 6:30 – 9:00 p.m. Gold Room The Mid-America Club, Aon Center ASCI Dinner & New Member AAP Member Banquet Induction Ceremony (Ticketed guests only) (Ticketed guests only) 7:00 – 10:00 p.m. 7:30 – 9:45 p.m. Imperial Ballroom, Level B2 Rouge, Lobby Level How to Solve a Scientific Puzzle: Speaker: Clara D. Bloomfield, MD Clues from Stockholm and Broadway The Ohio State University Comprehensive Cancer Center Speaker: Joe Goldstein, MD APSA Welcome Reception & University of Texas Southwestern Medical Center at Dallas Presidential Address APSA Dinner (Ticketed guests only) 9:00 p.m. – Midnight Signature Room, 360 Chicago, 7:30 – 9:00 p.m. John Hancock Center (off-site) Rouge, Lobby Level Speaker: Daniel DelloStritto, APSA President Finding One’s Scientific Niche: Musings from a Clinical Neuroscientist Speaker: Helen Mayberg, MD, Emory University Dessert Reception (open to all attendees) 10:00 p.m. – Midnight Imperial Foyer, Level B2 Sunday, April 17 APSA Future of Medicine and www.jointmeeting.org Residency Luncheon Noon – 2:00 p.m. Rouge, Lobby Level 2 www.jointmeeting.org Program Contents General Program Information 4 Continuing Medical Education Information 5 Faculty and Speaker Disclosures 7 Scientific Program Schedule 9 Speaker Biographies 16 Call for Nominations: 2017 Harrington Prize for Innovation in Medicine 26 AAP/ASCI/APSA Joint Meeting Faculty 27 Award Recipients 29 Call for Nominations: 2017 Harrington Scholar-Innovator Award 31 Call for Nominations: George M. -
Serine Proteases with Altered Sensitivity to Activity-Modulating
(19) & (11) EP 2 045 321 A2 (12) EUROPEAN PATENT APPLICATION (43) Date of publication: (51) Int Cl.: 08.04.2009 Bulletin 2009/15 C12N 9/00 (2006.01) C12N 15/00 (2006.01) C12Q 1/37 (2006.01) (21) Application number: 09150549.5 (22) Date of filing: 26.05.2006 (84) Designated Contracting States: • Haupts, Ulrich AT BE BG CH CY CZ DE DK EE ES FI FR GB GR 51519 Odenthal (DE) HU IE IS IT LI LT LU LV MC NL PL PT RO SE SI • Coco, Wayne SK TR 50737 Köln (DE) •Tebbe, Jan (30) Priority: 27.05.2005 EP 05104543 50733 Köln (DE) • Votsmeier, Christian (62) Document number(s) of the earlier application(s) in 50259 Pulheim (DE) accordance with Art. 76 EPC: • Scheidig, Andreas 06763303.2 / 1 883 696 50823 Köln (DE) (71) Applicant: Direvo Biotech AG (74) Representative: von Kreisler Selting Werner 50829 Köln (DE) Patentanwälte P.O. Box 10 22 41 (72) Inventors: 50462 Köln (DE) • Koltermann, André 82057 Icking (DE) Remarks: • Kettling, Ulrich This application was filed on 14-01-2009 as a 81477 München (DE) divisional application to the application mentioned under INID code 62. (54) Serine proteases with altered sensitivity to activity-modulating substances (57) The present invention provides variants of ser- screening of the library in the presence of one or several ine proteases of the S1 class with altered sensitivity to activity-modulating substances, selection of variants with one or more activity-modulating substances. A method altered sensitivity to one or several activity-modulating for the generation of such proteases is disclosed, com- substances and isolation of those polynucleotide se- prising the provision of a protease library encoding poly- quences that encode for the selected variants. -
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. -
Jararhagin ECD-Containing Disintegrin Domain: Expression in Escherichia Coli and Inhibition of the Platelet–Collagen Interaction
Archives of Biochemistry and Biophysics Vol. 369, No. 2, September 15, pp. 295–301, 1999 Article ID abbi.1999.1372, available online at http://www.idealibrary.com on Jararhagin ECD-Containing Disintegrin Domain: Expression in Escherichia coli and Inhibition of the Platelet–Collagen Interaction Ana M. Moura-da-Silva,*,†,‡,1 Alex Lı´nica,* Maisa S. Della-Casa,* Aura S. Kamiguti,§ Paulo L. Ho,¶ Julian M. Crampton,† and R. David G. Theakston‡ *Laborato´rio de Imunopatologia and ¶Laborato´rio de Biotecnologia Molecular, Instituto Butantan, Av. Vital Brasil, 1500, 05503-900, Sa˜o Paulo, Brazil; §Department of Haematology, University of Liverpool, Prescot Street, Liverpool, L69 3BX, United Kingdom; and †Molecular Genetics Unit and ‡Alistair Reid Venom Research Unit, Liverpool School of Tropical Medicine, Pembroke Place, L3 5QA, Liverpool, United Kingdom Received May 17, 1999, and in revised form July 6, 1999 demonstrating that these antibodies recognize the Jararhagin, a hemorrhagin from Bothrops jararaca parent jararhagin molecule. Treatment of the fusion venom, is a soluble snake venom component compris- protein with enterokinase, followed by further cap- ing metalloproteinase and disintegrin cysteine-rich ture of the enzyme, resulted in a band of 30 kDa, the domains and, therefore, is structurally closely related expected size for jararhagin-C. Further purification of to the membrane-bound A Disintegrin And Metallo- the cleaved disintegrin using FPLC Mono-Q columns proteinase (ADAMs) protein family. Its hemorrhagic resulted in one fraction capable of efficiently inhibit- activity is associated with the effects of both metallo- ing collagen-induced platelet aggregation in a dose- proteinase and disintegrin domains; the metallopro- dependent manner (IC50 of 8.5 mg/ml). -
Characterization of a Novel Metalloproteinase in Duvernoy's Gland of Rhabdophis Tigrinus Tigrinus
The Journal of Toxicological Sciences, 157 Vol.31, No.2, 157-168, 2006 CHARACTERIZATION OF A NOVEL METALLOPROTEINASE IN DUVERNOY’S GLAND OF RHABDOPHIS TIGRINUS TIGRINUS Koji KOMORI1, Motomi KONISHI1, Yuji MARUTA1, Michihisa TORIBA2, Atsushi SAKAI2, Akira MATSUDA3, Takamitsu HORI3, Mitsuko NAKATANI4, Naoto MINAMINO4 and Toshifumi AKIZAWA1 1Department of Analytical Chemistry, Faculty of Pharmaceutical Sciences, Setsunan University, 45-1 Nagaotogecho, Hirakata, Osaka 573-0101, Japan 2The Japan Snake Institute, 3318 Yabuzuka Ota, Gunma 379-2301, Japan 3Department of Biochemistry, Faculty of Pharmaceutical Sciences, Hiroshima International University, 5-1-1 Hirokoshingai, Kure, Hiroshima 737-0112, Japan 4Department of Pharmacology, National Cardiovascular Center Research Institute, 5-7-1 Fujishirodai, Suita, Osaka 565-8565, Japan (Received January 31, 2006; Accepted February 20, 2006) ABSTRACT — During the characterization of hemorrhagic factor in venom of Rhabdophis tigrinus tigri- nus, so-called Yamakagashi in Japan, one of the Colubridae family, a novel metalloproteinase with molec- ular weight of 38 kDa in the Duvernoy’s gland of Yamakagashi was identified by gelatin zymography and by monitoring its proteolytic activity using a fluorescence peptide substrate, MOCAc-PLGLA2pr(Dnp)AR-NH2, which was developed for measuring the well-known matrix metalloproteinase (MMP) activity. After purification by gel filtration HPLC and/or column switch HPLC system consisting of an affin- ity column, which was immobilized with a synthetic BS-10 peptide (MQKPRCGVPD) originating from propeptide domain of MMP-7 and a reversed-phase column, the N-terminal amino acid sequence of the 38 kDa metalloproteinase was identified as FNTFPGDLK which shared a high homology to Xenopus MMP-9. The 38 kDa metalloproteinase required Zn2+ and Ca2+ ions for its proteolytic activity. -
George Michael Humphrey Birchenough
GEORGE MICHAEL HUMPHREY BIRCHENOUGH Analysis of intestinal factors contributing to the age- dependency of systemic neuropathogenic Escherichia coli K1 infection in the neonatal rat Thesis submitted in accordance with the requirements of the UCL School of Pharmacy for the degree of Doctor of Philosophy Microbiology Group, Department of Pharmaceutics, UCL School of Pharmacy July 2012 PLAGIARISM STATEMENT This thesis describes research conducted in the UCL School of Pharmacy between October 2008 and July 2012 under the supervision of Professor Peter W. Taylor. I certify that the research described is original and that any parts of the work that have been conducted by collaboration are clearly indicated. I also certify that I have written all the text herein and have clearly indicated by suitable citation any part of the dissertation that has already appeared in publication. Signature: Date: Acknowledgements Firstly I wish to thank my supervisor, Professor Peter Taylor, for giving me the opportunity to work on such an interesting and rewarding project. Your continued support and enthusiasm has been a constant source of encouragement and I greatly appreciate all the advice and help (both scientific and general!) that you have provided over the last four years. I owe you a lot of beer. I also wish to thank my amazing parents for all their love and support over the eight years of my higher education. Without your enthusiasm and belief I would not have been able to follow this path. I sincerely promise I will now get a job! Furthermore, I wish to thank colleagues at the London School of Hygiene & Tropical Medicine, Dr. -
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 -
Handbook of Proteolytic Enzymes Second Edition Volume 1 Aspartic and Metallo Peptidases
Handbook of Proteolytic Enzymes Second Edition Volume 1 Aspartic and Metallo Peptidases Alan J. Barrett Neil D. Rawlings J. Fred Woessner Editor biographies xxi Contributors xxiii Preface xxxi Introduction ' Abbreviations xxxvii ASPARTIC PEPTIDASES Introduction 1 Aspartic peptidases and their clans 3 2 Catalytic pathway of aspartic peptidases 12 Clan AA Family Al 3 Pepsin A 19 4 Pepsin B 28 5 Chymosin 29 6 Cathepsin E 33 7 Gastricsin 38 8 Cathepsin D 43 9 Napsin A 52 10 Renin 54 11 Mouse submandibular renin 62 12 Memapsin 1 64 13 Memapsin 2 66 14 Plasmepsins 70 15 Plasmepsin II 73 16 Tick heme-binding aspartic proteinase 76 17 Phytepsin 77 18 Nepenthesin 85 19 Saccharopepsin 87 20 Neurosporapepsin 90 21 Acrocylindropepsin 9 1 22 Aspergillopepsin I 92 23 Penicillopepsin 99 24 Endothiapepsin 104 25 Rhizopuspepsin 108 26 Mucorpepsin 11 1 27 Polyporopepsin 113 28 Candidapepsin 115 29 Candiparapsin 120 30 Canditropsin 123 31 Syncephapepsin 125 32 Barrierpepsin 126 33 Yapsin 1 128 34 Yapsin 2 132 35 Yapsin A 133 36 Pregnancy-associated glycoproteins 135 37 Pepsin F 137 38 Rhodotorulapepsin 139 39 Cladosporopepsin 140 40 Pycnoporopepsin 141 Family A2 and others 41 Human immunodeficiency virus 1 retropepsin 144 42 Human immunodeficiency virus 2 retropepsin 154 43 Simian immunodeficiency virus retropepsin 158 44 Equine infectious anemia virus retropepsin 160 45 Rous sarcoma virus retropepsin and avian myeloblastosis virus retropepsin 163 46 Human T-cell leukemia virus type I (HTLV-I) retropepsin 166 47 Bovine leukemia virus retropepsin 169 48 -
Structural, Functional and Therapeutic Aspects of Snake Venom Metal- Loproteinases
Send Orders for Reprints to [email protected] 28 Mini-Reviews in Organic Chemistry, 2014, 11, 28-44 Structural, Functional and Therapeutic Aspects of Snake Venom Metal- loproteinases P. Chellapandi* Department of Bioinformatics, School of Life Sciences, Bharathidasan University, Tiruchirappalli-620024, Tamil Nadu, India Abstract: Snake venoms are rich sources of metalloproteinases that are of biological interest due to their diverse molecu- lar diversity and selective therapeutic applications. Snake venoms metalloproteinases (SVMPs) belong to the MEROPS peptidase family M12B or reprolysin subfamily, which are consisted of four major domains include a reprolysin catalytic domain, a disintegrin domain, a reprolysin family propeptide domain and a cysteine-rich domain. The appropriate struc- tural and massive sequences information have been available for SVMPs family of enzymes in the Protein Data Bank and National Center for Biotechnology Information, respectively. Functional essentiality of every domain and a crucial contri- bution of binding geometry, primary specificity site, and structural motifs have been studied in details, pointing the way for designing potential anti-coagulation, antitumor, anti-complementary and anti-inflammatory drugs or peptides. These enzymes have been reported to degrade fibrinogen, fibrin and collagens, and to prevent progression of clot formation. An- giotensin-converting enzyme activity, antibacterial properties, haemorrhagic activity and platelet aggregation response of SVMPs have been studied earlier. Structural information of these enzymes together with recombinant DNA technology would strongly promote the construction of many recombinant therapeutic peptides, particularly fibrinogenases and vac- cines. We have comprehensively reviewed the structure-function-evolution relationships of SVMPs family proteins and their advances in the promising target models for structure-based inhibitors and peptides design.