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  • 1
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    Reconstructing the Evolutionary History of Transposable Elements (2013)
    Oxford University Press
    Details
    Publication Date: 2013-01-19
    Description: The impact of transposable elements (TEs) on genome structure, plasticity, and evolution is still not well understood. The recent availability of complete genome sequences makes it possible to get new insights on the evolutionary dynamics of TEs from the phylogenetic analysis of their multiple copies in a wide range of species. However, this source of information is not always fully exploited. Here, we show how the history of transposition activity may be qualitatively and quantitatively reconstructed by considering the distribution of transposition events in the phylogenetic tree, along with the tree topology. Using statistical models developed to infer speciation and extinction rates in species phylogenies, we demonstrate that it is possible to estimate the past transposition rate of a TE family, as well as how this rate varies with time. This methodological framework may not only facilitate the interpretation of genomic data, but also serve as a basis to develop new theoretical and statistical models.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Polymerase {eta}-mediated chemoresistance to cisplatin [Biochemistry] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-05-09
    Description: Cisplatin (cis-diamminedichloroplatinum) and related compounds cause DNA damage and are widely used as anticancer agents. Chemoresistance to cisplatin treatment is due in part to translesion synthesis by human DNA polymerase η (hPol η). Here, we report crystal structures of hPol η complexed with intrastrand cisplatin-1,2–cross-linked DNA, representing four consecutive steps in translesion synthesis. In contrast to the generally enlarged and nondiscriminating active site of Y-family polymerases like Dpo4, Pol η is specialized for efficient bypass of UV–cross-linked pyrimidine dimers. Human Pol η differs from the yeast homolog in its binding of DNA template. To incorporate deoxycytidine opposite cisplatin–cross-linked guanines, hPol η undergoes a specific backbone rearrangement to accommodate the larger base dimer and minimizes the DNA distortion around the lesion. Our structural analyses show why Pol η is inefficient at extending primers after cisplatin lesions, which necessitates a second translesion DNA polymerase to complete bypass in vivo. A hydrophobic pocket near the primer-binding site in human Pol η is identified as a potential drug target for inhibiting translesion synthesis and, thereby, reducing chemoresistance.
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 3
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    Programming the magnitude and persistence of antibody responses with innate immunity (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-02-26
    Description: Many successful vaccines induce persistent antibody responses that can last a lifetime. The mechanisms by which they do so remain unclear, but emerging evidence indicates that they activate dendritic cells via Toll-like receptors (TLRs). For example, the yellow fever vaccine YF-17D, one of the most successful empiric vaccines ever developed, activates dendritic cells via multiple TLRs to stimulate proinflammatory cytokines. Triggering specific combinations of TLRs in dendritic cells can induce synergistic production of cytokines, which results in enhanced T-cell responses, but its impact on antibody responses remain unknown. Learning the critical parameters of innate immunity that program such antibody responses remains a major challenge in vaccinology. Here we demonstrate that immunization of mice with synthetic nanoparticles containing antigens plus ligands that signal through TLR4 and TLR7 induces synergistic increases in antigen-specific, neutralizing antibodies compared to immunization with nanoparticles containing antigens plus a single TLR ligand. Consistent with this there was enhanced persistence of germinal centres and of plasma-cell responses, which persisted in the lymph nodes for 〉1.5 years. Surprisingly, there was no enhancement of the early short-lived plasma-cell response relative to that observed with single TLR ligands. Molecular profiling of activated B cells, isolated 7 days after immunization, indicated that there was early programming towards B-cell memory. Antibody responses were dependent on direct triggering of both TLRs on B cells and dendritic cells, as well as on T-cell help. Immunization protected completely against lethal avian and swine influenza virus strains in mice, and induced robust immunity against pandemic H1N1 influenza in rhesus macaques.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3057367/" 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/PMC3057367/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kasturi, Sudhir Pai -- Skountzou, Ioanna -- Albrecht, Randy A -- Koutsonanos, Dimitrios -- Hua, Tang -- Nakaya, Helder I -- Ravindran, Rajesh -- Stewart, Shelley -- Alam, Munir -- Kwissa, Marcin -- Villinger, Francois -- Murthy, Niren -- Steel, John -- Jacob, Joshy -- Hogan, Robert J -- Garcia-Sastre, Adolfo -- Compans, Richard -- Pulendran, Bali -- HHSN266200700006C/PHS HHS/ -- HHSN266200700010C/PHS HHS/ -- N01 AI50025/AI/NIAID NIH HHS/ -- R01 AI048638/AI/NIAID NIH HHS/ -- R01 AI048638-07/AI/NIAID NIH HHS/ -- R01 AI048638-08/AI/NIAID NIH HHS/ -- R01 DK057665/DK/NIDDK NIH HHS/ -- R01 DK057665-09/DK/NIDDK NIH HHS/ -- R01 DK057665-10/DK/NIDDK NIH HHS/ -- R01 DK057665-11/DK/NIDDK NIH HHS/ -- R01 DK057665-12/DK/NIDDK NIH HHS/ -- R01 DK057665-13/DK/NIDDK NIH HHS/ -- R01DK057665/DK/NIDDK NIH HHS/ -- R37 AI048638/AI/NIAID NIH HHS/ -- R37 AI048638-09A1/AI/NIAID NIH HHS/ -- R37 AI048638-10/AI/NIAID NIH HHS/ -- R37 AI048638-11/AI/NIAID NIH HHS/ -- R37AI48638/AI/NIAID NIH HHS/ -- R56 AI048638/AI/NIAID NIH HHS/ -- R56 AI048638-09/AI/NIAID NIH HHS/ -- U01AI070469/AI/NIAID NIH HHS/ -- U19AI057266/AI/NIAID NIH HHS/ -- U19AI090023/AI/NIAID NIH HHS/ -- U54AI057157/AI/NIAID NIH HHS/ -- U54AI57158/AI/NIAID NIH HHS/ -- England -- Nature. 2011 Feb 24;470(7335):543-7. doi: 10.1038/nature09737.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Emory Vaccine Center, Emory University, Atlanta, Georgia 30329, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21350488" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Antibodies, Neutralizing/biosynthesis/*immunology ; Antibodies, Viral/biosynthesis/*immunology ; Antibody Formation/*immunology ; Dendritic Cells/cytology/immunology ; Hemagglutinin Glycoproteins, Influenza Virus/immunology ; Immunity, Innate/*immunology ; Immunologic Memory/*immunology ; Influenza A Virus, H1N1 Subtype/immunology ; Influenza A Virus, H5N1 Subtype/immunology ; Influenza Vaccines/administration & dosage/*immunology ; Lactic Acid ; Ligands ; Lymph Nodes/cytology/immunology ; Lymphocyte Activation ; Macaca mulatta/immunology/virology ; Mice ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Nanoparticles/administration & dosage ; Plasma Cells/cytology/immunology/metabolism ; Polyglycolic Acid ; T-Lymphocytes/immunology ; Toll-Like Receptors/immunology/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Molecular characterization and functional analysis of daf-16-2b gene in the pine wood nematode, Bursaphelenchus xylophilus (2019)
    Wiley
    Details
    Publication Date: 2019-03-12
    Print ISSN: 1437-4781
    Electronic ISSN: 1439-0329
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Wiley
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  • 5
    Electronic Resource
    Electronic Resource
    Cryopreservation of human semen
    Amsterdam : Elsevier
    Cryobiology 24 (1987), S. 585 
    Details
    ISSN: 0011-2240
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/0011-2240(87)90164-7
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    Paper (German National Licenses)
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  • 6
    Electronic Resource
    Electronic Resource
    Analysis of the tokamak sheath region with in-sheath ionization and transport of surface emitted particles (1994)
    [S.l.] : American Institute of Physics (AIP)
    Physics of Plasmas 1 (1994), S. 3607-3613 
    Details
    ISSN: 1089-7674
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A self-consistent numerical analysis has been performed of the oblique incidence magnetic field tokamak sheath, with in-sheath ionization and transport of surface desorbed and reflected hydrogen molecules and atoms, and sputtered and evaporated surface atoms. The analysis uses the newly developed bphi Monte Carlo/cloud-in-cell kinetic code together with particle–surface interaction models. For typical plasma boundary conditions (Te=100 eV, ne=1×1020 m−3), nearly all desorbed hydrogen molecules are ionized in the sheath; this lowers sheath potential by up to 30% and increases heat transmission by up to 150%. Backscattered hydrogen, and elastic collisions between primary ions and hydrogen molecules, in contrast, have a negligible effect on sheath parameters. The magnetic sheath region has a significant effect on sputtered tungsten atoms, resulting in high local redeposition, but is not itself changed by the sputtering. Ionization of thermally evaporated surface atoms (from overheating) can increase sheath heat transmission significantly, a process which may contribute to surface hot-spot formation.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.870896
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  • 7
    Electronic Resource
    Electronic Resource
    Cyclopeptides from the roots of Pseudostellaria heterophylla
    Amsterdam : Elsevier
    Phytochemistry 32 (1993), S. 1327-1330 
    Details
    ISSN: 0031-9422
    Keywords: Caryophyllaceae ; Pseudostellaria heterophylla ; cyclopeptides ; heterophyllin A, B. ; roots
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/S0031-9422(00)95114-8
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  • 8
    Electronic Resource
    Electronic Resource
    Superconductivity, magnetic susceptibility and thermal relaxation in amorphous CuZr
    Amsterdam : Elsevier
    Solid State Communications 40 (1981), S. 221-224 
    Details
    ISSN: 0038-1098
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0038-1098(81)90744-4
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  • 9
    Electronic Resource
    Electronic Resource
    Magnetic properties of rapidly crystallized Nd-Fe-B glassy alloys
    Amsterdam : Elsevier
    Journal of Magnetism and Magnetic Materials 81 (1989), S. 168-172 
    Details
    ISSN: 0304-8853
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0304-8853(89)90247-3
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  • 10
    Electronic Resource
    Electronic Resource
    A simplified analysis of the dynamic stress-intensity factors for the part-through surface crack in an elastic plate (1990)
    Springer
    Computational mechanics 5 (1990), S. 469-478 
    Details
    ISSN: 1432-0924
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Line-spring model was used for the simplified analysis of dynamic stress-intensity factor for part-through surface crack. Methods were presented for both evaluation of dynamic compliance of the line-spring and of dynamic stress-intensity factor along the crack front. It was found that the value of the dynamic compliance coefficient of the line-spring does not vary with the frequency of applied load and is good agreement with the analytical result given by Rice and Levy under static load conditions. To verify the validity of the present model, the dynamic stress-intensity factors were calculated for edge cracked strips in plane strain. The results obtained from the present model coincide with those obtained from the finite element analysis using quarter-point singularity elements around the crack tip. As an example of the application of the present model, the dynamic response of a plate containing a semi-elliptical surface crack was analysed where the plate is subjected to a vibrating stress at its ends.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01113450
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