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Makova KD, Pickett BD, Harris RS, Hartley GA, Cechova M, Pal K, Nurk S, Yoo D, Li Q, Hebbar P, McGrath BC, Antonacci F, Aubel M, Biddanda A, Borchers M, Bomberg E, Bouffard GG, Brooks SY, Carbone L, Carrel L, Carroll A, Chang PC, Chin CS, Cook DE, Craig SJ, de Gennaro L, Diekhans M, Dutra A, Garcia GH, Grady PG, Green RE, Haddad D, Hallast P, Harvey WT, Hickey G, Hillis DA, Hoyt SJ, Jeong H, Kamali K, Kosakovsky Pond SL, LaPolice TM, Lee C, Lewis AP, Loh YHE, Masterson P, McCoy RC, Medvedev P, Miga KH, Munson KM, Pak E, Paten B, Pinto BJ, Potapova T, Rhie A, Rocha JL, Ryabov F, Ryder OA, Sacco S, Shafin K, Shepelev VA, Slon V, Solar SJ, Storer JM, Sudmant PH, Sweetalana, Sweeten A, Tassia MG, Thibaud-Nissen F, Ventura M, Wilson MA, Young AC, Zeng H, Zhang X, Szpiech ZA, Huber CD, Gerton JL, Yi SV, Schatz MC, Alexandrov IA, Koren S, O’Neill RJ, Eichler E, Phillippy AM. The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes. bioRxiv 2023:2023.11.30.569198. [PMID: 38077089 PMCID: PMC10705393 DOI: 10.1101/2023.11.30.569198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2023]

Abstract

Apes possess two sex chromosomes-the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and cognition. Variation in mating patterns and brain function among great apes suggests corresponding differences in their sex chromosome structure and evolution. However, due to their highly repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the state-of-the-art experimental and computational methods developed for the telomere-to-telomere (T2T) human genome, we produced gapless, complete assemblies of the X and Y chromosomes for five great apes (chimpanzee, bonobo, gorilla, Bornean and Sumatran orangutans) and a lesser ape, the siamang gibbon. These assemblies completely resolved ampliconic, palindromic, and satellite sequences, including the entire centromeres, allowing us to untangle the intricacies of ape sex chromosome evolution. We found that, compared to the X, ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements. This divergence on the Y arises from the accumulation of lineage-specific ampliconic regions and palindromes (which are shared more broadly among species on the X) and from the abundance of transposable elements and satellites (which have a lower representation on the X). Our analysis of Y chromosome genes revealed lineage-specific expansions of multi-copy gene families and signatures of purifying selection. In summary, the Y exhibits dynamic evolution, while the X is more stable. Finally, mapping short-read sequencing data from >100 great ape individuals revealed the patterns of diversity and selection on their sex chromosomes, demonstrating the utility of these reference assemblies for studies of great ape evolution. These complete sex chromosome assemblies are expected to further inform conservation genetics of nonhuman apes, all of which are endangered species.

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Affiliation(s)

Kateryna D. Makova Penn State University, University Park, PA, USA
Brandon D. Pickett National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Robert S. Harris Penn State University, University Park, PA, USA
Gabrielle A. Hartley University of Connecticut, Storrs, CT, USA
Monika Cechova University of California Santa Cruz, Santa Cruz, CA, USA
Karol Pal Penn State University, University Park, PA, USA
Sergey Nurk National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
DongAhn Yoo University of Washington School of Medicine, Seattle, WA, USA
Qiuhui Li Johns Hopkins University, Baltimore, MD, USA
Prajna Hebbar University of California Santa Cruz, Santa Cruz, CA, USA
Barbara C. McGrath Penn State University, University Park, PA, USA
Francesca Antonacci Università degli Studi di Bari Aldo Moro, Italy
Margaux Aubel University of Münster, Münster, Germany
Arjun Biddanda Johns Hopkins University, Baltimore, MD, USA
Matthew Borchers Stowers Institute, Kansas City, MO, USA
Erich Bomberg University of Münster, Münster, Germany MPI for Developmental Biology, Tübingen, Germany
Gerard G. Bouffard National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Shelise Y. Brooks National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Lucia Carbone Oregon Health & Science University, Portland, OR, USA Oregon National Primate Research Center, Hillsboro, OR, USA
Laura Carrel Penn State University School of Medicine, Hershey, PA, USA
Andrew Carroll Google, Mountain View, CA, USA
Pi-Chuan Chang Google, Mountain View, CA, USA
Chen-Shan Chin Foundation of Biological Data Sciences, Belmont, CA, USA
Daniel E. Cook Google, Mountain View, CA, USA
Sarah J.C. Craig Penn State University, University Park, PA, USA
Luciana de Gennaro Università degli Studi di Bari Aldo Moro, Italy
Mark Diekhans University of California Santa Cruz, Santa Cruz, CA, USA
Amalia Dutra National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Gage H. Garcia University of Washington School of Medicine, Seattle, WA, USA
Patrick G.S. Grady University of Connecticut, Storrs, CT, USA
Richard E. Green University of California Santa Cruz, Santa Cruz, CA, USA
Diana Haddad National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Pille Hallast The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
William T. Harvey University of Washington School of Medicine, Seattle, WA, USA
Glenn Hickey University of California Santa Cruz, Santa Cruz, CA, USA
David A. Hillis University of California Santa Barbara, Santa Barbara, CA, USA
Savannah J. Hoyt University of Connecticut, Storrs, CT, USA
Hyeonsoo Jeong University of Washington School of Medicine, Seattle, WA, USA
Kaivan Kamali Penn State University, University Park, PA, USA
Sergei L. Kosakovsky Pond Temple University, Philadelphia, PA, USA
Troy M. LaPolice Penn State University, University Park, PA, USA
Charles Lee The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
Alexandra P. Lewis University of Washington School of Medicine, Seattle, WA, USA
Yong-Hwee E. Loh University of California Santa Barbara, Santa Barbara, CA, USA
Patrick Masterson National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Rajiv C. McCoy Johns Hopkins University, Baltimore, MD, USA
Paul Medvedev Penn State University, University Park, PA, USA
Karen H. Miga University of California Santa Cruz, Santa Cruz, CA, USA
Katherine M. Munson University of Washington School of Medicine, Seattle, WA, USA
Evgenia Pak National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Benedict Paten University of California Santa Cruz, Santa Cruz, CA, USA
Brendan J. Pinto Arizona State University, Tempe, AZ, USA
Tamara Potapova Stowers Institute, Kansas City, MO, USA
Arang Rhie National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Joana L. Rocha University of California Berkeley, Berkeley, CA, USA
Fedor Ryabov Masters Program in National Research University Higher School of Economics, Moscow, Russia
Oliver A. Ryder San Diego Zoological Society, San Diego, CA, USA
Samuel Sacco University of California Santa Cruz, Santa Cruz, CA, USA
Kishwar Shafin Google, Mountain View, CA, USA
Valery A. Shepelev Institute of Molecular Genetics, Moscow, Russia
Viviane Slon Tel Aviv University, Israel
Steven J. Solar National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Jessica M. Storer University of Connecticut, Storrs, CT, USA
Peter H. Sudmant University of California Berkeley, Berkeley, CA, USA
Sweetalana Penn State University, University Park, PA, USA
Alex Sweeten National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA Johns Hopkins University, Baltimore, MD, USA
Michael G. Tassia Johns Hopkins University, Baltimore, MD, USA
Françoise Thibaud-Nissen National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
Mario Ventura Università degli Studi di Bari Aldo Moro, Italy
Melissa A. Wilson Arizona State University, Tempe, AZ, USA
Alice C. Young National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Huiqing Zeng Penn State University, University Park, PA, USA
Xinru Zhang Penn State University, University Park, PA, USA
Zachary A. Szpiech Penn State University, University Park, PA, USA
Christian D. Huber Penn State University, University Park, PA, USA
Jennifer L. Gerton Stowers Institute, Kansas City, MO, USA
Soojin V. Yi University of California Santa Barbara, Santa Barbara, CA, USA
Michael C. Schatz Johns Hopkins University, Baltimore, MD, USA
Ivan A. Alexandrov Tel Aviv University, Israel
Sergey Koren National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Rachel J. O’Neill University of Connecticut, Storrs, CT, USA
Evan Eichler University of Washington School of Medicine, Seattle, WA, USA Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
Adam M. Phillippy National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA

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Altemose N, Glennis A, Bzikadze AV, Sidhwani P, Langley SA, Caldas GV, Hoyt SJ, Uralsky L, Ryabov FD, Shew CJ, Sauria MEG, Borchers M, Gershman A, Mikheenko A, Shepelev VA, Dvorkina T, Kunyavskaya O, Vollger MR, Rhie A, McCartney AM, Asri M, Lorig-Roach R, Shafin K, Aganezov S, Olson D, de Lima LG, Potapova T, Hartley GA, Haukness M, Kerpedjiev P, Gusev F, Tigyi K, Brooks S, Young A, Nurk S, Koren S, Salama SR, Paten B, Rogaev EI, Streets A, Karpen GH, Dernburg AF, Sullivan BA, Straight AF, Wheeler TJ, Gerton JL, Eichler EE, Phillippy AM, Timp W, Dennis MY, O'Neill RJ, Zook JM, Schatz MC, Pevzner PA, Diekhans M, Langley CH, Alexandrov IA, Miga KH. Complete genomic and epigenetic maps of human centromeres. Science 2022;376:eabl4178. [PMID: 35357911 PMCID: PMC9233505 DOI: 10.1126/science.abl4178] [Citation(s) in RCA: 157] [Impact Index Per Article: 78.5] [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: 12/20/2022]

Affiliation(s)

Nicolas Altemose Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
A. Glennis Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
Andrey V. Bzikadze Graduate Program in Bioinformatics and Systems Biology, University of California San Diego, La Jolla, CA, USA
Pragya Sidhwani Department of Biochemistry, Stanford University, Stanford, CA, USA
Sasha A. Langley Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
Gina V. Caldas Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
Savannah J. Hoyt Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
Lev Uralsky Sirius University of Science and Technology, Sochi, Russia Vavilov Institute of General Genetics, Moscow, Russia
Fedor D. Ryabov Moscow Polytechnic University, Moscow, Russia
Colin J. Shew Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
Michael E. G. Sauria Department of Biology, Johns Hopkins University, Baltimore, MD, USA
Matthew Borchers Stowers Institute for Medical Research, Kansas City, MO, USA
Ariel Gershman Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
Alla Mikheenko Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
Valery A. Shepelev Vavilov Institute of General Genetics, Moscow, Russia
Tatiana Dvorkina Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
Olga Kunyavskaya Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia
Mitchell R. Vollger Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
Arang Rhie Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Ann M. McCartney Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Mobin Asri UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Ryan Lorig-Roach UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Kishwar Shafin UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Sergey Aganezov Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
Daniel Olson Department of Computer Science, University of Montana, Missoula, MT. USA
Leonardo Gomes de Lima Stowers Institute for Medical Research, Kansas City, MO, USA
Tamara Potapova Stowers Institute for Medical Research, Kansas City, MO, USA
Gabrielle A. Hartley Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
Marina Haukness UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Peter Kerpedjiev Reservoir Genomics, Oakland, CA
Fedor Gusev Vavilov Institute of General Genetics, Moscow, Russia
Kristof Tigyi UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA
Shelise Brooks NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Alice Young NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Sergey Nurk Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Sergey Koren Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Sofie R. Salama UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA
Benedict Paten UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
Evgeny I. Rogaev Sirius University of Science and Technology, Sochi, Russia Vavilov Institute of General Genetics, Moscow, Russia Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, USA Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
Aaron Streets Department of Bioengineering, University of California, Berkeley, Berkeley, CA, USA Chan Zuckerberg Biohub, San Francisco, CA, USA
Gary H. Karpen Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA BioEngineering and BioMedical Sciences Department, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
Abby F. Dernburg Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA
Beth A. Sullivan Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
Aaron F. Straight Department of Biochemistry, Stanford University, Stanford, CA, USA
Travis J. Wheeler Department of Computer Science, University of Montana, Missoula, MT. USA
Jennifer L. Gerton Stowers Institute for Medical Research, Kansas City, MO, USA University of Kansas Medical School, Department of Biochemistry and Molecular Biology and Cancer Center, University of Kansas, Kansas City, KS, USA
Evan E. Eichler Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA Howard Hughes Medical Institute, Chevy Chase, MD, USA
Adam M. Phillippy Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
Winston Timp Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
Megan Y. Dennis Genome Center, MIND Institute, and Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Davis, CA, USA
Rachel J. O'Neill Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
Justin M. Zook Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
Michael C. Schatz Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
Pavel A. Pevzner Department of Computer Science and Engineering, University of California at San Diego, San Diego, CA, USA
Mark Diekhans UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
Charles H. Langley Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
Ivan A. Alexandrov Vavilov Institute of General Genetics, Moscow, Russia Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University, Saint Petersburg, Russia Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
Karen H. Miga UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA

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Nurk S, Koren S, Rhie A, Rautiainen M, Bzikadze AV, Mikheenko A, Vollger MR, Altemose N, Uralsky L, Gershman A, Aganezov S, Hoyt SJ, Diekhans M, Logsdon GA, Alonge M, Antonarakis SE, Borchers M, Bouffard GG, Brooks SY, Caldas GV, Chen NC, Cheng H, Chin CS, Chow W, de Lima LG, Dishuck PC, Durbin R, Dvorkina T, Fiddes IT, Formenti G, Fulton RS, Fungtammasan A, Garrison E, Grady PG, Graves-Lindsay TA, Hall IM, Hansen NF, Hartley GA, Haukness M, Howe K, Hunkapiller MW, Jain C, Jain M, Jarvis ED, Kerpedjiev P, Kirsche M, Kolmogorov M, Korlach J, Kremitzki M, Li H, Maduro VV, Marschall T, McCartney AM, McDaniel J, Miller DE, Mullikin JC, Myers EW, Olson ND, Paten B, Peluso P, Pevzner PA, Porubsky D, Potapova T, Rogaev EI, Rosenfeld JA, Salzberg SL, Schneider VA, Sedlazeck FJ, Shafin K, Shew CJ, Shumate A, Sims Y, Smit AFA, Soto DC, Sović I, Storer JM, Streets A, Sullivan BA, Thibaud-Nissen F, Torrance J, Wagner J, Walenz BP, Wenger A, Wood JMD, Xiao C, Yan SM, Young AC, Zarate S, Surti U, McCoy RC, Dennis MY, Alexandrov IA, Gerton JL, O’Neill RJ, Timp W, Zook JM, Schatz MC, Eichler EE, Miga KH, Phillippy AM. The complete sequence of a human genome. Science 2022;376:44-53. [PMID: 35357919 PMCID: PMC9186530 DOI: 10.1126/science.abj6987] [Citation(s) in RCA: 887] [Impact Index Per Article: 443.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]

Affiliation(s)

Sergey Nurk Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Sergey Koren Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Arang Rhie Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Mikko Rautiainen Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Andrey V. Bzikadze Graduate Program in Bioinformatics and Systems Biology, University of California, San Diego; La Jolla, CA, USA
Alla Mikheenko Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
Mitchell R. Vollger Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
Nicolas Altemose Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA
Lev Uralsky Sirius University of Science and Technology; Sochi, Russia Vavilov Institute of General Genetics; Moscow, Russia
Ariel Gershman Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA
Sergey Aganezov Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Savannah J. Hoyt Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
Mark Diekhans UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Glennis A. Logsdon Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
Michael Alonge Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Stylianos E. Antonarakis University of Geneva Medical School; Geneva, Switzerland
Matthew Borchers Stowers Institute for Medical Research; Kansas City, MO, USA
Gerard G. Bouffard NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Shelise Y. Brooks NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Gina V. Caldas Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA, USA
Nae-Chyun Chen Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Haoyu Cheng Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA Department of Biomedical Informatics, Harvard Medical School; Boston, MA
Chen-Shan Chin DNAnexus; Mountain View, CA, USA
William Chow Wellcome Sanger Institute; Cambridge, UK
Leonardo G. de Lima Stowers Institute for Medical Research; Kansas City, MO, USA
Philip C. Dishuck Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
Richard Durbin Wellcome Sanger Institute; Cambridge, UK Department of Genetics, University of Cambridge; Cambridge, UK
Tatiana Dvorkina Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia
Ian T. Fiddes Inscripta; Boulder, CO, USA
Giulio Formenti Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA Howard Hughes Medical Institute; Chevy Chase, MD, USA
Robert S. Fulton Department of Genetics, Washington University School of Medicine; St. Louis, MO, USA
Arkarachai Fungtammasan DNAnexus; Mountain View, CA, USA
Erik Garrison UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA University of Tennessee Health Science Center; Memphis, TN, USA
Patrick G.S. Grady Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
Tina A. Graves-Lindsay McDonnell Genome Institute, Washington University in St. Louis; St. Louis, MO, USA
Ira M. Hall Department of Genetics, Yale University School of Medicine; New Haven, CT, USA
Nancy F. Hansen Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Gabrielle A. Hartley Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
Marina Haukness UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Kerstin Howe Wellcome Sanger Institute; Cambridge, UK
Michael W. Hunkapiller Pacific Biosciences; Menlo Park, CA, USA
Chirag Jain Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA Department of Computational and Data Sciences, Indian Institute of Science; Bangalore KA, India
Miten Jain UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Erich D. Jarvis Laboratory of Neurogenetics of Language and The Vertebrate Genome Lab, The Rockefeller University; New York, NY, USA Howard Hughes Medical Institute; Chevy Chase, MD, USA
Peter Kerpedjiev Reservoir Genomics LLC; Oakland, CA
Melanie Kirsche Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Mikhail Kolmogorov Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
Jonas Korlach Pacific Biosciences; Menlo Park, CA, USA
Milinn Kremitzki McDonnell Genome Institute, Washington University in St. Louis; St. Louis, MO, USA
Heng Li Department of Data Sciences, Dana-Farber Cancer Institute; Boston, MA Department of Biomedical Informatics, Harvard Medical School; Boston, MA
Valerie V. Maduro Undiagnosed Diseases Program, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Tobias Marschall Heinrich Heine University Düsseldorf, Medical Faculty, Institute for Medical Biometry and Bioinformatics; Düsseldorf, Germany
Ann M. McCartney Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Jennifer McDaniel Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
Danny E. Miller Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children’s Hospital; Seattle, WA, USA
James C. Mullikin NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA Comparative Genomics Analysis Unit, Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Eugene W. Myers Max-Planck Institute of Molecular Cell Biology and Genetics; Dresden, Germany
Nathan D. Olson Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
Benedict Paten UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Paul Peluso Pacific Biosciences; Menlo Park, CA, USA
Pavel A. Pevzner Department of Computer Science and Engineering, University of California, San Diego; San Diego, CA, USA
David Porubsky Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA
Tamara Potapova Stowers Institute for Medical Research; Kansas City, MO, USA
Evgeny I. Rogaev Sirius University of Science and Technology; Sochi, Russia Vavilov Institute of General Genetics; Moscow, Russia Department of Psychiatry, University of Massachusetts Medical School; Worcester, MA, USA Faculty of Biology, Lomonosov Moscow State University; Moscow, Russia
Jeffrey A. Rosenfeld Cancer Institute of New Jersey; New Brunswick, NJ, USA
Steven L. Salzberg Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
Valerie A. Schneider National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
Fritz J. Sedlazeck Human Genome Sequencing Center, Baylor College of Medicine; Houston TX, USA
Kishwar Shafin UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA
Colin J. Shew Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
Alaina Shumate Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
Ying Sims Wellcome Sanger Institute; Cambridge, UK
Arian F. A. Smit Institute for Systems Biology; Seattle, WA, USA
Daniela C. Soto Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
Ivan Sović Pacific Biosciences; Menlo Park, CA, USA Digital BioLogic d.o.o.; Ivanić-Grad, Croatia
Jessica M. Storer Institute for Systems Biology; Seattle, WA, USA
Aaron Streets Department of Bioengineering, University of California, Berkeley; Berkeley, CA, USA Chan Zuckerberg Biohub; San Francisco, CA, USA
Beth A. Sullivan Department of Molecular Genetics and Microbiology, Duke University School of Medicine; Durham, NC, USA
Françoise Thibaud-Nissen National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
James Torrance Wellcome Sanger Institute; Cambridge, UK
Justin Wagner Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
Brian P. Walenz Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA
Aaron Wenger Pacific Biosciences; Menlo Park, CA, USA
Jonathan M. D. Wood Wellcome Sanger Institute; Cambridge, UK
Chunlin Xiao National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health; Bethesda, MD, USA
Stephanie M. Yan Department of Biology, Johns Hopkins University; Baltimore, MD, USA
Alice C. Young NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD, USA
Samantha Zarate Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA
Urvashi Surti Department of Pathology, University of Pittsburgh; Pittsburgh, PA, USA
Rajiv C. McCoy Department of Biology, Johns Hopkins University; Baltimore, MD, USA
Megan Y. Dennis Genome Center, MIND Institute, Department of Biochemistry and Molecular Medicine, University of California, Davis; CA, USA
Ivan A. Alexandrov Center for Algorithmic Biotechnology, Institute of Translational Biomedicine, Saint Petersburg State University; Saint Petersburg, Russia Vavilov Institute of General Genetics; Moscow, Russia Research Center of Biotechnology of the Russian Academy of Sciences; Moscow, Russia
Jennifer L. Gerton Stowers Institute for Medical Research; Kansas City, MO, USA Department of Biochemistry and Molecular Biology, University of Kansas Medical School; Kansas City, MO, USA
Rachel J. O’Neill Institute for Systems Genomics and Department of Molecular and Cell Biology, University of Connecticut; Storrs, CT, USA
Winston Timp Department of Molecular Biology and Genetics, Johns Hopkins University; Baltimore, MD, USA Department of Biomedical Engineering, Johns Hopkins University; Baltimore, MD, USA
Justin M. Zook Biosystems and Biomaterials Division, National Institute of Standards and Technology; Gaithersburg, MD, USA
Michael C. Schatz Department of Computer Science, Johns Hopkins University; Baltimore, MD, USA Department of Biology, Johns Hopkins University; Baltimore, MD, USA
Evan E. Eichler Department of Genome Sciences, University of Washington School of Medicine; Seattle, WA, USA Howard Hughes Medical Institute; Chevy Chase, MD, USA
Karen H. Miga UC Santa Cruz Genomics Institute, University of California, Santa Cruz; Santa Cruz, CA, USA Department of Biomolecular Engineering, University of California Santa Cruz, CA, USA
Adam M. Phillippy Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD USA

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Pertl K, Borchers M, Baumgärtner W, Wohlsein P. Expression of Neuroectodermal Markers in Atypical Fibromas in Two Dwarf Hamsters (Phodopus spp.). J Comp Pathol 2019;172:53-57. [PMID: 31690416 DOI: 10.1016/j.jcpa.2019.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/14/2019] [Accepted: 09/04/2019] [Indexed: 10/25/2022]

Graw MF, D'Angelo G, Borchers M, Thurber AR, Johnson JE, Zhang C, Liu H, Colwell FS. Energy Gradients Structure Microbial Communities Across Sediment Horizons in Deep Marine Sediments of the South China Sea. Front Microbiol 2018;9:729. [PMID: 29696012 PMCID: PMC5905238 DOI: 10.3389/fmicb.2018.00729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/28/2018] [Indexed: 01/28/2023] Open

Abstract

The deep marine subsurface is a heterogeneous environment in which the assembly of microbial communities is thought to be controlled by a combination of organic matter deposition, electron acceptor availability, and sedimentology. However, the relative importance of these factors in structuring microbial communities in marine sediments remains unclear. The South China Sea (SCS) experiences significant variability in sedimentation across the basin and features discrete changes in sedimentology as a result of episodic deposition of turbidites and volcanic ashes within lithogenic clays and siliceous or calcareous ooze deposits throughout the basin's history. Deep subsurface microbial communities were recently sampled by the International Ocean Discovery Program (IODP) at three locations in the SCS with sedimentation rates of 5, 12, and 20 cm per thousand years. Here, we used Illumina sequencing of the 16S ribosomal RNA gene to characterize deep subsurface microbial communities from distinct sediment types at these sites. Communities across all sites were dominated by several poorly characterized taxa implicated in organic matter degradation, including Atribacteria, Dehalococcoidia, and Aerophobetes. Sulfate-reducing bacteria comprised only 4% of the community across sulfate-bearing sediments from multiple cores and did not change in abundance in sediments from the methanogenic zone at the site with the lowest sedimentation rate. Microbial communities were significantly structured by sediment age and the availability of sulfate as an electron acceptor in pore waters. However, microbial communities demonstrated no partitioning based on the sediment type they inhabited. These results indicate that microbial communities in the SCS are structured by the availability of electron donors and acceptors rather than sedimentological characteristics.

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Lingen M, Albers L, Borchers M, Haass S, Gärtner J, Schröder S, Goldbeck L, von Kries R, Brockmann K, Zirn B. Obtaining a genetic diagnosis in a child with disability: impact on parental quality of life. Clin Genet 2015;89:258-66. [PMID: 26084449 DOI: 10.1111/cge.12629] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 06/16/2015] [Accepted: 06/16/2015] [Indexed: 12/14/2022]

Affiliation(s)

M Lingen Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
L Albers Institute of Social Paediatrics and Adolescent Medicine, Division of Epidemiology, Ludwig Maximilians University Munich, Munich, Germany
M Borchers Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
S Haass Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
J Gärtner Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
S Schröder Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
L Goldbeck Department of Child and Adolescent Psychiatry/Psychotherapy, University Ulm, Ulm, Germany
R von Kries Institute of Social Paediatrics and Adolescent Medicine, Division of Epidemiology, Ludwig Maximilians University Munich, Munich, Germany
K Brockmann Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany
B Zirn Interdisciplinary Pediatric Center for Children with Developmental Disabilities and Severe Chronic Disorders, Department of Paediatrics and Adolescent Medicine, University of Göttingen, Göttingen, Germany.,Genetikum, Genetic Counselling and Diagnostics, Stuttgart, Germany

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Shoukier M, Klein N, Auber B, Wickert J, Schröder J, Zoll B, Burfeind P, Bartels I, Alsat EA, Lingen M, Grzmil P, Schulze S, Keyser J, Weise D, Borchers M, Hobbiebrunken E, Röbl M, Gärtner J, Brockmann K, Zirn B. Array CGH in patients with developmental delay or intellectual disability: are there phenotypic clues to pathogenic copy number variants? Clin Genet 2013;83:53-65. [DOI: 10.1111/j.1399-0004.2012.01850.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]

Kaiser T, Esen C, Moritz H, Borchers M, Schweiger G. Observation of Fluorescence Background Suppression in Raman Scattering on Single Microparticles. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19961000206] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]

Borchers M, von der Mülbe B, Teikemeier F, Theegarten D. [Pulmonary nocardiasis with abscesses spreading to cerebrum, cerebellum and orbits]. Dtsch Med Wochenschr 2006;131:1085-8. [PMID: 16685629 DOI: 10.1055/s-2006-941724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 10/24/2022]

Stucki A, Borchers M, Stucki G, Cieza A, Amann E, Ruof J. Content comparison of health status measures for obesity based on the international classification of functioning, disability and health. Int J Obes (Lond) 2006;30:1791-9. [PMID: 16585945 DOI: 10.1038/sj.ijo.0803335] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [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: 01/21/2023]

Abstract

OBJECTIVE

To compare the content covered by twelve obesity-specific health status measures using the International Classification of Functioning, Disability and Health (ICF).

DESIGN

Obesity-specific health status measures were identified and then linked to the ICF separately by two trained health professionals according to standardized guidelines. The degree of agreement between health professionals was calculated by means of the kappa (kappa) statistic. Bootstrapped confidence intervals (CI) were calculated. The obesity-specific health-status measures were compared on the component and category level of the ICF.

MEASUREMENTS

welve condition-specific health-status measures were identified and included in this study, namely the obesity-related problem scale, the obesity eating problems scale, the obesity-related coping and obesity-related distress questionnaire, the impact of weight on quality of life questionnaire (short version), the health-related quality of life questionnaire, the obesity adjustment survey (short form), the short specific quality of life scale, the obesity-related well-being questionnaire, the bariatric analysis and reporting outcome system, the bariatric quality of life index, the obesity and weight loss quality of life questionnaire and the weight-related symptom measure.

RESULTS

In the 280 items of the eight measures, a total of 413 concepts were identified and linked to the 87 different ICF categories. The measures varied strongly in the number of concepts contained and the number of ICF categories used to map these concepts. Items on body functions varied form 12% in the obesity-related problem scale to 95% in the weight-related symptom measure. The estimated kappa coefficients ranged between 0.79 (CI: 0.72, 0.86) at the component ICFs level and 0.97 (CI: 0.93, 1.0) at the third ICF's level.

CONCLUSION

The ICF proved highly useful for the content comparison of obesity-specific health-status measures. The results may provide clinicians and researchers with new insights when selecting health-status measures for clinical studies in obesity.

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Borchers M, Kröling P, Sigl T, Stucki G. ICF-basiertes Assessment in der rehabilitativen Therapie - dargestellt anhand des ICF-Modellblatts am Beispiel Kniegelenkarthrose. Phys Med Rehab Kuror 2005. [DOI: 10.1055/s-2005-866881] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]

Bischoff-Ferrari HA, Borchers M, Gudat F, Dürmüller U, Stähelin HB, Dick W. Vitamin D receptor expression in human muscle tissue decreases with age. J Bone Miner Res 2004;19:265-9. [PMID: 14969396 DOI: 10.1359/jbmr.2004.19.2.265] [Citation(s) in RCA: 356] [Impact Index Per Article: 17.8] [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] [Received: 04/11/2003] [Revised: 09/09/2003] [Accepted: 09/10/2003] [Indexed: 12/21/2022]

Abstract

UNLABELLED

Intracellular 1,25-dihydroxyvitamin D receptor (VDR) is expressed in human skeletal muscle tissue. However, it is unknown whether VDR expression in vivo is related to age or vitamin D status, or whether VDR expression differs between skeletal muscle groups.

INTRODUCTION

We investigated these factors and their relation to 1,25-dihydroxyvitamin D receptor (VDR) expression in freshly removed human muscle tissue.

MATERIALS AND METHODS

We investigated biopsy specimens of the gluteus medius taken at surgery from 20 female patients undergoing total hip arthroplasty (mean age, 71.6 +/- 14.5; 72% > 65 years) and biopsy specimens of the transversospinalis muscle taken at surgery from 12 female patients with spinal operations (mean age, 55.2 +/- 19.6; 28% > 65 years). The specimens were obtained by immunohistological staining of the VDR using a monoclonal rat antibody to the VDR (Clone no. 9A7). Quantitative VDR expression (number of VDR positive nuclei) was assessed by counting 500 nuclei per specimen and person. Serum concentrations of 25-hydroxyvitamin D and 1,25-dihydroxyvitamin D were assessed at day of admission to surgery.

RESULTS

All muscle biopsy specimens stained positive for VDR. In the univariate analyses, increased age was associated with decreased VDR expression (r = 0.5: p = 0.004), whereas there were no significant correlations between VDR expression and 25-hydroxyvitamin D or 1,25-dihydroxyvitamin D levels. VDR expression did not differ between patients with hip and spinal surgery. In the multivariate analysis, older age was a significant predictor of decreased VDR expression after controlling biopsy location (gluteus medius or the transversospinalis muscle), and 25-hydroxyvitamin D levels (linear regression analysis: beta-estimate = -2.56; p = 0.047).

CONCLUSIONS

Intranuclear immunostaining of the VDR was present in muscle biopsy specimens of all orthopedic patients. Older age was significantly associated with decreased VDR expression, independent of biopsy location and serum 25-hydroxyvitamin D levels.

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Borchers M, Schwarzkopf S, Stucki G. A Multidisciplinary, Multimodal Daycare Concept for Patients with Osteoarthritis - First Results. AKTUEL RHEUMATOL 2003. [DOI: 10.1055/s-2003-37164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]

Bischoff HA, Borchers M, Gudat F, Duermueller U, Theiler R, Stähelin HB, Dick W. In situ detection of 1,25-dihydroxyvitamin D3 receptor in human skeletal muscle tissue. Histochem J 2001;33:19-24. [PMID: 11352397 DOI: 10.1023/a:1017535728844] [Citation(s) in RCA: 347] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]

Denzler KL, Farmer SC, Crosby JR, Borchers M, Cieslewicz G, Larson KA, Cormier-Regard S, Lee NA, Lee JJ. Eosinophil major basic protein-1 does not contribute to allergen-induced airway pathologies in mouse models of asthma. J Immunol 2000;165:5509-17. [PMID: 11067904 DOI: 10.4049/jimmunol.165.10.5509] [Citation(s) in RCA: 102] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]

Leipner C, Grün K, Borchers M, Stelzner A. The outcome of coxsackievirus B3-(CVB3-) induced myocarditis is influenced by the cellular immune status. Herz 2000;25:245-8. [PMID: 10904846 DOI: 10.1007/s000590050014] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [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: 11/28/2022]

Leipner C, Borchers M, Merkle I, Stelzner A. Coxsackievirus B3-induced myocarditis in MHC class II-deficient mice. J Hum Virol 1999;2:102-14. [PMID: 10225212] [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] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]

Balasubramaniam A, Ujhelyi M, Borchers M, Huang Y, Zhai W, Zhou Y, Johnson M, Sheriff S, Fischer JE. Antagonistic properties of centrally truncated analogs of [D-Trp(32)]NPY. J Med Chem 1996;39:1142-7. [PMID: 8676351 DOI: 10.1021/jm9505371] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [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: 02/01/2023]

Abstract

We have previously shown that [D-Trp(32)]NPY can competitively antagonize NPY-induced feeding in rats (Balasubramaniam et al. J. Med. Chem. 1994, 37, 811-815). This peptide, however, did not bind to SK-N-MC cells with Y-1 receptors. Since centrally truncated NPY analogs have been shown to bind Y-1 receptors, we synthesized similar analogs of [D-Trp(32)]NPY and investigated their Y-1 (SK-N-MC) and Y-2 (SK-N-BE2) receptor affinities and their properties in human erythroleukemia (HEL) cells. None of the analogs with D-Trp(32) mobilized intracellular calcium, [Ca2]i, in HEL cells. Although Des-AA(6-24)[Aoc(6)]NPY and the corresponding D-Trp(32) analog exhibited no affinity to Y-1 receptors, Des-AA(7-24)[Aoc(6),D-Trp(32)] NPY(6) exhibited weak binding. Replacing Pro(5) in 6 with D-Ala to stabilize the central chain reversal, and hence the antiparallel alignment of the N- and C-terminal regions known to be important for Y-1 binding, resulted in an analog, Des-AA(7-24)[D-Ala(5),Aoc(6),D-Trp(32)]NPY (7), which exhibited moderate antagonist potency in attenuating NPY effects on cAMP and [Ca2+]i, in SK-N-MC and HEL cells, respectively. This analog also shifted the dose-response curve of NPY on blood pressure in anesthetized rats. Deletion of only the 7-17 and/or the incorporation of N-Me-Ala(5), superior beta-turn stabilizer, in 7 did not improve the Y-1 receptor affinity. Des-AA(7-24)[D-Ala(5), Gly(6),D-Trp(32)]NPY exhibited an affinity similar to that of 7, suggesting that a long spacer arm is not necessary for efficient Y-1 receptor interaction. Locking the antiparallel alignment via a 2/26 or 2/27 lactam bridge did not improve the binding. Finally, replacement of D-Ala(5) in 7 with D-Trp dramatically increased both the binding and the antagonistic potencies. Modeling based on the avian pancreatic polypeptide X-ray structure suggested that analogs which have the N- and C-terminal regions in close proximity might exhibit good binding, and that the D-Trp(32) substitution may induce a beta-turn that could be important for exhibiting antagonism. A systematic investigation has resulted in the development of relatively potent Y-1 receptor antagonists. Further structure-activity studies with these compounds and those previously reported by us and other investigators should result in the development of long-acting and receptor selective antagonists.

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Chance WT, Balasubramaniam A, Borchers M, Fischer JE. Refractory hypothalamic adenylate cyclase in anorectic tumor-bearing rats: implications for NPY-induced feeding. Brain Res 1995;691:180-4. [PMID: 8590051 DOI: 10.1016/0006-8993(95)00716-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [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: 01/31/2023]