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  • Cell Press  (19)
  • American Society of Hematology  (16)
  • American Association for the Advancement of Science (AAAS)  (5)
  • 2010-2014  (40)
  • 1925-1929
  • 2014  (23)
  • 2010  (17)
  • 1
    Publikationsdatum: 2010-05-22
    Beschreibung: The human microbiome refers to the community of microorganisms, including prokaryotes, viruses, and microbial eukaryotes, that populate the human body. The National Institutes of Health launched an initiative that focuses on describing the diversity of microbial species that are associated with health and disease. The first phase of this initiative includes the sequencing of hundreds of microbial reference genomes, coupled to metagenomic sequencing from multiple body sites. Here we present results from an initial reference genome sequencing of 178 microbial genomes. From 547,968 predicted polypeptides that correspond to the gene complement of these strains, previously unidentified ("novel") polypeptides that had both unmasked sequence length greater than 100 amino acids and no BLASTP match to any nonreference entry in the nonredundant subset were defined. This analysis resulted in a set of 30,867 polypeptides, of which 29,987 (approximately 97%) were unique. In addition, this set of microbial genomes allows for approximately 40% of random sequences from the microbiome of the gastrointestinal tract to be associated with organisms based on the match criteria used. Insights into pan-genome analysis suggest that we are still far from saturating microbial species genetic data sets. In addition, the associated metrics and standards used by our group for quality assurance are presented.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940224/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940224/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Human Microbiome Jumpstart Reference Strains Consortium -- Nelson, Karen E -- Weinstock, George M -- Highlander, Sarah K -- Worley, Kim C -- Creasy, Heather Huot -- Wortman, Jennifer Russo -- Rusch, Douglas B -- Mitreva, Makedonka -- Sodergren, Erica -- Chinwalla, Asif T -- Feldgarden, Michael -- Gevers, Dirk -- Haas, Brian J -- Madupu, Ramana -- Ward, Doyle V -- Birren, Bruce W -- Gibbs, Richard A -- Methe, Barbara -- Petrosino, Joseph F -- Strausberg, Robert L -- Sutton, Granger G -- White, Owen R -- Wilson, Richard K -- Durkin, Scott -- Giglio, Michelle Gwinn -- Gujja, Sharvari -- Howarth, Clint -- Kodira, Chinnappa D -- Kyrpides, Nikos -- Mehta, Teena -- Muzny, Donna M -- Pearson, Matthew -- Pepin, Kymberlie -- Pati, Amrita -- Qin, Xiang -- Yandava, Chandri -- Zeng, Qiandong -- Zhang, Lan -- Berlin, Aaron M -- Chen, Lei -- Hepburn, Theresa A -- Johnson, Justin -- McCorrison, Jamison -- Miller, Jason -- Minx, Pat -- Nusbaum, Chad -- Russ, Carsten -- Sykes, Sean M -- Tomlinson, Chad M -- Young, Sarah -- Warren, Wesley C -- Badger, Jonathan -- Crabtree, Jonathan -- Markowitz, Victor M -- Orvis, Joshua -- Cree, Andrew -- Ferriera, Steve -- Fulton, Lucinda L -- Fulton, Robert S -- Gillis, Marcus -- Hemphill, Lisa D -- Joshi, Vandita -- Kovar, Christie -- Torralba, Manolito -- Wetterstrand, Kris A -- Abouellleil, Amr -- Wollam, Aye M -- Buhay, Christian J -- Ding, Yan -- Dugan, Shannon -- FitzGerald, Michael G -- Holder, Mike -- Hostetler, Jessica -- Clifton, Sandra W -- Allen-Vercoe, Emma -- Earl, Ashlee M -- Farmer, Candace N -- Liolios, Konstantinos -- Surette, Michael G -- Xu, Qiang -- Pohl, Craig -- Wilczek-Boney, Katarzyna -- Zhu, Dianhui -- HHSN272200900017C/PHS HHS/ -- N01 AI30071/AI/NIAID NIH HHS/ -- U54 HG003273/HG/NHGRI NIH HHS/ -- U54 HG003273-04/HG/NHGRI NIH HHS/ -- U54 HG003273-04S1/HG/NHGRI NIH HHS/ -- U54 HG003273-05/HG/NHGRI NIH HHS/ -- U54 HG003273-05S1/HG/NHGRI NIH HHS/ -- U54 HG003273-05S2/HG/NHGRI NIH HHS/ -- U54 HG003273-06/HG/NHGRI NIH HHS/ -- U54 HG003273-06S1/HG/NHGRI NIH HHS/ -- U54 HG003273-06S2/HG/NHGRI NIH HHS/ -- U54 HG003273-07/HG/NHGRI NIH HHS/ -- U54 HG003273-08/HG/NHGRI NIH HHS/ -- U54 HG004973/HG/NHGRI NIH HHS/ -- U54 HG004973-01/HG/NHGRI NIH HHS/ -- U54 HG004973-02/HG/NHGRI NIH HHS/ -- U54-AI084844/AI/NIAID NIH HHS/ -- U54-HG003079/HG/NHGRI NIH HHS/ -- U54-HG003273/HG/NHGRI NIH HHS/ -- U54-HG004968/HG/NHGRI NIH HHS/ -- U54-HG004969/HG/NHGRI NIH HHS/ -- U54-HG004973/HG/NHGRI NIH HHS/ -- Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2010 May 21;328(5981):994-9. doi: 10.1126/science.1183605.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20489017" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Bacteria/classification/genetics ; Bacterial Proteins/chemistry/genetics ; Biodiversity ; Computational Biology ; Databases, Genetic ; Gastrointestinal Tract/microbiology ; Genes, Bacterial ; Genetic Variation ; Genome, Archaeal ; *Genome, Bacterial ; Humans ; Metagenome/*genetics ; Metagenomics/methods/standards ; Mouth/microbiology ; Peptides/chemistry/genetics ; Phylogeny ; Respiratory System/microbiology ; *Sequence Analysis, DNA/standards ; Skin/microbiology ; Urogenital System/microbiology
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2010-08-07
    Beschreibung: Although practiced clinically for more than 40 years, the use of hematopoietic stem cell (HSC) transplants remains limited by the ability to expand these cells ex vivo. An unbiased screen with primary human HSCs identified a purine derivative, StemRegenin 1 (SR1), that promotes the ex vivo expansion of CD34+ cells. Culture of HSCs with SR1 led to a 50-fold increase in cells expressing CD34 and a 17-fold increase in cells that retain the ability to engraft immunodeficient mice. Mechanistic studies show that SR1 acts by antagonizing the aryl hydrocarbon receptor (AHR). The identification of SR1 and AHR modulation as a means to induce ex vivo HSC expansion should facilitate the clinical use of HSC therapy.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033342/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033342/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boitano, Anthony E -- Wang, Jian -- Romeo, Russell -- Bouchez, Laure C -- Parker, Albert E -- Sutton, Sue E -- Walker, John R -- Flaveny, Colin A -- Perdew, Gary H -- Denison, Michael S -- Schultz, Peter G -- Cooke, Michael P -- ES004869/ES/NIEHS NIH HHS/ -- ES007685/ES/NIEHS NIH HHS/ -- ES04699/ES/NIEHS NIH HHS/ -- P42 ES004699/ES/NIEHS NIH HHS/ -- P42 ES004699-24/ES/NIEHS NIH HHS/ -- R01 ES004869/ES/NIEHS NIH HHS/ -- R01 ES004869-23/ES/NIEHS NIH HHS/ -- R01 ES007685/ES/NIEHS NIH HHS/ -- R01 ES007685-11/ES/NIEHS NIH HHS/ -- New York, N.Y. -- Science. 2010 Sep 10;329(5997):1345-8. doi: 10.1126/science.1191536. Epub 2010 Aug 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20688981" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Animals ; Antigens, CD/analysis ; Antigens, CD34/analysis ; Aryl Hydrocarbon Hydroxylases/genetics/metabolism ; Cell Count ; Cell Lineage ; Cell Proliferation ; Cells, Cultured ; Cytochrome P-450 CYP1B1 ; Cytokines/pharmacology ; Glycoproteins/analysis ; Hematopoiesis ; *Hematopoietic Stem Cell Transplantation ; Hematopoietic Stem Cells/cytology/drug effects/metabolism/*physiology ; Humans ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Multipotent Stem Cells/cytology/drug effects/physiology ; Peptides/analysis ; Purines/*metabolism/*pharmacology ; Receptors, Aryl Hydrocarbon/*antagonists & inhibitors/metabolism ; Signal Transduction ; Small Molecule Libraries ; Species Specificity ; Tetrachlorodibenzodioxin/pharmacology
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2010-10-12
    Beschreibung: Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740384/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740384/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Arensburger, Peter -- Megy, Karine -- Waterhouse, Robert M -- Abrudan, Jenica -- Amedeo, Paolo -- Antelo, Beatriz -- Bartholomay, Lyric -- Bidwell, Shelby -- Caler, Elisabet -- Camara, Francisco -- Campbell, Corey L -- Campbell, Kathryn S -- Casola, Claudio -- Castro, Marta T -- Chandramouliswaran, Ishwar -- Chapman, Sinead B -- Christley, Scott -- Costas, Javier -- Eisenstadt, Eric -- Feschotte, Cedric -- Fraser-Liggett, Claire -- Guigo, Roderic -- Haas, Brian -- Hammond, Martin -- Hansson, Bill S -- Hemingway, Janet -- Hill, Sharon R -- Howarth, Clint -- Ignell, Rickard -- Kennedy, Ryan C -- Kodira, Chinnappa D -- Lobo, Neil F -- Mao, Chunhong -- Mayhew, George -- Michel, Kristin -- Mori, Akio -- Liu, Nannan -- Naveira, Horacio -- Nene, Vishvanath -- Nguyen, Nam -- Pearson, Matthew D -- Pritham, Ellen J -- Puiu, Daniela -- Qi, Yumin -- Ranson, Hilary -- Ribeiro, Jose M C -- Roberston, Hugh M -- Severson, David W -- Shumway, Martin -- Stanke, Mario -- Strausberg, Robert L -- Sun, Cheng -- Sutton, Granger -- Tu, Zhijian Jake -- Tubio, Jose Manuel C -- Unger, Maria F -- Vanlandingham, Dana L -- Vilella, Albert J -- White, Owen -- White, Jared R -- Wondji, Charles S -- Wortman, Jennifer -- Zdobnov, Evgeny M -- Birren, Bruce -- Christensen, Bruce M -- Collins, Frank H -- Cornel, Anthony -- Dimopoulos, George -- Hannick, Linda I -- Higgs, Stephen -- Lanzaro, Gregory C -- Lawson, Daniel -- Lee, Norman H -- Muskavitch, Marc A T -- Raikhel, Alexander S -- Atkinson, Peter W -- HHSN266200400001C/PHS HHS/ -- HHSN266200400039C/AI/NIAID NIH HHS/ -- HHSN266200400039C/PHS HHS/ -- N01-AI-30071/AI/NIAID NIH HHS/ -- N01AI30071/AI/NIAID NIH HHS/ -- ZIA AI000810-13/Intramural NIH HHS/ -- New York, N.Y. -- Science. 2010 Oct 1;330(6000):86-8. doi: 10.1126/science.1191864.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Center for Disease Vector Research, University of California Riverside, Riverside, CA 92521, USA. arensburger@gmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20929810" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Aedes/genetics ; Animals ; Anopheles gambiae/genetics ; Chromosome Mapping ; Chromosomes/*genetics ; Culex/classification/*genetics/physiology ; DNA Transposable Elements ; *Genes, Insect ; *Genome ; Insect Proteins/genetics/physiology ; Insect Vectors/genetics ; Molecular Sequence Data ; Multigene Family ; Phylogeny ; Receptors, Odorant/genetics ; Retroelements ; *Sequence Analysis, DNA
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    Publikationsdatum: 2014-05-17
    Beschreibung: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mengerink, Kathryn J -- Van Dover, Cindy L -- Ardron, Jeff -- Baker, Maria -- Escobar-Briones, Elva -- Gjerde, Kristina -- Koslow, J Anthony -- Ramirez-Llodra, Eva -- Lara-Lopez, Ana -- Squires, Dale -- Sutton, Tracey -- Sweetman, Andrew K -- Levin, Lisa A -- New York, N.Y. -- Science. 2014 May 16;344(6185):696-8. doi: 10.1126/science.1251458.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Environmental Law Institute, Washington, DC 20036, USA. Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, CA 92093-0202, USA. ; Marine Laboratory, Duke University, Beaufort, NC 28516, USA. ; Institute for Advanced Sustainability Studies, Potsdam, Germany. ; National Oceanography Centre, University of Southampton, Southampton, UK. ; Universidad Nacional Autonoma de Mexico, ICML, Mexico. ; Wycliffe Management, 05510 Warsaw, Poland. ; Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, CA 92093-0202, USA. ; Norwegian Institute for Water Research (NIVA), Oslo, Norway. ; Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Australia. ; University of California San Diego, La Jolla, CA 92093, USA. ; Oceanographic Center, College of Oceanography, Nova Southeastern University, Dania Beach, FL 33004, USA. ; International Research Institute of Stavanger, Norway. ; Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, CA 92093-0202, USA. llevin@ucsd.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24833377" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): *Air Pollutants ; Atmosphere ; Biodiversity ; *Carbon Dioxide ; Conservation of Natural Resources/*methods ; Minerals ; Mining ; Oceans and Seas ; *Seawater
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Publikationsdatum: 2014-08-16
    Beschreibung: Seven particles captured by the Stardust Interstellar Dust Collector and returned to Earth for laboratory analysis have features consistent with an origin in the contemporary interstellar dust stream. More than 50 spacecraft debris particles were also identified. The interstellar dust candidates are readily distinguished from debris impacts on the basis of elemental composition and/or impact trajectory. The seven candidate interstellar particles are diverse in elemental composition, crystal structure, and size. The presence of crystalline grains and multiple iron-bearing phases, including sulfide, in some particles indicates that individual interstellar particles diverge from any one representative model of interstellar dust inferred from astronomical observations and theory.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Westphal, Andrew J -- Stroud, Rhonda M -- Bechtel, Hans A -- Brenker, Frank E -- Butterworth, Anna L -- Flynn, George J -- Frank, David R -- Gainsforth, Zack -- Hillier, Jon K -- Postberg, Frank -- Simionovici, Alexandre S -- Sterken, Veerle J -- Nittler, Larry R -- Allen, Carlton -- Anderson, David -- Ansari, Asna -- Bajt, Sasa -- Bastien, Ron K -- Bassim, Nabil -- Bridges, John -- Brownlee, Donald E -- Burchell, Mark -- Burghammer, Manfred -- Changela, Hitesh -- Cloetens, Peter -- Davis, Andrew M -- Doll, Ryan -- Floss, Christine -- Grun, Eberhard -- Heck, Philipp R -- Hoppe, Peter -- Hudson, Bruce -- Huth, Joachim -- Kearsley, Anton -- King, Ashley J -- Lai, Barry -- Leitner, Jan -- Lemelle, Laurence -- Leonard, Ariel -- Leroux, Hugues -- Lettieri, Robert -- Marchant, William -- Ogliore, Ryan -- Ong, Wei Jia -- Price, Mark C -- Sandford, Scott A -- Sans Tresseras, Juan-Angel -- Schmitz, Sylvia -- Schoonjans, Tom -- Schreiber, Kate -- Silversmit, Geert -- Sole, Vicente A -- Srama, Ralf -- Stadermann, Frank -- Stephan, Thomas -- Stodolna, Julien -- Sutton, Stephen -- Trieloff, Mario -- Tsou, Peter -- Tyliszczak, Tolek -- Vekemans, Bart -- Vincze, Laszlo -- Von Korff, Joshua -- Wordsworth, Naomi -- Zevin, Daniel -- Zolensky, Michael E -- 30714 Stardust@home dusters -- New York, N.Y. -- Science. 2014 Aug 15;345(6198):786-91. doi: 10.1126/science.1252496.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Space Sciences Laboratory, University of California at Berkeley, Berkeley, CA, USA. westphal@ssl.berkeley.edu. ; Materials Science and Technology Division, Naval Research Laboratory, Washington, DC, USA. ; Advanced Light Source, Lawrence Berkeley Laboratory, Berkeley, CA, USA. ; Geoscience Institute, Goethe University Frankfurt, Frankfurt, Germany. ; Space Sciences Laboratory, University of California at Berkeley, Berkeley, CA, USA. ; State University of New York at Plattsburgh, Plattsburgh, NY, USA. ; Jacobs Technology/ESCG, NASA Johnson Space Center (JSC), Houston, TX, USA. ; Institut fur Geowissenschaften, University of Heidelberg, Germany. ; Institut des Sciences de la Terre, Observatoire des Sciences de l'Univers de Grenoble, Grenoble, France. ; Institut fur Raumfahrtsysteme (IRS), University of Stuttgart, Stuttgart, Germany. IGEP, TU Braunschweig, Braunschweig, Germany. Max Planck Institut fur Kernphysik, Heidelberg, Germany. International Space Sciences Institute, Bern, Switzerland. ; Carnegie Institution of Washington, Washington, DC, USA. ; Astromaterials Research and Exploration Science, NASA JSC, Houston, TX, USA. ; Field Museum of Natural History, Chicago, IL, USA. ; Deutsches Elektronen-Synchrotron, Hamburg, Germany. ; Space Research Centre, University of Leicester, Leicester, UK. ; Department of Astronomy, University of Washington, Seattle, WA, USA. ; University of Kent, Canterbury, Kent, UK. ; University of Ghent, Ghent, Belgium. ; University of New Mexico. ; European Synchrotron Radiation Facility (ESRF), Grenoble, France. ; University of Chicago, Chicago, IL, USA. ; Washington University, St. Louis, MO, USA. ; Max-Planck-Institut fur Kernphysik, Heidelberg, Germany. ; International Space Sciences Institute, Bern, Switzerland. ; Max-Planck-Institut fur Chemie, Mainz, Germany. ; 615 William Street, Apt 405, Midland, Ontario, Canada. ; Natural History Museum, London, UK. ; Advanced Photon Source, Argonne National Laboratory, Lemont, IL, USA. ; Ecole Normale Superieure de Lyon, Lyon, France. ; University Lille 1, France. ; University of Hawai'i at Manoa, Honolulu, HI, USA. ; NASA Ames Research Center, Moffett Field, CA, USA. ; IRS, University Stuttgart, Stuttgart, Germany. ; Jet Propulsion Laboratory, Pasadena, CA, USA. ; Wexbury, Farthing Green Lane, Stoke Poges, South Buckinghamshire, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25124433" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
  • 7
    Publikationsdatum: 2014-08-01
    Print ISSN: 0966-842X
    Digitale ISSN: 1878-4380
    Thema: Biologie
    Publiziert von Cell Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 2010-11-01
    Print ISSN: 0896-6273
    Digitale ISSN: 1097-4199
    Thema: Biologie , Medizin
    Publiziert von Cell Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
  • 10
    Publikationsdatum: 2014-12-06
    Beschreibung: Immunoglobulin (IG) G-switched chronic lymphocytic leukemia (G-CLL) is highly enriched for 3 stereotyped CLL subsets, utilizing either the IGHV4-34 gene, namely mutated subsets #4 and #16, or the IGHV4-39 gene, namely unmutated subset #8. These subsets, collectively accounting for ~30% of all G-CLL, are not represented within the common IgM/D variant, thus prompting speculations about distinct ontogenetic origin and/or immune triggering, as well as raising questions regarding the timing of class-switch recombination (CSR) in relation to malignant transformation. Considering the above, we sought to investigate the potential existence of B cells expressing clonotypic mu transcripts within the bulk of IgG-switched CLL cells in cases assigned to the aforementioned subsets. Using high-throughput next-generation sequencing (NGS, MiSeq Illumina), we interrogated the IgM+ B-cell repertoire of CLL subset #4 (n=8), subset #16 (n=1) and subset #8 (n=2) for the presence of clonotypic mu transcripts. PCR amplicons were generated from cDNA using a set of IGHV4/IGHM primers. The paired-end Illumina protocol allowed sequencing of the complementarity determining region 3 (CDR3) twice/read, thus increasing the accuracy of results. For 3/8 subset #4 cases multiple blood samples of the same time point were analyzed as reproducibility controls. A purpose-built bioinformatics algorithm was developed for raw NGS data processing, which included: (i) quality filtering of reads; (ii) merging of paired-end reads via local alignment; (iii) preparation of filtered-in fasta sequences for submission to the IMGT/HighV-QUEST tool; and, (iv) IMGT/HighV-QUEST metadata mining for subset-specific B-cell receptor (BcR) IG rearrangements. Subset-specific CDR3 motifs were defined according to established criteria. Overall, 7,125,958 IGHV-IGHD-IGHJ-IGHC rearrangements (189,988-673,835/sample) were included in the search for stereotyped motifs, corresponding to 1,056,967 distinct clonotypes (i.e. BcR IG rearrangements with a particular IGHV gene and amino acid CDR3 sequence) (7,163-123,276/sample, median=76,109). Regarding subset #4, 7/8 cases exhibited mu transcripts of subset #4-specific IG rearrangements ("subset #4 M-clonotypes"); by definition, these rearrangements utilized the IGHV4-34/IGHJ6 genes and had identical CDR3 length (20 amino acids), however their CDR3 amino acid composition varied (2-75 distinct subset #4 M-clonotypes/sample, median=8). In 5/7 cases these subset #4 M-clonotypes were characterized by CDR3s that were identical and/or highly similar (≤2 amino acid differences, ≥ 90% identity) to the CDR3 of the IgG-switched CLL clone. The M-clonotypes expressing CDR3s identical to those of the IgG-switched CLL clone represented the most expanded subset #4 M-clonotype within the sample, while the less expanded, "satellite" clonotypes may represent subclones that were selected against due to lower affinity with the driving antigen. The possibility that these “satellite” clonotypes derive from PCR and/or sequencing error cannot be a priori excluded, however replicate sample analysis produced identical subset #4 M-clonotypes in all cases tested, thus raising confidence in the accuracy of the data. Analysis of the subset #16 case yielded similar results, i.e. 2 subset #16 M-clonotypes, one of which was identical to the IgG-switched clonotypic BcR IG. Both subset #8 cases also carried subset #8 M-clonotypes, yet only one case exhibited an M-clonotype with a CDR3 identical to that of the respective G-CLL clone. Interestingly, this M-clonotype was accompanied by many highly similar, less expanded “satellite” clonotypes (n=109), raising the possibility that SHM may be occurring in (pre-)CLL clones carrying truly unmutated IGHV genes, but pass unnoticed due to negative selection. Although their actual frequency cannot be conclusively determined due to the inherent limitations of PCR-based NGS analysis, subset-specific rearrangements represented a very minor fraction of the sequenced IGHV4/IGHM clonotypes in all cases tested (median frequency 0.04%). Overall, our findings suggest that while CLL clones are primed prior to CSR for malignant transformation on the basis of their BcR IG features, G-CLL quickly transits through CSR either because full-blown malignant transformation occurs at a later time point, or because CSR offers a selective advantage to the malignant clone. Disclosures No relevant conflicts of interest to declare.
    Print ISSN: 0006-4971
    Digitale ISSN: 1528-0020
    Thema: Biologie , Medizin
    Standort Signatur Erwartet Verfügbarkeit
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