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  • 1
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    Ultrafast optical field-ionized gases--A laboratory platform for studying kinetic plasma instabilities (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉Kinetic instabilities arising from anisotropic electron velocity distributions are ubiquitous in ionospheric, cosmic, and terrestrial plasmas, yet there are only a handful of experiments that purport to validate their theory. It is known that optical field ionization of atoms using ultrashort laser pulses can generate plasmas with known anisotropic electron velocity distributions. Here, we show that following the ionization but before collisions thermalize the electrons, the plasma undergoes two-stream, filamentation, and Weibel instabilities that isotropize the electron distributions. The polarization-dependent frequency and growth rates of these kinetic instabilities, measured using Thomson scattering of a probe laser, agree well with the kinetic theory and simulations. Thus, we have demonstrated an easily deployable laboratory platform for studying kinetic instabilities in plasmas.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    A novel strain of cynomolgus macaque cytomegalovirus: implications for host-virus co-evolution (2016)
    BioMed Central
    Details
    Publication Date: 2016-04-06
    Description: Cytomegaloviruses belong to a large, ancient, genus of DNA viruses comprised of a wide array of species-specific strains that occur in diverse array of hosts.
    Electronic ISSN: 1471-2164
    Topics: Biology
    Published by BioMed Central
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  • 3
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    Dynamics of the Development of the Isle au Haut Gabbro-Diorite Layered Complex: Quantitative Implications for Mafic-Silicic Magma Interactions (2011)
    Oxford University Press
    Details
    Publication Date: 2011-11-27
    Description: The Isle au Haut Igneous Complex provides a unique opportunity to examine in detail the in situ physical and chemical interactions between contemporaneously emplaced mafic and silicic magmas. The complex contains a 600 m thick sequence of 11 alternating layers of gabbro and diorite (typically 15–40 m thick). Purely on the basis of density contrasts (2·65 g cm – 3 gabbro vs 2·55 g cm – 3 diorite), the entire system should have undergone wholesale instability and mixing; it is instead arrested in a grossly unstable state of interaction while molten. Chilled margins along the lower contacts of the gabbros and structural integrity of the diorite layers indicate that near-liquidus gabbroic magma invaded partly crystalline, cooler diorite. Mineral assemblages, chemical analyses, and phase equilibria calculations indicate initial temperatures during emplacement of ~1180°C (gabbro) and ~1000°C (diorite). Conductive thermal models yield solidification timescales of 15–60 years for single gabbro layers and about a thousand years for the entire complex. There is ample evidence for two phases of small-scale interfacial Rayleigh–Taylor type instabilities of dioritic melt into the gabbros. Phase I occurred immediately upon gabbro emplacement whereas evenly spaced, slender more silicic pipes represent a much later stage (Phase II). Pipe geometry and spacing, estimated viscosities of the gabbroic magma and silicic melt, and the sudden increase in silica near the upper contact of the diorite, all indicate a thin (~18–53 cm) buoyant layer at the upper contact of the diorite as the source of the pipes. Compaction of the diorite produced this layer over a period of about 10 years. Simultaneous solidification along the lower contact of the overlying gabbro, thickening inwards, increased viscosity enough to arrest pipe ascent after a few meters. Crystal size distribution analyses of the gabbro layers yield crystal growth rates [ G o = (2 – 4) x 10 – 10 cm s – 1 ] and nucleation rates ( J o = 10 –5 –10 –6 cm –3 s –1 ) indicative of conductive cooling coupled with some sluggish convective stirring owing to collapse of the roof-ward gabbro solidification fronts. Were the complex larger, with a much longer solidification time, all this evidence would have been lost, thus suggesting that in larger systems similar processes may commonly take place leaving little direct evidence of their operation apart from the ultimate final petrological product.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
    Published by Oxford University Press
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  • 4
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    Direct visualization of the E. coli Sec translocase engaging precursor proteins in lipid bilayers (2019)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2019
    Description: 〈p〉〈i〉Escherichia coli〈/i〉 exports proteins via a translocase comprising SecA and the translocon, SecYEG. Structural changes of active translocases underlie general secretory system function, yet directly visualizing dynamics has been challenging. We imaged active translocases in lipid bilayers as a function of precursor protein species, nucleotide species, and stage of translocation using atomic force microscopy (AFM). Starting from nearly identical initial states, SecA more readily dissociated from SecYEG when engaged with the precursor of outer membrane protein A as compared to the precursor of galactose-binding protein. For the SecA that remained bound to the translocon, the quaternary structure varied with nucleotide, populating SecA〈sub〉2〈/sub〉 primarily with adenosine diphosphate (ADP) and adenosine triphosphate, and the SecA monomer with the transition state analog ADP-AlF〈sub〉3〈/sub〉. Conformations of translocases exhibited precursor-dependent differences on the AFM imaging time scale. The data, acquired under near-native conditions, suggest that the translocation process varies with precursor species.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 5
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    Disruption of the nuclear membrane by perinuclear inclusions of mutant huntingtin causes cell-cycle re-entry and striatal cell death in mouse and cell models of Huntington's disease (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-26
    Description: Accumulation of N-terminal fragments of mutant huntingtin (mHTT) in the cytoplasm, nuclei and axons of neurons is a hallmark of Huntington's disease (HD), although how these fragments negatively impact neurons remains unclear. We followed the distribution of mHTT in the striata of transgenic R6/2-J2 HD mice as their motor function declined. The fraction of cells with diffuse, perinuclear or intranuclear mHTT changed in parallel with decreasing motor function. In transgenic mice, medium spiny neurons (MSNs) that exhibited perinuclear inclusions expressed cell-cycle markers typically not seen in the striata of normal mice, and these cells are preferentially lost as disease progresses. Electron microscopy reveals that perinuclear inclusions disrupt the nuclear envelope. The progression of perinuclear inclusions being accompanied by cell-cycle activation and culminating in cell death was also observed in 1° cortical neurons. These observations provide a strong correlation between the subcellular location of mHTT, disruption of the nucleus, re-entry into the cell-cycle and eventual neuronal death. They also highlight the fact that the subcellular distribution of mHTT is highly dynamic such that the distribution of mHTT observed depends greatly on the stage of the disease being examined.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Single-molecule observation of nucleotide induced conformational changes in basal SecA-ATP hydrolysis (2018)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2018
    Description: 〈p〉SecA is the critical adenosine triphosphatase that drives preprotein transport through the translocon, SecYEG, in 〈i〉Escherichia coli〈/i〉. This process is thought to be regulated by conformational changes of specific domains of SecA, but real-time, real-space measurement of these changes is lacking. We use single-molecule atomic force microscopy (AFM) to visualize nucleotide-dependent conformations and conformational dynamics of SecA. Distinct topographical populations were observed in the presence of specific nucleotides. AFM investigations during basal adenosine triphosphate (ATP) hydrolysis revealed rapid, reversible transitions between a compact and an extended state at the ~100-ms time scale. A SecA mutant lacking the precursor-binding domain (PBD) aided interpretation. Further, the biochemical activity of SecA prepared for AFM was confirmed by tracking inorganic phosphate release. We conclude that ATP-driven dynamics are largely due to PBD motion but that other segments of SecA contribute to this motion during the transition state of the ATP hydrolysis cycle.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing (2012)
    Nature Publishing Group (NPG)
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    Publication Date: 2012-06-23
    Description: Malaria elimination strategies require surveillance of the parasite population for genetic changes that demand a public health response, such as new forms of drug resistance. Here we describe methods for the large-scale analysis of genetic variation in Plasmodium falciparum by deep sequencing of parasite DNA obtained from the blood of patients with malaria, either directly or after short-term culture. Analysis of 86,158 exonic single nucleotide polymorphisms that passed genotyping quality control in 227 samples from Africa, Asia and Oceania provides genome-wide estimates of allele frequency distribution, population structure and linkage disequilibrium. By comparing the genetic diversity of individual infections with that of the local parasite population, we derive a metric of within-host diversity that is related to the level of inbreeding in the population. An open-access web application has been established for the exploration of regional differences in allele frequency and of highly differentiated loci in the P. falciparum genome.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738909/" 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/PMC3738909/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Manske, Magnus -- Miotto, Olivo -- Campino, Susana -- Auburn, Sarah -- Almagro-Garcia, Jacob -- Maslen, Gareth -- O'Brien, Jack -- Djimde, Abdoulaye -- Doumbo, Ogobara -- Zongo, Issaka -- Ouedraogo, Jean-Bosco -- Michon, Pascal -- Mueller, Ivo -- Siba, Peter -- Nzila, Alexis -- Borrmann, Steffen -- Kiara, Steven M -- Marsh, Kevin -- Jiang, Hongying -- Su, Xin-Zhuan -- Amaratunga, Chanaki -- Fairhurst, Rick -- Socheat, Duong -- Nosten, Francois -- Imwong, Mallika -- White, Nicholas J -- Sanders, Mandy -- Anastasi, Elisa -- Alcock, Dan -- Drury, Eleanor -- Oyola, Samuel -- Quail, Michael A -- Turner, Daniel J -- Ruano-Rubio, Valentin -- Jyothi, Dushyanth -- Amenga-Etego, Lucas -- Hubbart, Christina -- Jeffreys, Anna -- Rowlands, Kate -- Sutherland, Colin -- Roper, Cally -- Mangano, Valentina -- Modiano, David -- Tan, John C -- Ferdig, Michael T -- Amambua-Ngwa, Alfred -- Conway, David J -- Takala-Harrison, Shannon -- Plowe, Christopher V -- Rayner, Julian C -- Rockett, Kirk A -- Clark, Taane G -- Newbold, Chris I -- Berriman, Matthew -- MacInnis, Bronwyn -- Kwiatkowski, Dominic P -- 075491/Z/04/Wellcome Trust/United Kingdom -- 077012/Z/05/Z/Wellcome Trust/United Kingdom -- 082370/Wellcome Trust/United Kingdom -- 089275/Wellcome Trust/United Kingdom -- 090532/Wellcome Trust/United Kingdom -- 090532/Z/09/Z/Wellcome Trust/United Kingdom -- 090770/Wellcome Trust/United Kingdom -- 090770/Z/09/Z/Wellcome Trust/United Kingdom -- 092654/Wellcome Trust/United Kingdom -- 093956/Wellcome Trust/United Kingdom -- 098051/Wellcome Trust/United Kingdom -- 55005502/Howard Hughes Medical Institute/ -- G0600718/Medical Research Council/United Kingdom -- G19/9/Medical Research Council/United Kingdom -- Intramural NIH HHS/ -- England -- Nature. 2012 Jul 19;487(7407):375-9. doi: 10.1038/nature11174.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22722859" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; *Biodiversity ; Genome, Protozoan ; Genotype ; *High-Throughput Nucleotide Sequencing ; Humans ; Malaria, Falciparum/*parasitology ; Phylogeny ; Plasmodium falciparum/classification/*genetics ; Polymorphism, Single Nucleotide ; Principal Component Analysis
    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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  • 8
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    Single-molecule observation of nucleotide induced conformational changes in basal SecA-ATP hydrolysis (2018)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2018-10-25
    Description: SecA is the critical adenosine triphosphatase that drives preprotein transport through the translocon, SecYEG, in Escherichia coli . This process is thought to be regulated by conformational changes of specific domains of SecA, but real-time, real-space measurement of these changes is lacking. We use single-molecule atomic force microscopy (AFM) to visualize nucleotide-dependent conformations and conformational dynamics of SecA. Distinct topographical populations were observed in the presence of specific nucleotides. AFM investigations during basal adenosine triphosphate (ATP) hydrolysis revealed rapid, reversible transitions between a compact and an extended state at the ~100-ms time scale. A SecA mutant lacking the precursor-binding domain (PBD) aided interpretation. Further, the biochemical activity of SecA prepared for AFM was confirmed by tracking inorganic phosphate release. We conclude that ATP-driven dynamics are largely due to PBD motion but that other segments of SecA contribute to this motion during the transition state of the ATP hydrolysis cycle.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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  • 9
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    The selection landscape of malaria parasites (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-05-15
    Description: Malaria parasites have to survive and transmit within a highly selective and ever-changing host environment. Because immunity to malaria is nonsterilizing and builds up slowly through repeated infections, commonly the parasite invades a host that is immunologically and physiologically different from its previous host. During the course of infection, the parasite must also keep pace with changes in host immune responses and red-blood-cell physiology. Here, we describe the "selection landscape" of the most virulent of the human malaria parasites, Plasmodium falciparum, and the adaptive mechanisms it uses to navigate through that landscape. Taking a cost-benefit view of parasite fitness, we consider the evolutionary outcomes of the most important forces of selection operating on the parasite, namely immunity, host death, drugs, mosquito availability, and coinfection. Given the huge potential for malaria parasite evolution in the context of the recently renewed effort to eradicate malaria, a deeper understanding of P. falciparum adaptation is essential.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mackinnon, M J -- Marsh, K -- 077092/Wellcome Trust/United Kingdom -- 088634/Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2010 May 14;328(5980):866-71. doi: 10.1126/science.1185410.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Kenya Medical Research Institute-Wellcome Trust Research Programme, Post Office Box 230, Kilifi, Kenya. mmackinnon@kilifi.kemri-wellcome.org〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20466925" target="_blank"〉PubMed〈/a〉
    Keywords: Adaptation, Physiological ; Animals ; Antigenic Variation ; Antigens, Protozoan/immunology ; Antimalarials/pharmacology ; Culicidae/parasitology ; Drug Resistance ; Genes, Protozoan ; Genetic Fitness ; Genome, Protozoan ; Humans ; Immune Evasion ; Insect Vectors/parasitology ; Malaria, Falciparum/drug therapy/*parasitology/prevention & control/transmission ; Plasmodium falciparum/drug effects/*genetics/immunology/*physiology ; Protozoan Proteins/genetics/immunology ; *Selection, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    A LAIR1 insertion generates broadly reactive antibodies against malaria variant antigens (2015)
    Nature Publishing Group (NPG)
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    Publication Date: 2015-12-25
    Description: Plasmodium falciparum antigens expressed on the surface of infected erythrocytes are important targets of naturally acquired immunity against malaria, but their high number and variability provide the pathogen with a powerful means of escape from host antibodies. Although broadly reactive antibodies against these antigens could be useful as therapeutics and in vaccine design, their identification has proven elusive. Here we report the isolation of human monoclonal antibodies that recognize erythrocytes infected by different P. falciparum isolates and opsonize these cells by binding to members of the RIFIN family. These antibodies acquired broad reactivity through a novel mechanism of insertion of a large DNA fragment between the V and DJ segments. The insert, which is both necessary and sufficient for binding to RIFINs, encodes the entire 98 amino acid collagen-binding domain of LAIR1, an immunoglobulin superfamily inhibitory receptor encoded on chromosome 19. In each of the two donors studied, the antibodies are produced by a single expanded B-cell clone and carry distinct somatic mutations in the LAIR1 domain that abolish binding to collagen and increase binding to infected erythrocytes. These findings illustrate, with a biologically relevant example, a novel mechanism of antibody diversification by interchromosomal DNA transposition and demonstrate the existence of conserved epitopes that may be suitable candidates for the development of a malaria vaccine.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Tan, Joshua -- Pieper, Kathrin -- Piccoli, Luca -- Abdi, Abdirahman -- Foglierini, Mathilde -- Geiger, Roger -- Tully, Claire Maria -- Jarrossay, David -- Ndungu, Francis Maina -- Wambua, Juliana -- Bejon, Philip -- Fregni, Chiara Silacci -- Fernandez-Rodriguez, Blanca -- Barbieri, Sonia -- Bianchi, Siro -- Marsh, Kevin -- Thathy, Vandana -- Corti, Davide -- Sallusto, Federica -- Bull, Peter -- Lanzavecchia, Antonio -- 077092/Wellcome Trust/United Kingdom -- 084113/Z/07/Z/Wellcome Trust/United Kingdom -- 084378/Z/07/A/Wellcome Trust/United Kingdom -- 084535/Wellcome Trust/United Kingdom -- 084538/Wellcome Trust/United Kingdom -- 092654/Wellcome Trust/United Kingdom -- 092741/Wellcome Trust/United Kingdom -- 099811/Wellcome Trust/United Kingdom -- England -- Nature. 2016 Jan 7;529(7584):105-9. doi: 10.1038/nature16450. Epub 2015 Dec 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Research in Biomedicine, Universita della Svizzera Italiana, Via Vincenzo Vela 6, 6500 Bellinzona, Switzerland. ; KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230, 80108 Kilifi, Kenya. ; Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. ; Institute for Microbiology, ETH Zurich, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland. ; Humabs BioMed SA, 6500 Bellinzona, Switzerland.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26700814" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Antibodies, Monoclonal/chemistry/genetics/*immunology/therapeutic use ; *Antibody Specificity ; Antigenic Variation/*immunology ; Antigens, Protozoan/*immunology ; B-Lymphocytes/cytology/immunology ; Clone Cells/cytology/immunology ; Collagen/immunology/metabolism ; Conserved Sequence/immunology ; DNA Transposable Elements/genetics/immunology ; Epitopes, B-Lymphocyte/chemistry/immunology ; Erythrocytes/immunology/metabolism/parasitology ; Humans ; Kenya ; Malaria/*immunology/parasitology ; Malaria Vaccines/chemistry/immunology ; Membrane Proteins/chemistry/immunology ; Molecular Sequence Data ; Mutagenesis, Insertional/*genetics ; Plasmodium falciparum/*immunology ; Protein Structure, Tertiary/genetics ; Protozoan Proteins/chemistry/immunology ; Receptors, Immunologic/chemistry/genetics/*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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