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  • 1
    Publication Date: 2000-12-16
    Description: This report presents full-genome evidence that bacterial cells use discrete transcription patterns to control cell cycle progression. Global transcription analysis of synchronized Caulobacter crescentus cells was used to identify 553 genes (19% of the genome) whose messenger RNA levels varied as a function of the cell cycle. We conclude that in bacteria, as in yeast, (i) genes involved in a given cell function are activated at the time of execution of that function, (ii) genes encoding proteins that function in complexes are coexpressed, and (iii) temporal cascades of gene expression control multiprotein structure biogenesis. A single regulatory factor, the CtrA member of the two-component signal transduction family, is directly or indirectly involved in the control of 26% of the cell cycle-regulated genes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Laub, M T -- McAdams, H H -- Feldblyum, T -- Fraser, C M -- Shapiro, L -- GM32506/GM/NIGMS NIH HHS/ -- GM51426/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2000 Dec 15;290(5499):2144-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Developmental Biology, Beckman Center, Stanford University School of Medicine, Stanford, CA 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11118148" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/genetics/metabolism ; Binding Sites ; Caulobacter crescentus/*cytology/*genetics/growth & development/physiology ; Cell Cycle/*genetics ; Chemotaxis/genetics ; *DNA-Binding Proteins ; DNA-Directed RNA Polymerases/genetics ; Fimbriae Proteins ; Flagella/metabolism ; Gene Expression Profiling ; *Gene Expression Regulation, Bacterial ; Interphase ; Membrane Proteins/genetics ; Oligonucleotide Array Sequence Analysis ; RNA, Bacterial/genetics/metabolism ; RNA, Messenger/genetics/metabolism ; S Phase ; Signal Transduction ; *Transcription Factors ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2002-04-20
    Description: Cadherins are transmembrane proteins that mediate adhesion between cells in the solid tissues of animals. Here we present the 3.1 angstrom resolution crystal structure of the whole, functional extracellular domain from C-cadherin, a representative "classical" cadherin. The structure suggests a molecular mechanism for adhesion between cells by classical cadherins, and it provides a new framework for understanding both cis (same cell) and trans (juxtaposed cell) cadherin interactions. The trans adhesive interface is a twofold symmetric interaction defined by a conserved tryptophan side chain at the membrane-distal end of a cadherin molecule from one cell, which inserts into a hydrophobic pocket at the membrane-distal end of a cadherin molecule from the opposing cell.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boggon, Titus J -- Murray, John -- Chappuis-Flament, Sophie -- Wong, Ellen -- Gumbiner, Barry M -- Shapiro, Lawrence -- NCI-P30-CA-08784/CI/NCPDCID CDC HHS/ -- R01 GM062270/GM/NIGMS NIH HHS/ -- R01 GM52717/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 May 17;296(5571):1308-13. Epub 2002 Apr 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, Columbia University College of Physicians and Surgeons, 630 West 168th Street, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11964443" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Binding Sites ; CHO Cells ; Cadherins/*chemistry/genetics/metabolism ; *Cell Adhesion ; Cricetinae ; Crystallography, X-Ray ; Dimerization ; Glycosylation ; Hydrogen Bonding ; Models, Molecular ; Molecular Sequence Data ; Protein Structure, Tertiary ; Recombinant Fusion Proteins/chemistry ; Tryptophan/chemistry ; Xenopus Proteins
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    Electronic ISSN: 1095-9203
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  • 3
    Publication Date: 1999-12-11
    Description: Tubby-like proteins (TULPs) are found in a broad range of multicellular organisms. In mammals, genetic mutation of tubby or other TULPs can result in one or more of three disease phenotypes: obesity (from which the name "tubby" is derived), retinal degeneration, and hearing loss. These disease phenotypes indicate a vital role for tubby proteins; however, no biochemical function has yet been ascribed to any member of this protein family. A structure-directed approach was employed to investigate the biological function of these proteins. The crystal structure of the core domain from mouse tubby was determined at a resolution of 1.9 angstroms. From primarily structural clues, experiments were devised, the results of which suggest that TULPs are a unique family of bipartite transcription factors.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Boggon, T J -- Shan, W S -- Santagata, S -- Myers, S C -- Shapiro, L -- New York, N.Y. -- Science. 1999 Dec 10;286(5447):2119-25.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Structural Biology Program, Department of Physiology and Biophysics, Ruttenberg Cancer Center, Mount Sinai School of Medicine of New York University, New York, NY 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10591637" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptor Proteins, Signal Transducing ; Alternative Splicing ; Amino Acid Sequence ; Animals ; Cell Line ; Cell Nucleus/chemistry ; Crystallography, X-Ray ; DNA/metabolism ; Eye Proteins/*chemistry/genetics/*metabolism ; Humans ; Models, Molecular ; Molecular Sequence Data ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Proteins/*chemistry/genetics/*metabolism ; Recombinant Proteins/chemistry/metabolism ; Sequence Alignment ; Transcription Factors/*chemistry/genetics/*metabolism ; Transcriptional Activation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
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  • 4
    Publication Date: 2001-05-26
    Description: Dysfunction of the tubby protein results in maturity-onset obesity in mice. Tubby has been implicated as a transcription regulator, but details of the molecular mechanism underlying its function remain unclear. Here we show that tubby functions in signal transduction from heterotrimeric GTP-binding protein (G protein)-coupled receptors. Tubby localizes to the plasma membrane by binding phosphatidylinositol 4,5-bisphosphate through its carboxyl terminal "tubby domain." X-ray crystallography reveals the atomic-level basis of this interaction and implicates tubby domains as phosphorylated-phosphatidyl- inositol binding factors. Receptor-mediated activation of G protein alphaq (Galphaq) releases tubby from the plasma membrane through the action of phospholipase C-beta, triggering translocation of tubby to the cell nucleus. The localization of tubby-like protein 3 (TULP3) is similarly regulated. These data suggest that tubby proteins function as membrane-bound transcription regulators that translocate to the nucleus in response to phosphoinositide hydrolysis, providing a direct link between G-protein signaling and the regulation of gene expression.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Santagata, S -- Boggon, T J -- Baird, C L -- Gomez, C A -- Zhao, J -- Shan, W S -- Myszka, D G -- Shapiro, L -- New York, N.Y. -- Science. 2001 Jun 15;292(5524):2041-50. Epub 2001 May 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ruttenberg Cancer Center, Structural Biology Program, Department of Physiology and Biophysics, Mount Sinai School of Medicine of New York University, 1425 Madison Avenue New York, NY 10029, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11375483" target="_blank"〉PubMed〈/a〉
    Keywords: Active Transport, Cell Nucleus ; Adaptor Proteins, Signal Transducing ; Amino Acid Sequence ; Animals ; Cell Membrane/metabolism ; Cell Nucleus/*metabolism ; Cells, Cultured ; Crystallography, X-Ray ; GTP-Binding Protein alpha Subunits, Gq-G11 ; Gene Expression Regulation ; Heterotrimeric GTP-Binding Proteins/*metabolism ; Humans ; Isoenzymes/*metabolism ; Membrane Lipids/metabolism ; Mice ; Models, Biological ; Molecular Sequence Data ; Nuclear Localization Signals ; Obesity/genetics/metabolism ; Phosphatidylinositol 4,5-Diphosphate/*metabolism ; Phosphatidylinositol Phosphates/metabolism ; Phospholipase C beta ; Phosphorylation ; Protein Structure, Tertiary ; Proteins/chemistry/genetics/*metabolism ; Receptor, Serotonin, 5-HT2C ; Receptors, Muscarinic/metabolism ; Receptors, Serotonin/metabolism ; Recombinant Fusion Proteins/metabolism ; *Signal Transduction ; Transcription Factors/chemistry/genetics/*metabolism ; Type C Phospholipases/*metabolism
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    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2002-12-10
    Description: Bacteria are often highly polarized, exhibiting specialized structures at or near the ends of the cell. Among such structures are actin-organizing centers, which mediate the movement of certain pathogenic bacteria within the cytoplasm of an animal host cell; organized arrays of membrane receptors, which govern chemosensory behavior in swimming bacteria; and asymmetrically positioned septa, which generate specialized progeny in differentiating bacteria. This polarization is orchestrated by complex and dynamic changes in the subcellular localization of signal transduction and cytoskeleton proteins as well as of specific regions of the chromosome. Recent work has provided information on how dynamic subcellular localization occurs and how it is exploited by the bacterial cell. The main task of a bacterial cell is to survive and duplicate itself. The bacterium must replicate its genetic material and divide at the correct site in the cell and at the correct time in the cell cycle with high precision. Each kind of bacterium also executes its own strategy to find nutrients in its habitat and to cope with conditions of stress from its environment. This involves moving toward food, adapting to environmental extremes, and, in many cases, entering and exploiting a eukaryotic host. These activities often involve processes that take place at or near the poles of the cell. Here we explore some of the schemes bacteria use to orchestrate dynamic changes at their poles and how these polar events execute cellular functions. In spite of their small size, bacteria have a remarkably complex internal organization and external architecture. Bacterial cells are inherently asymmetric, some more obviously so than others. The most easily recognized asymmetries involve surface structures, e.g., flagella, pili, and stalks that are preferentially assembled at one pole by many bacteria. "New" poles generated at the cell division plane differ from old poles from the previous round of cell division. Even in Escherichia coli, which is generally thought to be symmetrical, old poles are more static than new poles with respect to cell wall assembly (1), and they differ in the deposition of phospholipid domains (2). There are many instances of differential polar functions; among these is the preferential use of old poles when attaching to host cells as in the interaction of Bradyrhizobium with plant root hairs (3) or the polar pili-mediated attachment of the Pseudomonas aeruginosa pathogen to tracheal epithelia (4). An unusual polar organelle that mediates directed motility on solid surfaces is found in the nonpathogenic bacterium Myxococcus xanthus. The gliding motility of this bacterium is propelled by a nozzle-like structure that squirts a polysaccharide-containing slime from the pole of the cell (5). Interestingly, M. xanthus, which has nozzles at both poles, can reverse direction by closing one nozzle and opening the other in response to end-to-end interactions between cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shapiro, Lucy -- McAdams, Harley H -- Losick, Richard -- GM18568/GM/NIGMS NIH HHS/ -- GM32506/GM/NIGMS NIH HHS/ -- GM51426/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 6;298(5600):1942-6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Developmental Biology, Stanford University School of Medicine, B300 Beckman Center, Stanford, CA 94305, USA. shapiro@cmgm.stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12471245" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/cytology/physiology ; Bacteria/cytology/metabolism/pathogenicity ; *Bacterial Physiological Phenomena ; Bacterial Proteins/*physiology ; Cell Division ; *Cell Polarity ; Chemotaxis ; Chromosomes, Bacterial/metabolism ; Cytoskeleton/metabolism ; Diffusion ; Replication Origin ; Signal Transduction ; Spores, Bacterial/physiology
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  • 6
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1998-12-29
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Losick, R -- Shapiro, L -- New York, N.Y. -- Science. 1998 Nov 20;282(5393):1430-1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. losick@biosun.harvard.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9867650" target="_blank"〉PubMed〈/a〉
    Keywords: Bacillus subtilis/growth & development/*metabolism ; Cell Nucleus/metabolism ; Chromosomes/metabolism ; Chromosomes, Bacterial/*metabolism ; *DNA Replication ; DNA, Bacterial/*biosynthesis ; DNA-Directed DNA Polymerase/*analysis/metabolism ; Models, Biological ; Recombinant Fusion Proteins/metabolism ; *Replication Origin
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  • 7
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 1990-04-13
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shapiro, J L -- New York, N.Y. -- Science. 1990 Apr 13;248(4952):145-6.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17740118" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
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  • 8
    Publication Date: 2007-02-10
    Description: The 5'-AMP (adenosine monophosphate)-activated protein kinase (AMPK) coordinates metabolic function with energy availability by responding to changes in intracellular ATP (adenosine triphosphate) and AMP concentrations. Here, we report crystal structures at 2.9 and 2.6 A resolution for ATP- and AMP-bound forms of a core alphabetagamma adenylate-binding domain from the fission yeast AMPK homolog. ATP and AMP bind competitively to a single site in the gamma subunit, with their respective phosphate groups positioned near function-impairing mutants. Unexpectedly, ATP binds without counterions, amplifying its electrostatic effects on a critical regulatory region where all three subunits converge.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Townley, Robert -- Shapiro, Lawrence -- New York, N.Y. -- Science. 2007 Mar 23;315(5819):1726-9. Epub 2007 Feb 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17289942" target="_blank"〉PubMed〈/a〉
    Keywords: AMP-Activated Protein Kinases ; Adenosine Monophosphate/metabolism ; Adenosine Triphosphate/metabolism ; Amino Acid Sequence ; Binding Sites ; Binding, Competitive ; Crystallization ; Crystallography, X-Ray ; Dimerization ; Hydrogen Bonding ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Protein Kinases/*chemistry/metabolism ; Protein Structure, Quaternary ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Protein-Serine-Threonine Kinases/*chemistry/metabolism ; Schizosaccharomyces/*enzymology
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    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 9
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2009-12-08
    Description: Despite their small size, bacteria have a remarkably intricate internal organization. Bacteria deploy proteins and protein complexes to particular locations and do so in a dynamic manner in lockstep with the organized deployment of their chromosome. The dynamic subcellular localization of protein complexes is an integral feature of regulatory processes of bacterial cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Shapiro, L -- McAdams, H H -- Losick, R -- GM07311/GM/NIGMS NIH HHS/ -- GM18568/GM/NIGMS NIH HHS/ -- GM325062/GM/NIGMS NIH HHS/ -- GM51426/GM/NIGMS NIH HHS/ -- R01 GM018568/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2009 Nov 27;326(5957):1225-8. doi: 10.1126/science.1175685.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA. shapiro@stanford.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19965466" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/cytology/*metabolism/ultrastructure ; Bacterial Proteins/*metabolism ; Cell Division ; Cell Membrane/physiology/ultrastructure ; Chemotaxis ; Chromosomes, Bacterial/physiology ; Diffusion ; Intracellular Space/metabolism ; Protein Binding
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  • 10
    Publication Date: 2011-08-13
    Description: Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution of antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3516815/" 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/PMC3516815/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wu, Xueling -- Zhou, Tongqing -- Zhu, Jiang -- Zhang, Baoshan -- Georgiev, Ivelin -- Wang, Charlene -- Chen, Xuejun -- Longo, Nancy S -- Louder, Mark -- McKee, Krisha -- O'Dell, Sijy -- Perfetto, Stephen -- Schmidt, Stephen D -- Shi, Wei -- Wu, Lan -- Yang, Yongping -- Yang, Zhi-Yong -- Yang, Zhongjia -- Zhang, Zhenhai -- Bonsignori, Mattia -- Crump, John A -- Kapiga, Saidi H -- Sam, Noel E -- Haynes, Barton F -- Simek, Melissa -- Burton, Dennis R -- Koff, Wayne C -- Doria-Rose, Nicole A -- Connors, Mark -- NISC Comparative Sequencing Program -- Mullikin, James C -- Nabel, Gary J -- Roederer, Mario -- Shapiro, Lawrence -- Kwong, Peter D -- Mascola, John R -- 5U19 AI 067854-06/AI/NIAID NIH HHS/ -- R01 AI033292/AI/NIAID NIH HHS/ -- U19 AI067854/AI/NIAID NIH HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2011 Sep 16;333(6049):1593-602. doi: 10.1126/science.1207532. Epub 2011 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Vaccine Research Center, National Institutes of Health, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21835983" target="_blank"〉PubMed〈/a〉
    Keywords: AIDS Vaccines ; Amino Acid Sequence ; Antibodies, Neutralizing/*chemistry/genetics/*immunology/isolation & purification ; Antibody Affinity ; Antibody Specificity ; Antigens, CD4/metabolism ; Base Sequence ; Binding Sites ; Binding Sites, Antibody ; Complementarity Determining Regions/genetics ; Crystallography, X-Ray ; Epitopes ; *Evolution, Molecular ; Genes, Immunoglobulin Heavy Chain ; HIV Antibodies/*chemistry/genetics/*immunology/isolation & purification ; HIV Envelope Protein gp120/chemistry/*immunology/metabolism ; HIV Infections/immunology ; HIV-1/chemistry/*immunology ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulin Fab Fragments/chemistry/immunology ; Immunoglobulin Heavy Chains/chemistry/immunology ; Immunoglobulin J-Chains/genetics ; Immunoglobulin Light Chains/chemistry/immunology ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Sequence Analysis, DNA
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