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Investigating the Origin of Observed Central Dips in Radial Metallicity Profiles [article]

Bethan Easeman, Patricia Schady, Stijn Wuyts, Robert M. Yates
2022 arXiv   pre-print
Kobulnicky et al. 1999; Stasińska 2005; Kewley & Ellison 2008; Yates et al. 2020) .  ...  We applied a lower limit on the H𝛼EW of the spaxels considered, removing any spaxels with H𝛼EW < 50Å, as used by Yates et al. (2020) .  ... 
arXiv:2201.03296v1 fatcat:7rlt2pd6bbacpl53hwkkaqasdm

Genenames.org: the HGNC resources in 2015

Kristian A. Gray, Bethan Yates, Ruth L. Seal, Mathew W. Wright, Elspeth A. Bruford
2014 Nucleic Acids Research  
The HUGO Gene Nomenclature Committee (HGNC) based at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. To date the HGNC have assigned over 39 000 gene names and, representing an increase of over 5000 entries in the past two years. As well as increasing the size of our database, we have continued redesigning our website http://www.genenames.org and have modified, updated and improved many aspects of the site including a faster and more powerful
more » ... ch, a vastly improved HCOP tool and a REST service to increase the number of ways users can retrieve our data. This article provides an overview of our current online data and resources, and highlights the changes we have made in recent years.
doi:10.1093/nar/gku1071 pmid:25361968 pmcid:PMC4383909 fatcat:6bgwdrhfizcmtfnls2i7s3iwly

Updates to HCOP: the HGNC comparison of orthology predictions tool

Bethan Yates, Kristian A Gray, Tamsin E M Jones, Elspeth A Bruford
2021 Briefings in Bioinformatics  
Multiple resources currently exist that predict orthologous relationships between genes. These resources differ both in the methodologies used and in the species they make predictions for. The HGNC Comparison of Orthology Predictions (HCOP) search tool integrates and displays data from multiple ortholog prediction resources for a specified human gene or set of genes. An indication of the reliability of a prediction is provided by the number of resources that support it. HCOP was originally
more » ... ned to show orthology predictions between human and mouse but has been expanded to include data from a current total of 20 selected vertebrate and model organism species. The HCOP pipeline used to fetch and integrate the information from the disparate ortholog and nomenclature data resources has recently been rewritten, both to enable the inclusion of new data and to take advantage of modern web technologies. Data from HCOP are used extensively in our work naming genes as the Vertebrate Gene Nomenclature Committee (https://vertebrate.genenames.org).
doi:10.1093/bib/bbab155 pmid:33959747 pmcid:PMC8574622 fatcat:meot4jf5hzhbne24n2plo6dtiq

Genenames.org: the HGNC and VGNC resources in 2017

Bethan Yates, Bryony Braschi, Kristian A. Gray, Ruth L. Seal, Susan Tweedie, Elspeth A. Bruford
2016 Nucleic Acids Research  
The HUGO Gene Nomenclature Committee (HGNC) based at the European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. Currently the HGNC database contains almost 40 000 approved gene symbols, over 19 000 of which represent protein-coding genes. In addition to naming genomic loci we manually curate genes into family sets based on shared characteristics such as homology, function or phenotype. We have recently updated our gene family resources and introduced new
more » ... proved visualizations which can be seen alongside our gene symbol reports on our primary website http://www.genenames.org. In 2016 we expanded our remit and formed the Vertebrate Gene Nomenclature Committee (VGNC) which is responsible for assigning names to vertebrate species lacking a dedicated nomenclature group. Using the chimpanzee genome as a pilot project we have approved symbols and names for over 14 500 proteincoding genes in chimpanzee, and have developed a new website http://vertebrate.genenames.org to distribute these data. Here, we review our online data and resources, focusing particularly on the improvements and new developments made during the last two years.
doi:10.1093/nar/gkw1033 pmid:27799471 pmcid:PMC5210531 fatcat:4lums3a3tffutdx2wgv77gsoki

Genenames.org: the HGNC and VGNC resources in 2019

Bryony Braschi, Paul Denny, Kristian Gray, Tamsin Jones, Ruth Seal, Susan Tweedie, Bethan Yates, Elspeth Bruford
2018 Nucleic Acids Research  
The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 40 000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. The Vertebrate Gene Nomenclature Committee (VGNC) was established in 2016 to assign standardized nomenclature in line with human for vertebrate species that lack their own nomenclature committees. The VGNC initially assigned
more » ... menclature for over 15000 proteincoding genes in chimpanzee. We have extended this process to other vertebrate species, naming over 14000 protein-coding genes in cow and dog and over 13 000 in horse to date. Our HGNC website https://www.genenames.org has undergone a major design update, simplifying the homepage to provide easy access to our search tools and making the site more mobile friendly. Our gene families pages are now known as 'gene groups' and have increased in number to over 1200, with nearly half of all named genes currently assigned to at least one gene group. This article provides an overview of our online data and resources, focusing on our work over the last two years.
doi:10.1093/nar/gky930 pmid:30304474 fatcat:fhml3cnddvgcrjz54mjwoczc2e

Genenames.org: the HGNC and VGNC resources in 2021

Susan Tweedie, Bryony Braschi, Kristian Gray, Tamsin E M Jones, Ruth L Seal, Bethan Yates, Elspeth A Bruford
2020 Nucleic Acids Research  
The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problematic symbols, we are working towards stabilizing symbols where possible; over 2000 symbols for disease associated genes are now marked as stable in our symbol reports. All of our
more » ... a is available at the HGNC website https://www.genenames.org. The Vertebrate Gene Nomenclature Committee (VGNC) was established to assign standardized nomenclature in line with human for vertebrate species lacking their own nomenclature committee. In addition to the previous VGNC core species of chimpanzee, cow, horse and dog, we now name genes in cat, macaque and pig. Gene groups have been added to VGNC and currently include two complex families: olfactory receptors (ORs) and cytochrome P450s (CYPs). In collaboration with specialists we have also named CYPs in species beyond our core set. All VGNC data is available at https://vertebrate.genenames.org/. This article provides an overview of our online data and resources, focusing on updates over the last two years.
doi:10.1093/nar/gkaa980 pmid:33152070 fatcat:jthxpdwn4vckbehpjauj4lafwy

Endo-lysosomal TRP mucolipin-1 channels trigger global ER Ca2+release and Ca2+influx

Bethan S. Kilpatrick, Elizabeth Yates, Christian Grimm, Anthony H. Schapira, Sandip Patel
2016 Journal of Cell Science  
Transient receptor potential (TRP) mucolipins (TRPMLs), encoded by the MCOLN genes, are patho-physiologically relevant endolysosomal ion channels crucial for membrane trafficking. Several lines of evidence suggest that TRPMLs mediate localised Ca 2+ release but their role in Ca 2+ signalling is not clear. Here, we show that activation of endogenous and recombinant TRPMLs with synthetic agonists evoked global Ca 2+ signals in human cells. These signals were blocked by a dominant-negative TRPML1
more » ... onstruct and a TRPML antagonist. We further show that, despite a predominant lysosomal localisation, TRPML1 supports both Ca 2+ release and Ca 2+ entry. Ca 2+ release required lysosomal and ER Ca 2+ stores suggesting that TRPMLs, like other endo-lysosomal Ca 2+ channels, are capable of 'chatter' with ER Ca 2+ channels. Our data identify new modalities for TRPML1 action.
doi:10.1242/jcs.190322 pmid:27577094 pmcid:PMC5087663 fatcat:w3p6rvkkkjghvf6nd5mkstzsde

An Endosomal NAADP-Sensitive Two-Pore Ca 2+ Channel Regulates ER-Endosome Membrane Contact Sites to Control Growth Factor Signaling

Bethan S. Kilpatrick, Emily R. Eden, Leanne N. Hockey, Elizabeth Yates, Clare E. Futter, Sandip Patel
2017 Cell Reports  
Membrane contact sites are regions of close apposition between organelles that facilitate information transfer. Here, we reveal an essential role for Ca2+ derived from the endo-lysosomal system in maintaining contact between endosomes and the endoplasmic reticulum (ER). Antagonizing action of the Ca2+-mobilizing messenger NAADP, inhibiting its target endo-lysosomal ion channel, TPC1, and buffering local Ca2+ fluxes all clustered and enlarged late endosomes/lysosomes. We show that TPC1 localizes
more » ... to ER-endosome contact sites and is required for their formation. Reducing NAADP-dependent contacts delayed EGF receptor de-phosphorylation consistent with close apposition of endocytosed receptors with the ER-localized phosphatase PTP1B. In accord, downstream MAP kinase activation and mobilization of ER Ca2+ stores by EGF were exaggerated upon NAADP blockade. Membrane contact sites between endosomes and the ER thus emerge as Ca2+-dependent hubs for signaling.
doi:10.1016/j.celrep.2017.01.052 pmid:28199837 pmcid:PMC5318655 fatcat:gkpucfsafjbwxcwuhcczakp4ge

Mining of Ebola virus entry inhibitors identifies approved drugs as two-pore channel pore blockers

Christopher J. Penny, Kristin Vassileva, Archana Jha, Yu Yuan, Xavier Chee, Elizabeth Yates, Michela Mazzon, Bethan S. Kilpatrick, Shmuel Muallem, Mark Marsh, Taufiq Rahman, Sandip Patel
2019 BBA - Molecular Cell Research  
Two-pore channels (TPCs) are Ca2+-permeable ion channels localised to the endo-lysosomal system where they regulate trafficking of various cargoes including viruses. As a result, TPCs are emerging as important drug targets. However, their pharmacology is ill-defined. There are no approved drugs to target them. And their mechanism of ligand activation is largely unknown. Here, we identify a number of FDA-approved drugs as TPC pore blockers. Using a model of the pore of human TPC2 based on recent
more » ... structures of mammalian TPCs, we virtually screened a database of ~1500 approved drugs. Because TPCs have recently emerged as novel host factors for Ebola virus entry, we reasoned that Ebola virus entry inhibitors may exert their effects through inhibition of TPCs. Cross-referencing hits from the TPC virtual screen with two recent high throughput anti-Ebola screens yielded approved drugs targeting dopamine and estrogen receptors as common hits. These compounds inhibited endogenous NAADP-evoked Ca2+ release from sea urchin egg homogenates, NAADP-mediated channel activity of TPC2 re-routed to the plasma membrane, and PI(3,5)P2-mediated channel activity of TPC2 expressed in enlarged lysosomes. Mechanistically, single channel analyses showed that the drugs reduced mean open time consistent with a direct action on the pore. Functionally, drug potency in blocking TPC2 activity correlated with inhibition of Ebola virus-like particle entry. Our results expand TPC pharmacology through the identification of approved drugs as novel blockers, support a role for TPCs in Ebola virus entry, and provide insight into the mechanisms underlying channel regulation. This article is part of a Special Issue entitled: ECS Meeting edited by Claus Heizmann, Joachim Krebs and Jacques Haiech.
doi:10.1016/j.bbamcr.2018.10.022 pmid:30408544 pmcid:PMC7114365 fatcat:z7wq5gmfdvgxzhfjy6yygm66m4

What is the nature and extent of evidence on methodologies for monitoring and evaluating marine spatial management measures in UK and similar coastal waters? A systematic map protocol

Bethan C. O'Leary, Bryce D. Stewart, Emma McKinley, Prue F. E. Addison, Chris Williams, Griffin Carpenter, David Righton, Katherine L. Yates
2019 Environmental Evidence  
Anthropogenic degradation of marine ecosystems is widely accepted as a major social-ecological problem. The growing urgency to better manage marine ecosystems has led to the increasing application of 'spatial management measures' including marine protected areas, sectoral (e.g. fishery) closures, and marine spatial planning. However, the designation of varied spatial management regimes is just the first step; achievement of objectives relies upon effective implementation, monitoring, evaluation
more » ... and adaptation. Despite spatial management being a core component of the marine management portfolio, to our knowledge, there is no systematic overview of the evidence on methodologies available, and employed, to monitor and evaluate their effectiveness across social, economic and ecological outcomes. Methods: This systematic map will examine existing evidence describing methodologies for monitoring the effects, and evaluating the effectiveness, of marine spatial management across ecological, social and economic outcomes. Our aim is to provide a resource for decision-makers, primarily in the UK but also internationally, that supports effective marine management, and to describe the current evidence base. Identification and evaluation of relevant studies will therefore be restricted to coastal countries identified by our Stakeholder Group as being relevant to the UK, and searches will be restricted to the period 2009 to 2019 to align with the current UK policy context. Searches for relevant grey and academic literature, published in English, will be conducted in four bibliographic search engines, Google Scholar, 38 organisational websites and one specialist data repository. Eligibility screening will be conducted first at title and abstract level, and then at full text. Coding and meta-data extraction from eligible studies will include: bibliographic information, general information about the spatial management measure studied, and methodological information on the monitoring and evaluation undertaken. Consistency checking amongst reviewers will be undertaken during screening, coding and data extraction phases. The outcome of the systematic map will be a database that displays the meta-data of identified relevant studies. Findings will be presented in a descriptive report detailing the evaluation approaches and analytical methodologies employed, and data collection methods applied and/or data required by relevant studies to inform evaluations on the effectiveness of marine spatial management measures.
doi:10.1186/s13750-019-0178-y fatcat:ma6tkbr5mbdp5lfrq7v54idawi

The nature and extent of evidence on methodologies for monitoring and evaluating marine spatial management measures in the UK and similar coastal waters: a systematic map

Bethan C. O'Leary, Joshua P. Copping, Nibedita Mukherjee, Sandra L. Dorning, Bryce D. Stewart, Emma McKinley, Prue F. E. Addison, Chris Williams, Griffin Carpenter, David Righton, Katherine L. Yates
2021 Environmental Evidence  
Background Anthropogenic degradation of marine ecosystems is widely accepted as a major social-ecological problem. The growing urgency to manage marine ecosystems more effectively has led to increasing application of spatial management measures (marine protected areas [MPAs], sectoral [e.g. fishery] closures and marine spatial planning [marine plans]). Understanding the methodologies used to evaluate the effectiveness of these measures against social, economic, and ecological outcomes is key
more » ... designing effective monitoring and evaluation programmes. Methods We used a pre-defined and tested search string focusing on intervention and outcome terms to search for relevant studies across four bibliographic databases, Google Scholar, 39 organisational websites, and one specialist data repository. Searches were conducted in English and restricted to the period 2009 to 2019 to align with current UK marine policy contexts. Relevant studies were restricted to UK-relevant coastal countries, as identified by key stakeholders. Search results were screened for relevance against pre-defined eligibility criteria first at title and abstract level, and then at full text. Articles assessed as not relevant at full text were recorded with reasons for exclusion. Two systematic map databases of meta-data and coded data from relevant primary and secondary studies, respectively, were produced. Review findings Over 19,500 search results were identified, resulting in 391 relevant primary articles, 33 secondary articles and 49 tertiary reviews. Relevant primary articles evaluated spatial management measures across a total of 22 social, economic and ecological outcomes; only 2.8% considered all three disciplines, with most focused exclusively on ecological (67.8%) or social (13.3%) evaluations. Secondary articles predominately focused on ecological evaluations (75.8%). The majority of the primary and secondary evidence base aimed to evaluate the effectiveness of MPAs (85.7% and 90.9% respectively), followed by fisheries closures (12.5%; 3.0%) with only 1.8% of primary, and 6.1% of secondary, articles focused on marine plans or on MPAs and fisheries closures combined. Most evaluations reported within primary articles were conducted for a single site (60.4%) or multiple individual sites (32.5%), with few evaluating networks of sites (6.9%). Secondary articles mostly evaluated multiple individual sites (93.9%). Most (70.3%) primary articles conducted principal evaluations, i.e. basic description of effects; 29.4% explored causation; and 0.3% undertook benefit evaluations. Secondary articles predominately explored causation (66.7%) with the remainder conducting principal evaluations. Australia (27.4%), the USA (18.4%) and the UK (11.3%) were most frequently studied by primary articles, with secondary articles reporting mostly global (66.7%) or European (18.2%) syntheses. Conclusions The systematic map reveals substantial bodies of evidence relating to methods of evaluating MPAs against ecological outcomes. However, key knowledge gaps include evaluation across social and economic outcomes and of overall merit and/or worth (benefit evaluation), as well as of: marine plans; networks of sites; real-time, temporary or seasonal closures; spatial management within offshore waters, and lagoon or estuary environments. Although the evidence base has grown over the past two decades, information to develop comprehensive evaluation frameworks remains insufficient. Greater understanding on how to evaluate the effectiveness of spatial management measures is required to support improved management of global ocean resources and spaces.
doi:10.1186/s13750-021-00227-x fatcat:oijmvyuribbdhh2gz6okayk5ti

Ensembl 2014

Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García Girón (+40 others)
2013 Nucleic Acids Research  
Ensembl (http://www.ensembl.org) creates tools and data resources to facilitate genomic analysis in chordate species with an emphasis on human, major vertebrate model organisms and farm animals. Over the past year we have increased the number of species that we support to 77 and expanded our genome browser with a new scrollable overview and improved variation and phenotype views. We also report updates to our core datasets and improvements to our gene homology relationships from the addition of
more » ... new species. Our REST service has been extended with additional support for comparative genomics and ontology information. Finally, we provide updated information about our methods for data access and resources for user training.
doi:10.1093/nar/gkt1196 pmid:24316576 pmcid:PMC3964975 fatcat:knxp7akjtnbvnm7hlxajhvnzra

Ensembl 2013

Paul Flicek, Ikhlak Ahmed, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil (+43 others)
2012 Nucleic Acids Research  
The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets.
more » ... l data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.
doi:10.1093/nar/gks1236 pmid:23203987 pmcid:PMC3531136 fatcat:5hwmkwmozbcpbk3bzrzuhwdqhe

Page 169 of The Huntington Library Quarterly Vol. 1, Issue 2 [page]

1938 The Huntington Library Quarterly  
Beginning with an article in the Review of English Studies,’ Miss Yates demonstrated the satiri- cal purpose of the Ortho-epia Gallica as it applied to several Eliza- bethan conversation manuals written  ...  Yates, John Florio: The Life of an Italian in Shakespeare’s England (Cam- bridge, 1934). “Idem, A Study of LOVE’s LABOUR’s Lost (Cambridge, 1936). [ 169 J  ... 

Page 138 of Notes and Queries Vol. 15, Issue 4 [page]

1968 Notes and Queries  
Yates (London and Chicago, 1966), p. 49.  ...  Yates in Shakespeare Studies III, ed. by J. Leeds Barroll (Cincinnati 1967). I am extremely grateful to Dr. Yates for allowing me to see this article in typescript.  ... 
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