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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. -
S100B Promotes Glioma Growth Through Chemoattraction of Myeloid-Derived Macrophages
Published OnlineFirst May 29, 2013; DOI: 10.1158/1078-0432.CCR-12-3725 Clinical Cancer Human Cancer Biology Research S100B Promotes Glioma Growth through Chemoattraction of Myeloid-Derived Macrophages Huaqing Wang1, Leying Zhang5, Ian Y. Zhang5, Xuebo Chen2, Anna Da Fonseca8, Shihua Wu3, Hui Ren2, Sam Badie5, Sam Sadeghi5, Mao Ouyang4, Charles D. Warden6, and Behnam Badie5,7 Abstract þ Purpose: S100B is member of a multigenic family of Ca2 -binding proteins, which is overexpressed by gliomas. Recently, we showed that low concentrations of S100B attenuated microglia activation through the induction of Stat3. We hypothesized that overexpression of S100B in gliomas could promote tumor growth by modulating the activity of tumor-associated macrophages (TAM). Experimental Design: We stably transfected GL261 glioma cell lines with constructs that overexpressed (S100Bhigh) or underexpressed (S100Blow) S100B and compared their growth characteristics to intracranial wild-type (S100Bwt) tumors. Results: Downregulation of S100B in gliomas had no impact on cell division in vitro but abrogated tumor growth in vivo. Interestingly, compared to S100Blow tumors, S100Bwt and S100Bhigh intracranial gliomas exhi- bited higher infiltration of TAMs, stronger inflammatory cytokine expression, and increased vascularity. To identify the potential mechanisms involved, the expression of the S100B receptor, receptor for advanced glycation end products (RAGE), was evaluated in gliomas. Although S100B expression induced RAGE in vivo, RAGE ablation in mice did not significantly inhibit TAM infiltration into gliomas, suggesting that other pathways were involved in this process. To evaluate other mechanisms responsible for TAM chemoattraction, we then examined chemokine pathways and found that C-C motif ligand 2 (CCL2) was upregulated in S100Bhigh tumors. -
Abstracts Genome 10K & Genome Science 29 Aug - 1 Sept 2017 Norwich Research Park, Norwich, Uk
Genome 10K c ABSTRACTS GENOME 10K & GENOME SCIENCE 29 AUG - 1 SEPT 2017 NORWICH RESEARCH PARK, NORWICH, UK Genome 10K c 48 KEYNOTE SPEAKERS ............................................................................................................................... 1 Dr Adam Phillippy: Towards the gapless assembly of complete vertebrate genomes .................... 1 Prof Kathy Belov: Saving the Tasmanian devil from extinction ......................................................... 1 Prof Peter Holland: Homeobox genes and animal evolution: from duplication to divergence ........ 2 Dr Hilary Burton: Genomics in healthcare: the challenges of complexity .......................................... 2 INVITED SPEAKERS ................................................................................................................................. 3 Vertebrate Genomics ........................................................................................................................... 3 Alex Cagan: Comparative genomics of animal domestication .......................................................... 3 Plant Genomics .................................................................................................................................... 4 Ksenia Krasileva: Evolution of plant Immune receptors ..................................................................... 4 Andrea Harper: Using Associative Transcriptomics to predict tolerance to ash dieback disease in European ash trees ............................................................................................................ -
Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma
Anatomy and Pathology Whole-Genome Microarray Detects Deletions and Loss of Heterozygosity of Chromosome 3 Occurring Exclusively in Metastasizing Uveal Melanoma Sarah L. Lake,1 Sarah E. Coupland,1 Azzam F. G. Taktak,2 and Bertil E. Damato3 PURPOSE. To detect deletions and loss of heterozygosity of disease is fatal in 92% of patients within 2 years of diagnosis. chromosome 3 in a rare subset of fatal, disomy 3 uveal mela- Clinical and histopathologic risk factors for UM metastasis noma (UM), undetectable by fluorescence in situ hybridization include large basal tumor diameter (LBD), ciliary body involve- (FISH). ment, epithelioid cytomorphology, extracellular matrix peri- ϩ ETHODS odic acid-Schiff-positive (PAS ) loops, and high mitotic M . Multiplex ligation-dependent probe amplification 3,4 5 (MLPA) with the P027 UM assay was performed on formalin- count. Prescher et al. showed that a nonrandom genetic fixed, paraffin-embedded (FFPE) whole tumor sections from 19 change, monosomy 3, correlates strongly with metastatic death, and the correlation has since been confirmed by several disomy 3 metastasizing UMs. Whole-genome microarray analy- 3,6–10 ses using a single-nucleotide polymorphism microarray (aSNP) groups. Consequently, fluorescence in situ hybridization were performed on frozen tissue samples from four fatal dis- (FISH) detection of chromosome 3 using a centromeric probe omy 3 metastasizing UMs and three disomy 3 tumors with Ͼ5 became routine practice for UM prognostication; however, 5% years’ metastasis-free survival. to 20% of disomy 3 UM patients unexpectedly develop metas- tases.11 Attempts have therefore been made to identify the RESULTS. Two metastasizing UMs that had been classified as minimal region(s) of deletion on chromosome 3.12–15 Despite disomy 3 by FISH analysis of a small tumor sample were found these studies, little progress has been made in defining the key on MLPA analysis to show monosomy 3. -
The EMBL-European Bioinformatics Institute the Hub for Bioinformatics in Europe
The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe Blaise T.F. Alako, PhD [email protected] www.ebi.ac.uk What is EMBL-EBI? • Part of the European Molecular Biology Laboratory • International, non-profit research institute • Europe’s hub for biological data, services and research The European Molecular Biology Laboratory Heidelberg Hamburg Hinxton, Cambridge Basic research Structural biology Bioinformatics Administration Grenoble Monterotondo, Rome EMBO EMBL staff: 1500 people Structural biology Mouse biology >60 nationalities EMBL member states Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia Who we are ~500 members of staff ~400 work in services & support >53 nationalities ~120 focus on basic research EMBL-EBI’s mission • Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • Contribute to the advancement of biology through basic investigator-driven research in bioinformatics • Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • Help disseminate cutting-edge technologies to industry • Coordinate biological data provision throughout Europe Services Data and tools for molecular life science www.ebi.ac.uk/services Browse our services 9 What services do we provide? Labs around the -
Functional Effects Detailed Research Plan
GeCIP Detailed Research Plan Form Background The Genomics England Clinical Interpretation Partnership (GeCIP) brings together researchers, clinicians and trainees from both academia and the NHS to analyse, refine and make new discoveries from the data from the 100,000 Genomes Project. The aims of the partnerships are: 1. To optimise: • clinical data and sample collection • clinical reporting • data validation and interpretation. 2. To improve understanding of the implications of genomic findings and improve the accuracy and reliability of information fed back to patients. To add to knowledge of the genetic basis of disease. 3. To provide a sustainable thriving training environment. The initial wave of GeCIP domains was announced in June 2015 following a first round of applications in January 2015. On the 18th June 2015 we invited the inaugurated GeCIP domains to develop more detailed research plans working closely with Genomics England. These will be used to ensure that the plans are complimentary and add real value across the GeCIP portfolio and address the aims and objectives of the 100,000 Genomes Project. They will be shared with the MRC, Wellcome Trust, NIHR and Cancer Research UK as existing members of the GeCIP Board to give advance warning and manage funding requests to maximise the funds available to each domain. However, formal applications will then be required to be submitted to individual funders. They will allow Genomics England to plan shared core analyses and the required research and computing infrastructure to support the proposed research. They will also form the basis of assessment by the Project’s Access Review Committee, to permit access to data. -
Ahnaks Are a Class of Giant Propeller-Like Proteins That Associate with Calcium Channel Proteins of Cardiomyocytes and Other Cells
The AHNAKs are a class of giant propeller-like proteins that associate with calcium channel proteins of cardiomyocytes and other cells Akihiko Komuro*, Yutaka Masuda*, Koichi Kobayashi, Roger Babbitt, Murat Gunel, Richard A. Flavell, and Vincent T. Marchesi† Departments of Pathology and Immunobiology, Boyer Center for Molecular Medicine, Yale University School of Medicine, New Haven, CT 06510 Contributed by Vincent T. Marchesi, December 31, 2003 To explore the function of the giant AHNAK molecule, first de- mechanisms, one operating at the cell surface in collaboration with scribed in 1992 [Shtivelman, E., Cohen, F. E. & Bishop, J. M. (1992) calcium channels, and the second, PLC activation, which is a process Proc. Natl. Acad. Sci. USA 89, 5472–5476], we created AHNAK null that could potentially take place at multiple points throughout the mice by homologous recombination. Homozygous knockouts cell. showed no obvious phenotype, but revealed instead a second The arrangement of channel proteins at the cell surface is AHNAK-like molecule, provisionally designated AHNAK2. Like the believed to be controlled by multidomain polypeptides known as original AHNAK, AHNAK2 is a 600-kDa protein composed of a large scaffolding proteins that link together activated channels at specific number of highly conserved repeat segments. Structural predic- points on the membrane surface. Scaffolding proteins also coordi- tions suggest that the repeat segments of both AHNAKs may have nate the activities of multienzyme complexes by physically linking as their basic framework a series of linked, antiparallel -strands them together, and as in the case with AHNAK, they are often similar to those found in -propeller proteins. -
The for Report 07-08
THE CENTER FOR INTEGRATIVE GENOMICS REPORT 07-08 www.unil.ch/cig Table of Contents INTRODUCTION 2 The CIG at a glance 2 The CIG Scientific Advisory Committee 3 Message from the Director 4 RESEARCH 6 Richard Benton Chemosensory perception in Drosophila: from genes to behaviour 8 Béatrice Desvergne Networking activity of PPARs during development and in adult metabolic homeostasis 10 Christian Fankhauser The effects of light on plant growth and development 12 Paul Franken Genetics and energetics of sleep homeostasis and circadian rhythms 14 Nouria Hernandez Mechanisms of basal and regulated RNA polymerase II and III transcription of ncRNA in mammalian cells 16 Winship Herr Regulation of cell proliferation 18 Henrik Kaessmann Mammalian evolutionary genomics 20 Sophie Martin Molecular mechanisms of cell polarization 22 Liliane Michalik Transcriptional control of tissue repair and angiogenesis 24 Alexandre Reymond Genome structure and expression 26 Andrzej Stasiak Functional transitions of DNA structure 28 Mehdi Tafti Genetics of sleep and the sleep EEG 30 Bernard Thorens Molecular and physiological analysis of energy homeostasis in health and disease 32 Walter Wahli The multifaceted roles of PPARs 34 Other groups at the Génopode 37 CORE FACILITIES 40 Lausanne DNA Array Facility (DAFL) 42 Protein Analysis Facility (PAF) 44 Core facilities associated with the CIG 46 EDUCATION 48 Courses and lectures given by CIG members 50 Doing a PhD at the CIG 52 Seminars and symposia 54 The CIG annual retreat 62 The CIG and the public 63 Artist in residence at the CIG 63 PEOPLE 64 1 Introduction The Center for IntegratiVE Genomics (CIG) at A glance The Center for Integrative Genomics (CIG) is the newest depart- ment of the Faculty of Biology and Medicine of the University of Lausanne (UNIL). -
Evolution of Language: Lessons from the Genome
Psychon Bull Rev DOI 10.3758/s13423-016-1112-8 BRIEF REPORT Evolution of language: Lessons from the genome Simon E. Fisher1,2 # The Author(s) 2016. This article is published with open access at Springerlink.com Abstract The post-genomic era is an exciting time for re- Keywords Genetics and genomics . Speech and language . searchers interested in the biology of speech and language. Evolution . Ancient DNA . Model systems Substantive advances in molecular methodologies have opened up entire vistas of investigation that were not previ- ously possible, or in some cases even imagined. Speculations Our speech and language capacities enable us to acquire vocab- concerning the origins of human cognitive traits are being ularies of many thousands of words, assemble them into a myr- transformed into empirically addressable questions, generat- iad of structured meaningful expressions, and convey thoughts ing specific hypotheses that can be explicitly tested using data to others by mapping meaning to sound, and back again. In the collected from both the natural world and experimental set- twenty-first century, we are witnessing dramatic advances in tings. In this article, I discuss a number of promising lines of deciphering the genetic architecture underlying these fascinat- research in this area. For example, the field has begun to ing aspects of the human condition. By directly borrowing identify genes implicated in speech and language skills, in- state-of-the-art gene mapping approaches from studies of typi- cluding not just disorders but also the normal range of abili- cal biomedical traits, and applying them to scientific studies of ties. Such genes provide powerful entry points for gaining language for the first time, it has become feasible to start tracing insights into neural bases and evolutionary origins, using so- out relevant genetic networks (Graham & Fisher, 2015). -
Cabinet Agenda
Cabinet Agenda Members of the Cabinet: Cllr J Fuller (Chairman) Leader, External Affairs and Policy Cllr K Mason Billig (Vice Chairman) Governance and Efficiency Cllr Y Bendle Better Lives Cllr M Edney Clean and Safe Environment Cllr L Neal Stronger Economy Cllr A Thomas Customer Focus Cllr J Worley Finance and Resources Date & Time: Monday 19 April 2021 9.00 am Place: To be hosted remotely at: South Norfolk House, Cygnet Court, Long Stratton, Norwich, NR15 2XE Contact: Claire White tel (01508) 533669 Email: [email protected] Website: www.south-norfolk.gov.uk PUBLIC ATTENDANCE: This meeting will be live streamed for public viewing via the following link: https://www.youtube.com/channel/UCZciRgwo84-iPyRImsTCIng If a member of the public would like to attend to speak on an agenda item, please email your request to [email protected], no later than 5.00pm on Thursday 15 April 2021. Large print version can be made available If you have any special requirements in order to attend this meeting, please let us know in advance. 1 AGENDA 1. To report apologies for absence 2. Any items of business which the Chairman decides should be considered as a matter of urgency pursuant to section 100B(4)(b) of the Local Government Act, 1972. Urgent business may only be taken if, “by reason of special circumstances” (which will be recorded in the minutes), the Chairman of the meeting is of the opinion that the item should be considered as a matter of urgency 3. To receive Declarations of interest from Members (please see guidance – page 4) 4. -
1 Genomic Analysis of Family Data Reveals Additional Genetic Effects On
bioRxiv preprint doi: https://doi.org/10.1101/106203; this version posted February 6, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Genomic analysis of family data reveals additional genetic effects on intelligence and personality W. David Hill1,2*†, Ruben C. Arslan3,4†, Charley Xia†5, Michelle Luciano1,2, Carmen Amador5, Pau Navarro5, Caroline Hayward5, Reka Nagy5, David J. Porteous1,6,8, Andrew M. McIntosh1,9, Ian J. Deary1,2, Chris S. Haley5,10, and Lars Penke1,3,4 1 Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK 2 Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK 3 Georg Elias Müller Institute of Psychology, Georg August University Göttingen, Germany 4 Leibniz ScienceCampus Primate Cognition, Göttingen, Germany 5 MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK 6 Generation Scotland, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK 8 Medical Genetics Section, Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh 9 Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh EH10 5HF 10 The Roslin Institute and Royal (Dick) School of Veterinary Sciences, University of Edinburgh, UK * Corresponding author † These authors contributed equally Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh EH8 9JZ, UK, T: +44 (131) 650 8405, E: [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/106203; this version posted February 6, 2017. -
Papers Will Be Uploaded in Due Course
THE UNIVERSITY OF EDINBURGH BUSINESS FOR MEETING OF THE UNIVERSITY COURT to be held in the Raeburn Room, Old College on Monday, 9 December 2013 at 2.00 p.m. A buffet lunch will be available at 1.00 p.m. in the Lord Provost Elder Room, Old College This meeting of Court will be preceded by a presentation on the Research Excellence Framework (REF2014) delivered by Mrs Tracey Slaven, Deputy Secretary, Strategic Planning. A FORMAL BUSINESS 1. Minute of the meeting held on 4 November 2013 A1 2. Senate Assessor A2 B PRINCIPAL'S BUSINESS 1. Principal’s Communications B1 2. Vice-Principal update B2 C SUBSTANTIVE ITEMS 1. Report of the Finance and General Purposes Committee .1 Comments on the Report of the Central Management Group C1.1 .2 Report on Other Items C1.2 2. EUSA President’s Report C2 3. Risk Management Committee year end report C3 4. Risk Management – post year end Assurance Statement C4 5. Audit Committee Annual Report C5 6. Reports and Financial Statements .1 Annual Report and Accounts for year ended 31 July 2013 C6.1 .2 Letter of Representation C6.2 .3 Review of 2012/2013 Outturn versus Forecast C6.3 7. 2014-2017 Draft Outcome Agreement C7 8. Strategic Plan: Targets and KPIs Progress Report C8 9. Annual Review 2012-2013 C9 10. Report from Remuneration Committee C10 11. Report from Knowledge Strategy Committee C11 D ITEMS FOR FORMAL APPROVAL OR NOTE 1. Draft Resolutions D1 2. Risk Management Committee – Terms of Reference D2 3. Donations and Legacies D3 4.