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Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Author Correction: Universal DNA methylation age across mammalian tissues. Nat Aging 2023; 3:1462. [PMID: 37674040 PMCID: PMC10645586 DOI: 10.1038/s43587-023-00499-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Affiliation(s)
- A T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - Z Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, Riverside, CA, USA
| | - A Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - T R Robeck
- Zoological SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - J A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - R Lowe
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Q Yan
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - J Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - H Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - J Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - V A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - D M Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - J Almunia
- Loro Parque Fundacion, Puerto de la Cruz, Spain
| | - A Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - R Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C S Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - G Banks
- School of Science and Technology, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - K Belov
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - N C Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - P Black
- Busch Gardens Tampa, Tampa, FL, USA
| | - D T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - E K Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - C E Breeze
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - R T Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - J L Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - G G Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - A Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - J M Cavin
- Gulf World, Dolphin Company, Panama City Beach, FL, USA
| | - L Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - I Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - H Chen
- Department of Pharmacology, Addiction Science and Toxicology, the University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - P Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - O W Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S M Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - L N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - M L Cossette
- Department of Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - J Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - J DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S DiRocco
- SeaWorld of Florida, Orlando, FL, USA
| | - C Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | | | - C K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - S Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E Erbay
- Altos Labs, San Francisco, CA, USA
| | - C Erlacher-Reid
- SeaWorld of Florida, Orlando, FL, USA
- SeaWorld Orlando, Orlando, FL, USA
| | - C G Faulkes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - S H Ferguson
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - C J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - J M Gaillard
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - E Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - L Gerber
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - V N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - R G Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - M J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - C B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - M B Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - D W Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - M Haulena
- Vancouver Aquarium, Vancouver, British Columbia, Canada
| | - K Herrick
- SeaWorld of California, San Diego, CA, USA
| | - A N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C J Hogg
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - T A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - T Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
- Division of Genetics and Metabolism, Oishei Children's Hospital, Buffalo, NY, USA
| | | | - A J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - G Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - O Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - H Katcher
- Yuvan Research, Mountain View, CA, USA
| | | | - V Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - H Kiaris
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - P Kordowitzki
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn, Poland
- Institute for Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | - W R Koski
- LGL Limited, King City, Ontario, Canada
| | - M Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - S B Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Center for Tropical Research, Institute for the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - S G Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - J F Lemaitre
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - A J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - X Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A R Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - D T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - T J Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - N Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - D Maddox
- White Oak Conservation, Yulee, FL, USA
| | - C O Matkin
- North Gulf Oceanic Society, Homer, AK, USA
| | - J A Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - J Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - J J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - G A Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - K Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - J Munshi-South
- Louis Calder Center-Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - A Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M Nagy
- Museum fur Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - P Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - P W Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - N B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Niehrs
- Institute of Molecular Biology, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - J K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - P O'Tierney Ginn
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - D T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - A G Ophir
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - S Osborn
- SeaWorld of Texas, San Antonio, TX, USA
| | - E A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - K M Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - K C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - M Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - K J Peters
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - A B Pedersen
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - D W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - G M Pinho
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
| | - P Reddy
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - B Rey
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - B R Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - J Robbins
- Center for Coastal Studies, Provincetown, MA, USA
| | | | - J Russell
- SeaWorld of California, San Diego, CA, USA
| | - E Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - L L Sailer
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - A B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - K M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | - T Schmitt
- SeaWorld of California, San Diego, CA, USA
| | | | - L B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - K E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - A W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - A Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - A B A Shafer
- Department of Forensic Science, Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - D Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - A V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - K Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS University, Mumbai, India
| | - I Sinha
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - R G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - E Soltanmaohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | - L Staggs
- SeaWorld of Florida, Orlando, FL, USA
| | | | - K J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - D T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | - V J Sugrue
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - B Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - J S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M J Thompson
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Van Bonn
- John G. Shedd Aquarium, Chicago, IL, USA
| | - S C Vernes
- School of Biology, the University of St Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - D Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - H V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Division of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - N Wang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
| | - C K Williams
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - X W Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M Yao
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - B G Young
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - B Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - P Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Y Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - W Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Zimmermann
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Koblenz, Germany
| | - J Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - K Raj
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - S Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
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Lu AT, Fei Z, Haghani A, Robeck TR, Zoller JA, Li CZ, Lowe R, Yan Q, Zhang J, Vu H, Ablaeva J, Acosta-Rodriguez VA, Adams DM, Almunia J, Aloysius A, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter GG, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke SM, Cooper LN, Cossette ML, Day J, DeYoung J, DiRocco S, Dold C, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Gorbunova V, Goya RG, Grant MJ, Green CB, Hales EN, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaitre JF, Levine AJ, Li C, Li X, Lim AR, Lin DTS, Lindemann DM, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, O'Brien JK, O'Tierney Ginn P, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pellegrini M, Peters KJ, Pedersen AB, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Seluanov A, Shafer ABA, Shanmuganayagam D, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmaohammadi E, Spangler ML, Spriggs MC, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Wallingford MC, Wang N, Wayne RK, Wilkinson GS, Williams CK, Williams RW, Yang XW, Yao M, Young BG, Zhang B, Zhang Z, Zhao P, Zhao Y, Zhou W, Zimmermann J, Ernst J, Raj K, Horvath S. Universal DNA methylation age across mammalian tissues. Nat Aging 2023; 3:1144-1166. [PMID: 37563227 PMCID: PMC10501909 DOI: 10.1038/s43587-023-00462-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/21/2023] [Indexed: 08/12/2023]
Abstract
Aging, often considered a result of random cellular damage, can be accurately estimated using DNA methylation profiles, the foundation of pan-tissue epigenetic clocks. Here, we demonstrate the development of universal pan-mammalian clocks, using 11,754 methylation arrays from our Mammalian Methylation Consortium, which encompass 59 tissue types across 185 mammalian species. These predictive models estimate mammalian tissue age with high accuracy (r > 0.96). Age deviations correlate with human mortality risk, mouse somatotropic axis mutations and caloric restriction. We identified specific cytosines with methylation levels that change with age across numerous species. These sites, highly enriched in polycomb repressive complex 2-binding locations, are near genes implicated in mammalian development, cancer, obesity and longevity. Our findings offer new evidence suggesting that aging is evolutionarily conserved and intertwined with developmental processes across all mammals.
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Affiliation(s)
- A T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - Z Fei
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Statistics, University of California, Riverside, Riverside, CA, USA
| | - A Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - T R Robeck
- Zoological SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - J A Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Z Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - R Lowe
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - Q Yan
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
| | - J Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - H Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - J Ablaeva
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - V A Acosta-Rodriguez
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - D M Adams
- Department of Biology, University of Maryland, College Park, MD, USA
| | - J Almunia
- Loro Parque Fundacion, Puerto de la Cruz, Spain
| | - A Aloysius
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - R Ardehali
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A Arneson
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - C S Baker
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - G Banks
- School of Science and Technology, Clifton Campus, Nottingham Trent University, Nottingham, UK
| | - K Belov
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - N C Bennett
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - P Black
- Busch Gardens Tampa, Tampa, FL, USA
| | - D T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
- Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - E K Bors
- Marine Mammal Institute, Oregon State University, Newport, OR, USA
| | - C E Breeze
- Altius Institute for Biomedical Sciences, Seattle, WA, USA
| | - R T Brooke
- Epigenetic Clock Development Foundation, Los Angeles, CA, USA
| | - J L Brown
- Center for Species Survival, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - G G Carter
- Department of Evolution, Ecology and Organismal Biology, The Ohio State University, Columbus, OH, USA
| | - A Caulton
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - J M Cavin
- Gulf World, Dolphin Company, Panama City Beach, FL, USA
| | - L Chakrabarti
- School of Veterinary Medicine and Science, University of Nottingham, Nottingham, UK
| | - I Chatzistamou
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina, Columbia, SC, USA
| | - H Chen
- Department of Pharmacology, Addiction Science and Toxicology, the University of Tennessee Health Science Center, Memphis, TN, USA
| | - K Cheng
- Medical Informatics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - P Chiavellini
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - O W Choi
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S M Clarke
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | - L N Cooper
- Department of Anatomy and Neurobiology, Northeast Ohio Medical University, Rootstown, OH, USA
| | - M L Cossette
- Department of Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - J Day
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - J DeYoung
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - S DiRocco
- SeaWorld of Florida, Orlando, FL, USA
| | - C Dold
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | | | - C K Emmons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - S Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E Erbay
- Altos Labs, San Francisco, CA, USA
| | - C Erlacher-Reid
- SeaWorld of Florida, Orlando, FL, USA
- SeaWorld Orlando, Orlando, FL, USA
| | - C G Faulkes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - S H Ferguson
- Fisheries and Oceans Canada, Freshwater Institute, Winnipeg, Manitoba, Canada
- Department of Biological Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - C J Finno
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | | | - J M Gaillard
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - E Garde
- Greenland Institute of Natural Resources, Nuuk, Greenland
| | - L Gerber
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia
| | - V N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - R G Goya
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - M J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - C B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - E N Hales
- Department of Population Health and Reproduction, University of California, Davis School of Veterinary Medicine, Davis, CA, USA
| | - M B Hanson
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - D W Hart
- Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - M Haulena
- Vancouver Aquarium, Vancouver, British Columbia, Canada
| | - K Herrick
- SeaWorld of California, San Diego, CA, USA
| | - A N Hogan
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - C J Hogg
- School of Life and Environmental Sciences, the University of Sydney, Sydney, New South Wales, Australia
| | - T A Hore
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - T Huang
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
- Division of Genetics and Metabolism, Oishei Children's Hospital, Buffalo, NY, USA
| | | | - A J Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - G Jones
- School of Biological Sciences, University of Bristol, Bristol, UK
| | | | - O Kashpur
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
| | - H Katcher
- Yuvan Research, Mountain View, CA, USA
| | | | - V Kaza
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
| | - H Kiaris
- Peromyscus Genetic Stock Center, University of South Carolina, Columbia, SC, USA
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M S Kobor
- Edwin S.H. Leong Healthy Aging Program, Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - P Kordowitzki
- Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Olsztyn, Poland
- Institute for Veterinary Medicine, Nicolaus Copernicus University, Torun, Poland
| | - W R Koski
- LGL Limited, King City, Ontario, Canada
| | - M Krützen
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
| | - S B Kwon
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Larison
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Center for Tropical Research, Institute for the Environment and Sustainability, UCLA, Los Angeles, CA, USA
| | - S G Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Lehmann
- Biochemistry Research Institute of La Plata, Histology and Pathology, School of Medicine, University of La Plata, La Plata, Argentina
| | - J F Lemaitre
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - A J Levine
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Li
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - X Li
- Technology Center for Genomics and Bioinformatics, Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - A R Lim
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - D T S Lin
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - T J Little
- Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - N Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - D Maddox
- White Oak Conservation, Yulee, FL, USA
| | - C O Matkin
- North Gulf Oceanic Society, Homer, AK, USA
| | - J A Mattison
- Translational Gerontology Branch, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, USA
| | | | - J Mergl
- Marineland of Canada, Niagara Falls, Ontario, Canada
| | - J J Meudt
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - G A Montano
- Zoological Operations, SeaWorld Parks and Entertainment, Orlando, FL, USA
| | - K Mozhui
- Department of Preventive Medicine, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - J Munshi-South
- Louis Calder Center-Biological Field Station, Department of Biological Sciences, Fordham University, Armonk, NY, USA
| | - A Naderi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M Nagy
- Museum fur Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - P Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - P W Nathanielsz
- Texas Pregnancy and Life-course Health Center, Southwest National Primate Research Center, San Antonio, TX, USA
- Department of Animal Science, College of Agriculture and Natural Resources, Laramie, WY, USA
| | - N B Nguyen
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - C Niehrs
- Institute of Molecular Biology, Mainz, Germany
- Division of Molecular Embryology, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - J K O'Brien
- Taronga Institute of Science and Learning, Taronga Conservation Society Australia, Mosman, New South Wales, Australia
| | - P O'Tierney Ginn
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Department of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - D T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Division of Regulatory Genomics and Cancer Evolution, Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - A G Ophir
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - S Osborn
- SeaWorld of Texas, San Antonio, TX, USA
| | - E A Ostrander
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - K M Parsons
- Conservation Biology Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - K C Paul
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - M Pellegrini
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - K J Peters
- Evolutionary Genetics Group, Department of Evolutionary Anthropology, University of Zurich, Zurich, Switzerland
- School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, Australia
| | - A B Pedersen
- Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | - D W Pietersen
- Mammal Research Institute, Department of Zoology and Entomology, University of Pretoria, Hatfield, South Africa
| | - G M Pinho
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Plassais
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - J R Poganik
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - N A Prado
- Department of Biology, College of Arts and Science, Adelphi University, Garden City, NY, USA
| | - P Reddy
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | - B Rey
- Universite de Lyon, Universite Lyon 1, CNRS, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, France
| | - B R Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Environmental Health Sciences, UCLA Fielding School of Public Health, Los Angeles, CA, USA
- Department of Neurology, UCLA David Geffen School of Medicine, Los Angeles, CA, USA
| | - J Robbins
- Center for Coastal Studies, Provincetown, MA, USA
| | | | - J Russell
- SeaWorld of California, San Diego, CA, USA
| | - E Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - L L Sailer
- Department of Psychology, Cornell University, Ithaca, NY, USA
| | - A B Salmon
- The Sam and Ann Barshop Institute for Longevity and Aging Studies and Department of Molecular Medicine, UT Health San Antonio and the Geriatric Research Education and Clinical Center, South Texas Veterans Healthcare System, San Antonio, TX, USA
| | | | - K M Schachtschneider
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, IL, USA
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - D Schmitt
- College of Agriculture, Missouri State University, Springfield, MO, USA
| | - T Schmitt
- SeaWorld of California, San Diego, CA, USA
| | | | - L B Schook
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | - K E Sears
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - A W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, USA
| | - A Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - A B A Shafer
- Department of Forensic Science, Environmental and Life Sciences, Trent University, Peterborough, Ontario, Canada
| | - D Shanmuganayagam
- Biomedical and Genomic Research Group, Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA
- Department of Surgery, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - A V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - K Singh
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM'S NMIMS University, Mumbai, India
| | - I Sinha
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - J Slone
- Division of Human Genetics, Department of Pediatrics, University at Buffalo, Buffalo, NY, USA
| | - R G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, the University of Auckland, Auckland, New Zealand
| | - E Soltanmaohammadi
- Department of Drug Discovery and Biomedical Sciences, College of Pharmacy, University of South Carolina, Columbia, SC, USA
| | - M L Spangler
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | - L Staggs
- SeaWorld of Florida, Orlando, FL, USA
| | | | - K J Steinman
- Species Preservation Laboratory, SeaWorld San Diego, San Diego, CA, USA
| | - D T Stewart
- Biology Department, Acadia University, Wolfville, Nova Scotia, Canada
| | - V J Sugrue
- Department of Anatomy, University of Otago, Dunedin, New Zealand
| | - B Szladovits
- Department of Pathobiology and Population Sciences, Royal Veterinary College, Hatfield, UK
| | - J S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Howard Hughes Medical Institute, Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - M Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - E C Teeling
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
| | - M J Thompson
- Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - B Van Bonn
- John G. Shedd Aquarium, Chicago, IL, USA
| | - S C Vernes
- School of Biology, the University of St Andrews, Fife, UK
- Neurogenetics of Vocal Communication Group, Max Planck Institute for Psycholinguistics, Nijmegen, the Netherlands
| | - D Villar
- Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - H V Vinters
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M C Wallingford
- Mother Infant Research Institute, Tufts Medical Center, Boston, MA, USA
- Division of Obstetrics and Gynecology, Tufts University School of Medicine, Boston, MA, USA
| | - N Wang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - R K Wayne
- Department of Ecology and Evolutionary Biology, UCLA, Los Angeles, CA, USA
| | - G S Wilkinson
- Department of Biology, University of Maryland, College Park, MD, USA
| | - C K Williams
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - R W Williams
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, College of Medicine, Memphis, TN, USA
| | - X W Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - M Yao
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - B G Young
- Fisheries and Oceans Canada, Winnipeg, Manitoba, Canada
| | - B Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Z Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - P Zhao
- Division of Cardiology, Department of Internal Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA, USA
| | - Y Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - W Zhou
- Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - J Zimmermann
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Koblenz, Germany
| | - J Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, USA
| | - K Raj
- Altos Labs, Cambridge Institute of Science, Cambridge, UK
| | - S Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
- Altos Labs, San Diego Institute of Science, San Diego, CA, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA.
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Brooks K, Farley J, Probert S, Hulk K, Rahimi O, McClure M, Eckmann M. Identifying the Upper Subscapular Nerve as a Target for Chronic Shoulder Pain. Muscles Ligaments Tendons J 2022. [DOI: 10.32098/mltj.03.2022.06] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Palmer E, Kegley E, Powell J, Wang X, Chai J, Chewning S, McClure M, Ball J, Zhao J. PSV-18 Characterization of rumen and fecal microbiota in heifer calves supplemented yeast products prior to and after weaning. J Anim Sci 2018. [DOI: 10.1093/jas/sky404.108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- E Palmer
- University of Arkansas Division of Agriculture,Fayetteville, AR, United States
| | - E Kegley
- University of Arkansas Division of Agriculture,Fayetteville, AR, United States
| | - J Powell
- University of Arkansas Division of Agriculture,Fayetteville, AR, United States
| | - X Wang
- University of Arkansas Division of Agriculture,Fayetteville, AR, United States
| | - J Chai
- University of Arkansas Division of Agriculture,Fayetteville, AR, United States
| | - S Chewning
- University of Arkansas Division of Agriculture,Fayetteville, AR, United States
| | - M McClure
- University of Arkansas Division of Agriculture,Fayetteville, AR, United States
| | - J Ball
- University of Arkansas Division of Agriculture,Fayetteville, AR, United States
| | - J Zhao
- University of Arkansas Division of Agriculture,Fayetteville, AR, United States
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Higgins M, Fitzsimons C, McClure M, McKenna C, Conroy S, Kenny D, McGee M, Waters S, Morris D. 289 Genome-wide association study and expression quantitative trait loci analysis identifies a single nucleotide polymorphism associated with both residual feed intake and GFRA2. J Anim Sci 2018. [DOI: 10.1093/jas/sky404.238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - C Fitzsimons
- Department of Agriculture,Ireland, Celbridge, Ireland
| | - M McClure
- Genus PLC,Basingstoke, United Kingdom
| | | | - S Conroy
- Irish Cattle Breeding Federation,Cork, Ireland
| | | | - M McGee
- Teagasc, Animal and Grassland Research and Innovation Centre,Dunsany, Ireland
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McClure M, Jones R. Update on Lupus Nephritis for GPs. Lupus 2018; 27:11-14. [PMID: 30452323 DOI: 10.1177/0961203318801687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- M McClure
- Vasculitis and Lupus Clinic, Addenbrooke's Hospital, Cambridge
| | - R Jones
- Vasculitis and Lupus Clinic, Addenbrooke's Hospital, Cambridge
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Purfield DC, McClure M, Berry DP. Justification for setting the individual animal genotype call rate threshold at eighty-five percent. J Anim Sci 2017; 94:4558-4569. [PMID: 27898963 DOI: 10.2527/jas.2016-0802] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Data quality of SNP arrays impacts the accuracy and precision of downstream data analyses. One such quality control measure often imposed is a threshold on individual animal call rate. Different call rate thresholds have been applied across studies; little is known, however, about the impact of these thresholds on the quality of the genotype data. The objective of the present study was to investigate the effect of different call rate thresholds on the integrity of the genotypes but also to quantify the contribution of different factors to the variability in animal call rate. Data included 142,342 samples genotyped on a custom Illumina genotype panel from 141,591 dairy and beef cattle; the number of Illumina SNP on the panel was 14,371. The mean animal call rate across all samples was 99.09%; 487 animals had both a low call rate (<99%) and a subsequent high call rate (≥99%) after resampling and regenotyping. Several factors were associated ( < 0.001) with individual call rate including animal sex, the sampling herd, the date of genotyping, the genotyping plate, and the plate well. The genotype and allele concordance between the genotypes of the 487 low- and high-call rate individuals improved at a diminishing rate as mean animal call rate increased. Mean genotype and allele concordance rates of 0.987 and 0.997, respectively, existed when animal call rate was between 85 and 90%, increasing to 0.998 and 0.999, respectively, when animal call rate was between 95 and <99%. The mean within-animal allele concordance rate of rare variants (i.e., minor allele frequency < 0.05) between low and high genotype call rate animals increased when animal call rate improved; an allele concordance rate of 1.00 was achieved when animal call rate was between 85 and <99%. The accuracy of imputation of the nonobserved genotypes in the low-call rate animals improved as animal call rate increased; the mean genotype concordance rate of the imputed nonobserved SNP was 0.41 when animal call rate was <40% but increased to 0.95 when animal call rate was between 95 and <99%. Parentage validation, determined by the count of opposing homozygotes in a parent-progeny pair, was unreliable when animal call rate was <85%. Therefore, to ensure the provision of high-quality genotypes while also considering the cost and inconvenience of resampling and regenotyping, we suggest a minimum animal call rate threshold of 85%.
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Berry DP, Wolfe A, O'Donovan J, Byrne N, Sayers RG, Dodds KG, McEwan JC, O'Connor RE, McClure M, Purfield DC. Characterization of an X-chromosomal non-mosaic monosomy (59, X0) dairy heifer detected using routinely available single nucleotide polymorphism genotype data1. J Anim Sci 2017; 95:1042-1049. [DOI: 10.2527/jas.2016.1279] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- D. P. Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - A. Wolfe
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - J. O'Donovan
- Department of Agriculture, Food and the Marine, Regional Veterinary Laboratory, Model Farm Road, Cork, T12 XD51, Ireland
| | - N. Byrne
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - R. G. Sayers
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - K. G. Dodds
- Department of Agriculture, AgResearch, Invermay Agricultural Centre, Mosgiel 9092, New Zealand
| | - J. C. McEwan
- Department of Agriculture, AgResearch, Invermay Agricultural Centre, Mosgiel 9092, New Zealand
| | - R. E. O'Connor
- Department of Agriculture, University of Kent, School of Biosciences, University of Kent, Canterbury, CT2 7AF, UK
| | - M. McClure
- Department of Agriculture, Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland
| | - D. C. Purfield
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
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Berry DP, Wolfe A, O’Donovan J, Byrne N, Sayers RG, Dodds KG, McEwan JC, O’Connor RE, McClure M, Purfield DC. Characterization of an X-chromosomal non-mosaic monosomy (59, X0) dairy heifer detected using routinely available single nucleotide polymorphism genotype data. J Anim Sci 2017. [DOI: 10.2527/jas2016.1279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Gurrala R, Lang Z, Shepherd L, Davidson D, Harrison E, McClure M, Kaye S, Toumazou C, Cooke GS. Novel pH sensing semiconductor for point-of-care detection of HIV-1 viremia. Sci Rep 2016; 6:36000. [PMID: 27829667 PMCID: PMC5103182 DOI: 10.1038/srep36000] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 10/11/2016] [Indexed: 11/10/2022] Open
Abstract
The timely detection of viremia in HIV-infected patients receiving antiviral treatment is key to ensuring effective therapy and preventing the emergence of drug resistance. In high HIV burden settings, the cost and complexity of diagnostics limit their availability. We have developed a novel complementary metal-oxide semiconductor (CMOS) chip based, pH-mediated, point-of-care HIV-1 viral load monitoring assay that simultaneously amplifies and detects HIV-1 RNA. A novel low-buffer HIV-1 pH-LAMP (loop-mediated isothermal amplification) assay was optimised and incorporated into a pH sensitive CMOS chip. Screening of 991 clinical samples (164 on the chip) yielded a sensitivity of 95% (in vitro) and 88.8% (on-chip) at >1000 RNA copies/reaction across a broad spectrum of HIV-1 viral clades. Median time to detection was 20.8 minutes in samples with >1000 copies RNA. The sensitivity, specificity and reproducibility are close to that required to produce a point-of-care device which would be of benefit in resource poor regions, and could be performed on an USB stick or similar low power device.
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Affiliation(s)
- R Gurrala
- Division of Infectious Diseases, Imperial College, London, England
| | - Z Lang
- DNA Electronics Ltd, Wood Lane, London, England
| | - L Shepherd
- DNA Electronics Ltd, Wood Lane, London, England
| | - D Davidson
- DNA Electronics Ltd, Wood Lane, London, England
| | - E Harrison
- DNA Electronics Ltd, Wood Lane, London, England
| | - M McClure
- Division of Infectious Diseases, Imperial College, London, England
| | - S Kaye
- Division of Infectious Diseases, Imperial College, London, England
| | - C Toumazou
- DNA Electronics Ltd, Wood Lane, London, England.,Department of Bioengineering, Imperial College, London, England
| | - G S Cooke
- Division of Infectious Diseases, Imperial College, London, England
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Woodhall SC, Wills G, Horner P, Craig R, Mindell JS, Murphy G, McClure M, Soldan K, Nardone A, Johnson AM. P08.12 Insights into chlamydia trachomatiscumulative incidence in the context of widespread opportunistic chlamydia screening in england: seroprevalence study using sera from a nationally-representative household survey. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Righarts AA, Dickson NP, Morgan J, Horner P, McClure M, Wills GS. P08.11 Chlamydia trachomatisincidence from self-reports and serology by age-period, sex and partner numbers in a birth cohort. Br J Vener Dis 2015. [DOI: 10.1136/sextrans-2015-052270.357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Tipple C, Hodson L, Jones R, Rayment M, Nwokolo N, McClure M, Taylor G. O05.2 Measuring Syphilis: Quantitative PCR Can Be Used to Monitor Treatment Response. Sex Transm Infect 2013. [DOI: 10.1136/sextrans-2013-051184.0108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Mallikarachchi D, Hodson L, Duckett C, Weerasinghe G, Buddhakorale K, McClure M, Taylor G, Tipple C. O21.6 A Tale of Two Cities: Treponema Pallidum Macrolide Resistance in Colombo (Sri Lanka) and London (United Kingdom). Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Horner P, Dickson N, Wills G, Righarts A, Vieira S, Young S, McClure M. P3.008 Epidemiological Correlates of Chlamydia Pgp3 Antibody in a Prospective Cohort of Men and Women. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Wills G, Samuel D, Warrener L, Horner P, McClure M. P3.018 Development of a C. Trachomatis-Specific Competitive Pgp3 ELISA. Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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White P, Fox J, MacDonald N, Weber J, McClure M, Fidler S, Ward H. O1-S11.03 How many infections are averted by behaviour change after early HIV diagnosis & counselling of MSM? Estimates from a stochastic individual-based model. Br J Vener Dis 2011. [DOI: 10.1136/sextrans-2011-050109.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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English S, Katzourakis A, Flanagan P, Duda A, Francis J, Matthews P, Prendergast A, Goulder P, Fidler S, Weber J, McClure M, Phillips R, Frater J. P07-09. Contemporaneous transmission of genetically distinct HIV variants from a single donor to two recipients. Retrovirology 2009. [PMCID: PMC2767590 DOI: 10.1186/1742-4690-6-s3-p107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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20
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Duda A, Lee-Turner L, Fox J, Robinson N, Dustan S, Kaye S, Fryer H, Carrington M, McClure M, McLean AR, Fidler S, Weber J, Phillips RE, Frater AJ. HLA-associated clinical progression correlates with epitope reversion rates in early human immunodeficiency virus infection. J Virol 2009; 83:1228-39. [PMID: 19019964 PMCID: PMC2620910 DOI: 10.1128/jvi.01545-08] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2008] [Accepted: 10/21/2008] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) can evade immunity shortly after transmission to a new host but the clinical significance of this early viral adaptation in HIV infection is not clear. We present an analysis of sequence variation from a longitudinal cohort study of HIV adaptation in 189 acute seroconverters followed for up to 3 years. We measured the rates of variation within well-defined epitopes to determine associations with the HLA-linked hazard of disease progression. We found early reversion across both the gag and pol genes, with a 10-fold faster rate of escape in gag (2.2 versus 0.27 forward mutations/1,000 amino acid sites). For most epitopes (23/34), variation in the HLA-matched and HLA-unmatched controls was similar. For a minority of epitopes (8/34, and generally associated with HLA class I alleles that confer clinical benefit), new variants appeared early and consistently over the first 3 years of infection. Reversion occurred early at a rate which was HLA-dependent and correlated with the HLA class 1-associated relative hazard of disease progression and death (P = 0.0008), reinforcing the association between strong cytotoxic T-lymphocyte responses, viral fitness, and disease status. These data provide a comprehensive overview of viral adaptation in the first 3 years of infection. Our findings of HLA-dependent reversion suggest that costs are borne by some escape variants which may benefit the host, a finding contrary to a simple immune evasion paradigm. These epitopes, which are both strongly and frequently recognized, and for which escape involves a high cost to the virus, have the potential to optimize vaccine design.
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Affiliation(s)
- A Duda
- Nuffield Department of Clinical Medicine, Peter Medawar Building for Pathogen Research, Oxford University, South Parks Road, Oxford OX1 3SY, United Kingdom
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Pelletier Y, Nie X, McClure M, Whitney S, Giguère MA. Behavior of bird cherry-oat aphid and green peach aphid in relation to potato virus Y transmission. J Econ Entomol 2008; 101:728-735. [PMID: 18613572 DOI: 10.1603/0022-0493(2008)101[728:bobcaa]2.0.co;2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Potato virus Y is transmitted to potato in a nonpersistent manner by many aphid species, some of which do not colonize this crop. The behavior of bird cherry-oat aphid, Rhopalosiphum padi (L.) on potato, Solanum tuberosum L., a plant species that is not colonized by this aphid, was described and compared with that of the potato-colonizing green peach aphid, Myzuspersicae (Sulzer). A higher proportion of winged morph of R. padi than M. persicae left the plant, but aphids that stayed in contact with the plant took the same mean time to initiate the first probe and it lasted the same mean time compared with M. persicae. Electronic penetration graph technique was used to study the probing behavior of the aphids during Potato virus Y (family Potyviridae, genus Potyvirus, PVY) transmission tests. Transmission rate decreased from 29 to 8% when the acquisition time increased from 5 min of continuous probing to 1 h with M. persicae, but it remained low (2 and 1%) with R. padi. Most of the difference in transmission rate between acquisition time with M. persicae and between aphid species was related to the change in the time and behavior taking place between the last cell puncture of the acquisition phase to the first cell puncture of the inoculation phase. Results presented here clearly demonstrated the importance of host plant selection and probing behavior in the transmission of nonpersistent plant viruses. They also stress the need to consider the behavior of the aphid in the design of laboratory tests of virus vector efficacy.
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Affiliation(s)
- Y Pelletier
- Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada.
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Fox J, Dustan S, McClure M, Weber J, Fidler S. Transmitted drug-resistant HIV-1 in primary HIV-1 infection; incidence, evolution and impact on response to antiretroviral therapy. HIV Med 2007; 7:477-83. [PMID: 16925735 DOI: 10.1111/j.1468-1293.2006.00412.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
OBJECTIVES The aim of the study was to determine the incidence and persistence of transmitted drug-resistant HIV-1 in an incident cohort between 2000 and 2004, and to investigate the impact of transmitted drug-resistant HIV-1 on the response to antiretroviral therapy (ART). METHODS A prospective, nonrandomized study was carried out on 140 individuals identified with primary HIV-1 infection (PHI). PHI was defined as an HIV-positive antibody test with an HIV antibody-negative result in the prior 6 months (n = 69); positive HIV DNA in the absence of antibody (n = 30); an evolving titre positive HIV antibody test (n = 23), or an incident 'detuned' assay (B clade viruses only) (n = 18). Genotypic resistance testing was performed at baseline, following ART and annually over a 4-year period. RESULTS The prevalence of transmitted drug-resistant HIV-1 infection between January 2000 and June 2004 was nine in 140 (6.0%) and the annual incidence was stable. Seven of these nine patients had a single point mutation conferring single-class drug resistance and the other two patients had multiple mutations conferring multiclass drug resistance (MDR). In eight of the nine cases, mutations conferring drug resistance persisted for more than 12 months off therapy. In contrast to transmitted MDR HIV-1, the virological response to initial ART and CD4 decline were comparable in those with wild-type virus, virus with 'polymorphisms' (secondary mutations) and virus with single drug-resistance mutations. CONCLUSIONS The incidence of transmitted drug-resistant HIV remained stable and low over a 4-year period. Although MDR remains rare, its presence significantly affects the response to first-line ART, predisposes towards the accumulation of new resistance mutations and is associated with a more rapid CD4 decline.
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Affiliation(s)
- J Fox
- Department of Infectious Diseases, Imperial College, London, UK.
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Taylor L, McClure M, Solomon M. 300 Keeping CF kids connected – Ability Online. J Cyst Fibros 2007. [DOI: 10.1016/s1569-1993(07)60275-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hogg R, Curry E, Muldrew A, Winder J, Stevenson M, McClure M, Chakravarthy U. Identification of lesion components that influence visual function in age related macular degeneration. Br J Ophthalmol 2003; 87:609-14. [PMID: 12714405 PMCID: PMC1771654 DOI: 10.1136/bjo.87.5.609] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AIMS To explore the relation between lesion composition as assessed by fundus photography and fluorescein angiography with clinical measures of vision in eyes of patients with age related macular degeneration (AMD). METHODS A standardised visual function assessment along with colour stereo pair fundus photography was carried out in both eyes of 58 subjects with a confirmed clinical diagnosis of AMD. The size, location, and composition of the macular lesion (blood, exudate, subretinal fluid, pigment, membrane, atrophy, and fibrosis) were measured on the colour photographs using computer assisted image analysis. Of the 58 subjects, 44 also had concurrent fluorescein angiography. Classic and occult choroidal neovascularisation (CNV), blood, blocked fluorescence, fibrosis, geographic atrophy, and the total area of abnormal fluorescence were measured. Multiple linear regression was used to examine the relation between clinical measures of vision and the location and extent of lesion components identified by both colour and fluorescein image capture. RESULTS The composition of the macular lesion strongly influenced visual function, with atrophy (p=0.001) and fibrosis (p=0.002) accounting for most of the variation. When the location of the lesion with respect to the fovea was examined, fibrosis within the fovea significantly influenced all clinical measures of vision (p=0.008). The regression model selected the total area of abnormal fluorescence and a composite parameter (a semiquantitative measure of the following characteristics: atrophy, exudates, blood, and fibrosis ) from colour photography (r(2) =0.52) as the variables that explained most of the variation in clinical measures of vision. CONCLUSIONS The composition and extent of the macular lesion strongly influences visual function in eyes with AMD. Both colour photography and angiography yielded information, which together explained considerably more of the variation in the clinical measures of vision than either on its own.
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Affiliation(s)
- R Hogg
- Queen's University Belfast, UK
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Linseman DA, Laessig T, Meintzer MK, McClure M, Barth H, Aktories K, Heidenreich KA. An essential role for Rac/Cdc42 GTPases in cerebellar granule neuron survival. J Biol Chem 2001; 276:39123-31. [PMID: 11509562 DOI: 10.1074/jbc.m103959200] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Rho family GTPases are critical molecular switches that regulate the actin cytoskeleton and cell function. In the current study, we investigated the involvement of Rho GTPases in regulating neuronal survival using primary cerebellar granule neurons. Clostridium difficile toxin B, a specific inhibitor of Rho, Rac, and Cdc42, induced apoptosis of granule neurons characterized by c-Jun phosphorylation, caspase-3 activation, and nuclear condensation. Serum and depolarization-dependent survival signals could not compensate for the loss of GTPase function. Unlike trophic factor withdrawal, toxin B did not affect the antiapoptotic kinase Akt or its target glycogen synthase kinase-3beta. The proapoptotic effects of toxin B were mimicked by Clostridium sordellii lethal toxin, a selective inhibitor of Rac/Cdc42. Although Rac/Cdc42 GTPase inhibition led to F-actin disruption, direct cytoskeletal disassembly with Clostridium botulinum C2 toxin was insufficient to induce c-Jun phosphorylation or apoptosis. Granule neurons expressed high basal JNK and low p38 mitogen-activated protein kinase activities that were unaffected by toxin B. However, pyridyl imidazole inhibitors of JNK/p38 attenuated c-Jun phosphorylation. Moreover, both pyridyl imidazoles and adenoviral dominant-negative c-Jun attenuated apoptosis, suggesting that JNK/c-Jun signaling was required for cell death. The results indicate that Rac/Cdc42 GTPases, in addition to trophic factors, are critical for survival of cerebellar granule neurons.
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Affiliation(s)
- D A Linseman
- Department of Pharmacology, University of Colorado Health Sciences Center and the Denver Veterans Affairs Medical Center, Denver, Colorado 80220, USA.
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Mallah MK, Hart PM, McClure M, Stevenson MR, Silvestri G, White ST, Chakravarthy U. Improvements in measures of vision and self-reported visual function after cataract extraction in patients with late-stage age-related maculopathy. Optom Vis Sci 2001; 78:683-8. [PMID: 11587203 DOI: 10.1097/00006324-200109000-00014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
PURPOSE A recent study indicated that patients with cataracts and early age-related maculopathy may benefit from cataract extraction. To ascertain whether cataract extraction in the presence of concurrent advanced age-related maculopathy was also associated with a clear benefit, we studied visual function and self-reported visual functioning in a cohort of 12 patients pre- and post-phakoemulsification. METHODS. All 12 patients had a diagnosis of advanced age-related maculopathy in the eye scheduled for cataract surgery. Preoperative assessment included refraction and recording of best corrected distance and near acuity and contrast sensitivity in both eyes. The Daily Living Tasks Dependent on Vision questionnaire was administered. After phakoemulsification and intraocular lens implantation, all patients were reviewed and assessed. RESULTS After surgery, improvement in acuity was recorded in nine operated eyes, whereas acuity remained unchanged in three eyes. Improvement in contrast sensitivity in the operated eye occurred in 10 patients, but in two patients contrast was reduced postoperatively. In terms of self-reported visual functioning, improvement in the ability to undertake many daily living tasks dependent on vision was recorded after cataract surgery. CONCLUSIONS Significant improvements in specific areas of self-reported visual functioning and measures of vision were recorded after cataract surgery. During the follow-up period, none of the operated eyes suffered a fall in visual acuity. There was also no evidence of worsening of the pre-existing macular lesion as judged by clinical examination and fundus photography.
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Affiliation(s)
- M K Mallah
- Ophthalmology and Vision Science, Royal Victoria Hospital and Queen's University of Belfast, United Kingdom
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Trotter JF, Talamantes M, McClure M, Wachs M, Bak T, Trouillot T, Kugelmas M, Everson GT, Kam I. Right hepatic lobe donation for living donor liver transplantation: impact on donor quality of life. Liver Transpl 2001; 7:485-93. [PMID: 11443574 DOI: 10.1053/jlts.2001.24646] [Citation(s) in RCA: 199] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Adult right hepatic lobe living donor liver transplantation (LDLT) has rapidly gained widespread acceptance as an effective procedure for selected patients with end-stage liver disease. However, there are currently no published data on the effect of this procedure on the quality of life of donors. We report the results of a survey of our living liver transplant donors to determine the effect of right hepatic lobe donation on quality of life. We have performed 30 LDLTs since 1997; 24 of these have a follow-up of 4 months or longer. In August 2000, these patients were sent a questionnaire (including a Medical Outcomes Study 36-Item Short-Form Survey) regarding psychosocial outcomes and symptoms after surgery. Major complications occurred in 4 of 24 patients (16%), and minor complications, in 4 of 24 patients (16%). Complete recovery occurred in 75% of patients at a mean time of 3.4 months. Ninety-six percent of patients returned to the same predonation job after a mean time of 2.4 months, and 66% of patients required a period of light-duty work for a mean of 2.8 months before returning to full-duty work. A change in body image was reported in 42% of patients, and 71% reported mild ongoing symptoms (primarily abdominal discomfort) that they related to the donor surgery for which 29% sought evaluation by a physician. The donor's relationship with the recipient was the same or better in 96% of donors, and the relationship with the donor's significant other was the same or better in 88% of donors. Mean out-of-pocket expenses incurred by donors were $3,660. Sixty-three percent of donors reported experiencing more pain than anticipated. All patients would donate again if necessary, and 96% benefited from the donor experience. In conclusion, (1) all our donors are alive and well after donation; (2) almost all donors were able to return to predonation employment status within a few months; (3) most donors have mild persistent abdominal symptoms, and some donors had a change in body image that they attribute to the donor surgery; and (4) this information should be provided to potential donors so they may better understand the impact of donor surgery.
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Affiliation(s)
- J F Trotter
- Division of Gastroenterology/Hepatology, University of Colorado Health Sciences Center, Denver, CO 80262, USA.
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Abstract
Construction of four dams on the lower Snake River (in northwestern United States) between 1961 and 1975 altered salmon spawning habitat, elevated smolt and adult migration mortality, and contributed to severe declines of Snake River salmon populations. By applying a matrix model to long-term population data, we found that (i) dam passage improvements have dramatically mitigated direct mortality associated with dams; (ii) even if main stem survival were elevated to 100%, Snake River spring/summer chinook salmon (Oncorhynchus tshawytscha) would probably continue to decline toward extinction; and (iii) modest reductions in first-year mortality or estuarine mortality would reverse current population declines.
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Affiliation(s)
- P Kareiva
- National Marine Fisheries Service, Northwest Fisheries Science Center, 2725 Montlake Boulevard East, Seattle, WA 98112, USA
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Sorkin A, McClure M, Huang F, Carter R. Interaction of EGF receptor and grb2 in living cells visualized by fluorescence resonance energy transfer (FRET) microscopy. Curr Biol 2000; 10:1395-8. [PMID: 11084343 DOI: 10.1016/s0960-9822(00)00785-5] [Citation(s) in RCA: 233] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The interaction of activated epidermal growth factor receptor (EGFR) with the Src homology 2 (SH2) domain of the growth-factor-receptor binding protein Grb2 initiates signaling through Ras and mitogen-activated protein kinase (MAP kinase) [1,2]. Activation of EGFRs by ligand also triggers rapid endocytosis of EGF-receptor complexes. To analyze the spatiotemporal regulation of EGFR-Grb2 interactions in living cells, we have combined imaging microscopy with a modified method of measuring fluorescence resonance energy transfer (FRET) on a pixel-by-pixel basis using EGFR fused to cyan fluorescent protein (CFP) and Grb2 fused to yellow fluorescent protein (YFP). Efficient energy transfer between CFP and YFP should only occur if CFP and YFP are less than 50A apart, which requires direct interaction of the EGFR and Grb2 fused to these fluorescent moieties [3]. Stimulation by EGF resulted in the recruitment of Grb2-YFP to cellular compartments that contained EGFR-CFP and a large increase in FRET signal amplitude. In particular, FRET measurements indicated that activated EGFR-CFP interacted with Grb2-YFP in membrane ruffles and endosomes. These results demonstrate that signaling via EGFRs can occur in the endosomal compartment. The work also highlights the potential of FRET microscopy in the study of subcellular compartmentalization of protein-protein interactions in living cells.
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Affiliation(s)
- A Sorkin
- Department of Pharmacology, University of Colorado Health Sciences Center, Denver, Colorado 80111, USA.
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Doyle F, McClure M. Hey, dot-com! What's your value proposition? Mater Manag Health Care 2000; 9:18-21. [PMID: 11186018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Dranoff JA, McClure M, Burgstahler AD, Denson LA, Crawford AR, Crawford JM, Karpen SJ, Nathanson MH. Short-term regulation of bile acid uptake by microfilament-dependent translocation of rat ntcp to the plasma membrane. Hepatology 1999; 30:223-9. [PMID: 10385660 DOI: 10.1002/hep.510300136] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The Na+-taurocholate cotransport polypeptide (ntcp) is the primary transporter for the uptake of bile acids in the liver. The second messenger adenosine 3':5'-cyclic monophosphate (cAMP) rapidly increases ntcp protein concentration in the plasma membrane, yet the mechanism is unknown. To investigate this, HepG2 cells were transiently transfected with a carboxy-terminal-tagged green fluorescence protein (GFP) conjugate of ntcp, and then examined by confocal video microscopy. Transporter activity was directly assayed with 3H-taurocholic acid (TC) scintigraphy. ntcp-GFP targeted to the plasma membrane in transfected cells, and the conjugate protein transported 3H-TC as effectively as unmodified rat ntcp. Stimulation of ntcp-GFP cells with cAMP increased GFP fluorescence in the plasma membrane by 40% (P <.0001) within 2.5 minutes and by 55% within 10 minutes. Similarly, cAMP increased transport of bile acids by 30%. Cytochalasin D, an inhibitor of microfilaments, did not prevent ntcp-GFP from targeting to the plasma membrane, but completely abolished the increase in GFP fluorescence seen in response to cAMP. In contrast, the microtubule inhibitor, nocodazole, prevented development of membrane fluorescence in 48 (96%) of 50 cells. Cells regained plasma membrane fluorescence within 2 hours after nocodazole removal. These findings suggest that targeting of ntcp to the plasma membrane consists of 2 steps: 1) delivery of ntcp to the region of the plasma membrane via microtubules; and 2) insertion of ntcp into the plasma membrane, in a microfilament- and cAMP-sensitive fashion.
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Affiliation(s)
- J A Dranoff
- Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
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Abstract
Pigmentation patterns in vertebrates have become an important model for those interested in mechanisms of pattern determination. I present detailed information on the development of melanophore patterns in the zebrafish, Danio rerio, five close relatives of that species, and an outgroup. The comparison of the ontogeny of melanophore patterns in this group is an important first step towards understanding the developmental basis of the interspecific variation. Pigment patterns in this group range from no distinct patterning at all to stripes of differing numbers and widths to reticulated stripes. Species examined form identical larval patterns and follow a common sequence of events from which different elements are eliminated or altered to produce the variety of patterns seen in the group. As flexion is completed, melanophores move from larval positions onto the flanks of the fish. In D. rerio, D. rerio 'leo,' D. kerri, and D. malabaricus, xanthophores become established on the body of the fish as the melanophores move; erythrophores become established on the flanks of D. albolineatus and D. sp. cf. aequipinnatus. An increase in melanophore number, begun at this time, continues at a higher rate in D. rerio, D. kerri, D. sp. cf. aequipinnatus and Tanichthys albonubes than in the other three species. This results in a greater number of melanophores on adults in those species with a higher rate of melanophore increase. No distinct pattern forms, except on the caudal peduncle, in D. albolineatus. In all other Danio species, melanophore stripes form first below then above the horizontal myoseptum. Additional stripes are added first below then above these initial two stripes. D. kerri develops fewer, wider melanophore stripes than D. rerio. After initial stripe formation, D. malabaricus and D. sp. cf. aequipinnatus both developed vertical pattern elements and reticulations in the melanophore pattern. Differences in patterns between species are similar in several cases to described mutants of the zebrafish, suggesting that some aspects of interspecific pigmentation pattern variation may be under relatively simple genetic control. Copyright 1999 Wiley-Liss, Inc.
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Affiliation(s)
- M McClure
- Section of Ecology and Systematics, Cornell University, Ithaca, New York
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Raskin S, Phillips JA, Kaplan G, McClure M, Vnencak-Jones C, Rozov T, Cardieri JM, Marostica P, Abreu F, Giugliani R, Reis F, Rosario NA, Ludwig N, Pereira L, Faucz F, Gabardo J, Culpi L. Geographic heterogeneity of 4 common worldwide cystic fibrosis non-DF508 mutations in Brazil. Hum Biol 1999; 71:111-21. [PMID: 9972102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Cystic fibrosis (CF) is an autosomal recessive disease caused by at least 750 different mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The frequency of the most common mutation (DF508) in Brazilian patients of European origin is 47%. To determine the frequency of 4 other common CF mutations (G542X, G551D, R553X, and N1303K) in Brazilian patients of European origin, we used direct polymerase chain reaction (PCR) amplification of DNA obtained from dried blood spots on Guthrie cards. The DNA came from 247 non-DF508 chromosomes from 172 Brazilian CF patients ascertained from 5 different states of Brazil. The results show that the 4 mutations account for 17% of the non-DF508 alleles and only 9% of the total number of Brazilian CF alleles. Overall, the frequency of each mutation is different from northern European and North American populations but similar to southern European populations, mainly the Italian and Spanish populations. When Brazilian patients of European origin are grouped according to state of birth, the frequencies of the mutations are significantly different between southern and southeastern states of Brazil. Therefore there are serious implication for risk assessment of DNA-based tests in heterogeneous populations such as Brazilians. Further studies are needed to identify the remaining 44% of CF mutations for the different populations and regions of Brazil.
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Affiliation(s)
- S Raskin
- Vanderbilt University, Nashville, TN, USA.
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McClure M, Kleiman N, Berdan L, Sparapani R, Topol E, Diaz R, Califf R, Gretler D, Karsch K, Harrington R. Thrombocytopenia in a large, international trial of the GP IIb/IIIa inhibitor eptitibatide in patients with acute coronary syndromes. J Am Coll Cardiol 1998. [DOI: 10.1016/s0735-1097(98)81047-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Vehmanen P, Friedman LS, Eerola H, McClure M, Ward B, Sarantaus L, Kainu T, Syrjäkoski K, Pyrhönen S, Kallioniemi OP, Muhonen T, Luce M, Frank TS, Nevanlinna H. Low proportion of BRCA1 and BRCA2 mutations in Finnish breast cancer families: evidence for additional susceptibility genes. Hum Mol Genet 1997; 6:2309-15. [PMID: 9361038 DOI: 10.1093/hmg/6.13.2309] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
One hundred breast and breast-ovarian cancer families identified at the Helsinki University Central Hospital in southern Finland and previously screened for mutations in the BRCA2 gene were now analyzed for mutations in the BRCA1 gene. The coding region and splice boundaries of BRCA1 were analyzed by protein truncation test (PTT) and heteroduplex analysis (HA)/SSCP in all 100 families, and 70 were also screened by direct sequencing. Contrary to expectations based on Finnish population history and strong founder effects in several monogenic diseases in Finland, a wide spectrum of BRCA1 and BRCA2 mutations was found. In the BRCA1 gene, 10 different protein truncating mutations were found each in one family. Six of these are novel Finnish mutations and four have been previously found in other European populations. Six different BRCA2 mutations were found in 11 families. Altogether only 21% of the breast cancer families were accounted for by mutations in these two genes. Linkage to both chromosome 17q21 (BRCA1) and 13q12 (BRCA2) was also excluded in a subset of seven mutation-negative families with four or more cases of breast or ovarian cancer. These data indicate that additional breast and breast-ovarian cancer susceptibility genes are likely to be important in Finland.
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Affiliation(s)
- P Vehmanen
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Haartmaninkatu 2, 00290 Helsinki, Finland
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Shattuck-Eidens D, Oliphant A, McClure M, McBride C, Gupte J, Rubano T, Pruss D, Tavtigian SV, Teng DH, Adey N, Staebell M, Gumpper K, Lundstrom R, Hulick M, Kelly M, Holmen J, Lingenfelter B, Manley S, Fujimura F, Luce M, Ward B, Cannon-Albright L, Steele L, Offit K, Thomas A. BRCA1 sequence analysis in women at high risk for susceptibility mutations. Risk factor analysis and implications for genetic testing. JAMA 1997; 278:1242-50. [PMID: 9333265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
CONTEXT A mutation in the BRCA1 gene may confer substantial risk for breast and/or ovarian cancer. However, knowledge regarding all possible mutations and the relationship between risk factors and mutations is incomplete. OBJECTIVES To identify BRCA1 mutations and to determine factors that best predict presence of a deleterious BRCA1 mutation in patients with breast and/or ovarian cancer. DESIGN A complete sequence analysis of the BRCA1 coding sequence and flanking intronic regions was performed in 798 women in a collaborative effort involving institutions from the United States, Italy, Germany, Finland, and Switzerland. PARTICIPANTS Institutions selected 798 persons representing families (1 person for each family) thought to be at elevated a priori risk of BRCA1 mutation due to potential risk factors, such as multiple cases of breast cancer, early age of breast cancer diagnosis, and cases of ovarian cancer. No participant was from a family in which genetic markers showed linkage to the BRCA1 locus. MAJOR OUTCOME MEASURES Sequence variants detected in this sample are presented along with analyses designed to determine predictive characteristics of those testing positive for BRCA1 mutations. RESULTS In 102 women (12.8%), clearly deleterious mutations were detected. Fifty new genetic alterations were found including 24 deleterious mutations, 24 variants of unknown significance, and 2 rare polymorphisms. In a subset of 71 Ashkenazi Jewish women, only 2 distinct deleterious mutations were found: 185delAG in 17 cases and 5382insC in 7 cases. A bias in prior reports for mutations in exon 11 was revealed. Characteristics of a patient's specific diagnosis (unilateral or bilateral breast cancer, with or without ovarian cancer), early age at diagnosis, Ashkenazi Jewish ethnicity, and family history of cancer were positively associated with the probability of her carrying a deleterious BRCA1 mutation. CONCLUSIONS Using logistic regression analysis, we provide a method for evaluating the probability of a woman's carrying a deleterious BRCA1 mutation for a wide range of cases, which can be an important tool for clinicians as they incorporate genetic susceptibility testing into their medical practice.
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Jackson AJ, Barnett ES, Stevens AB, McClure M, Patterson C, McReynolds MJ. Vision screening, eye examination and risk assessment of display screen users in a large regional teaching hospital. Ophthalmic Physiol Opt 1997; 17:187-95. [PMID: 9196660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
In January 1993 the Royal Group of Hospitals Trust, which employs approximately 5000 staff, implemented the Health and Safety (Display Screen Equipment) Northern Ireland Regulations (1992). During 1994 all regular display screen equipment users were offered a vision screening test. In total 571 employees were screened using computerized vision screening software (City Visual Systems Ltd). Risk assessments were completed for 293 display screen work-stations. One hundred and twelve full eye examinations, carried out by optometrists, were performed on those who failed vision screening and on those who specifically requested an optometric assessment. Results indicate that whereas the proportion of users experiencing visual and general symptoms differed markedly from department to department (28-82%), the median number of individuals failing the screening test was 25% (range 9-40%). Those involved in uninterrupted display screen equipment work for prolonged periods reported visual and general work-related symptoms twice as frequently as those who spent less time working with DSE. The outcome of full eye examinations confirmed that less than 5% of display screen users required spectacles solely for display screen use. Work-station analysis indicated that ergonomic problems were common. The authors conclude that the successful management of health risks from display screen equipment requires simultaneous attention to work-place design, working patterns and eye care.
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Affiliation(s)
- A J Jackson
- Eye and Ear Clinic, Royal Group of Hospitals Trust, Belfast, Northern Ireland
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Jackson AJ, Barnett ES, Stevens AB, McClure M, Patterson C, McReynolds MJ. Vision screening, eye examination and risk assessment of display screen users in a large regional teaching hospital. Ophthalmic Physiol Opt 1997. [DOI: 10.1111/j.1475-1313.1997.0_853.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- A. J. Jackson
- Eye and Ear Clinic, Royal Group of Hospitals Trust, Belfast BT 12 6BA, Northern Ireland
- Department of Ophthalmology, The Queen's University, Belfast, Northern Ireland
| | - E. S. Barnett
- Eye and Ear Clinic, Royal Group of Hospitals Trust, Belfast BT 12 6BA, Northern Ireland
| | - A. B. Stevens
- Department of Occupational Health, Royal Group of Hospitals Trust, Belfast BT 12 6BA, Northern Ireland
- Department of Public Health Medicine, The Queen's University, Belfast, Northern Ireland
| | - M. McClure
- Eye and Ear Clinic, Royal Group of Hospitals Trust, Belfast BT 12 6BA, Northern Ireland
| | - C. Patterson
- Department of Medical Statistics, The Queen's University, Belfast, Northern Ireland
| | - M. J. McReynolds
- Directorate of Development, Information Systems and Patient Records, Royal Group of Hospitals Trust, Belfast BT 12 6BA, Northern Ireland
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Jackson AJ, Barnett ES, Stevens AB, McClure M, Patterson C, McReynolds MJ. Vision screening, eye examination and risk assessment of display screen users in a large regional teaching hospital. Ophthalmic Physiol Opt 1997. [DOI: 10.1111/j.1475-1313.1997.tb00045.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Horner PJ, Cain D, McClure M, Thomas BJ, Gilroy C, Ali M, Weber JN, Taylor-Robinson D. Association of antibodies to Chlamydia trachomatis heat-shock protein 60 kD with chronic nongonococcal urethritis. Clin Infect Dis 1997; 24:653-60. [PMID: 9145740 DOI: 10.1093/clind/24.4.653] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Ninety male patients with acute nongonococcal urethritis (NGU) who presented for follow-up 10-92 days after initiation of treatment were evaluated. A polymerase chain reaction assay and direct fluorescence antibody test were used to detect Chlamydia trachomatis at presentation and during follow-up. Chlamydial heat-shock protein 60 kD (hsp60) serology with an enzyme-linked immunosorbent assay and C. trachomatis serology with a microimmunofluoresence test were undertaken. In 62 (69%) of the men, evidence of chronic urethritis was noted during follow-up. C. trachomatis was detected in only two patients during follow-up. Chlamydial hsp60 antibody was associated with the development of chronic urethritis between 10 and 92 days after treatment began (P < .04), that is, at 10-29 days (P < .02) and at 30-92 days (P < .008). These results are consistent with the theory that immune response to hsp60 is important in the development of this chronic disease. The results also suggest that chronic NGU is not a consequence of continued production of hsp60 by C. trachomatis.
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Affiliation(s)
- P J Horner
- Department of Genitourinary Medicine and Communicable Diseases, Imperial College School of Medicine at St. Mary's, London, United Kingdom
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Aarons E, Fernandez M, Rees A, McClure M, Weber J. CC-chemokine receptor 5 genotypes and in vitro susceptibility to HIV-1 of a cohort of British HIV-exposed uninfected homosexual men. AIDS 1997; 11:688-9. [PMID: 9108955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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Stafford MK, Cain D, Rosenstein I, Fontaine EA, McClure M, Flanagan AM, Smith JR, Taylor-Robinson D, Weber J, Kitchen VS. A placebo-controlled, double-blind prospective study in healthy female volunteers of dextrin sulphate gel: a novel potential intravaginal virucide. J Acquir Immune Defic Syndr Hum Retrovirol 1997; 14:213-8. [PMID: 9117452 DOI: 10.1097/00042560-199703010-00003] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A double-blind, placebo-controlled study was designed to evaluate the safety and tolerability of intravaginal dextrin sulphate (D2S) gel to assess its preliminary suitability as a potential vaginal virucide. Tolerability was assessed by questionnaire and patient interview. Colposcopy with vaginal biopsy was performed to assess the macroscopic and microscopic evidence of inflammation. The potential impact of the gel on normal vaginal flora was examined by quantitative lactobacilli culture with assessment of the ratio of peroxide to nonperoxide-producing organisms. Colposcopy revealed mild erythema in five of 24 subjects receiving active gel and in none of the 12 placebo recipients, but histology in all subjects revealed no evidence of inflammation. No impact on vaginal lactobacilli was found. We conclude that D2S gel is safe and well tolerated intravaginally at the dosing schedule used in this study.
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Affiliation(s)
- M K Stafford
- Department of Genitourinary Medicine and Communicable Diseases (Clinical Trials Centre, Jefferiss Research Trust Laboratories and MRC Sexually Transmitted Diseases Research Group), Chelsea and Westminister Hospital, London, England
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McClure M, Barnett S, Jackson AJ. An evaluation of vision screening and eye examinations performed on display screen equipment users. Ophthalmic Physiol Opt 1996. [DOI: 10.1046/j.1475-1313.1996.96849969.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Durocher F, Shattuck-Eidens D, McClure M, Labrie F, Skolnick MH, Goldgar DE, Simard J. Comparison of BRCA1 polymorphisms, rare sequence variants and/or missense mutations in unaffected and breast/ovarian cancer populations. Hum Mol Genet 1996; 5:835-42. [PMID: 8776600 DOI: 10.1093/hmg/5.6.835] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Inherited mutations in the BRCA1 gene are known to confer a predisposition to breast and ovarian cancer. We have first characterized 19 sequence variants in the BRCA1 gene during mutation screening by direct sequencing using DNA samples from breast/ovarian cancer patients or obligate carriers. The frequencies of these sequence variants were then compared with those found in control populations of women. Among the 10 sequence variants showing an estimated frequency of the less common allele above 0.05, Q/R356, L/P871, E/G1038, K/R1183 and S/G1613 result in a change of amino acids, 2201C/T, 2430T/C and 4427C/T are silent mutations and the two others, 4209-141C/A and 5272 + 66A/G, are intronic polymorphisms. These frequent polymorphisms, with the exception of Q/R356, were in complete or significant pairwise linkage disequilibrium as evaluated in our control populations. With one exception (L/P871), none of these variants had statistically significant (P < 0.05) differences in allele frequency between breast/ovarian cancer patients or obligate carriers and our control populations. Four rare sequence variants designated 710C-->T, D693N, R841W and S1040N were found in both unaffected and breast/ovarian cancer populations, while the missense mutations M1008I, E1219D, R1347G, T1561I and M1628V were detected only once in our patient population. When a functional test is available, it will be important to determine the consequence on the BRCA1 activity of these rare sequence variants and missense mutations.
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Affiliation(s)
- F Durocher
- Medical Research Council Group in Molecular Endocrinology, CHUL Research Center, Quebec City, Canada
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Liu Q, Neuhausen S, McClure M, Frye C, Weaver-Feldhaus J, Gruis NA, Eddington K, Allalunis-Turner MJ, Skolnick MH, Fujimura FK. CDKN2 (MTS1) tumor suppressor gene mutations in human tumor cell lines. Oncogene 1995; 11:2455. [PMID: 8570198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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McClure M, Bohonak AJ. Non-selectivity in extinction of bivalves in the Late Cretaceous of the Atlantic and Gulf Coastal Plain of North America. J Evol Biol 1995. [DOI: 10.1046/j.1420-9101.1995.8060779.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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