Genome-wide signals of positive selection in human evolution

PubMed Central

Enard, David; Messer, Philipp W.; Petrov, Dmitri A.

2014-01-01

The role of positive selection in human evolution remains controversial. On the one hand, scans for positive selection have identified hundreds of candidate loci, and the genome-wide patterns of polymorphism show signatures consistent with frequent positive selection. On the other hand, recent studies have argued that many of the candidate loci are false positives and that most genome-wide signatures of adaptation are in fact due to reduction of neutral diversity by linked deleterious mutations, known as background selection. Here we analyze human polymorphism data from the 1000 Genomes Project and detect signatures of positive selection once we correct for the effects of background selection. We show that levels of neutral polymorphism are lower near amino acid substitutions, with the strongest reduction observed specifically near functionally consequential amino acid substitutions. Furthermore, amino acid substitutions are associated with signatures of recent adaptation that should not be generated by background selection, such as unusually long and frequent haplotypes and specific distortions in the site frequency spectrum. We use forward simulations to argue that the observed signatures require a high rate of strongly adaptive substitutions near amino acid changes. We further demonstrate that the observed signatures of positive selection correlate better with the presence of regulatory sequences, as predicted by the ENCODE Project Consortium, than with the positions of amino acid substitutions. Our results suggest that adaptation was frequent in human evolution and provide support for the hypothesis of King and Wilson that adaptive divergence is primarily driven by regulatory changes. PMID:24619126

Solar cycle evolution of solar wind speed structure between 1973 and 1985 observed with the interplanetary scintillation method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kojima, M.; Kakinuma, T.

1987-07-01

The solar cycle evolution of solar wind speed structure was studied for the years from 1973 to 1985 on a basis of interplanetary scintillation observations using a new method for mapping solar wind speed to the source surface. The major minimum-speed regions are distributed along a neutral line through the whole period of a solar cycle: when solar activity is low, they are distributed on the wavy neutral line along the solar equator; in the active phase they also tend to be distributed along the neutral line, which has a large latitudinal amplitude. The minimum-speed regions tend to be distributedmore » not only along the neutral line but also at low magnetic intensity regions and/or coronal bright regions which do not correspond to the neutral line. As the polar high-speed regions extend equatorward around the minimum phase, the latitudinal gradient of speed increases at the boundaries of the low-speed region, and the width of the low-speed region decreases. One or two years before the minimum of solar activity, two localized minimum-speed regions appear on the neutral line, and their locations are longitudinally separated by 180. copyright American Geophysical Union 1987« less

Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans.

PubMed

Rand, D M; Kann, L M

1996-07-01

Recent studies of mitochondrial DNA (mtDNA) variation in mammals and Drosophila have shown an excess of amino acid variation within species (replacement polymorphism) relative to the number of silent and replacement differences fixed between species. To examine further this pattern of nonneutral mtDNA evolution, we present sequence data for the ND3 and ND5 genes from 59 lines of Drosophila melanogaster and 29 lines of D. simulans. Of interest are the frequency spectra of silent and replacement polymorphisms, and potential variation among genes and taxa in the departures from neutral expectations. The Drosophila ND3 and ND5 data show no significant excess of replacement polymorphism using the McDonald-Kreitman test. These data are in contrast to significant departures from neutrality for the ND3 gene in mammals and other genes in Drosophila mtDNA (cytochrome b and ATPase 6). Pooled across genes, however, both Drosophila and human mtDNA show very significant excesses of amino acid polymorphism. Silent polymorphisms at ND5 show a significantly higher variance in frequency than replacement polymorphisms, and the latter show a significant skew toward low frequencies (Tajima's D = -1.954). These patterns are interpreted in light of the nearly neutral theory where mildly deleterious amino acid haplotypes are observed as ephemeral variants within species but do not contribute to divergence. The patterns of polymorphism and divergence at charge-altering amino acid sites are presented for the Drosophila ND5 gene to examine the evolution of functionally distinct mutations. Excess charge-altering polymorphism is observed at the carboxyl terminal and excess charge-altering divergence is detected at the amino terminal. While the mildly deleterious model fits as a net effect in the evolution of nonrecombining mitochondrial genomes, these data suggest that opposing evolutionary pressures may act on different regions of mitochondrial genes and genomes.

Evolution of the human immunodeficiency virus type 2 envelope in the first years of infection is associated with the dynamics of the neutralizing antibody response

DOE PAGES

Rocha, Cheila; Calado, Rita; Borrego, Pedro; ...

2013-10-24

Background: therapy and the majority of HIV-2 infected individuals survive as elite controllers with normal CD4 + T cell counts and low or undetectable plasma viral load. Neutralizing antibodies (Nabs) are thought to play a central role in HIV-2 evolution and pathogenesis. However, the dynamic of the Nab response and resulting HIV-2 escape during acute infection and their impact in HIV-2 evolution and disease progression remain largely unknown. Our objective was to characterize the Nab response and the molecular and phenotypic evolution of HIV-2 in association with Nab escape in the first years of infection in two children infected atmore » birth. As a result, CD4 + T cells decreased from about 50% to below 30% in both children in the first five years of infection and the infecting R5 viruses were replaced by X4 viruses within the same period. With antiretroviral therapy, viral load in child 1 decreased to undetectable levels and CD4 + T cells recovered to normal levels, which have been sustained at least until the age of 12. In contrast, viral load increased in child 2 and she progressed to AIDS and death at age 9. Beginning in the first year of life, child 1 raised high titers of antibodies that neutralized primary R5 isolates more effectively than X4 isolates, both autologous and heterologous. Child 2 raised a weak X4-specific Nab response that decreased sharply as disease progressed. Rate of evolution, nucleotide and amino acid diversity, and positive selection, were significantly higher in the envelope of child 1 compared to child 2. Rates of R5-to-X4 tropism switch, of V1 and V3 sequence diversification, and of convergence of V3 to a β-hairpin structure were related with rate of escape from the neutralizing antibodies. Finally, our data suggests that the molecular and phenotypic evolution of the human immunodeficiency virus type 2 envelope are related with the dynamics of the neutralizing antibody response providing further support for a model in which Nabs play an important role in HIV-2 pathogenesis.« less

Evolution of the human immunodeficiency virus type 2 envelope in the first years of infection is associated with the dynamics of the neutralizing antibody response

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rocha, Cheila; Calado, Rita; Borrego, Pedro

Background: therapy and the majority of HIV-2 infected individuals survive as elite controllers with normal CD4 + T cell counts and low or undetectable plasma viral load. Neutralizing antibodies (Nabs) are thought to play a central role in HIV-2 evolution and pathogenesis. However, the dynamic of the Nab response and resulting HIV-2 escape during acute infection and their impact in HIV-2 evolution and disease progression remain largely unknown. Our objective was to characterize the Nab response and the molecular and phenotypic evolution of HIV-2 in association with Nab escape in the first years of infection in two children infected atmore » birth. As a result, CD4 + T cells decreased from about 50% to below 30% in both children in the first five years of infection and the infecting R5 viruses were replaced by X4 viruses within the same period. With antiretroviral therapy, viral load in child 1 decreased to undetectable levels and CD4 + T cells recovered to normal levels, which have been sustained at least until the age of 12. In contrast, viral load increased in child 2 and she progressed to AIDS and death at age 9. Beginning in the first year of life, child 1 raised high titers of antibodies that neutralized primary R5 isolates more effectively than X4 isolates, both autologous and heterologous. Child 2 raised a weak X4-specific Nab response that decreased sharply as disease progressed. Rate of evolution, nucleotide and amino acid diversity, and positive selection, were significantly higher in the envelope of child 1 compared to child 2. Rates of R5-to-X4 tropism switch, of V1 and V3 sequence diversification, and of convergence of V3 to a β-hairpin structure were related with rate of escape from the neutralizing antibodies. Finally, our data suggests that the molecular and phenotypic evolution of the human immunodeficiency virus type 2 envelope are related with the dynamics of the neutralizing antibody response providing further support for a model in which Nabs play an important role in HIV-2 pathogenesis.« less

Forward jet and particle production at HERA

NASA Astrophysics Data System (ADS)

Adloff, C.; Anderson, M.; Andreev, V.; Andrieu, B.; Arkadov, V.; Arndt, C.; Ayyaz, I.; Babaev, A.; Bähr, J.; Bán, J.; Baranov, P.; Barrelet, E.; Bartel, W.; Bassler, U.; Bate, P.; Beck, M.; Beglarian, A.; Behnke, O.; Behrend, H.-J.; Beier, C.; Belousov, A.; Berger, Ch.; Bernardi, G.; Bertrand-Coremans, G.; Biddulph, P.; Bizot, J. C.; Boudry, V.; Braunschweig, W.; Brisson, V.; Brown, D. P.; Brückner, W.; Bruel, P.; Bruncko, D.; Bürger, J.; Büsser, F. W.; Buniatian, A.; Burke, S.; Buschhorn, G.; Calvet, D.; Campbell, A. J.; Carli, T.; Chabert, E.; Charlet, M.; Clarke, D.; Clerbaux, B.; Cocks, S.; Contreras, J. G.; Cormack, C.; Coughlan, J. A.; Cousinou, M.-C.; Cox, B. E.; Cozzika, G.; Cvach, J.; Dainton, J. B.; Dau, W. D.; Daum, K.; David, M.; Davidsson, M.; De Roeck, A.; De Wolf, E. A.; Delcourt, B.; Demirchyan, R.; Diaconu, C.; Dirkmann, M.; Dixon, P.; Dlugosz, W.; Donovan, K. T.; Dowell, J. D.; Droutskoi, A.; Ebert, J.; Eckerlin, G.; Eckstein, D.; Efremenko, V.; Egli, S.; Eichler, R.; Eisele, F.; Eisenhandler, E.; Elsen, E.; Enzenberger, M.; Erdmann, M.; Fahr, A. B.; Favart, L.; Fedotov, A.; Felst, R.; Feltesse, J.; Ferencei, J.; Ferrarotto, F.; Fleischer, M.; Flügge, G.; Fomenko, A.; Formánek, J.; Foster, J. M.; Franke, G.; Gabathuler, E.; Gabathuler, K.; Gaede, F.; Garvey, J.; Gayler, J.; Gerhards, R.; Ghazaryan, S.; Glazov, A.; Goerlich, L.; Gogitidze, N.; Goldberg, M.; Gorelov, I.; Grab, C.; Grässler, H.; Greenshaw, T.; Griffiths, R. K.; Grindhammer, G.; Hadig, T.; Haidt, D.; Hajduk, L.; Haller, T.; Hampel, M.; Haustein, V.; Haynes, W. J.; Heinemann, B.; Heinzelmann, G.; Henderson, R. C. W.; Hengstmann, S.; Henschel, H.; Heremans, R.; Herynek, I.; Hewitt, K.; Hiller, K. H.; Hilton, C. D.; Hladký, J.; Hoffmann, D.; Holtom, T.; Horisberger, R.; Hudgson, V. L.; Hurling, S.; Ibbotson, M.; İşsever, Ç.; Itterbeck, H.; Jacquet, M.; Jaffre, M.; Jansen, D. M.; Jönsson, L.; Johnson, D. P.; Jung, H.; Kästli, H. K.; Kander, M.; Kant, D.; Kapichine, M.; Karlsson, M.; Karschnik, O.; Katzy, J.; Kaufmann, O.; Kausch, M.; Kenyon, I. R.; Kermiche, S.; Keuker, C.; Kiesling, C.; Klein, M.; Kleinwort, C.; Knies, G.; Köhne, J. H.; Kolanoski, H.; Kolya, S. D.; Korbel, V.; Kostka, P.; Kotelnikov, S. K.; Krämerkämper, T.; Krasny, M. W.; Krehbiel, H.; Krücker, D.; Krüger, K.; Küpper, A.; Küster, H.; Kuhlen, M.; Kurča, T.; Laforge, B.; Lahmann, R.; Landon, M. P. J.; Lange, W.; Langenegger, U.; Lebedev, A.; Lehner, F.; Lemaitre, V.; Lendermann, V.; Levonian, S.; Lindstroem, M.; List, B.; Lobo, G.; Lobodzinska, E.; Lubimov, V.; Lüke, D.; Lytkin, L.; Magnussen, N.; Mahlke-Krüger, H.; Malinovski, E.; Maraček, R.; Marage, P.; Marks, J.; Marshall, R.; Martin, G.; Martyn, H.-U.; Martyniak, J.; Maxfield, S. J.; McMahon, S. J.; McMahon, T. R.; Mehta, A.; Meier, K.; Merkel, P.; Metlica, F.; Meyer, A.; Meyer, A.; Meyer, H.; Meyer, J.; Meyer, P.-O.; Mikochi, S.; Milstead, D.; Moeck, J.; Mohr, R.; Mohrdieck, S.; Moreau, F.; Morris, J. V.; Müller, D.; Müller, K.; Murín, P.; Nagovizin, V.; Naroska, B.; Naumann, Th.; Négri, I.; Newman, P. R.; Nguyen, H. K.; Nicholls, T. C.; Niebergall, F.; Niebuhr, C.; Niedzballa, Ch.; Niggli, H.; Nikitin, D.; Nix, O.; Nowak, G.; Nunnemann, T.; Oberlack, H.; Olsson, J. E.; Ozerov, D.; Palmen, P.; Panassik, V.; Pascaud, C.; Passaggio, S.; Patel, G. D.; Pawletta, H.; Perez, E.; Phillips, J. P.; Pieuchot, A.; Pitzl, D.; Pöschl, R.; Pope, G.; Povh, B.; Rabbertz, K.; Rauschenberger, J.; Reimer, P.; Reisert, B.; Rick, H.; Riess, S.; Rizvi, E.; Robmann, P.; Roosen, R.; Rosenbauer, K.; Rostovtsev, A.; Rouse, F.; Royon, C.; Rusakov, S.; Rybicki, K.; Sankey, D. P. C.; Schacht, P.; Scheins, J.; Schleif, S.; Schleper, P.; Schmidt, D.; Schmidt, D.; Schoeffel, L.; Schröder, V.; Schultz-Coulon, H.-C.; Schwab, B.; Sefkow, F.; Semenov, A.; Shekelyan, V.; Sheviakov, I.; Shtarkov, L. N.; Siegmon, G.; Sirois, Y.; Sloan, T.; Smirnov, P.; Smith, M.; Solochenko, V.; Soloviev, Y.; Spaskov, V.; Specka, A.; Spiekermann, J.; Spitzer, H.; Squinabol, F.; Steffen, P.; Steinberg, R.; Steinhart, J.; Stella, B.; Stellberger, A.; Stiewe, J.; Straumann, U.; Struczinski, W.; Sutton, J. P.; Swart, M.; Tapprogge, S.; Taševský, M.; Tchernyshov, V.; Tchetchelnitski, S.; Theissen, J.; Thompson, G.; Thompson, P. D.; Tobien, N.; Todenhagen, R.; Truöl, P.; Tsipolitis, G.; Turnau, J.; Tzamariudaki, E.; Udluft, S.; Usik, A.; Valkár, S.; Valkárová, A.; Vallée, C.; Van Esch, P.; Van Haecke, A.; Van Mechelen, P.; Vazdik, Y.; Villet, G.; Wacker, K.; Wallny, R.; Walter, T.; Waugh, B.; Weber, G.; Weber, M.; Wegener, D.; Wegner, A.; Wengler, T.; Werner, M.; West, L. R.; Wiesand, S.; Wilksen, T.; Willard, S.; Winde, M.; Winter, G.-G.; Wittek, C.; Wittmann, E.; Wobisch, M.; Wollatz, H.; Wünsch, E.; Žáček, J.; Zálešák, J.; Zhang, Z.; Zhokin, A.; Zini, P.; Zomer, F.; Zsembery, J.; zurNedden, M.; H1 Collaboration

1999-01-01

Single particles and jets in deeply inelastic scattering at low x are measured with the H1 detector in the region away from the current jet and towards the proton remnant, known as the forward region. Hadronic final state measurements in this region are expected to be particularly sensitive to QCD evolution effects. Jet cross sections are presented as a function of Bjorken- x for forward jets produced with a polar angle to the proton direction, θjet, in the range 7° < θjet < 20°. Azimuthal correlations are studied between the forward jet and the scattered lepton. Charged and neutral single particle production in the forward region are measured as a function of Bjorken- x, in the range 5° < θ < 25°, for particle transverse momenta larger than 1 GeV. QCD based Monte Carlo predictions and analytical calculations based on BFKL, CCFM and DGLAP evolution are compared to the data. Predictions based on the DGLAP approach fail to describe the data, except for those which allow for a resolved photon contribution.

MARTINI: An event generator for relativistic heavy-ion collisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schenke, Bjoern; Gale, Charles; Jeon, Sangyong

2009-11-15

We introduce the modular algorithm for relativistic treatment of heavy ion interactions (MARTINI), a comprehensive event generator for the hard and penetrating probes in high-energy nucleus-nucleus collisions. Its main components are a time-evolution model for the soft background, PYTHIA 8.1, and the McGill-Arnold, Moore, and Yaffe (AMY) parton-evolution scheme, including radiative as well as elastic processes. This allows us to generate full event configurations in the high p{sub T} region that take into account thermal quantum chromodynamic (QCD) and quantum electrodynamic (QED) effects as well as effects of the evolving medium. We present results for the neutral pion nuclear modificationmore » factor in Au+Au collisions at the BNL Relativistic Heavy Ion Collider as a function of p{sub T} for different centralities and also as a function of the angle with respect to the reaction plane for noncentral collisions. Furthermore, we study the production of high-transverse-momentum photons, incorporating a complete set of photon-production channels.« less

Neutral biogeography and the evolution of climatic niches.

PubMed

Boucher, Florian C; Thuiller, Wilfried; Davies, T Jonathan; Lavergne, Sébastien

2014-05-01

Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than from adaptive scenarios. We developed a model inspired by neutral biodiversity theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sampled the climatic niches of species according to their geographic position and showed that even when species evolve independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time.

Biological and genetic evolution of HIV type 1 in two siblings with different patterns of disease progression.

PubMed

Ripamonti, Chiara; Leitner, Thomas; Laurén, Anna; Karlsson, Ingrid; Pastore, Angela; Cavarelli, Mariangela; Antonsson, Liselotte; Plebani, Anna; Fenyö, Eva Maria; Scarlatti, Gabriella

2007-12-01

To investigate the immunological and virological factors that may lead to different patterns of disease progression characteristic of HIV-1-infected children, two HIV-1-infected siblings, a slow and a fast progressor, were followed prospectively before the onset of highly active antiretroviral therapy. Viral coreceptor usage, including the use of CCR5/CXCR4 chimeric receptors, macrophage tropism, and sensitivity to the CC-chemokine RANTES, has been studied. An autologous and heterologous neutralizing antibody response has been documented using peripheral blood mononuclear cells- and GHOST(3) cell line-based assays. Viral evolution was investigated by env C2-V3 region sequence analysis. Although both siblings were infected with HIV-1 of the R5 phenotype, their viruses showed important biological differences. In the fast progressor there was a higher RANTES sensitivity of the early virus, an increased trend to change the mode of CCR5 receptor use, and a larger genetic evolution. Both children developed an autologous neutralizing antibody response starting from the second year with evidence of the continuous emergence of resistant variants. A marked viral genetic and phenotypic evolution was documented in the fast progressor sibling, which is accompanied by a high viral RANTES sensitivity and persistent neutralizing antibodies.

Neutral biogeography and the evolution of climatic niches

PubMed Central

Boucher, Florian C.; Thuiller, Wilfried; Davies, T. Jonathan; Lavergne, Sébastien

2014-01-01

Recent debate on whether climatic niches are conserved through time has focused on how phylogenetic niche conservatism can be measured by deviations from a Brownian motion model of evolutionary change. However, there has been no evaluation of this methodological approach. In particular, the fact that climatic niches are usually obtained from distribution data and are thus heavily influenced by biogeographic factors has largely been overlooked. Our main objective here was to test whether patterns of climatic niche evolution that are frequently observed might arise from neutral dynamics rather than adaptive scenarios. We develop a model inspired by Neutral Biodiversity Theory, where individuals disperse, compete, and undergo speciation independently of climate. We then sample the climatic niches of species according to their geographic position and show that even when species evolved independently of climate, their niches can nonetheless exhibit evolutionary patterns strongly differing from Brownian motion. Indeed, climatic niche evolution is better captured by a model of punctuated evolution with constraints due to landscape boundaries, two features that are traditionally interpreted as evidence for selective processes acting on the niche. We therefore suggest that deviation from Brownian motion alone should not be used as evidence for phylogenetic niche conservatism, but that information on phenotypic traits directly linked to physiology is required to demonstrate that climatic niches have been conserved through time. PMID:24739191

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A.

HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here in this paper, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of themore » study period, VRC01-lineage clades showed continuous evolution, with rates of ~2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization.« less

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.

PubMed

Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A; Joyce, M Gordon; Kwon, Young Do; Zhou, Tongqing; Sheng, Zizhang; Zhang, Baoshan; O'Dell, Sijy; McKee, Krisha; Georgiev, Ivelin S; Chuang, Gwo-Yu; Longo, Nancy S; Lynch, Rebecca M; Saunders, Kevin O; Soto, Cinque; Srivatsan, Sanjay; Yang, Yongping; Bailer, Robert T; Louder, Mark K; Mullikin, James C; Connors, Mark; Kwong, Peter D; Mascola, John R; Shapiro, Lawrence

2015-04-23

HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of the study period, VRC01-lineage clades showed continuous evolution, with rates of ∼2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization. Copyright © 2015 Elsevier Inc. All rights reserved.

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

DOE PAGES

Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A.; ...

2015-04-09

HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here in this paper, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of themore » study period, VRC01-lineage clades showed continuous evolution, with rates of ~2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization.« less

Multiplexed screening of natural humoral immunity identifies antibodies at fine specificity for complex and dynamic viral targets.

PubMed

McCutcheon, Krista M; Gray, Julia; Chen, Natalie Y; Liu, Keyi; Park, Minha; Ellsworth, Stote; Tripp, Ralph A; Tompkins, S Mark; Johnson, Scott K; Samet, Shelly; Pereira, Lenore; Kauvar, Lawrence M

2014-01-01

Viral entry targets with therapeutic neutralizing potential are subject to multiple escape mechanisms, including antigenic drift, immune dominance of functionally irrelevant epitopes, and subtle variations in host cell mechanisms. A surprising finding of recent years is that potent neutralizing antibodies to viral epitopes independent of strain exist, but are poorly represented across the diverse human population. Identifying these antibodies and understanding the biology mediating the specific immune response is thus difficult. An effective strategy for meeting this challenge is to incorporate multiplexed antigen screening into a high throughput survey of the memory B cell repertoire from immune individuals. We used this approach to discover suites of cross-clade antibodies directed to conformational epitopes in the stalk region of the influenza A hemagglutinin (HA) protein and to select high-affinity anti-peptide antibodies to the glycoprotein B (gB) of human cytomegalovirus. In each case, our screens revealed a restricted VH and VL germline usage, including published and previously unidentified gene families. The in vivo evolution of paratope specificity with optimal neutralizing activity was understandable after correlating biological activities with kinetic binding and epitope recognition. Iterative feedback between antigen probe design based on structure and function information with high throughput multiplexed screening demonstrated a generally applicable strategy for efficient identification of safe, native, finely tuned antibodies with the potential for high genetic barriers to viral escape.

Functionalized carbon nanotube based hybrid electrochemical capacitors using neutral bromide redox-active electrolyte for enhancing energy density

NASA Astrophysics Data System (ADS)

Tang, Xiaohui; Lui, Yu Hui; Chen, Bolin; Hu, Shan

2017-06-01

A hybrid electrochemical capacitor (EC) with enhanced energy density is realized by integrating functionalized carbon nanotube (FCNT) electrodes with redox-active electrolyte that has a neutral pH value (1 M Na2SO4 and 0.5 M KBr mixed aqueous solution). The negative electrode shows an electric double layer capacitor-type behavior. On the positive electrode, highly reversible Br-/Br3- redox reactions take place, presenting a battery-type behavior, which contributes to increase the capacitance of the hybrid cell. The voltage window of the whole cell is extended up to 1.5 V because of the high over-potentials of oxygen and hydrogen evolution reactions in the neutral electrolyte. Compared with raw CNT, the FCNT has better wettability in the aqueous electrolyte and contributes to increase the electric double layer capacitance of the cell. As a result, the maximum energy density of 28.3 Wh kg-1 is obtained from the hybrid EC at 0.5 A g-1 without sacrificing its power density, which is around 4 times larger than that of the electrical double layer capacitor constructed by FCNT electrodes and 1 M Na2SO4 electrolyte. Moreover, the discharge capacity retained 86.3% of its initial performance after 10000 cycles of galvanostatic charge and discharge test (10 A/g), suggesting its long life cycle even at high current loading.

Interaction of Tryptophane and Phenylalanine with Cadmium and Molybdenum Ferrocyanides and Its Implications in Chemical Evolution and Origins of Life.

NASA Astrophysics Data System (ADS)

Tewari, Brij

2016-07-01

Insoluble metal hexacyanoferrate(II) complexes could have concentrated biomonomers from dilute prebiotic soup during course of chemical evolution and origin of life or primitive earth. In the light of above hypothesis, adsorption of tryptophane and phenylalanine was studied on cadmium and molybdenum ferrocyanides at neutral pH (7.0 ± 0.01) and at a temperature of 30 ± 1º C. Interaction of amino acids with metal ferrocyanides are found to be maximum at neutral pH. Neutral pH is chosen for the adsorption studies because most of the reactions in biological systems taken place at neutral pH range. Adsorption trend follow Langmuir isotherm model. The Langmuir constants b and Qo were calculated at neutral pH, tryptophane was found to more adsorbed than phenylalanine on both metal ferrocyanides studied. Molybdenum ferrocyanides studied. Molybdenum ferrocyanides was found to have more uptake capacity for both adsorbates than cadmium ferrocyanides. The present study suggests that metal ferrocyanides might have played a role in the stabilization of biomolecules through their surface activity during course of chemical solution and origins of life on primitive earth.

Stability and Evolution of Supernova Fallback Disks

NASA Astrophysics Data System (ADS)

Menou, Kristen; Perna, Rosalba; Hernquist, Lars

2001-10-01

We show that thin accretion disks made of carbon or oxygen are subject to the same thermal ionization instability as hydrogen and helium disks. We argue that the instability applies to disks of any metal content. The relevance of the instability to supernova fallback disks probably means that their power-law evolution breaks down when they first become neutral. We construct simple analytical models for the viscous evolution of fallback disks to show that it is possible for these disks to become neutral when they are still young (ages of a few 103 to 104 yr), compact in size (a few 109 to 1011 cm) and generally accreting at sub-Eddington rates (M~a few 1014-1018 g s-1). Based on recent results on the nature of viscosity in the disks of close binaries, we argue that this time may also correspond to the end of the disk activity period. Indeed, in the absence of a significant source of viscosity in the neutral phase, the entire disk will likely turn to dust and become passive. We discuss various applications of the evolutionary model, including anomalous X-ray pulsars and young radio pulsars. Our analysis indicates that metal-rich fallback disks around newly born neutron stars and black holes become neutral generally inside the tidal truncation radius (Roche limit) for planets at ~1011 cm. Consequently, the efficiency of the planetary formation process in this context will mostly depend on the ability of the resulting disk of rocks to spread via collisions beyond the Roche limit. It appears easier for the merger product of a doubly degenerate binary, whether it is a massive white dwarf or a neutron star, to harbor planets because its remnant disk has a rather large initial angular momentum, which allows it to spread beyond the Roche limit before becoming neutral. The early super-Eddington phase of accretion is a source of uncertainty for the disk evolution models presented here.

Mutation exposed: a neutral explanation for extreme base composition of an endosymbiont genome.

PubMed

Wernegreen, Jennifer J; Funk, Daniel J

2004-12-01

The influence of neutral mutation pressure versus selection on base composition evolution is a subject of considerable controversy. Yet the present study represents the first explicit population genetic analysis of this issue in prokaryotes, the group in which base composition variation is most dramatic. Here, we explore the impact of mutation and selection on the dynamics of synonymous changes in Buchnera aphidicola, the AT-rich bacterial endosymbiont of aphids. Specifically, we evaluated three forms of evidence. (i) We compared the frequencies of directional base changes (AT-->GC vs. GC-->AT) at synonymous sites within and between Buchnera species, to test for selective preference versus effective neutrality of these mutational categories. Reconstructed mutational changes across a robust intraspecific phylogeny showed a nearly 1:1 AT-->GC:GC-->AT ratio. Likewise, stationarity of base composition among Buchnera species indicated equal rates of AT-->GC and GC-->AT substitutions. The similarity of these patterns within and between species supported the neutral model. (ii) We observed an equivalence of relative per-site AT mutation rate and current AT content at synonymous sites, indicating that base composition is at mutational equilibrium. (iii) We demonstrated statistically greater equality in the frequency of mutational categories in Buchnera than in parallel mammalian studies that documented selection on synonymous sites. Our results indicate that effectively neutral mutational pressure, rather than selection, represents the major force driving base composition evolution in Buchnera. Thus they further corroborate recent evidence for the critical role of reduced N(e) in the molecular evolution of bacterial endosymbionts.

Divergent oviposition preferences of sister species are not driven by nest survival: The evidence for neutrality

EPA Science Inventory

Both adaptive and neutral trait evolution can contribute to divergence, but the relative contributions of the two remain unclear. Oviposition preference, a trait that has been demonstrated to contribute to divergence among populations, is often presumed to be an adaptive trait. F...

Detuning dependence of Rabi oscillations in an InAs self-assembled quantum dot ensemble

NASA Astrophysics Data System (ADS)

Suzuki, Takeshi; Singh, Rohan; Bayer, Manfred; Ludzwig, Arne; Wieck, Andreas D.; Cundiff, Steven T.

2018-04-01

We study the coherent evolution of an InAs self-assembled quantum dot (QD) ensemble in the ultrafast regime. The evolution of the entire frequency distribution is revealed by performing prepulse two-dimensional (2D) coherent spectroscopy. Charged and neutral QDs display distinct nonlinear responses arising from two-level trion and four-level exciton-biexciton systems, respectively, and each signal is clearly separated in 2D spectra. Whereas the signals for charged QDs are symmetric with respect to the detuning, those for neutral QDs are asymmetric due to the asymmetric four-level energy structure. Experimental results for charged and neutral QDs are well reproduced by solving the optical Bloch equations, including detuning and excitation-induced dephasing (EID) effects. The temperature dependence suggests that wetting-layer carriers play an important role in EID.

Extreme Conservation and Non-Neutral Evolution of the cpmA Circadian Locus in a Globally Distributed Chroococcidiopsis sp. from Naturally Stressful Habitats

PubMed Central

Dvornyk, Volodymyr; Jahan, Akhee Sabiha

2012-01-01

Cyanobacteria are among the most ancient organisms known to have circadian rhythms. The cpmA gene is involved in controlling the circadian output signal. We studied polymorphism and divergence of this gene in six populations of a stress-tolerant cyanobacterium, Chroococcidiopsis sp., sampled in extreme habitats across the globe. Despite high haplotype diversity (0.774), nucleotide diversity of cpmA is very low (π = 0.0034): the gene appears to be even more conserved than housekeeping genes. Even though the populations were sampled thousands kilometers apart, they manifested virtually no genetic differentiation at this locus (FST = 0.0228). Using various tests for neutrality, we determined that evolution of cpmA significantly departures from the neutral model and is governed by episodic positive selection. PMID:22844070

Speciation and Neutral Molecular Evolution in One-Dimensional Closed Population

NASA Astrophysics Data System (ADS)

Semovski, Sergei V.; Bukin, Yuri S.; Sherbakov, Dmitry Yu.

Models are presented suitable for a description of speciation processes arising due to reproductive isolation depending on genetic distance. The main attention is paid to the model of a one-dimensional closed population, which describes the evolution of littoral benthic organisms. In order to correspond the modeling results to the results obtained in the course of experimental phylogenetic studies, all individual-based models described here involve neutrally evolving and maternally inherited DNA sequence. Sub-samples of the resulting sequences were used for a posteriori phylogenetic inferences which then were compared to the "true" evolutionary histories.

Cultural selection drives the evolution of human communication systems

PubMed Central

Tamariz, Monica; Ellison, T. Mark; Barr, Dale J.; Fay, Nicolas

2014-01-01

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems. PMID:24966310

Cultural selection drives the evolution of human communication systems.

PubMed

Tamariz, Monica; Ellison, T Mark; Barr, Dale J; Fay, Nicolas

2014-08-07

Human communication systems evolve culturally, but the evolutionary mechanisms that drive this evolution are not well understood. Against a baseline that communication variants spread in a population following neutral evolutionary dynamics (also known as drift models), we tested the role of two cultural selection models: coordination- and content-biased. We constructed a parametrized mixed probabilistic model of the spread of communicative variants in four 8-person laboratory micro-societies engaged in a simple communication game. We found that selectionist models, working in combination, explain the majority of the empirical data. The best-fitting parameter setting includes an egocentric bias and a content bias, suggesting that participants retained their own previously used communicative variants unless they encountered a superior (content-biased) variant, in which case it was adopted. This novel pattern of results suggests that (i) a theory of the cultural evolution of human communication systems must integrate selectionist models and (ii) human communication systems are functionally adaptive complex systems.

Chemical communication, sexual selection, and introgression in wall lizards.

PubMed

MacGregor, Hannah E A; Lewandowsky, Rachel A M; d'Ettorre, Patrizia; Leroy, Chloé; Davies, Noel W; While, Geoffrey M; Uller, Tobias

2017-10-01

Divergence in communication systems should influence the likelihood that individuals from different lineages interbreed, and consequently shape the direction and rate of hybridization. Here, we studied the role of chemical communication in hybridization, and its contribution to asymmetric and sexually selected introgression between two lineages of the common wall lizard (Podarcis muralis). Males of the two lineages differed in the chemical composition of their femoral secretions. Chemical profiles provided information regarding male secondary sexual characters, but the associations were variable and inconsistent between lineages. In experimental contact zones, chemical composition was weakly associated with male reproductive success, and did not predict the likelihood of hybridization. Consistent with these results, introgression of chemical profiles in a natural hybrid zone resembled that of neutral nuclear genetic markers overall, but one compound in particular (tocopherol methyl ether) matched closely the introgression of visual sexual characters. These results imply that associations among male chemical profiles, sexual characters, and reproductive success largely reflect transient and environmentally driven effects, and that genetic divergence in chemical composition is largely neutral. We therefore suggest that femoral secretions in wall lizards primarily provide information about residency and individual identity rather than function as sexual signals. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Fluctuating Selection in the Moran

PubMed Central

Dean, Antony M.; Lehman, Clarence; Yi, Xiao

2017-01-01

Contrary to classical population genetics theory, experiments demonstrate that fluctuating selection can protect a haploid polymorphism in the absence of frequency dependent effects on fitness. Using forward simulations with the Moran model, we confirm our analytical results showing that a fluctuating selection regime, with a mean selection coefficient of zero, promotes polymorphism. We find that increases in heterozygosity over neutral expectations are especially pronounced when fluctuations are rapid, mutation is weak, the population size is large, and the variance in selection is big. Lowering the frequency of fluctuations makes selection more directional, and so heterozygosity declines. We also show that fluctuating selection raises dn/ds ratios for polymorphism, not only by sweeping selected alleles into the population, but also by purging the neutral variants of selected alleles as they undergo repeated bottlenecks. Our analysis shows that randomly fluctuating selection increases the rate of evolution by increasing the probability of fixation. The impact is especially noticeable when the selection is strong and mutation is weak. Simulations show the increase in the rate of evolution declines as the rate of new mutations entering the population increases, an effect attributable to clonal interference. Intriguingly, fluctuating selection increases the dn/ds ratios for divergence more than for polymorphism, a pattern commonly seen in comparative genomics. Our model, which extends the classical neutral model of molecular evolution by incorporating random fluctuations in selection, accommodates a wide variety of observations, both neutral and selected, with economy. PMID:28108586

Does evolution lead to maximizing behavior?

PubMed

Lehmann, Laurent; Alger, Ingela; Weibull, Jörgen

2015-07-01

A long-standing question in biology and economics is whether individual organisms evolve to behave as if they were striving to maximize some goal function. We here formalize this "as if" question in a patch-structured population in which individuals obtain material payoffs from (perhaps very complex multimove) social interactions. These material payoffs determine personal fitness and, ultimately, invasion fitness. We ask whether individuals in uninvadable population states will appear to be maximizing conventional goal functions (with population-structure coefficients exogenous to the individual's behavior), when what is really being maximized is invasion fitness at the genetic level. We reach two broad conclusions. First, no simple and general individual-centered goal function emerges from the analysis. This stems from the fact that invasion fitness is a gene-centered multigenerational measure of evolutionary success. Second, when selection is weak, all multigenerational effects of selection can be summarized in a neutral type-distribution quantifying identity-by-descent between individuals within patches. Individuals then behave as if they were striving to maximize a weighted sum of material payoffs (own and others). At an uninvadable state it is as if individuals would freely choose their actions and play a Nash equilibrium of a game with a goal function that combines self-interest (own material payoff), group interest (group material payoff if everyone does the same), and local rivalry (material payoff differences). © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Transition to an Aquatic Habitat Permitted the Repeated Loss of the Pleiotropic KLK8 Gene in Mammals.

PubMed

Hecker, Nikolai; Sharma, Virag; Hiller, Michael

2017-11-01

Kallikrein related peptidase 8 (KLK8; also called neuropsin) is a serine protease that plays distinct roles in the skin and hippocampus. In the skin, KLK8 influences keratinocyte proliferation and desquamation, and activates antimicrobial peptides in sweat. In the hippocampus, KLK8 affects memory acquisition. Here, we examined the evolution of KLK8 in mammals and discovered that, out of 70 placental mammals, KLK8 is exclusively lost in three independent fully-aquatic lineages, comprising dolphin, killer whale, minke whale, and manatee. In addition, while the sperm whale has an intact KLK8 reading frame, the gene evolves neutrally in this species. We suggest that the distinct functions of KLK8 likely became obsolete in the aquatic environment, leading to the subsequent loss of KLK8 in several fully-aquatic mammalian lineages. First, the cetacean and manatee skin lacks sweat glands as an adaptation to the aquatic environment, which likely made the epidermal function of KLK8 obsolete. Second, cetaceans and manatees exhibit a proportionally small hippocampus, which may have rendered the hippocampal functions of KLK8 obsolete. Together, our results shed light on the genomic changes that correlate with skin and neuroanatomical differences of aquatic mammals, and show that even pleiotropic genes can be lost during evolution if an environmental change nullifies the need for the different functions of such genes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

PubMed Central

Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun

2012-01-01

Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272

Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes.

PubMed

Figuet, Emeric; Nabholz, Benoît; Bonneau, Manon; Mas Carrio, Eduard; Nadachowska-Brzyska, Krystyna; Ellegren, Hans; Galtier, Nicolas

2016-06-01

The nearly neutral theory of molecular evolution predicts that small populations should accumulate deleterious mutations at a faster rate than large populations. The analysis of nonsynonymous (dN) versus synonymous (dS) substitution rates in birds versus mammals, however, has provided contradictory results, questioning the generality of the nearly neutral theory. Here we analyzed the impact of life history traits, taken as proxies of the effective population size, on molecular evolutionary and population genetic processes in amniotes, including the so far neglected reptiles. We report a strong effect of species body mass, longevity, and age of sexual maturity on genome-wide patterns of polymorphism and divergence across the major groups of amniotes, in agreement with the nearly neutral theory. Our results indicate that the rate of protein evolution in amniotes is determined in the first place by the efficiency of purifying selection against deleterious mutations-and this is true of both radical and conservative amino acid changes. Interestingly, the among-species distribution of dN/dS in birds did not follow this general trend: dN/dS was not higher in large, long-lived than in small, short-lived species of birds. We show that this unexpected pattern is not due to a more narrow range of life history traits, a lack of correlation between traits and Ne, or a peculiar distribution of fitness effects of mutations in birds. Our analysis therefore highlights the bird dN/dS ratio as a molecular evolutionary paradox and a challenge for future research. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Electroweak splitting functions and high energy showering

NASA Astrophysics Data System (ADS)

Chen, Junmou; Han, Tao; Tweedie, Brock

2017-11-01

We derive the electroweak (EW) collinear splitting functions for the Standard Model, including the massive fermions, gauge bosons and the Higgs boson. We first present the splitting functions in the limit of unbroken SU(2) L × U(1) Y and discuss their general features in the collinear and soft-collinear regimes. These are the leading contributions at a splitting scale ( k T ) far above the EW scale ( v). We then systematically incorporate EW symmetry breaking (EWSB), which leads to the emergence of additional "ultra-collinear" splitting phenomena and naive violations of the Goldstone-boson Equivalence Theorem. We suggest a particularly convenient choice of non-covariant gauge (dubbed "Goldstone Equivalence Gauge") that disentangles the effects of Goldstone bosons and gauge fields in the presence of EWSB, and allows trivial book-keeping of leading power corrections in v/ k T . We implement a comprehensive, practical EW showering scheme based on these splitting functions using a Sudakov evolution formalism. Novel features in the implementation include a complete accounting of ultra-collinear effects, matching between shower and decay, kinematic back-reaction corrections in multi-stage showers, and mixed-state evolution of neutral bosons ( γ/ Z/ h) using density-matrices. We employ the EW showering formalism to study a number of important physical processes at O (1-10 TeV) energies. They include (a) electroweak partons in the initial state as the basis for vector-boson-fusion; (b) the emergence of "weak jets" such as those initiated by transverse gauge bosons, with individual splitting probabilities as large as O (35%); (c) EW showers initiated by top quarks, including Higgs bosons in the final state; (d) the occurrence of O (1) interference effects within EW showers involving the neutral bosons; and (e) EW corrections to new physics processes, as illustrated by production of a heavy vector boson ( W ') and the subsequent showering of its decay products.

Positive selection drives the evolution of a major histocompatibility complex gene in an endangered Mexican salamander species complex.

PubMed

Tracy, Karen E; Kiemnec-Tyburczy, Karen M; DeWoody, J Andrew; Parra-Olea, Gabriela; Zamudio, Kelly R

2015-06-01

Immune gene evolution can be critical to species survival in the face of infectious disease. In particular, polymorphism in the genes of the major histocompatibility complex (MHC) helps vertebrates combat novel and diverse pathogens by increasing the number of pathogen-derived proteins that can initiate the host's acquired immune response. In this study, we used a combination of presumably adaptive and neutral markers to investigate MHC evolution in populations of five salamander species within the Ambystoma velasci complex, a group consisting of 15 recently diverged species, several of which are endangered. We isolated 31 unique MHC class II β alleles from 75 total individuals from five species in this complex. MHC heterozygosity was significantly lower than expected for all five species, and we found no clear relationship between number of MHC alleles and species range, life history, or level of heterozygosity. We inferred a phylogeny representing the evolutionary history of Ambystoma MHC, with which we found signatures of positive selection on the overall gene, putative peptide-binding residues, and allelic lineages. We identified several instances of trans-species polymorphism, a hallmark of balancing selection observed in other groups of closely related species. In contrast, we did not detect comparable allelic diversity or signatures of selection on neutral loci. Additionally, we identified 17 supertypes among the 44 unique Ambystoma alleles, indicating that these sequences may encode functionally distinct MHC variants. We therefore have strong evidence that positive selection is a major evolutionary force driving patterns of MHC polymorphism in this recently radiated species complex.

Hard and Soft Selection Revisited: How Evolution by Natural Selection Works in the Real World.

PubMed

Reznick, David

2016-01-01

The modern synthesis of evolutionary biology unified Darwin's natural selection with Mendelian genetics, but at the same time it created the dilemma of genetic load. Lewontin and Hubby's (1966) and Harris's (1966) characterization of genetic variation in natural populations increased the apparent burden of this load. Neutrality or near neutrality of genetic variation was one mechanism proposed for the revealed excessive genetic variation. Bruce Wallace coined the term "soft selection" to describe an alternative way for natural selection to operate that was consistent with observed variation. He envisioned nature as presenting ecological vacancies that could be filled by diverse genotypes. Survival and successful reproduction was a combined function of population density, genotype, and genotype frequencies, rather than a fixed value of the relative fitness of each genotype. My goal in this review is to explore the importance of soft selection in the real world. My motive and that of my colleagues as described here is not to explain what maintains genetic variation in natural populations, but rather to understand the factors that shape how organisms adapt to natural environments. We characterize how feedbacks between ecology and evolution shape both evolution and ecology. These feedbacks are mediated by density- and frequency-dependent selection, the mechanisms that underlie soft selection. Here, I report on our progress in characterizing these types of selection with a combination of a consideration of the published literature and the results from my collaborators' and my research on natural populations of guppies. © The American Genetic Association. 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Tumor evolution: Linear, branching, neutral or punctuated?☆

PubMed Central

Davis, Alexander; Gao, Ruli; Navin, Nicholas

2017-01-01

Intratumor heterogeneity has been widely reported in human cancers, but our knowledge of how this genetic diversity emerges over time remains limited. A central challenge in studying tumor evolution is the difficulty in collecting longitudinal samples from cancer patients. Consequently, most studies have inferred tumor evolution from single time-point samples, providing very indirect information. These data have led to several competing models of tumor evolution: linear, branching, neutral and punctuated. Each model makes different assumptions regarding the timing of mutations and selection of clones, and therefore has different implications for the diagnosis and therapeutic treatment of cancer patients. Furthermore, emerging evidence suggests that models may change during tumor progression or operate concurrently for different classes of mutations. Finally, we discuss data that supports the theory that most human tumors evolve from a single cell in the normal tissue. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby. PMID:28110020

Three species one-dimensional kinetic model for weakly ionized plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gonzalez, J., E-mail: jorge.gonzalez@upm.es; Donoso, J. M.; Tierno, S. P.

2016-06-15

A three species one-dimensional kinetic model is presented for a spatially homogeneous weakly ionized plasma subjected to the action of a time varying electric field. Planar geometry is assumed, which means that the plasma evolves in the privileged direction of the field. The energy transmitted to the electric charges is channelized to the neutrals thanks to collisions, a mechanism that influences the plasma dynamics. Charge-charge interactions have been designed as a one-dimensional collision term equivalent to the Landau operator used for fully ionized plasmas. Charge-neutral collisions are modelled by a conservative drift-diffusion operator in the Dougherty's form. The resulting setmore » of coupled integro-differential equations is solved with the stable and robust propagator integral method. This semi–analytical method feasibility accounts for non–linear effects without appealing to linearisation or simplifications, providing conservative physically meaningful solutions even for initial or emerging sharp velocity distribution function profiles. It is found that charge-neutral collisions exert a significant effect since a quite different plasma evolution arises if compared to the collisionless limit. In addition, substantial differences in the system motion are found for constant and temperature dependent collision frequencies cases.« less

On the relative roles of background selection and genetic hitchhiking in shaping human cytomegalovirus genetic diversity.

PubMed

Renzette, Nicholas; Kowalik, Timothy F; Jensen, Jeffrey D

2016-01-01

A central focus of population genetics has been examining the contribution of selective and neutral processes in shaping patterns of intraspecies diversity. In terms of selection specifically, surveys of higher organisms have shown considerable variation in the relative contributions of background selection and genetic hitchhiking in shaping the distribution of polymorphisms, although these analyses have rarely been extended to bacteria and viruses. Here, we study the evolution of a ubiquitous, viral pathogen, human cytomegalovirus (HCMV), by analysing the relationship among intraspecies diversity, interspecies divergence and rates of recombination. We show that there is a strong correlation between diversity and divergence, consistent with expectations of neutral evolution. However, after correcting for divergence, there remains a significant correlation between intraspecies diversity and recombination rates, with additional analyses suggesting that this correlation is largely due to the effects of background selection. In addition, a small number of loci, centred on long noncoding RNAs, also show evidence of selective sweeps. These data suggest that HCMV evolution is dominated by neutral mechanisms as well as background selection, expanding our understanding of linked selection to a novel class of organisms. © 2015 John Wiley & Sons Ltd.

Adaptation and colonization history affect the evolution of clines in two introduced species.

PubMed

Keller, Stephen R; Sowell, Dexter R; Neiman, Maurine; Wolfe, Lorne M; Taylor, Douglas R

2009-08-01

Phenotypic and genetic clines have long been synonymous with adaptive evolution. However, other processes (for example, migration, range expansion, invasion) may generate clines in traits or loci across geographical and environmental gradients. It is therefore important to distinguish between clines that represent adaptive evolution and those that result from selectively neutral demographic or genetic processes. We tested for the differentiation of phenotypic traits along environmental gradients using two species in the genus Silene, whilst statistically controlling for colonization history and founder effects. We sampled seed families from across the native and introduced ranges, genotyped individuals and estimated phenotypic differentiation in replicated common gardens. The results suggest that post-glacial expansion of S. vulgaris and S. latifolia involved both neutral and adaptive genetic differentiation (clines) of life history traits along major axes of environmental variation in Europe and North America. Phenotypic clines generally persisted when tested against the neutral expectation, although some clines disappeared (and one cline emerged) when the effects of genetic ancestry were statistically removed. Colonization history, estimated using genetic markers, is a useful null model for tests of adaptive trait divergence, especially during range expansion and invasion when selection and gene flow may not have reached equilibrium.

Sexual selection and population divergence II. Divergence in different sexual traits and signal modalities in field crickets (Teleogryllus oceanicus).

PubMed

Pascoal, Sonia; Mendrok, Magdalena; Wilson, Alastair J; Hunt, John; Bailey, Nathan W

2017-06-01

Sexual selection can target many different types of traits. However, the relative influence of different sexually selected traits during evolutionary divergence is poorly understood. We used the field cricket Teleogryllus oceanicus to quantify and compare how five traits from each of three sexual signal modalities and components diverge among allopatric populations: male advertisement song, cuticular hydrocarbon (CHC) profiles and forewing morphology. Population divergence was unexpectedly consistent: we estimated the among-population (genetic) variance-covariance matrix, D, for all 15 traits, and D max explained nearly two-thirds of its variation. CHC and wing traits were most tightly integrated, whereas song varied more independently. We modeled the dependence of among-population trait divergence on genetic distance estimated from neutral markers to test for signatures of selection versus neutral divergence. For all three sexual trait types, phenotypic variation among populations was largely explained by a neutral model of divergence. Our findings illustrate how phenotypic integration across different types of sexual traits might impose constraints on the evolution of mating isolation and divergence via sexual selection. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Rapid evolution of RNA editing sites in a small non-essential plastid gene

PubMed Central

Fiebig, Andreas; Stegemann, Sandra; Bock, Ralph

2004-01-01

Chloroplast RNA editing proceeds by C-to-U transitions at highly specific sites. Here, we provide a phylogenetic analysis of RNA editing in a small plastid gene, petL, encoding subunit VI of the cytochrome b6f complex. Analyzing representatives from most major groups of seed plants, we find an unexpectedly high frequency and dynamics of RNA editing. High-frequency editing has previously been observed in plastid ndh genes, which are remarkable in that their mutational inactivation does not produce an obvious mutant phenotype. In order to test the idea that reduced functional constraints allow for more flexible evolution of RNA editing sites, we have created petL knockout plants by tobacco chloroplast transformation. We find that, in the higher plant tobacco, targeted inactivation of petL does not impair plant growth under a variety of conditions markedly contrasting the important role of petL in photosynthesis in the green alga Chlamydomonas reinhardtii. Together with a low number of editing sites in plastid genes that are essential to gene expression and photosynthetic activity, these data suggest that RNA editing sites may evolve more readily in those genes whose transitory loss of function can be tolerated. Accumulated evidence for this ‘relative neutrality hypothesis for the evolution of plastid editing sites’ is discussed. PMID:15240834

Fitness Landscapes of Functional RNAs.

PubMed

Kun, Ádám; Szathmáry, Eörs

2015-08-21

The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world.

Fluctuating Selection in the Moran.

PubMed

Dean, Antony M; Lehman, Clarence; Yi, Xiao

2017-03-01

Contrary to classical population genetics theory, experiments demonstrate that fluctuating selection can protect a haploid polymorphism in the absence of frequency dependent effects on fitness. Using forward simulations with the Moran model, we confirm our analytical results showing that a fluctuating selection regime, with a mean selection coefficient of zero, promotes polymorphism. We find that increases in heterozygosity over neutral expectations are especially pronounced when fluctuations are rapid, mutation is weak, the population size is large, and the variance in selection is big. Lowering the frequency of fluctuations makes selection more directional, and so heterozygosity declines. We also show that fluctuating selection raises d n / d s ratios for polymorphism, not only by sweeping selected alleles into the population, but also by purging the neutral variants of selected alleles as they undergo repeated bottlenecks. Our analysis shows that randomly fluctuating selection increases the rate of evolution by increasing the probability of fixation. The impact is especially noticeable when the selection is strong and mutation is weak. Simulations show the increase in the rate of evolution declines as the rate of new mutations entering the population increases, an effect attributable to clonal interference. Intriguingly, fluctuating selection increases the d n / d s ratios for divergence more than for polymorphism, a pattern commonly seen in comparative genomics. Our model, which extends the classical neutral model of molecular evolution by incorporating random fluctuations in selection, accommodates a wide variety of observations, both neutral and selected, with economy. Copyright © 2017 by the Genetics Society of America.

Examination of Signatures of Recent Positive Selection on Genes Involved in Human Sialic Acid Biology.

PubMed

Moon, Jiyun M; Aronoff, David M; Capra, John A; Abbot, Patrick; Rokas, Antonis

2018-03-28

Sialic acids are nine carbon sugars ubiquitously found on the surfaces of vertebrate cells and are involved in various immune response-related processes. In humans, at least 58 genes spanning diverse functions, from biosynthesis and activation to recycling and degradation, are involved in sialic acid biology. Because of their role in immunity, sialic acid biology genes have been hypothesized to exhibit elevated rates of evolutionary change. Consistent with this hypothesis, several genes involved in sialic acid biology have experienced higher rates of non-synonymous substitutions in the human lineage than their counterparts in other great apes, perhaps in response to ancient pathogens that infected hominins millions of years ago (paleopathogens). To test whether sialic acid biology genes have also experienced more recent positive selection during the evolution of the modern human lineage, reflecting adaptation to contemporary cosmopolitan or geographically-restricted pathogens, we examined whether their protein-coding regions showed evidence of recent hard and soft selective sweeps. This examination involved the calculation of four measures that quantify changes in allele frequency spectra, extent of population differentiation, and haplotype homozygosity caused by recent hard and soft selective sweeps for 55 sialic acid biology genes using publicly available whole genome sequencing data from 1,668 humans from three ethnic groups. To disentangle evidence for selection from confounding demographic effects, we compared the observed patterns in sialic acid biology genes to simulated sequences of the same length under a model of neutral evolution that takes into account human demographic history. We found that the patterns of genetic variation of most sialic acid biology genes did not significantly deviate from neutral expectations and were not significantly different among genes belonging to different functional categories. Those few sialic acid biology genes that significantly deviated from neutrality either experienced soft sweeps or population-specific hard sweeps. Interestingly, while most hard sweeps occurred on genes involved in sialic acid recognition, most soft sweeps involved genes associated with recycling, degradation and activation, transport, and transfer functions. We propose that the lack of signatures of recent positive selection for the majority of the sialic acid biology genes is consistent with the view that these genes regulate immune responses against ancient rather than contemporary cosmopolitan or geographically restricted pathogens. Copyright © 2018 Moon et al.

Phylogeny of Banana Streak Virus reveals recent and repetitive endogenization in the genome of its banana host (Musa sp.).

PubMed

Gayral, Philippe; Iskra-Caruana, Marie-Line

2009-07-01

Banana streak virus (BSV) is a plant dsDNA pararetrovirus (family Caulimoviridae, genus badnavirus). Although integration is not an essential step in the BSV replication cycle, the nuclear genome of banana (Musa sp.) contains BSV endogenous pararetrovirus sequences (BSV EPRVs). Some BSV EPRVs are infectious by reconstituting a functional viral genome. Recent studies revealed a large molecular diversity of episomal BSV viruses (i.e., nonintegrated) while others focused on BSV EPRV sequences only. In this study, the evolutionary history of badnavirus integration in banana was inferred from phylogenetic relationships between BSV and BSV EPRVs. The relative evolution rates and selective pressures (d(N)/d(S) ratio) were also compared between endogenous and episomal viral sequences. At least 27 recent independent integration events occurred after the divergence of three banana species, indicating that viral integration is a recent and frequent phenomenon. Relaxation of selective pressure on badnaviral sequences that experienced neutral evolution after integration in the plant genome was recorded. Additionally, a significant decrease (35%) in the EPRV evolution rate was observed compared to BSV, reflecting the difference in the evolution rate between episomal dsDNA viruses and plant genome. The comparison of our results with the evolution rate of the Musa genome and other reverse-transcribing viruses suggests that EPRVs play an active role in episomal BSV diversity and evolution.

Lyman-α emitters gone missing: the different evolution of the bright and faint populations

NASA Astrophysics Data System (ADS)

Weinberger, Lewis H.; Kulkarni, Girish; Haehnelt, Martin G.; Choudhury, Tirthankar Roy

2018-06-01

We model the transmission of the Lyman-α line through the circum- and intergalactic media around dark matter haloes expected to host Lyman-alpha emitters (LAEs) at z ≥ 5.7, using the high-dynamic-range Sherwood simulations. We find very different CGM environments around more massive haloes (˜1011M⊙) compared to less massive haloes (˜109M⊙) at these redshifts, which can contribute to a different evolution of the Lyα transmission from LAEs within these haloes. Additionally we confirm that part of the differential evolution could result from bright LAEs being more likely to reside in larger ionized regions. We conclude that a combination of the CGM environment and the IGM ionization structure is likely to be responsible for the differential evolution of the bright and faint ends of the LAE luminosity function at z ≥ 6. More generally, we confirm the suggestion that the self-shielded neutral gas in the outskirts of the host halo can strongly attenuate the Lyα emission from high redshift galaxies. We find that this has a stronger effect on the more massive haloes hosting brighter LAEs. The faint-end of the LAE luminosity function is thus a more reliable probe of the average ionization state of the IGM. Comparing our model for LAEs with a range of observational data we find that the favoured reionization histories are our previously advocated `Late' and `Very Late' reionization histories, in which reionization finishes rather rapidly at around z ≃ 6.

Does constructive neutral evolution play an important role in the origin of cellular complexity? Making sense of the origins and uses of biological complexity.

PubMed

Speijer, Dave

2011-05-01

Recently, constructive neutral evolution has been touted as an important concept for the understanding of the emergence of cellular complexity. It has been invoked to help explain the development and retention of, amongst others, RNA splicing, RNA editing and ribosomal and mitochondrial respiratory chain complexity. The theory originated as a welcome explanation of isolated small scale cellular idiosyncrasies and as a reaction to 'overselectionism'. Here I contend, that in its extended form, it has major conceptual problems, can not explain observed patterns of complex processes, is too easily dismissive of alternative selectionist models, underestimates the creative force of complexity as such, and--if seen as a major evolutionary mechanism for all organisms--could stifle further thought regarding the evolution of highly complex biological processes. Copyright © 2011 WILEY Periodicals, Inc.

Blood tolerant laccase by directed evolution.

PubMed

Mate, Diana M; Gonzalez-Perez, David; Falk, Magnus; Kittl, Roman; Pita, Marcos; De Lacey, Antonio L; Ludwig, Roland; Shleev, Sergey; Alcalde, Miguel

2013-02-21

High-redox potential laccases are powerful biocatalysts with a wide range of applications in biotechnology. We have converted a thermostable laccase from a white-rot fungus into a blood tolerant laccase. Adapting the fitness of this laccase to the specific composition of human blood (above neutral pH, high chloride concentration) required several generations of directed evolution in a surrogate complex blood medium. Our evolved laccase was tested in both human plasma and blood, displaying catalytic activity while retaining a high redox potential at the T1 copper site. Mutations introduced in the second coordination sphere of the T1 site shifted the pH activity profile and drastically reduced the inhibitory effect of chloride. This proof of concept that laccases can be adapted to function in extreme conditions opens an array of opportunities for implantable nanobiodevices, chemical syntheses, and detoxification. Copyright © 2013 Elsevier Ltd. All rights reserved.

Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes

PubMed Central

Newton, Matilda S.; Arcus, Vickery L.; Patrick, Wayne M.

2015-01-01

The evolution of enzymes is often viewed as following a smooth and steady trajectory, from barely functional primordial catalysts to the highly active and specific enzymes that we observe today. In this review, we summarize experimental data that suggest a different reality. Modern examples, such as the emergence of enzymes that hydrolyse human-made pesticides, demonstrate that evolution can be extraordinarily rapid. Experiments to infer and resurrect ancient sequences suggest that some of the first organisms present on the Earth are likely to have possessed highly active enzymes. Reconciling these observations, we argue that rapid bursts of strong selection for increased catalytic efficiency are interspersed with much longer periods in which the catalytic power of an enzyme erodes, through neutral drift and selection for other properties such as cellular energy efficiency or regulation. Thus, many enzymes may have already passed their catalytic peaks. PMID:25926697

Star formation in a hierarchical model for Cloud Complexes

NASA Astrophysics Data System (ADS)

Sanchez, N.; Parravano, A.

The effects of the external and initial conditions on the star formation processes in Molecular Cloud Complexes are examined in the context of a schematic model. The model considers a hierarchical system with five predefined phases: warm gas, neutral gas, low density molecular gas, high density molecular gas and protostars. The model follows the mass evolution of each substructure by computing its mass exchange with their parent and children. The parent-child mass exchange depends on the radiation density at the interphase, which is produced by the radiation coming from the stars that form at the end of the hierarchical structure, and by the external radiation field. The system is chaotic in the sense that its temporal evolution is very sensitive to small changes in the initial or external conditions. However, global features such as the star formation efficience and the Initial Mass Function are less affected by those variations.

Cobalt-embedded nitrogen-rich carbon nanotubes efficiently catalyze hydrogen evolution reaction at all pH values.

PubMed

Zou, Xiaoxin; Huang, Xiaoxi; Goswami, Anandarup; Silva, Rafael; Sathe, Bhaskar R; Mikmeková, Eliška; Asefa, Tewodros

2014-04-22

Despite being technically possible, splitting water to generate hydrogen is still practically unfeasible due mainly to the lack of sustainable and efficient catalysts for the half reactions involved. Herein we report the synthesis of cobalt-embedded nitrogen-rich carbon nanotubes (NRCNTs) that 1) can efficiently electrocatalyze the hydrogen evolution reaction (HER) with activities close to that of Pt and 2) function well under acidic, neutral or basic media alike, allowing them to be coupled with the best available oxygen-evolving catalysts-which also play crucial roles in the overall water-splitting reaction. The materials are synthesized by a simple, easily scalable synthetic route involving thermal treatment of Co(2+) -embedded graphitic carbon nitride derived from inexpensive starting materials (dicyandiamide and CoCl2 ). The materials' efficient catalytic activity is mainly attributed to their nitrogen dopants and concomitant structural defects. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Coverage of Human Evolution in High School Biology Textbooks in the 20th Century and in Current State Science Standards

ERIC Educational Resources Information Center

Skoog, Gerald

2005-01-01

Efforts to eliminate or neutralize the coverage of evolution in high school biology textbooks in the United States have persisted with varying degrees of intensity and success since the 1920s. In particular, the coverage of human evolution has been impacted by these efforts. Evidence of the success of these efforts can be chronicled by the…

Self-shielding of hydrogen in the IGM during the epoch of reionization

NASA Astrophysics Data System (ADS)

Chardin, Jonathan; Kulkarni, Girish; Haehnelt, Martin G.

2018-04-01

We investigate self-shielding of intergalactic hydrogen against ionizing radiation in radiative transfer simulations of cosmic reionization carefully calibrated with Lyα forest data. While self-shielded regions manifest as Lyman-limit systems in the post-reionization Universe, here we focus on their evolution during reionization (redshifts z = 6-10). At these redshifts, the spatial distribution of hydrogen-ionizing radiation is highly inhomogeneous, and some regions of the Universe are still neutral. After masking the neutral regions and ionizing sources in the simulation, we find that the hydrogen photoionization rate depends on the local hydrogen density in a manner very similar to that in the post-reionization Universe. The characteristic physical hydrogen density above which self-shielding becomes important at these redshifts is about nH ˜ 3 × 10-3 cm-3, or ˜20 times the mean hydrogen density, reflecting the fact that during reionization photoionization rates are typically low enough that the filaments in the cosmic web are often self-shielded. The value of the typical self-shielding density decreases by a factor of 3 between redshifts z = 3 and 10, and follows the evolution of the average photoionization rate in ionized regions in a simple fashion. We provide a simple parameterization of the photoionization rate as a function of density in self-shielded regions during the epoch of reionization.

Self-shielding of hydrogen in the IGM during the epoch of reionization

NASA Astrophysics Data System (ADS)

Chardin, Jonathan; Kulkarni, Girish; Haehnelt, Martin G.

2018-07-01

We investigate self-shielding of intergalactic hydrogen against ionizing radiation in radiative transfer simulations of cosmic reionization carefully calibrated with Lyα forest data. While self-shielded regions manifest as Lyman limit systems in the post-reionization Universe, here we focus on their evolution during reionization (redshifts z = 6-10). At these redshifts, the spatial distribution of hydrogen-ionizing radiation is highly inhomogeneous, and some regions of the Universe are still neutral. After masking the neutral regions and ionizing sources in the simulation, we find that the hydrogen photoionization rate depends on the local hydrogen density in a manner very similar to that in the post-reionization Universe. The characteristic physical hydrogen density above which self-shielding becomes important at these redshifts is about nH ˜ 3 × 10-3 cm-3, or ˜20 times the mean hydrogen density, reflecting the fact that during reionization photoionization rates are typically low enough that the filaments in the cosmic web are often self-shielded. The value of the typical self-shielding density decreases by a factor of 3 between redshifts z = 3 and 10, and follows the evolution of the average photoionization rate in ionized regions in a simple fashion. We provide a simple parametrization of the photoionization rate as a function of density in self-shielded regions during the epoch of reionization.

Photo-Oxidative Stress-Driven Mutagenesis and Adaptive Evolution on the Marine Diatom Phaeodactylum tricornutum for Enhanced Carotenoid Accumulation.

PubMed

Yi, Zhiqian; Xu, Maonian; Magnusdottir, Manuela; Zhang, Yuetuan; Brynjolfsson, Sigurdur; Fu, Weiqi

2015-09-29

Marine diatoms have recently gained much attention as they are expected to be a promising resource for sustainable production of bioactive compounds such as carotenoids and biofuels as a future clean energy solution. To develop photosynthetic cell factories, it is important to improve diatoms for value-added products. In this study, we utilized UVC radiation to induce mutations in the marine diatom Phaeodactylum tricornutum and screened strains with enhanced accumulation of neutral lipids and carotenoids. Adaptive laboratory evolution (ALE) was also used in parallel to develop altered phenotypic and biological functions in P. tricornutum and it was reported for the first time that ALE was successfully applied on diatoms for the enhancement of growth performance and productivity of value-added carotenoids to date. Liquid chromatography-mass spectrometry (LC-MS) was utilized to study the composition of major pigments in the wild type P. tricornutum, UV mutants and ALE strains. UVC radiated strains exhibited higher accumulation of fucoxanthin as well as neutral lipids compared to their wild type counterpart. In addition to UV mutagenesis, P. tricornutum strains developed by ALE also yielded enhanced biomass production and fucoxanthin accumulation under combined red and blue light. In short, both UV mutagenesis and ALE appeared as an effective approach to developing desired phenotypes in the marine diatoms via electromagnetic radiation-induced oxidative stress.

Photo-Oxidative Stress-Driven Mutagenesis and Adaptive Evolution on the Marine Diatom Phaeodactylum tricornutum for Enhanced Carotenoid Accumulation

PubMed Central

Yi, Zhiqian; Xu, Maonian; Magnusdottir, Manuela; Zhang, Yuetuan; Brynjolfsson, Sigurdur; Fu, Weiqi

2015-01-01

Marine diatoms have recently gained much attention as they are expected to be a promising resource for sustainable production of bioactive compounds such as carotenoids and biofuels as a future clean energy solution. To develop photosynthetic cell factories, it is important to improve diatoms for value-added products. In this study, we utilized UVC radiation to induce mutations in the marine diatom Phaeodactylum tricornutum and screened strains with enhanced accumulation of neutral lipids and carotenoids. Adaptive laboratory evolution (ALE) was also used in parallel to develop altered phenotypic and biological functions in P. tricornutum and it was reported for the first time that ALE was successfully applied on diatoms for the enhancement of growth performance and productivity of value-added carotenoids to date. Liquid chromatography-mass spectrometry (LC-MS) was utilized to study the composition of major pigments in the wild type P. tricornutum, UV mutants and ALE strains. UVC radiated strains exhibited higher accumulation of fucoxanthin as well as neutral lipids compared to their wild type counterpart. In addition to UV mutagenesis, P. tricornutum strains developed by ALE also yielded enhanced biomass production and fucoxanthin accumulation under combined red and blue light. In short, both UV mutagenesis and ALE appeared as an effective approach to developing desired phenotypes in the marine diatoms via electromagnetic radiation-induced oxidative stress. PMID:26426027

Evolution dynamics of a model for gene duplication under adaptive conflict

NASA Astrophysics Data System (ADS)

Ancliff, Mark; Park, Jeong-Man

2014-06-01

We present and solve the dynamics of a model for gene duplication showing escape from adaptive conflict. We use a Crow-Kimura quasispecies model of evolution where the fitness landscape is a function of Hamming distances from two reference sequences, which are assumed to optimize two different gene functions, to describe the dynamics of a mixed population of individuals with single and double copies of a pleiotropic gene. The evolution equations are solved through a spin coherent state path integral, and we find two phases: one is an escape from an adaptive conflict phase, where each copy of a duplicated gene evolves toward subfunctionalization, and the other is a duplication loss of function phase, where one copy maintains its pleiotropic form and the other copy undergoes neutral mutation. The phase is determined by a competition between the fitness benefits of subfunctionalization and the greater mutational load associated with maintaining two gene copies. In the escape phase, we find a dynamics of an initial population of single gene sequences only which escape adaptive conflict through gene duplication and find that there are two time regimes: until a time t* single gene sequences dominate, and after t* double gene sequences outgrow single gene sequences. The time t* is identified as the time necessary for subfunctionalization to evolve and spread throughout the double gene sequences, and we show that there is an optimum mutation rate which minimizes this time scale.

Propagation of large amplitude Alfven waves in the solar wind neutral sheet

NASA Technical Reports Server (NTRS)

Malara, F.; Primavera, L.; Veltri, P.

1995-01-01

Analysis of solar wind fluctuation data show that the correlation between velocity and magnetic field fluctuations decreases when going farther away from the Sun. This decorrelation can be attributed either to the time evolution of the fluctuations, carried away by the solar wind, or to the interaction between the solar wind neutral sheet and Alfven waves. To check this second hypothesis we have numerically studied the propagation of Alfven waves in the solar wind neutral sheet. The initial conditions have been set up in order to guarantee B(exp 2) = const, so that the following numerical evolution is only due to the inhomogeneity in the background magnetic field. The analysis of the results shows that compressive structures are formed, mainly in the neutral sheet where they have been identified as pressure balanced structures, i.e., tangential discontinuities. Fast perturbations, which are also produced, have a tendency to leave the simulation domain, propagating also perpendicularly to the mean magnetic field. For this reason the level of fast perturbations is always smaller with respect to the previously cited plasma balanced structures, which are slow mode perturbations. A comparison between the numerical results and some particular observational issues is also presented.

Testing natural selection vs. genetic drift in phenotypic evolution using quantitative trait locus data.

PubMed Central

Orr, H A

1998-01-01

Evolutionary biologists have long sought a way to determine whether a phenotypic difference between two taxa was caused by natural selection or random genetic drift. Here I argue that data from quantitative trait locus (QTL) analyses can be used to test the null hypothesis of neutral phenotypic evolution. I propose a sign test that compares the observed number of plus and minus alleles in the "high line" with that expected under neutrality, conditioning on the known phenotypic difference between the taxa. Rejection of the null hypothesis implies a role for directional natural selection. This test is applicable to any character in any organism in which QTL analysis can be performed. PMID:9691061

On the Rayleigh-Taylor Instability in Presence of a Background Shear

NASA Astrophysics Data System (ADS)

Shvydkoy, Roman

2018-01-01

In this note we revisit the classical subject of the Rayleigh-Taylor instability in presence of an incompressible background shear flow. We derive a formula for the essential spectral radius of the evolution group generated by the linearization near the steady state and reveal that the velocity variations neutralize shortwave instabilities. The formula is a direct generalization of the result of Hwang and Guo (Arch Ration Mech Anal 167(3):235-253, (2003). Furthermore, we construct a class of steady states which posses unstable discrete spectrum with neutral essential spectrum. The technique involves the WKB analysis of the evolution equation and contains novel compactness criterion for pseudo-differential operators on unbounded domains.

Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses

DOE PAGES

Moody, M.  Anthony; Gao, Feng; Gurley, Thaddeus  C.; ...

2015-09-09

The third variable (V3) loop and the CD4 binding site (CD4bs) of the viral envelope are frequently targeted by neutralizing antibodies (nAbs) in HIV-1-infected individuals. In chronic infection, virus escape mutants repopulate the plasma and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize, but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tiermore » 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.« less

Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moody, M.  Anthony; Gao, Feng; Gurley, Thaddeus  C.

The third variable (V3) loop and the CD4 binding site (CD4bs) of the viral envelope are frequently targeted by neutralizing antibodies (nAbs) in HIV-1-infected individuals. In chronic infection, virus escape mutants repopulate the plasma and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize, but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tiermore » 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses.« less

Anisotropies in the linear polarization of vacancy photoluminescence in diamond induced by crystal rotations and strong magnetic fields

NASA Astrophysics Data System (ADS)

Braukmann, D.; Popov, V. P.; Glaser, E. R.; Kennedy, T. A.; Bayer, M.; Debus, J.

2018-03-01

We study the linear polarization properties of the photoluminescence of ensembles of neutral and negatively charged nitrogen vacancies and neutral vacancies in diamond crystals as a function of their symmetry and their response to strong external magnetic fields. The linear polarization degree, which exceeds 10% at room temperature, and rotation of the polarization plane of their zero-phonon lines significantly depend on the crystal rotation around specific axes demonstrating anisotropic angular evolutions. The sign of the polarization plane rotation is changed periodically through the crystal rotation, which indicates a switching between electron excited states of orthogonal linear polarizations. At external magnetic fields of up to 10 T, the angular dependencies of the linear polarization degree experience a remarkable phase shift. Moreover, the rotation of the linear polarization plane increases linearly with rising magnetic field at 6 K and room temperature, for the negatively charged nitrogen vacancies, which is attributed to magneto-optical Faraday rotation.

The importance of selection in the evolution of blindness in cavefish.

PubMed

Cartwright, Reed A; Schwartz, Rachel S; Merry, Alexandra L; Howell, Megan M

2017-02-07

Blindness has evolved repeatedly in cave-dwelling organisms, and many hypotheses have been proposed to explain this observation, including both accumulation of neutral loss-of-function mutations and adaptation to darkness. Investigating the loss of sight in cave dwellers presents an opportunity to understand the operation of fundamental evolutionary processes, including drift, selection, mutation, and migration. Here we model the evolution of blindness in caves. This model captures the interaction of three forces: (1) selection favoring alleles causing blindness, (2) immigration of sightedness alleles from a surface population, and (3) mutations creating blindness alleles. We investigated the dynamics of this model and determined selection-strength thresholds that result in blindness evolving in caves despite immigration of sightedness alleles from the surface. We estimate that the selection coefficient for blindness would need to be at least 0.005 (and maybe as high as 0.5) for blindness to evolve in the model cave-organism, Astyanax mexicanus. Our results indicate that strong selection is required for the evolution of blindness in cave-dwelling organisms, which is consistent with recent work suggesting a high metabolic cost of eye development.

Etch Profile Simulation Using Level Set Methods

NASA Technical Reports Server (NTRS)

Hwang, Helen H.; Meyyappan, Meyya; Arnold, James O. (Technical Monitor)

1997-01-01

Etching and deposition of materials are critical steps in semiconductor processing for device manufacturing. Both etching and deposition may have isotropic and anisotropic components, due to directional sputtering and redeposition of materials, for example. Previous attempts at modeling profile evolution have used so-called "string theory" to simulate the moving solid-gas interface between the semiconductor and the plasma. One complication of this method is that extensive de-looping schemes are required at the profile corners. We will present a 2D profile evolution simulation using level set theory to model the surface. (1) By embedding the location of the interface in a field variable, the need for de-looping schemes is eliminated and profile corners are more accurately modeled. This level set profile evolution model will calculate both isotropic and anisotropic etch and deposition rates of a substrate in low pressure (10s mTorr) plasmas, considering the incident ion energy angular distribution functions and neutral fluxes. We will present etching profiles of Si substrates in Ar/Cl2 discharges for various incident ion energies and trench geometries.

High Epstein-Barr Virus Load and Genomic Diversity Are Associated with Generation of gp350-Specific Neutralizing Antibodies following Acute Infectious Mononucleosis

PubMed Central

Weiss, Eric R.; Alter, Galit; Ogembo, Javier Gordon; Henderson, Jennifer L.; Tabak, Barbara; Bakiş, Yasin; Somasundaran, Mohan; Garber, Manuel; Selin, Liisa

2016-01-01

ABSTRACT The Epstein-Barr virus (EBV) gp350 glycoprotein interacts with the cellular receptor to mediate viral entry and is thought to be the major target for neutralizing antibodies. To better understand the role of EBV-specific antibodies in the control of viral replication and the evolution of sequence diversity, we measured EBV gp350-specific antibody responses and sequenced the gp350 gene in samples obtained from individuals experiencing primary EBV infection (acute infectious mononucleosis [AIM]) and again 6 months later (during convalescence [CONV]). EBV gp350-specific IgG was detected in the sera of 17 (71%) of 24 individuals at the time of AIM and all 24 (100%) individuals during CONV; binding antibody titers increased from AIM through CONV, reaching levels equivalent to those in age-matched, chronically infected individuals. Antibody-dependent cell-mediated phagocytosis (ADCP) was rarely detected during AIM (4 of 24 individuals; 17%) but was commonly detected during CONV (19 of 24 individuals; 79%). The majority (83%) of samples taken during AIM neutralized infection of primary B cells; all samples obtained at 6 months postdiagnosis neutralized EBV infection of cultured and primary target cells. Deep sequencing revealed interpatient gp350 sequence variation but conservation of the CR2-binding site. The levels of gp350-specific neutralizing activity directly correlated with higher peripheral blood EBV DNA levels during AIM and a greater evolution of diversity in gp350 nucleotide sequences from AIM to CONV. In summary, we conclude that the viral load and EBV gp350 diversity during early infection are associated with the development of neutralizing antibody responses following AIM. IMPORTANCE Antibodies against viral surface proteins can blunt the spread of viral infection by coating viral particles, mediating uptake by immune cells, or blocking interaction with host cell receptors, making them a desirable component of a sterilizing vaccine. The EBV surface protein gp350 is a major target for antibodies. We report the detection of EBV gp350-specific antibodies capable of neutralizing EBV infection in vitro. The majority of gp350-directed vaccines focus on glycoproteins from lab-adapted strains, which may poorly reflect primary viral envelope diversity. We report some of the first primary gp350 sequences, noting that the gp350 host receptor binding site is remarkably stable across patients and time. However, changes in overall gene diversity were detectable during infection. Patients with higher peripheral blood viral loads in primary infection and greater changes in viral diversity generated more efficient antibodies. Our findings provide insight into the generation of functional antibodies, necessary for vaccine development. PMID:27733645

High Epstein-Barr Virus Load and Genomic Diversity Are Associated with Generation of gp350-Specific Neutralizing Antibodies following Acute Infectious Mononucleosis.

PubMed

Weiss, Eric R; Alter, Galit; Ogembo, Javier Gordon; Henderson, Jennifer L; Tabak, Barbara; Bakiş, Yasin; Somasundaran, Mohan; Garber, Manuel; Selin, Liisa; Luzuriaga, Katherine

2017-01-01

The Epstein-Barr virus (EBV) gp350 glycoprotein interacts with the cellular receptor to mediate viral entry and is thought to be the major target for neutralizing antibodies. To better understand the role of EBV-specific antibodies in the control of viral replication and the evolution of sequence diversity, we measured EBV gp350-specific antibody responses and sequenced the gp350 gene in samples obtained from individuals experiencing primary EBV infection (acute infectious mononucleosis [AIM]) and again 6 months later (during convalescence [CONV]). EBV gp350-specific IgG was detected in the sera of 17 (71%) of 24 individuals at the time of AIM and all 24 (100%) individuals during CONV; binding antibody titers increased from AIM through CONV, reaching levels equivalent to those in age-matched, chronically infected individuals. Antibody-dependent cell-mediated phagocytosis (ADCP) was rarely detected during AIM (4 of 24 individuals; 17%) but was commonly detected during CONV (19 of 24 individuals; 79%). The majority (83%) of samples taken during AIM neutralized infection of primary B cells; all samples obtained at 6 months postdiagnosis neutralized EBV infection of cultured and primary target cells. Deep sequencing revealed interpatient gp350 sequence variation but conservation of the CR2-binding site. The levels of gp350-specific neutralizing activity directly correlated with higher peripheral blood EBV DNA levels during AIM and a greater evolution of diversity in gp350 nucleotide sequences from AIM to CONV. In summary, we conclude that the viral load and EBV gp350 diversity during early infection are associated with the development of neutralizing antibody responses following AIM. Antibodies against viral surface proteins can blunt the spread of viral infection by coating viral particles, mediating uptake by immune cells, or blocking interaction with host cell receptors, making them a desirable component of a sterilizing vaccine. The EBV surface protein gp350 is a major target for antibodies. We report the detection of EBV gp350-specific antibodies capable of neutralizing EBV infection in vitro The majority of gp350-directed vaccines focus on glycoproteins from lab-adapted strains, which may poorly reflect primary viral envelope diversity. We report some of the first primary gp350 sequences, noting that the gp350 host receptor binding site is remarkably stable across patients and time. However, changes in overall gene diversity were detectable during infection. Patients with higher peripheral blood viral loads in primary infection and greater changes in viral diversity generated more efficient antibodies. Our findings provide insight into the generation of functional antibodies, necessary for vaccine development. Copyright © 2016 American Society for Microbiology.

Large shield volcanos on Venus: The effect of neutral buoyancy zone development on evolution and altitude distribution

NASA Technical Reports Server (NTRS)

Keddie, S.; Head, James W., III

1992-01-01

The Magellan mission to Venus has emphasized the importance of volcanism in shaping the surface of the planet. Volcanic plains make up 80 percent of the terrain and hundreds of regions of localized eruptions have been identified. Large volcanos, defined as edifices with diameters greater than 100 km, are the sites of some of the most voluminous eruptions. Head et al. have identified 158 of these structures. Their spatial distribution is neither random nor arranged in linear chains as on the Earth; large volcanos on Venus are concentrated in two large, near-equatorial clusters that are also the site of many other forms of volcanic activity. The set of conditions that must be met on Venus that controls the change from widespread, distributed volcanism to focused, shield-building volcanism is not well understood. Future studies of transitional features will help to address this problem. It is likely, however, that the formation and evolution of a neutral buoyancy zone (NBZ) plays an important role in both determining the style of the volcanism and the development of the volcanic feature once it has begun to erupt. Head and Wilson have suggested that the high surface pressure on Venus may inhibit volatile exsolution, which may influence the density distribution of the upper crust and hence control the nature and location of a NBZ. The extreme variations in pressure with elevation may result in significantly different characteristics of such a NBZ at different locations on the planet. In order to test these ideas regarding the importance of NBZ development in the evolution of a large shield and to determine the style of volcanism, three large volcanos that occur at different basal elevations were examined and the distribution of large volcanos as a function of altitude was determined.

Hepatitis C virus quasispecies and pseudotype analysis from acute infection to chronicity in HIV-1 co-infected individuals.

PubMed

Ferns, R Bridget; Tarr, Alexander W; Hue, Stephane; Urbanowicz, Richard A; McClure, C Patrick; Gilson, Richard; Ball, Jonathan K; Nastouli, Eleni; Garson, Jeremy A; Pillay, Deenan

2016-05-01

HIV-1 infected patients who acquire HCV infection have higher rates of chronicity and liver disease progression than patients with HCV mono-infection. Understanding early events in this pathogenic process is important. We applied single genome sequencing of the E1 to NS3 regions and viral pseudotype neutralization assays to explore the consequences of viral quasispecies evolution from pre-seroconversion to chronicity in four co-infected individuals (mean follow up 566 days). We observed that one to three founder viruses were transmitted. Relatively low viral sequence diversity, possibly related to an impaired immune response, due to HIV infection was observed in three patients. However, the fourth patient, after an early purifying selection displayed increasing E2 sequence evolution, possibly related to being on suppressive antiretroviral therapy. Viral pseudotypes generated from HCV variants showed relative resistance to neutralization by autologous plasma but not to plasma collected from later time points, confirming ongoing virus escape from antibody neutralization. Copyright © 2016 Elsevier Inc. All rights reserved.

Characterizing Phase Transitions in a Model of Neutral Evolutionary Dynamics

NASA Astrophysics Data System (ADS)

Scott, Adam; King, Dawn; Bahar, Sonya

2013-03-01

An evolutionary model was recently introduced for sympatric, phenotypic evolution over a variable fitness landscape with assortative mating (Dees & Bahar 2010). Organisms in the model are described by coordinates in a two-dimensional phenotype space, born at random coordinates with limited variation from their parents as determined by a mutation parameter, mutability. The model has been extended to include both neutral evolution and asexual reproduction in Scott et al (submitted). It has been demonstrated that a second order, non-equilibrium phase transition occurs for the temporal dynamics as the mutability is varied, for both the original model and for neutral conditions. This transition likely belongs to the directed percolation universality class. In contrast, the spatial dynamics of the model shows characteristics of an ordinary percolation phase transition. Here, we characterize the phase transitions exhibited by this model by determining critical exponents for the relaxation times, characteristic lengths, and cluster (species) mass distributions. Missouri Research Board; J.S. McDonnell Foundation

A New Constraint on Reionization from the Evolution of the Lyα Luminosity Function at z ˜ 6-7 Probed by a Deep Census of z = 7.0 Lyα Emitter Candidates to 0.3L *

NASA Astrophysics Data System (ADS)

Ota, Kazuaki; Iye, Masanori; Kashikawa, Nobunari; Konno, Akira; Nakata, Fumiaki; Totani, Tomonori; Kobayashi, Masakazu A. R.; Fudamoto, Yoshinobu; Seko, Akifumi; Toshikawa, Jun; Ichikawa, Akie; Shibuya, Takatoshi; Onoue, Masafusa

2017-07-01

We detect 20 z = 7.0 Lyα emitter (LAE) candidates to L(Lyα) ˜ 2 × 1042 erg s-1 or 0.3 {L}z=7* and in a volume of 6.1 × 105 Mpc3 in the Subaru Deep Field and the Subaru/XMM-Newton Deep Survey field by 82 hr and 37 hr of Subaru Suprime-Cam narrowband NB973 and reddest optical y-band imaging. We compare their Lyα and UV luminosity functions (LFs) and densities and Lyα equivalent widths (EWs) to those of z = 5.7, 6.6, and 7.3 LAEs from previous Suprime-Cam surveys. The Lyα LF (density) rapidly declines by a factor of ×1.5 (1.9) in L(Lyα) at z = 5.7-6.6 (160 Myr), ×1.5 (1.6) at z = 6.6-7.0 (60 Myr) at the faint end, and ×2.0 (3.8) at z = 7.0-7.3 (40 Myr). Also, in addition to the systematic decrease in EW at z = 5.7-6.6 previously found, two-thirds of the z = 7.0 LAEs detected in the UV continuum exhibit lower EWs than the z = 6.6 ones. Moreover, while the UV LF and density do not evolve at z = 5.7-6.6, they modestly decline at z = 6.6-7.0, implying galaxy evolution contributing to the decline of the Lyα LF. Comparison of the z = 7.0 Lyα LF to the one predicted by an LAE evolution model further reveals that galaxy evolution alone cannot explain all of the decline of the Lyα LF. If we attribute the discrepancy to Lyα attenuation by neutral hydrogen, the intergalactic medium transmission of Lyα photons at z = 7.0 would be {T}{Lyα }{IGM}≤slant 0.6{--}0.7. It is lower (higher) than the {T}{Lyα }{IGM} at z = 6.6 (7.3) derived by previous studies, suggesting rapid increase in neutral fraction at z > 6. Based on data collected at Subaru Telescope, which is operated by the National Astronomical Observatory of Japan.

Ion and neutral dynamics in Hall plasma accelerator ionization instabilities

NASA Astrophysics Data System (ADS)

Lucca Fabris, Andrea; Young, Christopher; Cappelli, Mark

2015-09-01

Hall thrusters, the extensively studied E × B devices used for space propulsion applications, are rife with instabilities and fluctuations. Many are thought to be fundamentally linked to microscopic processes like electron transport across magnetic field lines and propellant ionization that in turn affect macroscopic properties like device performance and lifetime. One of the strongest oscillatory regimes is the ``breathing mode,'' characterized by a propagating ionization front, time-varying ion acceleration profiles, and quasi-periodic 10-50 kHz current oscillations. Determining the temporal and spatial evolution of plasma properties is critical to achieving a fundamental physical understanding of these processes. We present non-intrusive laser-induced fluorescence measurements of the local ion and neutral velocity distribution functions synchronized with the breathing mode oscillations. Measurements reveal strong ion velocity fluctuations, multiple ion populations arising in narrow time windows throughout the near-field plume, and the periodic population and depopulation of neutral excited states. Analyzing these detailed experimental results in the context of the existing literature clarifies the fundamental physical processes underlying the breathing mode. This work is sponsored by the U.S. Air Force Office of Scientific Research with Dr. M. Birkan as program manager. C.Y. acknowledges support from the DOE NSSA Stewardship Science Graduate Fellowship under contract DE-FC52-08NA28752.

Theory-driven design of high-valence metal sites for water oxidation confirmed using in situ soft X-ray absorption

NASA Astrophysics Data System (ADS)

Zheng, Xueli; Zhang, Bo; de Luna, Phil; Liang, Yufeng; Comin, Riccardo; Voznyy, Oleksandr; Han, Lili; García de Arquer, F. Pelayo; Liu, Min; Dinh, Cao Thang; Regier, Tom; Dynes, James J.; He, Sisi; Xin, Huolin L.; Peng, Huisheng; Prendergast, David; Du, Xiwen; Sargent, Edward H.

2018-02-01

The efficiency with which renewable fuels and feedstocks are synthesized from electrical sources is limited at present by the sluggish oxygen evolution reaction (OER) in pH-neutral media. We took the view that generating transition-metal sites with high valence at low applied bias should improve the activity of neutral OER catalysts. Here, using density functional theory, we find that the formation energy of desired Ni4+ sites is systematically modulated by incorporating judicious combinations of Co, Fe and non-metal P. We therefore synthesized NiCoFeP oxyhydroxides and probed their oxidation kinetics with in situ soft X-ray absorption spectroscopy (sXAS). In situ sXAS studies of neutral-pH OER catalysts indicate ready promotion of Ni4+ under low overpotential conditions. The NiCoFeP catalyst outperforms IrO2 and retains its performance following 100 h of operation. We showcase NiCoFeP in a membrane-free CO2 electroreduction system that achieves a 1.99 V cell voltage at 10 mA cm-2, reducing CO2 into CO and oxidizing H2O to O2 with a 64% electricity-to-chemical-fuel efficiency.

Theory-driven design of high-valence metal sites for water oxidation confirmed using in situ soft X-ray absorption

DOE PAGES

Zheng, Xueli; Zhang, Bo; De Luna, Phil; ...

2017-11-20

The efficiency with which renewable fuels and feedstocks are synthesized from electrical sources is limited at present by the sluggish oxygen evolution reaction (OER) in pH-neutral media. Here, we took the view that generating transition metal sites with high valence at low applied bias should improve the activity of neutral OER catalysts. Using density functional theory, we find that the formation energy of desired Ni 4+ sites is systematically modulated by incorporating judicious combinations of Co, Fe and non-metal phosphorus. Here we synthesized NiCoFeP oxyhydroxides and probed their oxidation kinetics by employing in situ soft X-ray absorption (sXAS). In situmore » sXAS studies of neutral-pH OER catalysts indicate ready promotion of Ni 4+ under low overpotential conditions. NiCoFeP catalyst outperforms IrO 2 and retains its performance following 100 hours of operation. We showcase NiCoFeP in a membrane-free CO 2 electroreduction system that achieves a 1.99 V cell voltage at 10 mA cm -2, reducing CO 2 into CO and oxidizing H 2O to O 2 with a 64% electricity-to-chemical-fuel efficiency.« less

Theory-driven design of high-valence metal sites for water oxidation confirmed using in situ soft X-ray absorption

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, Xueli; Zhang, Bo; De Luna, Phil

The efficiency with which renewable fuels and feedstocks are synthesized from electrical sources is limited at present by the sluggish oxygen evolution reaction (OER) in pH-neutral media. Here, we took the view that generating transition metal sites with high valence at low applied bias should improve the activity of neutral OER catalysts. Using density functional theory, we find that the formation energy of desired Ni 4+ sites is systematically modulated by incorporating judicious combinations of Co, Fe and non-metal phosphorus. Here we synthesized NiCoFeP oxyhydroxides and probed their oxidation kinetics by employing in situ soft X-ray absorption (sXAS). In situmore » sXAS studies of neutral-pH OER catalysts indicate ready promotion of Ni 4+ under low overpotential conditions. NiCoFeP catalyst outperforms IrO 2 and retains its performance following 100 hours of operation. We showcase NiCoFeP in a membrane-free CO 2 electroreduction system that achieves a 1.99 V cell voltage at 10 mA cm -2, reducing CO 2 into CO and oxidizing H 2O to O 2 with a 64% electricity-to-chemical-fuel efficiency.« less

Theory-driven design of high-valence metal sites for water oxidation confirmed using in situ soft X-ray absorption.

PubMed

Zheng, Xueli; Zhang, Bo; De Luna, Phil; Liang, Yufeng; Comin, Riccardo; Voznyy, Oleksandr; Han, Lili; García de Arquer, F Pelayo; Liu, Min; Dinh, Cao Thang; Regier, Tom; Dynes, James J; He, Sisi; Xin, Huolin L; Peng, Huisheng; Prendergast, David; Du, Xiwen; Sargent, Edward H

2018-02-01

The efficiency with which renewable fuels and feedstocks are synthesized from electrical sources is limited at present by the sluggish oxygen evolution reaction (OER) in pH-neutral media. We took the view that generating transition-metal sites with high valence at low applied bias should improve the activity of neutral OER catalysts. Here, using density functional theory, we find that the formation energy of desired Ni 4+ sites is systematically modulated by incorporating judicious combinations of Co, Fe and non-metal P. We therefore synthesized NiCoFeP oxyhydroxides and probed their oxidation kinetics with in situ soft X-ray absorption spectroscopy (sXAS). In situ sXAS studies of neutral-pH OER catalysts indicate ready promotion of Ni 4+ under low overpotential conditions. The NiCoFeP catalyst outperforms IrO 2 and retains its performance following 100 h of operation. We showcase NiCoFeP in a membrane-free CO 2 electroreduction system that achieves a 1.99 V cell voltage at 10 mA cm -2 , reducing CO 2 into CO and oxidizing H 2 O to O 2 with a 64% electricity-to-chemical-fuel efficiency.

Evolution of Field-Aligned Electron and Ion Densities From Whistler Mode Radio Soundings During Quiet to Moderately Active Period and Comparisons With SAMI2 Simulations

NASA Astrophysics Data System (ADS)

Reddy, A.; Sonwalkar, V. S.; Huba, J. D.

2018-02-01

Knowledge of field-aligned electron and ion distributions is necessary for understanding the physical processes causing variations in field-aligned electron and ion densities. Using whistler mode sounding by Radio Plasma Imager/Imager for Magnetopause-to-Aurora Global Exploration (RPI/IMAGE), we determined the evolution of dayside electron and ion densities along L ˜ 2 and L ˜ 3 (90-4,000 km) during a 7 day (21-27 November 2005) geomagnetically quiet to moderately active period. Over this period the O+/H+ transition height was ˜880 ± 60 km and ˜1000 ± 100 km, respectively, at L ˜ 2 and L ˜ 3. The electron density varied in a complex manner; it was different at L ˜ 2 and L ˜ 3 and below and above the O+/H+ transition height. The measured electron and ion densities are consistent with those from Challenging Minisatellite Payload (CHAMP) and Defense Meteorological Satellite Program (DMSP) and other past measurements, but they deviated from bottomside sounding and International Reference Ionosphere (IRI) 2012 empirical model results. Using SAMI2 (Naval Research Laboratory (NRL) ionosphere model) with reasonably adjusted values of inputs (neutral densities, winds, electric fields, and photoelectron heating), we simulated the evolution of O+/H+ transition height and field-aligned electron and ion densities so that a fair agreement was obtained between the simulation results and observations. Simulation studies indicated that reduced neutral densities (H and/or O) with time limited O+-H charge exchange process. This reduction in neutral densities combined with changes in neutral winds and plasma temperature led to the observed variations in the electron and ion densities. The observation/simulation method presented here can be extended to investigate the role of neutral densities and composition, disturbed winds, and prompt penetration electric fields in the storm time ionosphere/plasmasphere dynamics.

Divertor, scrape-off layer and pedestal particle dynamics in the ELM cycle on ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Laggner, F. M.; Keerl, S.; Gnilsen, J.; Wolfrum, E.; Bernert, M.; Carralero, D.; Guimarais, L.; Nikolaeva, V.; Potzel, S.; Cavedon, M.; Mink, F.; Dunne, M. G.; Birkenmeier, G.; Fischer, R.; Viezzer, E.; Willensdorfer, M.; Wischmeier, M.; Aumayr, F.; the EUROfusion MST1 Team; the ASDEX Upgrade Team

2018-02-01

In addition to the relaxation of the pedestal, edge localised modes (ELMs) introduce changes to the divertor and scrape-off layer (SOL) conditions. Their impact on the inter-ELM pedestal recovery is investigated, with emphasis on the electron density (n e) evolution. The typical ELM cycle occurring in an exemplary ASDEX Upgrade discharge interval at moderate applied gas puff and heating power is characterised, utilising several divertor, SOL and pedestal diagnostics. In the studied discharge interval the inner divertor target is detached before the ELM crash, while the outer target is attached. The particles and power expelled by the ELM crash lead to a re-attachment of the inner target plasma. After the ELM crash, the outer divertor target moves into a high recycling regime with large n e in front of the plate, which is accompanied by high main chamber neutral fluxes. On similar timescales, the inner target fully detaches and the high field side high density region (HFSHD) is formed reaching up to the high field side midplane. This state evolves again to the pre-ELM state, when the main chamber neutral fluxes are reduced later in the ELM cycle. Neither the timescale of the appearance of the HFSHD nor the increase of the main chamber neutral fluxes fit the timescale of the n e pedestal, which is faster. It is found that during the n e pedestal recovery, the magnetic activity at the low field side midplane is strongly reduced indicating a lower level of fluctuations. A rough estimation of the particle flux across the pedestal suggests that the particle flux is reduced in this period. In conclusion, the evolution of the n e pedestal is determined by a combination of neutral fluxes, HFSHD and reduced particle flux across the pedestal. A reduced particle flux explains the fast, experimentally observed re-establishment of the n e pedestal best, whereas neutrals and HFSHD impact on the evolution of the SOL and separatrix conditions.

Space weathering on near-Earth objects investigated by neutral-particle detection

NASA Astrophysics Data System (ADS)

Plainaki, C.; Milillo, A.; Orsini, S.; Mura, A.; De Angelis, E.; Di Lellis, A. M.; Dotto, E.; Livi, S.; Mangano, V.; Massetti, S.; Palumbo, M. E.

2009-03-01

The ion-sputtering (IS) process is active in many planetary environments in the solar system where plasma precipitates directly on the surface (for instance, Mercury, Moon and Europa). In particular, solar wind sputtering is one of the most important agents for the surface erosion of a near-Earth object (NEO), acting together with other surface release processes, such as photon stimulated desorption (PSD), thermal desorption (TD) and micrometeoroid impact vaporization (MIV). The energy distribution of the IS-released neutrals peaks at a few eVs and extends up to hundreds of eVs. Since all other release processes produce particles of lower energies, the presence of neutral atoms in the energy range above 10 eV and below a few keVs (sputtered high-energy atoms (SHEA)) identifies the IS process. SHEA easily escape from the NEO, due to NEO's extremely weak gravity. Detection and analysis of SHEA will give important information on surface-loss processes as well as on surface elemental composition. The investigation of the active release processes, as a function of the external conditions and the NEO surface properties, is crucial for obtaining a clear view of the body's present loss rate as well as for getting clues on its evolution, which depends significantly on space weather. In this work, an attempt to analyze processes that take place on the surface of these small airless bodies, as a result of their exposure to the space environment, has been realized. For this reason, a new space weathering model (space weathering on NEO-SPAWN) is presented. Moreover, an instrument concept of a neutral-particle analyzer specifically designed for the measurement of neutral density and the detection of SHEA from a NEO is proposed.

Space weathering on near-Earth objects investigated by neutral-particle detection

NASA Astrophysics Data System (ADS)

Plainaki, C.; Milillo, A.; Orsini, S.; Mura, A.; de Angelis, E.; di Lellis, A. M.; Dotto, E.; Livi, S.; Mangano, V.; Palumbo, M. E.

2009-04-01

The ion-sputtering (IS) process is active in many planetary environments in the solar system where plasma precipitates directly on the surface (for instance, Mercury, Moon and Europa). In particular, solar wind sputtering is one of the most important agents for the surface erosion of a near-Earth object (NEO), acting together with other surface release processes, such as photon stimulated desorption (PSD), thermal desorption (TD) and micrometeoroid impact vaporization (MIV). The energy distribution of the IS-released neutrals peaks at a few eVs and extends up to hundreds of eVs. Since all other release processes produce particles of lower energies, the presence of neutral atoms in the energy range above 10 eV and below a few keVs (sputtered high-energy atoms (SHEA)) identifies the IS process. SHEA easily escape from the NEO, due to NEO's extremely weak gravity. Detection and analysis of SHEA will give important information on surface-loss processes as well as on surface elemental composition. The investigation of the active release processes, as a function of the external conditions and the NEO surface properties, is crucial for obtaining a clear view of the body's present loss rate as well as for getting clues on its evolution, which depends significantly on space weather. In this work, an attempt to analyze processes that take place on the surface of these small airless bodies, as a result of their exposure to the space environment, has been realized. For this reason, a new space weathering model (space weathering on NEO-SPAWN) is presented. Moreover, an instrument concept of a neutral-particle analyzer specifically designed for the measurement of neutral density and the detection of SHEA from a NEO is proposed.

Structure and composition of the neutral upper atmosphere of Mars from the MAVEN NGIMS investigation

PubMed Central

Benna, M.; Elrod, M.; Yelle, R. V.; Bougher, S. W.; Stone, S. W.; Jakosky, B. M.

2015-01-01

Abstract The Mars Atmosphere and Volatile EvolutioN (MAVEN) Neutral Gas and Ion Mass Spectrometer (NGIMS) provides sensitive detections of neutral gas and ambient ion composition. NGIMS measurements of nine atomic and molecular neutral species, and their variation with altitude, latitude, and solar zenith angle are reported over several months of operation of the MAVEN mission. Sampling NGIMS signals from multiple neutral species every several seconds reveals persistent and unexpectedly large amplitude density structures. The scale height temperatures are mapped over the course of the first few months of the mission from high down to midlatitudes. NGIMS measurements near the homopause of 40Ar/N2 ratios agree with those reported by the Sample Analysis at Mars investigation and allow the altitude of the homopause for the most abundant gases to be established. PMID:27667873

Large-scale analyses of synonymous substitution rates can be sensitive to assumptions about the process of mutation.

PubMed

Aris-Brosou, Stéphane; Bielawski, Joseph P

2006-08-15

A popular approach to examine the roles of mutation and selection in the evolution of genomes has been to consider the relationship between codon bias and synonymous rates of molecular evolution. A significant relationship between these two quantities is taken to indicate the action of weak selection on substitutions among synonymous codons. The neutral theory predicts that the rate of evolution is inversely related to the level of functional constraint. Therefore, selection against the use of non-preferred codons among those coding for the same amino acid should result in lower rates of synonymous substitution as compared with sites not subject to such selection pressures. However, reliably measuring the extent of such a relationship is problematic, as estimates of synonymous rates are sensitive to our assumptions about the process of molecular evolution. Previous studies showed the importance of accounting for unequal codon frequencies, in particular when synonymous codon usage is highly biased. Yet, unequal codon frequencies can be modeled in different ways, making different assumptions about the mutation process. Here we conduct a simulation study to evaluate two different ways of modeling uneven codon frequencies and show that both model parameterizations can have a dramatic impact on rate estimates and affect biological conclusions about genome evolution. We reanalyze three large data sets to demonstrate the relevance of our results to empirical data analysis.

Mr. Red in the American South: A Response to Lisa Borgerding

ERIC Educational Resources Information Center

Meadows, Lee

2017-01-01

This review essay affirms the work Mr. Red does with his students to support their learning about evolution and how his approach agrees with the realities of teaching evolution in the American South. It then shows how focusing on understanding, but not necessarily belief, adds to Mr. Red's apparent neutrality a complimentary pedagogical approach…

Reasons Given by UK Churchgoers for Their Stance on Evolution

ERIC Educational Resources Information Center

Village, Andrew; Baker, Sylvia

2013-01-01

A sample of 661 churchgoers from a range of Christian denominations in the United Kingdom was asked about Darwinian evolution (defined as the common origin of all species, including humans). Respondents were categorised as those who accepted the idea, those who rejected it, and those who were unsure or neutral. People in each category were given a…

Ion neutral mass spectrometer results from the first flyby of Titan.

PubMed

Waite, J Hunter; Niemann, Hasso; Yelle, Roger V; Kasprzak, Wayne T; Cravens, Thomas E; Luhmann, Janet G; McNutt, Ralph L; Ip, Wing-Huen; Gell, David; De La Haye, Virginie; Müller-Wordag, Ingo; Magee, Brian; Borggren, Nathan; Ledvina, Steve; Fletcher, Greg; Walter, Erin; Miller, Ryan; Scherer, Stefan; Thorpe, Rob; Xu, Jing; Block, Bruce; Arnett, Ken

2005-05-13

The Cassini Ion Neutral Mass Spectrometer (INMS) has obtained the first in situ composition measurements of the neutral densities of molecular nitrogen, methane, molecular hydrogen, argon, and a host of stable carbon-nitrile compounds in Titan's upper atmosphere. INMS in situ mass spectrometry has also provided evidence for atmospheric waves in the upper atmosphere and the first direct measurements of isotopes of nitrogen, carbon, and argon, which reveal interesting clues about the evolution of the atmosphere. The bulk composition and thermal structure of the moon's upper atmosphere do not appear to have changed considerably since the Voyager 1 flyby.

Transition to an Aquatic Habitat Permitted the Repeated Loss of the Pleiotropic KLK8 Gene in Mammals

PubMed Central

Hecker, Nikolai; Sharma, Virag

2017-01-01

Abstract Kallikrein related peptidase 8 (KLK8; also called neuropsin) is a serine protease that plays distinct roles in the skin and hippocampus. In the skin, KLK8 influences keratinocyte proliferation and desquamation, and activates antimicrobial peptides in sweat. In the hippocampus, KLK8 affects memory acquisition. Here, we examined the evolution of KLK8 in mammals and discovered that, out of 70 placental mammals, KLK8 is exclusively lost in three independent fully-aquatic lineages, comprising dolphin, killer whale, minke whale, and manatee. In addition, while the sperm whale has an intact KLK8 reading frame, the gene evolves neutrally in this species. We suggest that the distinct functions of KLK8 likely became obsolete in the aquatic environment, leading to the subsequent loss of KLK8 in several fully-aquatic mammalian lineages. First, the cetacean and manatee skin lacks sweat glands as an adaptation to the aquatic environment, which likely made the epidermal function of KLK8 obsolete. Second, cetaceans and manatees exhibit a proportionally small hippocampus, which may have rendered the hippocampal functions of KLK8 obsolete. Together, our results shed light on the genomic changes that correlate with skin and neuroanatomical differences of aquatic mammals, and show that even pleiotropic genes can be lost during evolution if an environmental change nullifies the need for the different functions of such genes. PMID:29145610

Evolutionary dynamics on graphs: Efficient method for weak selection

NASA Astrophysics Data System (ADS)

Fu, Feng; Wang, Long; Nowak, Martin A.; Hauert, Christoph

2009-04-01

Investigating the evolutionary dynamics of game theoretical interactions in populations where individuals are arranged on a graph can be challenging in terms of computation time. Here, we propose an efficient method to study any type of game on arbitrary graph structures for weak selection. In this limit, evolutionary game dynamics represents a first-order correction to neutral evolution. Spatial correlations can be empirically determined under neutral evolution and provide the basis for formulating the game dynamics as a discrete Markov process by incorporating a detailed description of the microscopic dynamics based on the neutral correlations. This framework is then applied to one of the most intriguing questions in evolutionary biology: the evolution of cooperation. We demonstrate that the degree heterogeneity of a graph impedes cooperation and that the success of tit for tat depends not only on the number of rounds but also on the degree of the graph. Moreover, considering the mutation-selection equilibrium shows that the symmetry of the stationary distribution of states under weak selection is skewed in favor of defectors for larger selection strengths. In particular, degree heterogeneity—a prominent feature of scale-free networks—generally results in a more pronounced increase in the critical benefit-to-cost ratio required for evolution to favor cooperation as compared to regular graphs. This conclusion is corroborated by an analysis of the effects of population structures on the fixation probabilities of strategies in general 2×2 games for different types of graphs. Computer simulations confirm the predictive power of our method and illustrate the improved accuracy as compared to previous studies.

Unveiling the Diffuse, Neutral Interstellar Medium: Absorption Spectroscopy of Galactic Hydrogen

NASA Astrophysics Data System (ADS)

Murray, Claire Elizabeth

The formation of stars and evolution of galaxies depends on the cycle of interstellar matter between supernova-expelled plasma and molecule-rich gas. At the center of this cycle is multiphase neutral hydrogen (HI), whose physical conditions provide key ingredients to theoretical models. However, constraints for HI properties require measurements of gas emission and absorption which have been severely limited by previous observational capabilities. In this thesis, I present the largest survey of Galactic HI absorption ever undertaken with the Karl G. Jansky Very Large Array (VLA). The survey, 21 cm Spectral Line Observations of Neutral Gas with the VLA (21-SPONGE), is a statistical study of HI in all phases using direct absorption measurements. Leveraging novel calibration techniques, I demonstrate the capability of the VLA to detect a significant sample of 21 cm absorption lines from warm, diffuse HI. To maximize observational sensitivity, I stack the 21-SPONGE spectra and detect a pervasive signature of the warm neutral medium in absorption. The inferred excitation (or spin) temperature is consistent with existing estimates, yet higher than predictions from theoretical models of collisional HI excitation. This suggests that radiative feedback via resonant scattering of Lyalpha photons, known as the Wouthuysen-Field effect, is influential with important implications for cosmological 21 cm observations. Next, I compare 21-SPONGE with synthetic HI spectra from 3D numerical simulations using a new, objective decomposition and radiative transfer tool. I quantify the recovery of HI structures and their properties by Gaussian-fitted 21 cm spectral lines for the first time. I find that 21 cm absorption line shapes are sensitive to simulated physics, and demonstrate that my analysis method is a powerful tool for diagnosing neutral ISM conditions. Finally, I compare properties inferred from synthetic spectra with "true" simulation results to construct a bias correction function for estimating HI properties. I apply this correction to the mass distribution of HI as a function of temperature from 21-SPONGE, and find a significant fraction of thermally unstable gas. This confirms that non-steady radiative and dynamical processes, such as turbulence and supernovae, have a strong influence on the thermodynamic state of the ISM.

Strain-Specific V3 and CD4 Binding Site Autologous HIV-1 Neutralizing Antibodies Select Neutralization-Resistant Viruses.

PubMed

Moody, M Anthony; Gao, Feng; Gurley, Thaddeus C; Amos, Joshua D; Kumar, Amit; Hora, Bhavna; Marshall, Dawn J; Whitesides, John F; Xia, Shi-Mao; Parks, Robert; Lloyd, Krissey E; Hwang, Kwan-Ki; Lu, Xiaozhi; Bonsignori, Mattia; Finzi, Andrés; Vandergrift, Nathan A; Alam, S Munir; Ferrari, Guido; Shen, Xiaoying; Tomaras, Georgia D; Kamanga, Gift; Cohen, Myron S; Sam, Noel E; Kapiga, Saidi; Gray, Elin S; Tumba, Nancy L; Morris, Lynn; Zolla-Pazner, Susan; Gorny, Miroslaw K; Mascola, John R; Hahn, Beatrice H; Shaw, George M; Sodroski, Joseph G; Liao, Hua-Xin; Montefiori, David C; Hraber, Peter T; Korber, Bette T; Haynes, Barton F

2015-09-09

The third variable (V3) loop and the CD4 binding site (CD4bs) of the HIV-1 envelope are frequently targeted by neutralizing antibodies (nAbs) in infected individuals. In chronic infection, HIV-1 escape mutants repopulate the plasma, and V3 and CD4bs nAbs emerge that can neutralize heterologous tier 1 easy-to-neutralize but not tier 2 difficult-to-neutralize HIV-1 isolates. However, neutralization sensitivity of autologous plasma viruses to this type of nAb response has not been studied. We describe the development and evolution in vivo of antibodies distinguished by their target specificity for V3 and CD4bs epitopes on autologous tier 2 viruses but not on heterologous tier 2 viruses. A surprisingly high fraction of autologous circulating viruses was sensitive to these antibodies. These findings demonstrate a role for V3 and CD4bs antibodies in constraining the native envelope trimer in vivo to a neutralization-resistant phenotype, explaining why HIV-1 transmission generally occurs by tier 2 neutralization-resistant viruses. Copyright © 2015 Elsevier Inc. All rights reserved.

The Evolution of Finite Amplitude Wavetrains in Plane Channel Flow

NASA Technical Reports Server (NTRS)

Hewitt, R. E.; Hall, P.

1996-01-01

We consider a viscous incompressible fluid flow driven between two parallel plates by a constant pressure gradient. The flow is at a finite Reynolds number, with an 0(l) disturbance in the form of a traveling wave. A phase equation approach is used to discuss the evolution of slowly varying fully nonlinear two dimensional wavetrains. We consider uniform wavetrains in detail, showing that the development of a wavenumber perturbation is governed by Burgers equation in most cases. The wavenumber perturbation theory, constructed using the phase equation approach for a uniform wavetrain, is shown to be distinct from an amplitude perturbation expansion about the periodic flow. In fact we show that the amplitude equation contains only linear terms and is simply the heat equation. We review, briefly, the well known dynamics of Burgers equation, which imply that both shock structures and finite time singularities of the wavenumber perturbation can occur with respect to the slow scales. Numerical computations have been performed to identify areas of the (wavenumber, Reynolds number, energy) neutral surface for which each of these possibilities can occur. We note that the evolution equations will breakdown under certain circumstances, in particular for a weakly nonlinear secondary flow. Finally we extend the theory to three dimensions and discuss the limit of a weak spanwise dependence for uniform wavetrains, showing that two functions are required to describe the evolution. These unknowns are a phase and a pressure function which satisfy a pair of linearly coupled partial differential equations. The results obtained from applying the same analysis to the fully three dimensional problem are included as an appendix.

The Azomethine Ylide Route to Amine C–H Functionalization: Redox-Versions of Classic Reactions and a Pathway to New Transformations

PubMed Central

2016-01-01

Conspectus Redox-neutral methods for the functionalization of amine α-C–H bonds are inherently efficient because they avoid external oxidants and reductants and often do not generate unwanted byproducts. However, most of the current methods for amine α-C–H bond functionalization are oxidative in nature. While the most efficient variants utilize atmospheric oxygen as the terminal oxidant, many such transformations require the use of expensive or toxic oxidants, often coupled with the need for transition metal catalysts. Redox-neutral amine α-functionalizations that involve intramolecular hydride transfer steps provide viable alternatives to certain oxidative reactions. These processes have been known for some time and are particularly well suited for tertiary amine substrates. A mechanistically distinct strategy for secondary amines has emerged only recently, despite sharing common features with a range of classic organic transformations. Among those are such widely used reactions as the Strecker, Mannich, Pictet–Spengler, and Kabachnik–Fields reactions, Friedel–Crafts alkylations, and iminium alkynylations. In these classic processes, condensation of a secondary amine with an aldehyde (or a ketone) typically leads to the formation of an intermediate iminium ion, which is subsequently attacked by a nucleophile. The corresponding redox-versions of these transformations utilize identical starting materials but incorporate an isomerization step that enables α-C–H bond functionalization. Intramolecular versions of these reactions include redox-neutral amine α-amination, α-oxygenation, and α-sulfenylation. In all cases, a reductive N-alkylation is effectively combined with an oxidative α-functionalization, generating water as the only byproduct. Reactions are promoted by simple carboxylic acids and in some cases require no additives. Azomethine ylides, dipolar species whose usage is predominantly in [3 + 2] cycloadditions and other pericyclic processes, have been identified as common intermediates. Extension of this chemistry to amine α,β-difunctionalization has been shown to be possible by way of converting the intermediate azomethine ylides into transient enamines. This Account details the evolution of this general strategy and the progress made to date. Further included is a discussion of related decarboxylative reactions and transformations that result in the redox-neutral aromatization of (partially) saturated cyclic amines. These processes also involve azomethine ylides, reactive intermediates that appear to be far more prevalent in condensation chemistry of amines and carbonyl compounds than previously considered. In contrast, as exemplified by some redox transformations that have been studied in greater detail, iminium ions are not necessarily involved in all amine/aldehyde condensation reactions. PMID:25560649

The azomethine ylide route to amine C-H functionalization: redox-versions of classic reactions and a pathway to new transformations.

PubMed

Seidel, Daniel

2015-02-17

Conspectus Redox-neutral methods for the functionalization of amine α-C-H bonds are inherently efficient because they avoid external oxidants and reductants and often do not generate unwanted byproducts. However, most of the current methods for amine α-C-H bond functionalization are oxidative in nature. While the most efficient variants utilize atmospheric oxygen as the terminal oxidant, many such transformations require the use of expensive or toxic oxidants, often coupled with the need for transition metal catalysts. Redox-neutral amine α-functionalizations that involve intramolecular hydride transfer steps provide viable alternatives to certain oxidative reactions. These processes have been known for some time and are particularly well suited for tertiary amine substrates. A mechanistically distinct strategy for secondary amines has emerged only recently, despite sharing common features with a range of classic organic transformations. Among those are such widely used reactions as the Strecker, Mannich, Pictet-Spengler, and Kabachnik-Fields reactions, Friedel-Crafts alkylations, and iminium alkynylations. In these classic processes, condensation of a secondary amine with an aldehyde (or a ketone) typically leads to the formation of an intermediate iminium ion, which is subsequently attacked by a nucleophile. The corresponding redox-versions of these transformations utilize identical starting materials but incorporate an isomerization step that enables α-C-H bond functionalization. Intramolecular versions of these reactions include redox-neutral amine α-amination, α-oxygenation, and α-sulfenylation. In all cases, a reductive N-alkylation is effectively combined with an oxidative α-functionalization, generating water as the only byproduct. Reactions are promoted by simple carboxylic acids and in some cases require no additives. Azomethine ylides, dipolar species whose usage is predominantly in [3 + 2] cycloadditions and other pericyclic processes, have been identified as common intermediates. Extension of this chemistry to amine α,β-difunctionalization has been shown to be possible by way of converting the intermediate azomethine ylides into transient enamines. This Account details the evolution of this general strategy and the progress made to date. Further included is a discussion of related decarboxylative reactions and transformations that result in the redox-neutral aromatization of (partially) saturated cyclic amines. These processes also involve azomethine ylides, reactive intermediates that appear to be far more prevalent in condensation chemistry of amines and carbonyl compounds than previously considered. In contrast, as exemplified by some redox transformations that have been studied in greater detail, iminium ions are not necessarily involved in all amine/aldehyde condensation reactions.

Adiabatic Quantum Computing with Neutral Atoms

NASA Astrophysics Data System (ADS)

Hankin, Aaron; Biedermann, Grant; Burns, George; Jau, Yuan-Yu; Johnson, Cort; Kemme, Shanalyn; Landahl, Andrew; Mangan, Michael; Parazzoli, L. Paul; Schwindt, Peter; Armstrong, Darrell

2012-06-01

We are developing, both theoretically and experimentally, a neutral atom qubit approach to adiabatic quantum computation. Using our microfabricated diffractive optical elements, we plan to implement an array of optical traps for cesium atoms and use Rydberg-dressed ground states to provide a controlled atom-atom interaction. We will develop this experimental capability to generate a two-qubit adiabatic evolution aimed specifically toward demonstrating the two-qubit quadratic unconstrained binary optimization (QUBO) routine.

Testing the link between population genetic differentiation and clade diversification in Costa Rican orchids.

PubMed

Kisel, Yael; Moreno-Letelier, Alejandra C; Bogarín, Diego; Powell, Martyn P; Chase, Mark W; Barraclough, Timothy G

2012-10-01

Species population genetics could be an important factor explaining variation in clade species richness. Here, we use newly generated amplified fragment length polymorphism (AFLP) data to test whether five pairs of sister clades of Costa Rican orchids that differ greatly in species richness also differ in average neutral genetic differentiation within species, expecting that if the strength of processes promoting differentiation within species is phylogenetically heritable, then clades with greater genetic differentiation should diversify more. Contrary to expectation, neutral genetic differentiation does not correlate directly with total diversification in the clades studied. Neutral genetic differentiation varies greatly among species and shows no heritability within clades. Half of the variation in neutral genetic differentiation among populations can be explained by ecological variables, and species-level traits explain the most variation. Unexpectedly, we find no isolation by distance in any species, but genetic differentiation is greater between populations occupying different niches. This pattern corresponds with those observed for microscopic eukaryotes and could reflect effective widespread dispersal of tiny and numerous orchid seeds. Although not providing a definitive answer to whether population genetics processes affect clade diversification, this work highlights the potential for addressing new macroevolutionary questions using a comparative population genetic approach. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Empirical phylogenies and species abundance distributions are consistent with preequilibrium dynamics of neutral community models with gene flow.

PubMed

Bonnet-Lebrun, Anne-Sophie; Manica, Andrea; Eriksson, Anders; Rodrigues, Ana S L

2017-05-01

Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modeled communities-that is with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities-from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by gene flow. The former produced more realistic communities (shape of phylogenetic tree and species-abundance distribution), consistent with gene flow being a key process in macro-evolutionary dynamics. Earlier models struggled to capture the empirically observed branching tempo in phylogenetic trees, as measured by the gamma statistic. We show that the low gamma values typical of empirical trees can be obtained in models with protracted speciation, in preequilibrium communities developing from an initially abundant and widespread species. This was even more so in communities sampled incompletely, particularly if the unknown species are the youngest. Overall, our results demonstrate that the characteristics of empirical communities that we have studied can, to a large extent, be explained through a purely neutral model under preequilibrium conditions. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Two-fluid Numerical Simulations of Solar Spicules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kuźma, Błażej; Murawski, Kris; Kayshap, Pradeep

2017-11-10

We aim to study the formation and evolution of solar spicules by means of numerical simulations of the solar atmosphere. With the use of newly developed JOANNA code, we numerically solve two-fluid (for ions + electrons and neutrals) equations in 2D Cartesian geometry. We follow the evolution of a spicule triggered by the time-dependent signal in ion and neutral components of gas pressure launched in the upper chromosphere. We use the potential magnetic field, which evolves self-consistently, but mainly plays a passive role in the dynamics. Our numerical results reveal that the signal is steepened into a shock that propagatesmore » upward into the corona. The chromospheric cold and dense plasma lags behind this shock and rises into the corona with a mean speed of 20–25 km s{sup −1}. The formed spicule exhibits the upflow/downfall of plasma during its total lifetime of around 3–4 minutes, and it follows the typical characteristics of a classical spicule, which is modeled by magnetohydrodynamics. The simulated spicule consists of a dense and cold core that is dominated by neutrals. The general dynamics of ion and neutral spicules are very similar to each other. Minor differences in those dynamics result in different widths of both spicules with increasing rarefaction of the ion spicule in time.« less

Identification of amino acid substitutions with compensational effects in the attachment protein of canine distemper virus.

PubMed

Sattler, Ursula; Khosravi, Mojtaba; Avila, Mislay; Pilo, Paola; Langedijk, Johannes P; Ader-Ebert, Nadine; Alves, Lisa A; Plattet, Philippe; Origgi, Francesco C

2014-07-01

The hemagglutinin (H) gene of canine distemper virus (CDV) encodes the receptor-binding protein. This protein, together with the fusion (F) protein, is pivotal for infectivity since it contributes to the fusion of the viral envelope with the host cell membrane. Of the two receptors currently known for CDV (nectin-4 and the signaling lymphocyte activation molecule [SLAM]), SLAM is considered the most relevant for host susceptibility. To investigate how evolution might have impacted the host-CDV interaction, we examined the functional properties of a series of missense single nucleotide polymorphisms (SNPs) naturally accumulating within the H-gene sequences during the transition between two distinct but related strains. The two strains, a wild-type strain and a consensus strain, were part of a single continental outbreak in European wildlife and occurred in distinct geographical areas 2 years apart. The deduced amino acid sequence of the two H genes differed at 5 residues. A panel of mutants carrying all the combinations of the SNPs was obtained by site-directed mutagenesis. The selected mutant, wild type, and consensus H proteins were functionally evaluated according to their surface expression, SLAM binding, fusion protein interaction, and cell fusion efficiencies. The results highlight that the most detrimental functional effects are associated with specific sets of SNPs. Strikingly, an efficient compensational system driven by additional SNPs appears to come into play, virtually neutralizing the negative functional effects. This system seems to contribute to the maintenance of the tightly regulated function of the H-gene-encoded attachment protein. Importance: To investigate how evolution might have impacted the host-canine distemper virus (CDV) interaction, we examined the functional properties of naturally occurring single nucleotide polymorphisms (SNPs) in the hemagglutinin gene of two related but distinct strains of CDV. The hemagglutinin gene encodes the attachment protein, which is pivotal for infection. Our results show that few SNPs have a relevant detrimental impact and they generally appear in specific combinations (molecular signatures). These drastic negative changes are neutralized by compensatory mutations, which contribute to maintenance of an overall constant bioactivity of the attachment protein. This compensational mechanism might reflect the reaction of the CDV machinery to the changes occurring in the virus following antigenic variations critical for virulence. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Internucleotide correlations and nucleotide periodicity in Drosophila mtDNA: new evidence for panselective evolution.

PubMed

Valenzuela, Carlos Y

2010-01-01

Analysis for the homogeneity of the distribution of the second base of dinucleotides in relation to the first, whose bases are separated by 0, 1, 2,... 21 nucleotide sites, was performed with the VIH-1 genome (cDNA), the Drosophila mtDNA, the Drosophila Torso gene and the human p-globin gene. These four DNA segments showed highly significant heterogeneities of base distributions that cannot be accounted for by neutral or nearly neutral evolution or by the "neighbor influence" of nucleotides on mutation rates. High correlations are found in the bases of dinucleotides separated by 0, 1 and more number of sites. A periodicity of three consecutive significance values (measured by the x²9) was found only in Drosophila mtDNA. This periodicity may be due to an unknown structure or organization of mtDNA. This non-random distribution of the two bases of dinucleotides widespread throughout these DNA segments is rather compatible with panselective evolution and generalized internucleotide co-adaptation.

Rapid evolution of cis-regulatory sequences via local point mutations

NASA Technical Reports Server (NTRS)

Stone, J. R.; Wray, G. A.

2001-01-01

Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.

Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences.

PubMed

Saber, Morteza Mahmoudi; Adeyemi Babarinde, Isaac; Hettiarachchi, Nilmini; Saitou, Naruya

2016-07-12

Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions. © The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

On the Evolution of the Pulmonary Alveolar Lipofibroblast

PubMed Central

Torday, John S.; Rehan, Virender K.

2015-01-01

The pulmonary alveolar lipofibroblast was first reported in 1970. Since then its development, structure, function and molecular characteristics have been determined. Its capacity to actively absorb, store and ‘traffic’ neutral lipid for protection of the alveolus against oxidant injury, and for the active supply of substrate for lung surfactant phospholipid production have offered the opportunity to identify a number of specialized functions of these strategically placed cells. Namely, Parathyroid Hormone-related Protein (PTHrP) signaling, expression of Adipocyte Differentiation Related Protein, leptin, peroxisome proliferator activator receptor gamma, and the prostaglandin E2 receptor EP2-which are all stretch-regulated, explaining how and why surfactant production is ‘on-demand’ in service to ventilation-perfusion matching. Because of the central role of the lipofibroblast in vertebrate lung physiologic evolution, it is a Rosetta Stone for understanding how and why the lung evolved in adaptation to terrestrial life, beginning with the duplication of the PTHrP Receptor some 300 mya. Moreover, such detailed knowledge of the workings of the lipofibroblast have provided insight to the etiology and effective treatment of Bronchopulmonary Dysplasia based on physiologic principles rather than on pharmacology. PMID:26706109

Intra and Interspecific Variations of Gene Expression Levels in Yeast Are Largely Neutral: (Nei Lecture, SMBE 2016, Gold Coast).

PubMed

Yang, Jian-Rong; Maclean, Calum J; Park, Chungoo; Zhao, Huabin; Zhang, Jianzhi

2017-09-01

It is commonly, although not universally, accepted that most intra and interspecific genome sequence variations are more or less neutral, whereas a large fraction of organism-level phenotypic variations are adaptive. Gene expression levels are molecular phenotypes that bridge the gap between genotypes and corresponding organism-level phenotypes. Yet, it is unknown whether natural variations in gene expression levels are mostly neutral or adaptive. Here we address this fundamental question by genome-wide profiling and comparison of gene expression levels in nine yeast strains belonging to three closely related Saccharomyces species and originating from five different ecological environments. We find that the transcriptome-based clustering of the nine strains approximates the genome sequence-based phylogeny irrespective of their ecological environments. Remarkably, only ∼0.5% of genes exhibit similar expression levels among strains from a common ecological environment, no greater than that among strains with comparable phylogenetic relationships but different environments. These and other observations strongly suggest that most intra and interspecific variations in yeast gene expression levels result from the accumulation of random mutations rather than environmental adaptations. This finding has profound implications for understanding the driving force of gene expression evolution, genetic basis of phenotypic adaptation, and general role of stochasticity in evolution. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Neutral Community Dynamics and the Evolution of Species Interactions.

PubMed

Coelho, Marco Túlio P; Rangel, Thiago F

2018-04-01

A contemporary goal in ecology is to determine the ecological and evolutionary processes that generate recurring structural patterns in mutualistic networks. One of the great challenges is testing the capacity of neutral processes to replicate observed patterns in ecological networks, since the original formulation of the neutral theory lacks trophic interactions. Here, we develop a stochastic-simulation neutral model adding trophic interactions to the neutral theory of biodiversity. Without invoking ecological differences among individuals of different species, and assuming that ecological interactions emerge randomly, we demonstrate that a spatially explicit multitrophic neutral model is able to capture the recurrent structural patterns of mutualistic networks (i.e., degree distribution, connectance, nestedness, and phylogenetic signal of species interactions). Nonrandom species distribution, caused by probabilistic events of migration and speciation, create nonrandom network patterns. These findings have broad implications for the interpretation of niche-based processes as drivers of ecological networks, as well as for the integration of network structures with demographic stochasticity.

Possible modification of the cooling index of interstellar helium pickup ions by electron impact ionization in the inner heliosphere

NASA Astrophysics Data System (ADS)

Chen, Jun Hong; Bochsler, Peter; Möbius, Eberhard; Gloeckler, George

2014-09-01

Interstellar neutrals penetrating into the inner heliosphere are ionized by photoionization, charge exchange with solar wind ions, and electron impact ionization. These processes comprise the first step in the evolution of interstellar pickup ion (PUI) distributions. Typically, PUI distributions have been described in terms of velocity distribution functions that cool adiabatically under solar wind expansion, with a cooling index of 3/2. Recently, the cooling index has been determined experimentally in observations of He PUI distributions with Advanced Composition Explorer (ACE)/Solar Wind Ion Composition Spectrometer and found to vary substantially over the solar cycle. The experimental determination of the cooling index depends on the knowledge of the ionization rates and their spatial variation. Usually, ionization rates increase with 1/r2 as neutral particles approach the Sun, which is not exactly true for electron impact ionization, because the electron temperature increases with decreasing distance from the Sun due to the complexity of its distributions and different radial gradients in temperature. This different dependence on distance may become important in the study of the evolution of PUI distributions and is suspected as one of the potential reasons for the observed variation of the cooling index. Therefore, we investigate in this paper the impact of electron ionization on the variability of the cooling index. We find that the deviation of the electron ionization rate from the canonical 1/r2 behavior of other ionization processes plays only a minor role.

Mr. Red in the American South: a response to Lisa Borgerding

NASA Astrophysics Data System (ADS)

Meadows, Lee

2017-03-01

This review essay affirms the work Mr. Red does with his students to support their learning about evolution and how his approach agrees with the realities of teaching evolution in the American South. It then shows how focusing on understanding, but not necessarily belief, adds to Mr. Red's apparent neutrality a complimentary pedagogical approach that legitimizes more strongly accepted science while at the same time attending to the deep conflict many rural students feel when they are asked to learn evolution.

Effects of convincing power and neutrality on minority opinion spreading

NASA Astrophysics Data System (ADS)

Wu, Yue; Xiong, Xi; Zhang, Yi

2017-02-01

The dynamics evolution of the minority opinion in public debates is studied using a convincing power (CP) model with neutrality. In a given group, an agent with a definite standpoint (yes or no) can be persuaded to be a neutral agent, if its capacity of persuasion is lower than the average CP of its opponents. Besides that a neutral agent will change its state and follow a more persuasive opinion. Starting from two opposite opinions with different rates, repeated local discussions are found to drive the minority reversal. It reveals that in addition to the initial minority, the number of neutral agents is also an important factor to the eventual winners. During the process of consensus, there exists a threshold of initial fraction to guarantee one side win. The results have a guiding significance for designing strategies to win a public debate.

Superposed epoch analysis of ion temperatures during CME- and CIR/HSS-driven storms

NASA Astrophysics Data System (ADS)

Keesee, A. M.; Scime, E. E.

2012-12-01

The NASA Two Wide-angle Imaging Neutral atom Spectrometers (TWINS) Mission provides a global view of the magnetosphere with near-continuous coverage. Utilizing a novel technique to calculate ion temperatures from the TWINS energetic neutral atom (ENA) measurements, we generate ion temperature maps of the magnetosphere. These maps can be used to study ion temperature evolution during geomagnetic storms. A superposed epoch analysis of the ion temperature evolution during 48 storms will be presented. Zaniewski et al. [2006] performed a superposed epoch analysis of ion temperatures by storm interval using data from the MENA instrument on the IMAGE mission, demonstrating significant dayside ion heating during the main phase. The TWINS measurements provide more continuous coverage and improved spatial and temporal resolution. Denton and Borovsky [2008] noted differences in ion temperature evolution at geosynchronous orbit between coronal mass ejection (CME)- and corotating interaction region (CIR)/high speed stream (HSS)- driven storms. Using our global ion temperature maps, we have found consistent results for select individual storms [Keesee et al., 2012]. We will present superposed epoch analyses for the subgroups of CME- and CIR/HSS-driven storms to compare global ion temperature evolution during the two types of storms.

Neutral helium beam probe

NASA Astrophysics Data System (ADS)

Karim, Rezwanul

1999-10-01

This article discusses the development of a code where diagnostic neutral helium beam can be used as a probe. The code solves numerically the evolution of the population densities of helium atoms at their several different energy levels as the beam propagates through the plasma. The collisional radiative model has been utilized in this numerical calculation. The spatial dependence of the metastable states of neutral helium atom, as obtained in this numerical analysis, offers a possible diagnostic tool for tokamak plasma. The spatial evolution for several hypothetical plasma conditions was tested. Simulation routines were also run with the plasma parameters (density and temperature profiles) similar to a shot in the Princeton beta experiment modified (PBX-M) tokamak and a shot in Tokamak Fusion Test Reactor tokamak. A comparison between the simulation result and the experimentally obtained data (for each of these two shots) is presented. A good correlation in such comparisons for a number of such shots can establish the accurateness and usefulness of this probe. The result can possibly be extended for other plasma machines and for various plasma conditions in those machines.

HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage.

PubMed

Landais, Elise; Murrell, Ben; Briney, Bryan; Murrell, Sasha; Rantalainen, Kimmo; Berndsen, Zachary T; Ramos, Alejandra; Wickramasinghe, Lalinda; Smith, Melissa Laird; Eren, Kemal; de Val, Natalia; Wu, Mengyu; Cappelletti, Audrey; Umotoy, Jeffrey; Lie, Yolanda; Wrin, Terri; Algate, Paul; Chan-Hui, Po-Ying; Karita, Etienne; Ward, Andrew B; Wilson, Ian A; Burton, Dennis R; Smith, Davey; Pond, Sergei L Kosakovsky; Poignard, Pascal

2017-11-21

Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Neutrality in the field: alpha-function and the dreaming dyad in psychoanalytic process.

PubMed

Schwartz, Henry P

2013-07-01

Analysts have interpreted the concept of neutrality in a variety of ways, beginning with Strachey's use of that word to translate Freud's (1915) term, Indifferenz. In this paper, neutrality is linked to Freud's notions of free association and evenly suspended attention. A history of psychoanalytic attempts to clarify the concept are presented, with special attention to issues of ambiguity and the patient's role in the determination of neutrality. Neutrality is further elaborated in relation to the bipersonal field as described by the Barangers and contemporary field theorists. Understood in terms of the field, neutrality becomes a transpersonal concept, here conceived in terms of alpha-function and a dreaming dyad. Two clinical examples cast in the light of a Bionian perspective are discussed to suggest an alternative understanding of analytic impasses and their relation to alpha-function and neutrality. © 2013 The Psychoanalytic Quarterly, Inc.

The Quiet Revolution: A New Synthesis of Biological Knowledge

ERIC Educational Resources Information Center

Dyer, K. F.

1971-01-01

Reviews evidence from molecular genetics and biochemistry, which supports the idea of some evolution, due to chance and selectively neutral mutations, occurring independently of natural selection. (AL)

Composition dependence of the mercury vacancies energy levels in HgCdTe: Evolution of the “negative-U” property

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gemain, F.; Robin, I. C.; Feuillet, G.

2013-12-07

HgCdTe films grown by liquid phase epitaxy with different Cd compositions were post-annealed to control the Hg vacancy concentration. Then temperature-dependent Hall measurements and photoluminescence measurements allowed us to study the evolution of the Hg vacancy acceptor levels with the cadmium composition. For Cd compositions below 33% the Hg vacancies in HgCdTe present a negative-U property with the ionized state V{sup −} stabilized compared to the neutral state V{sup 0}. For Cd compositions higher than 45%, the Hg vacancies in HgCdTe present a more standard level ordering with the ionized state V{sup −} at higher energy than the neutral statemore » V{sup 0}.« less

A new technique for in situ measurement of the composition of neutral gas in interplanetary space

NASA Technical Reports Server (NTRS)

Gruntman, Michael A.

1993-01-01

Neutral atoms in interplanetary space play an important role in many processes relevant to the formation and evolution of the Solar System. An experimental approach is proposed for in situ atom detection based on the conversion of neutral atoms to negative ions at a specially prepared sensitive surface. Negative ions are subsequently analyzed and detected in an essentially noise-free mode. The use of the technique for in situ study of the composition of neutral interstellar atoms is considered. It is shown that interstellar H, D, and O atoms and possibly H2 molecules can be measured by the proposed technique. The experiment can be performed from a high-apogee Earth-orbiting satellite or from a deep space probe. Possible applications of the technique are discussed.

The response of plasma density to breaking inertial gravity wave in the lower regions of ionosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Wenbo, E-mail: Wenbo.Tang@asu.edu; Mahalov, Alex, E-mail: Alex.Mahalov@asu.edu

2014-04-15

We present a three-dimensional numerical study for the E and lower F region ionosphere coupled with the neutral atmosphere dynamics. This model is developed based on a previous ionospheric model that examines the transport patterns of plasma density given a prescribed neutral atmospheric flow. Inclusion of neutral dynamics in the model allows us to examine the charge-neutral interactions over the full evolution cycle of an inertial gravity wave when the background flow spins up from rest, saturates and eventually breaks. Using Lagrangian analyses, we show the mixing patterns of the ionospheric responses and the formation of ionospheric layers. The correspondingmore » plasma density in this flow develops complex wave structures and small-scale patches during the gravity wave breaking event.« less

Pump-probe studies of radiation induced defects and formation of warm dense matter with pulsed ion beams

NASA Astrophysics Data System (ADS)

Schenkel, T.; Persaud, A.; Gua, H.; Seidl, P. A.; Waldron, W. L.; Gilson, E. P.; Kaganovich, I. D.; Davidson, R. C.; Friedman, A.; Barnard, J. J.; Minior, A. M.

2014-10-01

We report results from the 2nd generation Neutralized Drift Compression Experiment at Berkeley Lab. NDCX-II is a pulsed, linear induction accelerator designed to drive thin foils to warm dense matter (WDM) states with peak temperatures of ~ 1 eV using intense, short pulses of 1.2 MeV lithium ions. Tunability of the ion beam enables pump-probe studies of radiation effects in solids as a function of excitation density, from isolated collision cascades to the onset of phase-transitions and WDM. Ion channeling is an in situ diagnostic of damage evolution during ion pulses with a sensitivity of <0.1% displacements per atom. We will report results from damage evolution studies in thin silicon crystals with Li + and K + beams. Detection of channeled ions tracks lattice disorder evolution with a resolution of ~ 1 ns using fast current measurements. We will discuss pump-probe experiments with pulsed ion beams and the development of diagnostics for WDM and multi-scale (ms to fs) access to the materials physics of collision cascades e.g. in fusion reactor materials. Work performed under auspices of the US DOE under Contract No. DE-AC02-05CH11231.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Price, Morgan N.; Arkin, Adam P.; Alm, Eric J.

Operons are a major feature of all prokaryotic genomes, but how and why operon structures vary is not well understood. To elucidate the life-cycle of operons, we compared gene order between Escherichia coli K12 and its relatives and identified the recently formed and destroyed operons in E. coli. This allowed us to determine how operons form, how they become closely spaced, and how they die. Our findings suggest that operon evolution is driven by selection on gene expression patterns. First, both operon creation and operon destruction lead to large changes in gene expression patterns. For example, the removal of lysAmore » and ruvA from ancestral operons that contained essential genes allowed their expression to respond to lysine levels and DNA damage, respectively. Second, some operons have undergone accelerated evolution, with multiple new genes being added during a brief period. Third, although most operons are closely spaced because of a neutral bias towards deletion and because of selection against large overlaps, highly expressed operons tend to be widely spaced because of regulatory fine-tuning by intervening sequences. Although operon evolution seems to be adaptive, it need not be optimal: new operons often comprise functionally unrelated genes that were already in proximity before the operon formed.« less

On the soft supersymmetry-breaking parameters in gauge-mediated models

NASA Astrophysics Data System (ADS)

Wagner, C. E. M.

1998-09-01

Gauge mediation of supersymmetry breaking in the observable sector is an attractive idea, which naturally alleviates the flavor changing neutral current problem of supersymmetric theories. Quite generally, however, the number and quantum number of the messengers are not known; nor is their characteristic mass scale determined by the theory. Using the recently proposed method to extract supersymmetry-breaking parameters from wave-function renormalization, we derived general formulae for the soft supersymmetry-breaking parameters in the observable sector, valid in the small and moderate tan β regimes, for the case of split messengers. The full leading-order effects of top Yukawa and gauge couplings on the soft supersymmetry-breaking parameters are included. We give a simple interpretation of the general formulae in terms of the renormalization group evolution of the soft supersymmetry-breaking parameters. As a by-product of this analysis, the one-loop renormalization group evolution of the soft supersymmetry-breaking parameters is obtained for arbitrary boundary conditions of the scalar and gaugino mass parameters at high energies.

DR-induced Hot Oxygen and Carbon Coronae of Early Mars

NASA Astrophysics Data System (ADS)

Zhao, J.; Chassefiere, E.; Tian, F.; Chaufray, J. Y.; Leblanc, F.

2017-12-01

The evolution of Martian atmosphere is a key aspect to understand the habitability of Mars in time. The distributions of neutral atoms above the exobase of ancient Mars (corona) is important for understanding the interactions between the corona and the solar wind, which could help improving our understanding of the evolution of Martian atmosphere. In this work, a 3-D Monte Carlo Model is built to simulate Martian corona in different period of Mars history based on thermosphere structure corresponding to 1, 3, 10, and 20 times present solar XUV conditions and dissociative recombination (DR) reaction profiles. DR reactions of O2+, CO2+, and CO+ are considered as the sources of primary O and C. Secondary O and C atoms, which are formed through collisions between primaries and background species. We will discuss the dependence of physical properties of Martian corona as functions of solar XUV flux and DR reactions. We will also discuss the potential importance of CO+ DR as a contributor to Martian corona.

Rapid bursts and slow declines: on the possible evolutionary trajectories of enzymes.

PubMed

Newton, Matilda S; Arcus, Vickery L; Patrick, Wayne M

2015-06-06

The evolution of enzymes is often viewed as following a smooth and steady trajectory, from barely functional primordial catalysts to the highly active and specific enzymes that we observe today. In this review, we summarize experimental data that suggest a different reality. Modern examples, such as the emergence of enzymes that hydrolyse human-made pesticides, demonstrate that evolution can be extraordinarily rapid. Experiments to infer and resurrect ancient sequences suggest that some of the first organisms present on the Earth are likely to have possessed highly active enzymes. Reconciling these observations, we argue that rapid bursts of strong selection for increased catalytic efficiency are interspersed with much longer periods in which the catalytic power of an enzyme erodes, through neutral drift and selection for other properties such as cellular energy efficiency or regulation. Thus, many enzymes may have already passed their catalytic peaks. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

A Janus cobalt-based catalytic material for electro-splitting of water

NASA Astrophysics Data System (ADS)

Cobo, Saioa; Heidkamp, Jonathan; Jacques, Pierre-André; Fize, Jennifer; Fourmond, Vincent; Guetaz, Laure; Jousselme, Bruno; Ivanova, Valentina; Dau, Holger; Palacin, Serge; Fontecave, Marc; Artero, Vincent

2012-09-01

The future of energy supply depends on innovative breakthroughs regarding the design of cheap, sustainable and efficient systems for the conversion and storage of renewable energy sources. The production of hydrogen through water splitting seems a promising and appealing solution. We found that a robust nanoparticulate electrocatalytic material, H2-CoCat, can be electrochemically prepared from cobalt salts in a phosphate buffer. This material consists of metallic cobalt coated with a cobalt-oxo/hydroxo-phosphate layer in contact with the electrolyte and mediates H2 evolution from neutral aqueous buffer at modest overpotentials. Remarkably, it can be converted on anodic equilibration into the previously described amorphous cobalt oxide film (O2-CoCat or CoPi) catalysing O2 evolution. The switch between the two catalytic forms is fully reversible and corresponds to a local interconversion between two morphologies and compositions at the surface of the electrode. After deposition, the noble-metal-free coating thus functions as a robust, bifunctional and switchable catalyst.

The Role of Genetic Drift in Shaping Modern Human Cranial Evolution: A Test Using Microevolutionary Modeling

PubMed Central

Smith, Heather F.

2011-01-01

The means by which various microevolutionary processes have acted in the past to produce patterns of cranial variation that characterize modern humans is not thoroughly understood. Applying a microevolutionary framework, within- and among-population variance/covariance (V/CV) structure was compared for several functional and developmental modules of the skull across a worldwide sample of modern humans. V/CV patterns in the basicranium, temporal bone, and face are proportional within and among groups, which is consistent with a hypothesis of neutral evolution; however, mandibular morphology deviated from this pattern. Degree of intergroup similarity in facial, temporal bone, and mandibular morphology is significantly correlated with geographic distance; however, much of the variance remains unexplained. These findings provide insight into the evolutionary history of modern human cranial variation by identifying signatures of genetic drift, gene flow, and migration and set the stage for inferences regarding selective pressures that early humans encountered since their initial migrations around the world. PMID:21461369

Faster-X evolution of gene expression is driven by recessive adaptive cis-regulatory variation in Drosophila.

PubMed

Llopart, Ana

2018-05-01

The hemizygosity of the X (Z) chromosome fully exposes the fitness effects of mutations on that chromosome and has evolutionary consequences on the relative rates of evolution of X and autosomes. Specifically, several population genetics models predict increased rates of evolution in X-linked loci relative to autosomal loci. This prediction of faster-X evolution has been evaluated and confirmed for both protein coding sequences and gene expression. In the case of faster-X evolution for gene expression divergence, it is often assumed that variation in 5' noncoding sequences is associated with variation in transcript abundance between species but a formal, genomewide test of this hypothesis is still missing. Here, I use whole genome sequence data in Drosophila yakuba and D. santomea to evaluate this hypothesis and report positive correlations between sequence divergence at 5' noncoding sequences and gene expression divergence. I also examine polymorphism and divergence in 9,279 noncoding sequences located at the 5' end of annotated genes and detected multiple signals of positive selection. Notably, I used the traditional synonymous sites as neutral reference to test for adaptive evolution, but I also used bases 8-30 of introns <65 bp, which have been proposed to be a better neutral choice. X-linked genes with high degree of male-biased expression show the most extreme adaptive pattern at 5' noncoding regions, in agreement with faster-X evolution for gene expression divergence and a higher incidence of positively selected recessive mutations. © 2018 The Authors. Molecular Ecology Published by John Wiley & Sons Ltd.

Coincidence degree and periodic solutions of neutral equations

NASA Technical Reports Server (NTRS)

Hale, J. K.; Mawhin, J.

1973-01-01

The problem of existence of periodic solutions for some nonautonomous neutral functional differential equations is examined. It is an application of a basic theorem on the Fredholm alternative for periodic solutions of some linear neutral equations and of a generalized Leray-Schauder theory. Although proofs are simple, the results are nontrivial extensions to the neutral case of existence theorems for periodic solutions of functional differential equations.

Atomic and molecular hydrogen gas temperatures in a low-pressure helicon plasma

NASA Astrophysics Data System (ADS)

Samuell, Cameron M.; Corr, Cormac S.

2015-08-01

Neutral gas temperatures in hydrogen plasmas are important for experimental and modelling efforts in fusion technology, plasma processing, and surface modification applications. To provide values relevant to these application areas, neutral gas temperatures were measured in a low pressure (< 10 mTorr) radiofrequency helicon discharge using spectroscopic techniques. The atomic and molecular species were not found to be in thermal equilibrium with the atomic temperature being mostly larger then the molecular temperature. In low power operation (< 1 kW), the molecular hydrogen temperature was observed to be linearly proportional to the pressure while the atomic hydrogen temperature was inversely proportional. Both temperatures were observed to rise linearly with input power. For high power operation (5-20 kW), the molecular temperature was found to rise with both power and pressure up to a maximum of approximately 1200 K. Spatially resolved measurements near a graphite target demonstrated localised cooling near the sample surface. The temporal evolution of the molecular gas temperature during a high power 1.1 ms plasma pulse was also investigated and found to vary considerably as a function of pressure.

Applying ecological models to communities of genetic elements: the case of neutral theory.

PubMed

Linquist, Stefan; Cottenie, Karl; Elliott, Tyler A; Saylor, Brent; Kremer, Stefan C; Gregory, T Ryan

2015-07-01

A promising recent development in molecular biology involves viewing the genome as a mini-ecosystem, where genetic elements are compared to organisms and the surrounding cellular and genomic structures are regarded as the local environment. Here, we critically evaluate the prospects of ecological neutral theory (ENT), a popular model in ecology, as it applies at the genomic level. This assessment requires an overview of the controversy surrounding neutral models in community ecology. In particular, we discuss the limitations of using ENT both as an explanation of community dynamics and as a null hypothesis. We then analyse a case study in which ENT has been applied to genomic data. Our central finding is that genetic elements do not conform to the requirements of ENT once its assumptions and limitations are made explicit. We further compare this genome-level application of ENT to two other, more familiar approaches in genomics that rely on neutral mechanisms: Kimura's molecular neutral theory and Lynch's mutational-hazard model. Interestingly, this comparison reveals that there are two distinct concepts of neutrality associated with these models, which we dub 'fitness neutrality' and 'competitive neutrality'. This distinction helps to clarify the various roles for neutral models in genomics, for example in explaining the evolution of genome size. © 2015 John Wiley & Sons Ltd.

Identification and analysis of evolutionary selection pressures acting at the molecular level in five forkhead subfamilies.

PubMed

Fetterman, Christina D; Rannala, Bruce; Walter, Michael A

2008-09-24

Members of the forkhead gene family act as transcription regulators in biological processes including development and metabolism. The evolution of forkhead genes has not been widely examined and selection pressures at the molecular level influencing subfamily evolution and differentiation have not been explored. Here, in silico methods were used to examine selection pressures acting on the coding sequence of five multi-species FOX protein subfamily clusters; FoxA, FoxD, FoxI, FoxO and FoxP. Application of site models, which estimate overall selection pressures on individual codons throughout the phylogeny, showed that the amino acid changes observed were either neutral or under negative selection. Branch-site models, which allow estimated selection pressures along specified lineages to vary as compared to the remaining phylogeny, identified positive selection along branches leading to the FoxA3 and Protostomia clades in the FoxA cluster and the branch leading to the FoxO3 clade in the FoxO cluster. Residues that may differentiate paralogs were identified in the FoxA and FoxO clusters and residues that differentiate orthologs were identified in the FoxA cluster. Neutral amino acid changes were identified in the forkhead domain of the FoxA, FoxD and FoxP clusters while positive selection was identified in the forkhead domain of the Protostomia lineage of the FoxA cluster. A series of residues under strong negative selection adjacent to the N- and C-termini of the forkhead domain were identified in all clusters analyzed suggesting a new method for refinement of domain boundaries. Extrapolation of domains among cluster members in conjunction with selection pressure information allowed prediction of residue function in the FoxA, FoxO and FoxP clusters and exclusion of known domain function in residues of the FoxA and FoxI clusters. Consideration of selection pressures observed in conjunction with known functional information allowed prediction of residue function and refinement of domain boundaries. Identification of residues that differentiate orthologs and paralogs provided insight into the development and functional consequences of paralogs and forkhead subfamily composition differences among species. Overall we found that after gene duplication of forkhead family members, rapid differentiation and subsequent fixation of amino acid changes through negative selection has occurred.

What Is the "One Thing" You Should Know before Teaching about Evolution?

ERIC Educational Resources Information Center

Billingsley, Berry

2014-01-01

In practice, in the classroom, teachers are still faced with the issue of what to say to children if they believe that evolution conflicts with their own or other people's religious faith. When asked how they plan to respond, most teacher trainees and teachers respond that they will be a neutral chair and try to give children a balanced view.…

Moran model as a dynamical process on networks and its implications for neutral speciation.

PubMed

de Aguiar, Marcus A M; Bar-Yam, Yaneer

2011-09-01

In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.

Moran model as a dynamical process on networks and its implications for neutral speciation

NASA Astrophysics Data System (ADS)

de Aguiar, Marcus A. M.; Bar-Yam, Yaneer

2011-03-01

In population genetics, the Moran model describes the neutral evolution of a biallelic gene in a population of haploid individuals subjected to mutations. We show in this paper that this model can be mapped into an influence dynamical process on networks subjected to external influences. The panmictic case considered by Moran corresponds to fully connected networks and can be completely solved in terms of hypergeometric functions. Other types of networks correspond to structured populations, for which approximate solutions are also available. This approach to the classic Moran model leads to a relation between regular networks based on spatial grids and the mechanism of isolation by distance. We discuss the consequences of this connection for topopatric speciation and the theory of neutral speciation and biodiversity. We show that the effect of mutations in structured populations, where individuals can mate only with neighbors, is greatly enhanced with respect to the panmictic case. If mating is further constrained by genetic proximity between individuals, a balance of opposing tendencies takes place: increasing diversity promoted by enhanced effective mutations versus decreasing diversity promoted by similarity between mates. Resolution of large enough opposing tendencies occurs through speciation via pattern formation. We derive an explicit expression that indicates when speciation is possible involving the parameters characterizing the population. We also show that the time to speciation is greatly reduced in comparison with the panmictic case.

Accelerated and Adaptive Evolution of Yeast Sexual Adhesins

PubMed Central

Xie, Xianfa; Qiu, Wei-Gang; Lipke, Peter N.

2011-01-01

There is a recent emergence of interest in the genes involved in gametic recognition as drivers of reproductive isolation. The recent population genomic sequencing of two species of sexually primitive yeasts (Liti G, Carter DM, Moses AM, Warringer J, Parts L, James SA, Davey RP, Roberts IN, Burt A, Koufopanou V et al. [23 co-authors]. 2009. Population genomics of domestic and wild yeasts. Nature 458:337–341.) has provided data for systematic study of the roles these genes play in the early evolution of sex and speciation. Here, we discovered that among genes encoding cell surface proteins, the sexual adhesin genes have evolved significantly more rapidly than others, both within and between Saccharomyces cerevisiae and its closest relative S. paradoxus. This result was supported by analyses using the PAML pairwise model, a modified McDonald–Kreitman test, and the PAML branch model. Moreover, using a combination of a new statistic of neutrality, an information theory–based measure of evolutionary variability, and functional characterization of amino acid changes, we found that a higher proportion of amino acid changes are fixed in the sexual adhesins than in other proteins and a greater proportion of the fixed amino acid changes either between the two species or the two subgroups of S. paradoxus are functionally dissimilar or radically different. These results suggest that the accelerated evolution of sexual adhesin genes may facilitate speciation, or incipient speciation, and promote sexual selection in general. PMID:21633112

Boosting heterosubtypic neutralization antibodies in recipients of 2009 pandemic H1N1 influenza vaccine.

PubMed

Qiu, Chao; Huang, Yang; Wang, Qian; Tian, Di; Zhang, Wanju; Hu, Yunwen; Yuan, Zhenghong; Zhang, Xiaoyan; Xu, Jianqing

2012-01-01

A mass vaccination has been implemented to prevent the spread of 2009 pandemic influenza virus in China. Highly limited information is available on whether this vaccine induces cross-reactive neutralization antibodies against other subtypes of influenza viruses. We employed pseudovirus-based assays to analyze heterosubtypic neutralization responses in serum samples of 23 recipients of 2009 pandemic influenza vaccine. One dose of pandemic vaccine not only stimulated good neutralization antibodies against cognate influenza virus 2009 influenza A (H1N1), but also raised broad cross-reactive neutralization activities against seasonal H3N2 and highly pathogenic avian influenza virus H5N1 and lesser to H2N2. The cross-reactive neutralization activities were completely abolished after the removal of immunoglobin G (IgG). In contrast, H1N1 vaccination alone in influenza-naive mice elicited only vigorous homologous neutralizing activities but not cross-reactive neutralization activities. Our data suggest that the cross-reactive neutralization epitopes do exist in this vaccine and could elicit significant cross-reactive neutralizing IgG antibodies in the presence of preexisting responses. The exposure to H1N1 vaccine is likely to modify the hierarchical order of preexisting immune responses to influenza viruses. These findings provide insights into the evolution of human immunity to influenza viruses after experiencing multiple influenza virus infections and vaccinations.

Neutral evolution in a biological population as diffusion in phenotype space: reproduction with local mutation but without selection.

PubMed

Lawson, Daniel John; Jensen, Henrik Jeldtoft

2007-03-02

The process of "evolutionary diffusion," i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.

Selection against Heteroplasmy Explains the Evolution of Uniparental Inheritance of Mitochondria

PubMed Central

Christie, Joshua R.; Schaerf, Timothy M.; Beekman, Madeleine

2015-01-01

Why are mitochondria almost always inherited from one parent during sexual reproduction? Current explanations for this evolutionary mystery include conflict avoidance between the nuclear and mitochondrial genomes, clearing of deleterious mutations, and optimization of mitochondrial-nuclear coadaptation. Mathematical models, however, fail to show that uniparental inheritance can replace biparental inheritance under any existing hypothesis. Recent empirical evidence indicates that mixing two different but normal mitochondrial haplotypes within a cell (heteroplasmy) can cause cell and organism dysfunction. Using a mathematical model, we test if selection against heteroplasmy can lead to the evolution of uniparental inheritance. When we assume selection against heteroplasmy and mutations are neither advantageous nor deleterious (neutral mutations), uniparental inheritance replaces biparental inheritance for all tested parameter values. When heteroplasmy involves mutations that are advantageous or deleterious (non-neutral mutations), uniparental inheritance can still replace biparental inheritance. We show that uniparental inheritance can evolve with or without pre-existing mating types. Finally, we show that selection against heteroplasmy can explain why some organisms deviate from strict uniparental inheritance. Thus, we suggest that selection against heteroplasmy explains the evolution of uniparental inheritance. PMID:25880558

Rapid evolution of troglomorphic characters suggests selection rather than neutral mutation as a driver of eye reduction in cave crabs.

PubMed

Klaus, Sebastian; Mendoza, José C E; Liew, Jia Huan; Plath, Martin; Meier, Rudolf; Yeo, Darren C J

2013-04-23

This study asked whether reductive traits in cave organisms evolve at a slower pace (suggesting neutral evolution under relaxed selection) than constructive changes, which are likely to evolve under directional selection. We investigated 11 subterranean and seven surface populations of Sundathelphusa freshwater crabs on Bohol Island, Philippines, and examined constructive traits associated with improved food finding in darkness (increased leg and setae length) and reductive traits (reduced cornea size and eyestalk length). All changes occurred rapidly, given that the age of the most recent common ancestor was estimated to be 722-271 ka based on three mitochondrial markers. In order to quantify the speed of character change, we correlated the degree of morphological change with genetic distances between surface and subterranean individuals. The temporal pattern of character change following the transition to subterranean life was indistinguishable for constructive and reductive traits, characterized by an immediate onset and rapid evolutionary change. We propose that the evolution of these reductive traits-just like constructive traits-is most likely driven by strong directional selection.

Carnivore-specific SINEs (Can-SINEs): distribution, evolution, and genomic impact.

PubMed

Walters-Conte, Kathryn B; Johnson, Diana L E; Allard, Marc W; Pecon-Slattery, Jill

2011-01-01

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics.

Carnivore-Specific SINEs (Can-SINEs): Distribution, Evolution, and Genomic Impact

PubMed Central

Johnson, Diana L.E.; Allard, Marc W.; Pecon-Slattery, Jill

2011-01-01

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics. PMID:21846743

Local Complex Potential Based Time Dependent Wave Packet Approach to Calculation of Vibrational Excitation Cross-sections in e-N2, e-H2 and e-CO Scattering

NASA Astrophysics Data System (ADS)

Sarma, Manabendra; Singh, Raman K.; Mishra, Manoj K.

2007-12-01

Vibrational excitation cross-sections σn←m(E) in resonant e-N2, e-CO and e-H2 scattering are calculated from transition matrix elements Tn←m(E) obtained using Fourier transform of the cross correlation function <φn(R)|ψm(R,t)> where ψm(R,t); e-iHA-(R)t/ℏφm(R). Time evolution under the influence of the resonance anionic Hamiltonian HA-(A- = N2-/CO/H2-) is effected using Lanczos and fast Fourier transforms and the target (A) vibrational eigenfunctions φm(R) and φn(R) are calculated using Fourier grid Hamiltonian method applied to PE curve of the neutral target. The resulting vibrational excitation cross-section profiles provide reasonable agreement with experimental results and the cross correlation functions offer an unequivocal differentiation between the boomerang and impulse models.

A case study of the thermospheric neutral wind response to geomagnetic storm

NASA Astrophysics Data System (ADS)

Jiang, Guoying; Zhang, Shunrong; Wang, Wenbin; Yuan, Wei; Wu, Qian; Xu, Jiyao

A minor geomagnetic storm (Kp=5) occurred on March 27-28, 2012. The response of the thermospheric neutral wind at ~ 250 km to this storm was investigated by the 630.0 nm nightglow measurements of Fabry-Perot interferometers (FPIs) over Xinglong (geographic location: 40.2N, 117.4E; geomagnetic location: 29.8N, 193.2E) and Millstone Hill (geographic location: 42.6N, 71.5W; geomagnetic location: 53.1N, 65.1W). Our results show that the minor storm on March 27-28, 2012 obviously effected on the thermospheric neutral winds over Xinglong and Millstone Hill, especially Millstone Hill had larger response because of its higher geomagnetic latitude. Another interesting result is that a small variation in geomagnetic activity (Kp=2.7) could enough introduce a clear disturbance in the nighttime thermospheric neutral wind over Millstone hill. NCAR-TIME-GCM (National Center for Atmospheric Research-Thermosphere Ionosphere Mesosphere Electrodynamics-General Circulation Model) was employed to study the evolution and mechanism of the thermospheric neutral wind response.

Evolution of the HIV-1 Envelope Glycoprotein Genes and Neutralizing Antibody Response in an Individual with Broadly Cross Neutralizing Antibodies

DTIC Science & Technology

2010-08-31

genital fluids HIV -1 infected cells are present in more substantial numbers than free virus, and the former may account for the majority of...Severe acquired immunodeficiency in male homosexuals, manifested by chronic perianal ulcerative herpes simplex lesions. N Engl J Med 1981 , 305:1439...1994,179:463-472. 59. Miller CJ: Localization of Simian immunodeficiency virus-infected cells in the genital tract of male and female Rhesus macaques. J

Manufacturing of a novel double-function ssDNA aptamer for sensitive diagnosis and efficient neutralization of SEA.

PubMed

Sedighian, Hamid; Halabian, Raheleh; Amani, Jafar; Heiat, Mohammad; Taheri, Ramezan Ali; Imani Fooladi, Abbas Ali

2018-05-01

Staphylococcal enterotoxin A (SEA) is an enterotoxin produced mainly by Staphylococcus aureus. In recent years, it has become the most prevalent compound for staphylococcal food poisoning (SFP) around the world. In this study, we isolate new dual-function single-stranded DNA (ssDNA) aptamers by using some new methods, such as the Taguchi method, by focusing on the detection and neutralization of SEA enterotoxin in food and clinical samples. For the asymmetric polymerase chain reaction (PCR) optimization of each round of systematic evolution of ligands by exponential enrichment (SELEX), we use Taguchi L9 orthogonal arrays, and the aptamer mobility shift assay (AMSA) is used for initial evaluation of the protein-DNA interactions on the last SELEX round. In our investigation the dissociation constant (K D ) value and the limit of detection (LOD) of the candidate aptamer were found to be 8.5 ± 0.91 of nM and 5 ng/ml using surface plasmon resonance (SPR). In the current study, the Taguchi and mobility shift assay methods were innovatively harnessed to improve the selection process and evaluate the protein-aptamer interactions. To the best of our knowledge, this is the first report on employing these two methods in aptamer technology especially against bacterial toxin. Copyright © 2018 Elsevier Inc. All rights reserved.

Evolution of RNA-Protein Interactions: Non-Specific Binding Led to RNA Splicing Activity of Fungal Mitochondrial Tyrosyl-tRNA Synthetases

PubMed Central

Lamech, Lilian T.; Mallam, Anna L.; Lambowitz, Alan M.

2014-01-01

The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mtTyrRS; CYT-18 protein) evolved a new function as a group I intron splicing factor by acquiring the ability to bind group I intron RNAs and stabilize their catalytically active RNA structure. Previous studies showed: (i) CYT-18 binds group I introns by using both its N-terminal catalytic domain and flexibly attached C-terminal anticodon-binding domain (CTD); and (ii) the catalytic domain binds group I introns specifically via multiple structural adaptations that occurred during or after the divergence of Peziomycotina and Saccharomycotina. However, the function of the CTD and how it contributed to the evolution of splicing activity have been unclear. Here, small angle X-ray scattering analysis of CYT-18 shows that both CTDs of the homodimeric protein extend outward from the catalytic domain, but move inward to bind opposite ends of a group I intron RNA. Biochemical assays show that the isolated CTD of CYT-18 binds RNAs non-specifically, possibly contributing to its interaction with the structurally different ends of the intron RNA. Finally, we find that the yeast mtTyrRS, which diverged from Pezizomycotina fungal mtTyrRSs prior to the evolution of splicing activity, binds group I intron and other RNAs non-specifically via its CTD, but lacks further adaptations needed for group I intron splicing. Our results suggest a scenario of constructive neutral (i.e., pre-adaptive) evolution in which an initial non-specific interaction between the CTD of an ancestral fungal mtTyrRS and a self-splicing group I intron was “fixed” by an intron RNA mutation that resulted in protein-dependent splicing. Once fixed, this interaction could be elaborated by further adaptive mutations in both the catalytic domain and CTD that enabled specific binding of group I introns. Our results highlight a role for non-specific RNA binding in the evolution of RNA-binding proteins. PMID:25536042

Evolution of RNA-protein interactions: non-specific binding led to RNA splicing activity of fungal mitochondrial tyrosyl-tRNA synthetases.

PubMed

Lamech, Lilian T; Mallam, Anna L; Lambowitz, Alan M

2014-12-01

The Neurospora crassa mitochondrial tyrosyl-tRNA synthetase (mtTyrRS; CYT-18 protein) evolved a new function as a group I intron splicing factor by acquiring the ability to bind group I intron RNAs and stabilize their catalytically active RNA structure. Previous studies showed: (i) CYT-18 binds group I introns by using both its N-terminal catalytic domain and flexibly attached C-terminal anticodon-binding domain (CTD); and (ii) the catalytic domain binds group I introns specifically via multiple structural adaptations that occurred during or after the divergence of Peziomycotina and Saccharomycotina. However, the function of the CTD and how it contributed to the evolution of splicing activity have been unclear. Here, small angle X-ray scattering analysis of CYT-18 shows that both CTDs of the homodimeric protein extend outward from the catalytic domain, but move inward to bind opposite ends of a group I intron RNA. Biochemical assays show that the isolated CTD of CYT-18 binds RNAs non-specifically, possibly contributing to its interaction with the structurally different ends of the intron RNA. Finally, we find that the yeast mtTyrRS, which diverged from Pezizomycotina fungal mtTyrRSs prior to the evolution of splicing activity, binds group I intron and other RNAs non-specifically via its CTD, but lacks further adaptations needed for group I intron splicing. Our results suggest a scenario of constructive neutral (i.e., pre-adaptive) evolution in which an initial non-specific interaction between the CTD of an ancestral fungal mtTyrRS and a self-splicing group I intron was "fixed" by an intron RNA mutation that resulted in protein-dependent splicing. Once fixed, this interaction could be elaborated by further adaptive mutations in both the catalytic domain and CTD that enabled specific binding of group I introns. Our results highlight a role for non-specific RNA binding in the evolution of RNA-binding proteins.

Neutral Evolution of Multiple Quantitative Characters: A Genealogical Approach

PubMed Central

Griswold, Cortland K.; Logsdon, Benjamin; Gomulkiewicz, Richard

2007-01-01

The G matrix measures the components of phenotypic variation that are genetically heritable. The structure of G, that is, its principal components and their associated variances, determines, in part, the direction and speed of multivariate trait evolution. In this article we present a framework and results that give the structure of G under the assumption of neutrality. We suggest that a neutral expectation of the structure of G is important because it gives a null expectation for the structure of G from which the unique consequences of selection can be determined. We demonstrate how the processes of mutation, recombination, and drift shape the structure of G. Furthermore, we demonstrate how shared common ancestry between segregating alleles shapes the structure of G. Our results show that shared common ancestry, which manifests itself in the form of a gene genealogy, causes the structure of G to be nonuniform in that the variances associated with the principal components of G decline at an approximately exponential rate. Furthermore we show that the extent of the nonuniformity in the structure of G is enhanced with declines in mutation rates, recombination rates, and numbers of loci and is dependent on the pattern and modality of mutation. PMID:17339224

Magma reservoirs and neutral buoyancy zones on Venus - Implications for the formation and evolution of volcanic landforms

NASA Technical Reports Server (NTRS)

Head, James W.; Wilson, Lionel

1992-01-01

The production of magma reservoirs and neutral buoyancy zones (NBZs) on Venus and the implications of their development for the formation and evolution of volcanic landforms are examined. The high atmospheric pressure on Venus reduces volatile exsolution and generally serves to inhibit the formation of NBZs and shallow magma reservoirs. For a range of common terrestrial magma-volatile contents, magma ascending and erupting near or below mean planetary radius (MPR) should not stall at shallow magma reservoirs; such eruptions are characterized by relatively high total volumes and effusion rates. For the same range of volatile contents at 2 km above MPR, about half of the cases result in the direct ascent of magma to the surface and half in the production of neutral buoyancy zones. NBZs and shallow magma reservoirs begin to appear as gas content increases and are nominally shallower on Venus than on earth. For a fixed volatile content, NBZs become deeper with increasing elevation: over the range of elevations treated in this study (-1 km to +4.4 km) depths differ by a factor of 2-4. Factors that may account for the low height of volcanoes on Venus are discussed.

Etching in Chlorine Discharges Using an Integrated Feature Evolution-Plasma Model

NASA Technical Reports Server (NTRS)

Hwang, Helen H.; Bose, Deepak; Govindan, T. R.; Meyyappan, M.; Biegel, Bryan (Technical Monitor)

2001-01-01

Etching of semiconductor materials is reliant on plasma properties. Quantities such as ion and neutral fluxes, both in magnitude and in direction, are often determined by reactor geometry (height, radius, position of the coils, etc.) In order to obtain accurate etching profiles, one must also model the plasma as a whole to obtain local fluxes and distributions. We have developed a set of three models that simulates C12 plasmas for etching of silicon, ion and neutral trajectories in the plasma, and feature profile evolution. We have found that the location of the peak in the ion densities in the reactor plays a major role in determining etching uniformity across the wafer. For a stove top coil inductively coupled plasma (ICP), the ion density is peaked at the top of the reactor. This leads to nearly uniform neutral and ion fluxes across the wafer. A side coil configuration causes the ion density to peak near the sidewalls. Ion fluxes are thus greater toward the wall's and decrease toward the center. In addition, the ions bombard the wafer at a slight angle. This angle is sufficient to cause slanted profiles, which is highly undesirable.

Are Synonymous Sites in Primates and Rodents Functionally Constrained?

PubMed

Price, Nicholas; Graur, Dan

2016-01-01

It has been claimed that synonymous sites in mammals are under selective constraint. Furthermore, in many studies the selective constraint at such sites in primates was claimed to be more stringent than that in rodents. Given the larger effective population sizes in rodents than in primates, the theoretical expectation is that selection in rodents would be more effective than that in primates. To resolve this contradiction between expectations and observations, we used processed pseudogenes as a model for strict neutral evolution, and estimated selective constraint on synonymous sites using the rate of substitution at pseudosynonymous and pseudononsynonymous sites in pseudogenes as the neutral expectation. After controlling for the effects of GC content, our results were similar to those from previous studies, i.e., synonymous sites in primates exhibited evidence for higher selective constraint that those in rodents. Specifically, our results indicated that in primates up to 24% of synonymous sites could be under purifying selection, while in rodents synonymous sites evolved neutrally. To further control for shifts in GC content, we estimated selective constraint at fourfold degenerate sites using a maximum parsimony approach. This allowed us to estimate selective constraint using mutational patterns that cause a shift in GC content (GT ↔ TG, CT ↔ TC, GA ↔ AG, and CA ↔ AC) and ones that do not (AT ↔ TA and CG ↔ GC). Using this approach, we found that synonymous sites evolve neutrally in both primates and rodents. Apparent deviations from neutrality were caused by a higher rate of C → A and C → T mutations in pseudogenes. Such differences are most likely caused by the shift in GC content experienced by pseudogenes. We conclude that previous estimates according to which 20-40% of synonymous sites in primates were under selective constraint were most likely artifacts of the biased pattern of mutation.

Three-dimensional Hybrid Simulation Study of Anisotropic Turbulence in the Proton Kinetic Regime

NASA Astrophysics Data System (ADS)

Vasquez, Bernard J.; Markovskii, Sergei A.; Chandran, Benjamin D. G.

2014-06-01

Three-dimensional numerical hybrid simulations with particle protons and quasi-neutralizing fluid electrons are conducted for a freely decaying turbulence that is anisotropic with respect to the background magnetic field. The turbulence evolution is determined by both the combined root-mean-square (rms) amplitude for fluctuating proton bulk velocity and magnetic field and by the ratio of perpendicular to parallel wavenumbers. This kind of relationship had been considered in the past with regard to interplanetary turbulence. The fluctuations nonlinearly evolve to a turbulent phase whose net wave vector anisotropy is usually more perpendicular than the initial one, irrespective of the initial ratio of perpendicular to parallel wavenumbers. Self-similar anisotropy evolution is found as a function of the rms amplitude and parallel wavenumber. Proton heating rates in the turbulent phase vary strongly with the rms amplitude but only weakly with the initial wave vector anisotropy. Even in the limit where wave vectors are confined to the plane perpendicular to the background magnetic field, the heating rate remains close to the corresponding case with finite parallel wave vector components. Simulation results obtained as a function of proton plasma to background magnetic pressure ratio β p in the range 0.1-0.5 show that the wave vector anisotropy also weakly depends on β p .

New insights on the collisional escape of light neutrals from Mars

NASA Astrophysics Data System (ADS)

Gacesa, Marko; Zahnle, Kevin

2017-04-01

Photodissociative recombination (PDR) of atmospheric molecules on Mars is a major mechanism of production of hot (suprathermal) atoms with sufficient kinetic energy to either directly escape to space or to eject other atmospheric species. This collisional ejection mechanism is important for evaluating the escape rates of all light neutrals that are too heavy to escape via Jeans escape. In particular, it plays a role in estimating the total volume of escaped water constituents (i.e., O and H) from Mars, as well as influences evolution of the atmospheric [D]/[H] ratio1. We present revised estimates of total collisional escape rates of neutral light elements including H, He, and H2, based on recent (years 2015-2016) atmospheric density profiles obtained from the NASA Mars Atmosphere and Volatile Evolution (MAVEN) mission. We also estimate the contribution to the collisional escape from Energetic Neutral Atoms (ENAs) produced in charge-exchange of solar wind H+ and He+ ions with atmospheric gases2,3. Scattering of hot oxygen and atmospheric species of interest is modeled using fully-quantum reactive scattering formalism1,3. The escape rates are evaluated using a 1D model of the atmosphere supplemented with MAVEN measurements of the neutrals. Finally, new estimates of contributions of these non-thermal mechanisms to the estimated PDR escape rates from young Mars4 are presented. [1] M. Gacesa and V. Kharchenko, "Non-thermal escape of molecular hydrogen from Mars", Geophys. Res. Lett., 39, L10203 (2012). [2] N. Lewkow and V. Kharchenko, "Precipitation of Energetic Neutral Atoms and Escape Fluxes induced from the Mars Atmosphere", Astroph. J., 790, 98 (2014). [3] M. Gacesa, N. Lewkow, and V. Kharchenko, "Non-thermal production and escape of OH from the upper atmosphere of Mars", Icarus 284, 90 (2017). [4] J. Zhao, F. Tian, Y. Ni, and X. Huang, "DR-induced escape of O and C from early Mars", Icarus 284, 305 (2017).

Biological signatures of dynamic river networks from a coupled landscape evolution and neutral community model

NASA Astrophysics Data System (ADS)

Stokes, M.; Perron, J. T.

2017-12-01

Freshwater systems host exceptionally species-rich communities whose spatial structure is dictated by the topology of the river networks they inhabit. Over geologic time, river networks are dynamic; drainage basins shrink and grow, and river capture establishes new connections between previously separated regions. It has been hypothesized that these changes in river network structure influence the evolution of life by exchanging and isolating species, perhaps boosting biodiversity in the process. However, no general model exists to predict the evolutionary consequences of landscape change. We couple a neutral community model of freshwater organisms to a landscape evolution model in which the river network undergoes drainage divide migration and repeated river capture. Neutral community models are macro-ecological models that include stochastic speciation and dispersal to produce realistic patterns of biodiversity. We explore the consequences of three modes of speciation - point mutation, time-protracted, and vicariant (geographic) speciation - by tracking patterns of diversity in time and comparing the final result to an equilibrium solution of the neutral model on the final landscape. Under point mutation, a simple model of stochastic and instantaneous speciation, the results are identical to the equilibrium solution and indicate the dominance of the species-area relationship in forming patterns of diversity. The number of species in a basin is proportional to its area, and regional species richness reaches its maximum when drainage area is evenly distributed among sub-basins. Time-protracted speciation is also modeled as a stochastic process, but in order to produce more realistic rates of diversification, speciation is not assumed to be instantaneous. Rather, each new species must persist for a certain amount of time before it is considered to be established. When vicariance (geographic speciation) is included, there is a transient signature of increased regional diversity after river capture. The results indicate that the mode of speciation and the rate of speciation relative to the rate of divide migration determine the evolutionary signature of river capture.

Naima: a Python package for inference of particle distribution properties from nonthermal spectra

NASA Astrophysics Data System (ADS)

Zabalza, V.

2015-07-01

The ultimate goal of the observation of nonthermal emission from astrophysical sources is to understand the underlying particle acceleration and evolution processes, and few tools are publicly available to infer the particle distribution properties from the observed photon spectra from X-ray to VHE gamma rays. Here I present naima, an open source Python package that provides models for nonthermal radiative emission from homogeneous distribution of relativistic electrons and protons. Contributions from synchrotron, inverse Compton, nonthermal bremsstrahlung, and neutral-pion decay can be computed for a series of functional shapes of the particle energy distributions, with the possibility of using user-defined particle distribution functions. In addition, naima provides a set of functions that allow to use these models to fit observed nonthermal spectra through an MCMC procedure, obtaining probability distribution functions for the particle distribution parameters. Here I present the models and methods available in naima and an example of their application to the understanding of a galactic nonthermal source. naima's documentation, including how to install the package, is available at http://naima.readthedocs.org.

Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations.

PubMed

Matsumoto, Tomotaka; John, Anoop; Baeza-Centurion, Pablo; Li, Boyang; Akashi, Hiroshi

2016-06-01

A growing number of molecular evolutionary studies are estimating the proportion of adaptive amino acid substitutions (α) from comparisons of ratios of polymorphic and fixed DNA mutations. Here, we examine how violations of two of the model assumptions, neutral evolution of synonymous mutations and stationary base composition, affect α estimation. We simulated the evolution of coding sequences assuming weak selection on synonymous codon usage bias and neutral protein evolution, α = 0. We show that weak selection on synonymous mutations can give polymorphism/divergence ratios that yield α-hat (estimated α) considerably larger than its true value. Nonstationary evolution (changes in population size, selection, or mutation) can exacerbate such biases or, in some scenarios, give biases in the opposite direction, α-hat < α. These results demonstrate that two factors that appear to be prevalent among taxa, weak selection on synonymous mutations and non-steady-state nucleotide composition, should be considered when estimating α. Estimates of the proportion of adaptive amino acid fixations from large-scale analyses of Drosophila melanogaster polymorphism and divergence data are positively correlated with codon usage bias. Such patterns are consistent with α-hat inflation from weak selection on synonymous mutations and/or mutational changes within the examined gene trees. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Frequency Spectrum Neutrality Tests: One for All and All for One

PubMed Central

Achaz, Guillaume

2009-01-01

Neutrality tests based on the frequency spectrum (e.g., Tajima's D or Fu and Li's F) are commonly used by population geneticists as routine tests to assess the goodness-of-fit of the standard neutral model on their data sets. Here, I show that these neutrality tests are specific instances of a general model that encompasses them all. I illustrate how this general framework can be taken advantage of to devise new more powerful tests that better detect deviations from the standard model. Finally, I exemplify the usefulness of the framework on SNP data by showing how it supports the selection hypothesis in the lactase human gene by overcoming the ascertainment bias. The framework presented here paves the way for constructing novel tests optimized for specific violations of the standard model that ultimately will help to unravel scenarios of evolution. PMID:19546320

Effect of ion-neutral collisions on the evolution of kinetic Alfvén waves in plasmas

NASA Astrophysics Data System (ADS)

Goyal, R.; Sharma, R. P.

2018-03-01

This paper studies the effect of ion-neutral collisions on the propagation of kinetic Alfvén waves (KAWs) in inhomogeneous magnetized plasma. The inhomogeneity in the plasma imposed by background density in a direction transverse as well as parallel to the ambient magnetic field plays a vital role in the localization process. The mass loading of ions takes place due to their collisions with neutral fluid leading to the damping of the KAWs. Numerical analysis of linear KAWs in inhomogeneous magnetized plasma is done for a fixed finite frequency taking into consideration the ion-neutral collisions. There is a prominent effect of collisional damping on the wave localization, wave magnetic field, and frequency spectrum. A semi-analytical technique has been employed to study the magnetic field amplitude decay process and the effect of wave frequency in the range of ion cyclotron frequency on the propagation of waves leading to damping.

The Role of Natural Killer (NK) Cells and NK Cell Receptor Polymorphisms in the Assessment of HIV-1 Neutralization

DTIC Science & Technology

2012-04-11

neutralization) and non-neutralizing antibody-dependent HIV inhibition, which may provide the opportunity to delineate the dominant antibody function (s) in...immunity, there has been a considerable effort to develop a vaccine that will elicit antibodies with some or all of these functions [19], and to... function (s) in polyclonal vaccine responses. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT Same as Report (SAR) 18

Demixing of polymers under nanoimprinting process

NASA Astrophysics Data System (ADS)

Wang, Zhen

Polymer blend has been an important area in polymer science for decades. The knowledge of polymer blend in bulk is well established and technologies based on it have created products ubiquitous in our daily life. More intriguing problem arises when the phase separation of a polymer blend occurs under physical confinement. In this thesis, we investigated the effect of interfacial interactions between constituent polymers and confinement environment on phase evolution. Specifically, morphologies of thin films of binary polymer blends were examined on chemically homogenous substrates (preferential surface, neutral surface), on chemical pattern, between two parallel rigid substrates, and under thermal embossing/step-and-flash nanoimprint lithography conditions. We found that preferential wetting of selective component dominates the phase evolution, which can be suppressed by the use of neutral surfaces or external pressure. By manipulating these factors, a wide range of unique non-equilibrium micro or nanostructures can thus be achieved.

R5 clade C SHIV strains with tier 1 or 2 neutralization sensitivity: tools to dissect env evolution and to develop AIDS vaccines in primate models.

PubMed

Siddappa, Nagadenahalli B; Watkins, Jennifer D; Wassermann, Klemens J; Song, Ruijiang; Wang, Wendy; Kramer, Victor G; Lakhashe, Samir; Santosuosso, Michael; Poznansky, Mark C; Novembre, Francis J; Villinger, François; Else, James G; Montefiori, David C; Rasmussen, Robert A; Ruprecht, Ruth M

2010-07-21

HIV-1 clade C (HIV-C) predominates worldwide, and anti-HIV-C vaccines are urgently needed. Neutralizing antibody (nAb) responses are considered important but have proved difficult to elicit. Although some current immunogens elicit antibodies that neutralize highly neutralization-sensitive (tier 1) HIV strains, most circulating HIVs exhibiting a less sensitive (tier 2) phenotype are not neutralized. Thus, both tier 1 and 2 viruses are needed for vaccine discovery in nonhuman primate models. We constructed a tier 1 simian-human immunodeficiency virus, SHIV-1157ipEL, by inserting an "early," recently transmitted HIV-C env into the SHIV-1157ipd3N4 backbone [1] encoding a "late" form of the same env, which had evolved in a SHIV-infected rhesus monkey (RM) with AIDS. SHIV-1157ipEL was rapidly passaged to yield SHIV-1157ipEL-p, which remained exclusively R5-tropic and had a tier 1 phenotype, in contrast to "late" SHIV-1157ipd3N4 (tier 2). After 5 weekly low-dose intrarectal exposures, SHIV-1157ipEL-p systemically infected 16 out of 17 RM with high peak viral RNA loads and depleted gut CD4+ T cells. SHIV-1157ipEL-p and SHIV-1157ipd3N4 env genes diverge mostly in V1/V2. Molecular modeling revealed a possible mechanism for the increased neutralization resistance of SHIV-1157ipd3N4 Env: V2 loops hindering access to the CD4 binding site, shown experimentally with nAb b12. Similar mutations have been linked to decreased neutralization sensitivity in HIV-C strains isolated from humans over time, indicating parallel HIV-C Env evolution in humans and RM. SHIV-1157ipEL-p, the first tier 1 R5 clade C SHIV, and SHIV-1157ipd3N4, its tier 2 counterpart, represent biologically relevant tools for anti-HIV-C vaccine development in primates.

Selfish genetic elements, genetic conflict, and evolutionary innovation.

PubMed

Werren, John H

2011-06-28

Genomes are vulnerable to selfish genetic elements (SGEs), which enhance their own transmission relative to the rest of an individual's genome but are neutral or harmful to the individual as a whole. As a result, genetic conflict occurs between SGEs and other genetic elements in the genome. There is growing evidence that SGEs, and the resulting genetic conflict, are an important motor for evolutionary change and innovation. In this review, the kinds of SGEs and their evolutionary consequences are described, including how these elements shape basic biological features, such as genome structure and gene regulation, evolution of new genes, origin of new species, and mechanisms of sex determination and development. The dynamics of SGEs are also considered, including possible "evolutionary functions" of SGEs.

Cryptic genetic variation, evolution's hidden substrate

PubMed Central

Paaby, Annalise B.; Rockman, Matthew V.

2016-01-01

Cryptic genetic variation is invisible under normal conditions but fuel for evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles in need of constant suppression. CGV emerges from both neutral and selective processes and it may inform how human populations respond to change. In experimental settings, CGV facilitates adaptation, but does it play an important role in the real world? We review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution. PMID:24614309

Neutral Evolution in a Biological Population as Diffusion in Phenotype Space: Reproduction with Local Mutation but without Selection

NASA Astrophysics Data System (ADS)

Lawson, Daniel John; Jensen, Henrik Jeldtoft

2007-03-01

The process of “evolutionary diffusion,” i.e., reproduction with local mutation but without selection in a biological population, resembles standard diffusion in many ways. However, evolutionary diffusion allows the formation of localized peaks that undergo drift, even in the infinite population limit. We relate a microscopic evolution model to a stochastic model which we solve fully. This allows us to understand the large population limit, relates evolution to diffusion, and shows that independent local mutations act as a diffusion of interacting particles taking larger steps.

Possible impact of multi-electron loss events on the average beam charge state in an HIF target chamber and a neutral beam approach

NASA Astrophysics Data System (ADS)

Grisham, L. R.

2001-05-01

Experiments were carried out during the early 1980s to assess the obtainable atomic neutralization of energetic beams of negative ions ranging from lithium to silicon. The experiments found (Grisham et al. Rev. Sci. Instrum. 53 (1982) 281; Princeton Plasma Physics Laboratory Report PPPL-1857, 1981) that, for higher atomic number elements than lithium, it appeared that a substantial fraction of the time more than one electron was being lost in a single collision. This result was inferred from the existence of more than one ionization state in the product beam for even the thinnest line densities at which any electron removal took place. Because of accelerator limitations, these experiments were limited to maximum energies of 7 MeV. However, based upon these results, it is possible that multi-electron loss events may also play a significant role in determining the average ion charge state of the much higher Z and more energetic beams traversing the medium in an heavy ion fusion chamber. This could result in the beam charge state being considerably higher than previously anticipated, and might require designers to consider harder vacuum ballistic focusing approaches, or the development of additional space charge neutralization schemes. This paper discusses the measurements that gave rise for these concerns, as well as a description of further measurements that are proposed to be carried out for atomic numbers and energies per amu which would be closer to those required for heavy ion fusion drivers. With a very low current beam of a massive, but low charge state energetic ion, the charge state distribution emerging from a target gas cell could be measured as a function of line density and medium composition. Varying the line density would allow one to simulate the charge state evolution of the beam as a function of distance into the target chamber. This paper also briefly discusses a possible alternative driver approach using photodetachment-neutralized atomic beams, which could reduce plasma complications far from the target, but which would impose more stringent limitations upon chamber pressure and repetition rate.

New method to determine the total carbonyl functional group content in extractable particulate organic matter by tandem mass spectrometry.

PubMed

Dron, J; Zheng, W; Marchand, N; Wortham, H

2008-08-01

A functional group analysis method was developed to determine the quantitative content of carbonyl functional groups in atmospheric particulate organic matter (POM) using constant neutral loss scanning-tandem mass spectrometry (CNLS-MS/MS). The neutral loss method consists in monitoring the loss of a neutral fragment produced by the fragmentation of a precursor ion in a collision cell. The only ions detected are the daughter ions resulting from the loss of the neutral fragment under study. Then, scanning the loss of a neutral fragment characteristic of a functional group enables the selective detection of the compounds bearing the chemical function under study within a complex mixture. The selective detection of carbonyl functional groups was achieved after derivatization with pentafluorophenylhydrazine (PFPH) by monitoring the neutral loss of C(6)F(5)N (181 amu), which was characteristic of a large panel of derivatized carbonyl compounds. The method was tested on 25 reference mixtures of different composition, all containing 24 carbonyl compounds at randomly determined concentrations. The repeatability and calibration tests were satisfying as they resulted in a relative standard deviation below 5% and a linear range between 0.01 and 0.65 mM with a calculated detection limit of 0.0035 mM. Also, the relative deviation induced by changing the composition of the mixture while keeping the total concentration of carbonyl functional groups constant was less than 20%. These reliability experiments demonstrate the high robustness of the developed procedure for accurate carbonyl functional group measurement, which was applied to atmospheric POM samples. Copyright (c) 2008 John Wiley & Sons, Ltd.

Molecular evolution across the Asteraceae: micro- and macroevolutionary processes.

PubMed

Kane, Nolan C; Barker, Michael S; Zhan, Shing H; Rieseberg, Loren H

2011-12-01

The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Ontology functional categories to compare rates of evolution over both short and long evolutionary timescales. Our results indicate that patterns of molecular change across the family are surprisingly consistent on a macroevolutionary timescale and much more so more than would be predicted from the analysis of one (or many) examples of microevolution. These analyses also point to particular classes of genes that may be crucial in shaping the radiation of this diverse plant family. Similar analyses of nuclear and chloroplast genes in six other plant families confirm that many of these patterns are common features of the plant kingdom.

A population memetics approach to cultural evolution in chaffinch song: meme diversity within populations.

PubMed

Lynch, A; Baker, A J

1993-04-01

We investigated cultural evolution in populations of common chaffinches (Fringilla coelebs) in the Atlantic islands (Azores, Madeira, Canaries) and neighboring continental regions (Morocco, Iberia) by employing a population memetics approach. To quantify variability within populations, we used the concept of a song meme, defined as a single syllable or a series of linked syllables capable of being transmitted. The frequency distribution of memes within populations generally fit a neutral model in which there is an equilibrium between mutation, migration, and drift, which suggests that memes are functionally equivalent. The diversity of memes of single syllables is significantly greater in the Azores compared to all other regions, consistent with higher population densities of chaffinches there. On the other hand, memes of two to five syllables have greater diversity in Atlantic island and Moroccan populations compared to their Iberian counterparts. This higher diversity emanates from a looser syntax and increased recombination in songs, presumably because of relaxed selection for distinctive songs in these peripheral and depauperate avifaunas. We urge comparative population memetic studies of other species of songbirds and predict that they will lead to a formulation of a general theory for the cultural evolution of bird song analogous to population genetics theory for biological traits.

Durable rechargeable zinc-air batteries with neutral electrolyte and manganese oxide catalyst

NASA Astrophysics Data System (ADS)

Sumboja, Afriyanti; Ge, Xiaoming; Zheng, Guangyuan; Goh, F. W. Thomas; Hor, T. S. Andy; Zong, Yun; Liu, Zhaolin

2016-11-01

Neutral chloride-based electrolyte and directly grown manganese oxide on carbon paper are used as the electrolyte and air cathode respectively for rechargeable Zn-air batteries. Oxygen reduction and oxygen evolution reactions on manganese oxide show dependence of activities on the pH of the electrolyte. Zn-air batteries with chloride-based electrolyte and manganese oxide catalyst exhibit satisfactory voltage profile (discharge and charge voltage of 1 and 2 V at 1 mA cm-2) and excellent cycling stability (≈90 days of continuous cycle test), which is attributed to the reduced carbon corrosion on the air cathode and decreased carbonation in neutral electrolyte. This work describes a robust electrolyte system that improves the cycle life of rechargeable Zn-air batteries.

Spontaneously Broken Neutral Symmetry in an Ecological System

NASA Astrophysics Data System (ADS)

Borile, C.; Muñoz, M. A.; Azaele, S.; Banavar, Jayanth R.; Maritan, A.

2012-07-01

Spontaneous symmetry breaking plays a fundamental role in many areas of condensed matter and particle physics. A fundamental problem in ecology is the elucidation of the mechanisms responsible for biodiversity and stability. Neutral theory, which makes the simplifying assumption that all individuals (such as trees in a tropical forest)—regardless of the species they belong to—have the same prospect of reproduction, death, etc., yields gross patterns that are in accord with empirical data. We explore the possibility of birth and death rates that depend on the population density of species, treating the dynamics in a species-symmetric manner. We demonstrate that dynamical evolution can lead to a stationary state characterized simultaneously by both biodiversity and spontaneously broken neutral symmetry.

Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution.

PubMed

Peabody, George; Winkler, James; Fountain, Weston; Castro, David A; Leiva-Aravena, Enzo; Kao, Katy C

2016-11-15

Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load. Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Benefits of a Recombination-Proficient Escherichia coli System for Adaptive Laboratory Evolution

PubMed Central

Peabody, George; Winkler, James; Fountain, Weston; Castro, David A.; Leiva-Aravena, Enzo

2016-01-01

ABSTRACT Adaptive laboratory evolution typically involves the propagation of organisms asexually to select for mutants with the desired phenotypes. However, asexual evolution is prone to competition among beneficial mutations (clonal interference) and the accumulation of hitchhiking and neutral mutations. The benefits of horizontal gene transfer toward overcoming these known disadvantages of asexual evolution were characterized in a strain of Escherichia coli engineered for superior sexual recombination (genderless). Specifically, we experimentally validated the capacity of the genderless strain to reduce the mutational load and recombine beneficial mutations. We also confirmed that inclusion of multiple origins of transfer influences both the frequency of genetic exchange throughout the chromosome and the linkage of donor DNA. We built a simple kinetic model to estimate recombination frequency as a function of transfer size and relative genotype enrichment in batch transfers; the model output correlated well with the experimental data. Our results provide strong support for the advantages of utilizing the genderless strain over its asexual counterpart during adaptive laboratory evolution for generating beneficial mutants with reduced mutational load. IMPORTANCE Over 80 years ago Fisher and Muller began a debate on the origins of sexual recombination. Although many aspects of sexual recombination have been examined at length, experimental evidence behind the behaviors of recombination in many systems and the means to harness it remain elusive. In this study, we sought to experimentally validate some advantages of recombination in typically asexual Escherichia coli and determine if a sexual strain of E. coli can become an effective tool for strain development. PMID:27613685

Variance to mean ratio, R(t), for poisson processes on phylogenetic trees.

PubMed

Goldman, N

1994-09-01

The ratio of expected variance to mean, R(t), of numbers of DNA base substitutions for contemporary sequences related by a "star" phylogeny is widely seen as a measure of the adherence of the sequences' evolution to a Poisson process with a molecular clock, as predicted by the "neutral theory" of molecular evolution under certain conditions. A number of estimators of R(t) have been proposed, all predicted to have mean 1 and distributions based on the chi 2. Various genes have previously been analyzed and found to have values of R(t) far in excess of 1, calling into question important aspects of the neutral theory. In this paper, I use Monte Carlo simulation to show that the previously suggested means and distributions of estimators of R(t) are highly inaccurate. The analysis is applied to star phylogenies and to general phylogenetic trees, and well-known gene sequences are reanalyzed. For star phylogenies the results show that Kimura's estimators ("The Neutral Theory of Molecular Evolution," Cambridge Univ. Press, Cambridge, 1983) are unsatisfactory for statistical testing of R(t), but confirm the accuracy of Bulmer's correction factor (Genetics 123: 615-619, 1989). For all three nonstar phylogenies studied, attained values of all three estimators of R(t), although larger than 1, are within their true confidence limits under simple Poisson process models. This shows that lineage effects can be responsible for high estimates of R(t), restoring some limited confidence in the molecular clock and showing that the distinction between lineage and molecular clock effects is vital.(ABSTRACT TRUNCATED AT 250 WORDS)

Beyond neutral and forbidden links: morphological matches and the assembly of mutualistic hawkmoth-plant networks.

PubMed

Sazatornil, Federico D; Moré, Marcela; Benitez-Vieyra, Santiago; Cocucci, Andrea A; Kitching, Ian J; Schlumpberger, Boris O; Oliveira, Paulo E; Sazima, Marlies; Amorim, Felipe W

2016-11-01

A major challenge in evolutionary ecology is to understand how co-evolutionary processes shape patterns of interactions between species at community level. Pollination of flowers with long corolla tubes by long-tongued hawkmoths has been invoked as a showcase model of co-evolution. Recently, optimal foraging models have predicted that there might be a close association between mouthparts' length and the corolla depth of the visited flowers, thus favouring trait convergence and specialization at community level. Here, we assessed whether hawkmoths more frequently pollinate plants with floral tube lengths similar to their proboscis lengths (morphological match hypothesis) against abundance-based processes (neutral hypothesis) and ecological trait mismatches constraints (forbidden links hypothesis), and how these processes structure hawkmoth-plant mutualistic networks from five communities in four biogeographical regions of South America. We found convergence in morphological traits across the five communities and that the distribution of morphological differences between hawkmoths and plants is consistent with expectations under the morphological match hypothesis in three of the five communities. In the two remaining communities, which are ecotones between two distinct biogeographical areas, interactions are better predicted by the neutral hypothesis. Our findings are consistent with the idea that diffuse co-evolution drives the evolution of extremely long proboscises and flower tubes, and highlight the importance of morphological traits, beyond the forbidden links hypothesis, in structuring interactions between mutualistic partners, revealing that the role of niche-based processes can be much more complex than previously known. © 2016 The Authors. Journal of Animal Ecology © 2016 British Ecological Society.

Femtosecond Multidimensional Imaging - Watching Chemistry from the Molecule's Point of View

NASA Astrophysics Data System (ADS)

Geßner, O.; Lee, A. M. D.; Chrysostom, E. t.-H.; Hayden, C. C.; Stolow, Albert

Using Femtosecond Multidimensional Imaging we disentangle the complex neutral dissociation mechanism of the NO dimer. We characterize all electronic configurations from start to finish and directly observe the evolution of intramolecular vibrational energy redistribution (IVR).

Functional Stability of HIV-1 Envelope Trimer Affects Accessibility to Broadly Neutralizing Antibodies at Its Apex.

PubMed

Gift, Syna Kuriakose; Leaman, Daniel P; Zhang, Lei; Kim, Arthur S; Zwick, Michael B

2017-12-15

The trimeric envelope glycoprotein spike (Env) of HIV-1 is the target of vaccine development to elicit broadly neutralizing antibodies (bnAbs). Env trimer instability and heterogeneity in principle make subunit interfaces inconsistent targets for the immune response. Here, we investigate how functional stability of Env relates to neutralization sensitivity to V2 bnAbs and V3 crown antibodies that engage subunit interfaces upon binding to unliganded Env. Env heterogeneity was inferred when antibodies neutralized a mutant Env with a plateau of less than 100% neutralization. A statistically significant correlation was found between the stability of mutant Envs and the MPN of V2 bnAb, PG9, as well as an inverse correlation between stability of Env and neutralization by V3 crown antibody, 447-52D. A number of Env-stabilizing mutations and V2 bnAb-enhancing mutations were identified in Env, but they did not always overlap, indicating distinct requirements of functional stabilization versus antibody recognition. Blocking complex glycosylation of Env affected V2 bnAb recognition, as previously described, but also notably increased functional stability of Env. This study shows how instability and heterogeneity affect antibody sensitivity of HIV-1 Env, which is relevant to vaccine design involving its dynamic apex. IMPORTANCE The Env trimer is the only viral protein on the surface of HIV-1 and is the target of neutralizing antibodies that reduce viral infectivity. Quaternary epitopes at the apex of the spike are recognized by some of the most potent and broadly neutralizing antibodies to date. Being that their glycan-protein hybrid epitopes are at subunit interfaces, the resulting heterogeneity can lead to partial neutralization. Here, we screened for mutations in Env that allowed for complete neutralization by the bnAbs. We found that when mutations outside V2 increased V2 bnAb recognition, they often also increased Env stability-of-function and decreased binding by narrowly neutralizing antibodies to the V3 crown. Three mutations together increased neutralization by V2 bnAb and eliminated binding by V3 crown antibodies. These results may aid the design of immunogens that elicit antibodies to the trimer apex. Copyright © 2017 American Society for Microbiology.

Functional Stability of HIV-1 Envelope Trimer Affects Accessibility to Broadly Neutralizing Antibodies at Its Apex

PubMed Central

Gift, Syna Kuriakose; Leaman, Daniel P.; Zhang, Lei; Kim, Arthur S.

2017-01-01

ABSTRACT The trimeric envelope glycoprotein spike (Env) of HIV-1 is the target of vaccine development to elicit broadly neutralizing antibodies (bnAbs). Env trimer instability and heterogeneity in principle make subunit interfaces inconsistent targets for the immune response. Here, we investigate how functional stability of Env relates to neutralization sensitivity to V2 bnAbs and V3 crown antibodies that engage subunit interfaces upon binding to unliganded Env. Env heterogeneity was inferred when antibodies neutralized a mutant Env with a plateau of less than 100% neutralization. A statistically significant correlation was found between the stability of mutant Envs and the MPN of V2 bnAb, PG9, as well as an inverse correlation between stability of Env and neutralization by V3 crown antibody, 447-52D. A number of Env-stabilizing mutations and V2 bnAb-enhancing mutations were identified in Env, but they did not always overlap, indicating distinct requirements of functional stabilization versus antibody recognition. Blocking complex glycosylation of Env affected V2 bnAb recognition, as previously described, but also notably increased functional stability of Env. This study shows how instability and heterogeneity affect antibody sensitivity of HIV-1 Env, which is relevant to vaccine design involving its dynamic apex. IMPORTANCE The Env trimer is the only viral protein on the surface of HIV-1 and is the target of neutralizing antibodies that reduce viral infectivity. Quaternary epitopes at the apex of the spike are recognized by some of the most potent and broadly neutralizing antibodies to date. Being that their glycan-protein hybrid epitopes are at subunit interfaces, the resulting heterogeneity can lead to partial neutralization. Here, we screened for mutations in Env that allowed for complete neutralization by the bnAbs. We found that when mutations outside V2 increased V2 bnAb recognition, they often also increased Env stability-of-function and decreased binding by narrowly neutralizing antibodies to the V3 crown. Three mutations together increased neutralization by V2 bnAb and eliminated binding by V3 crown antibodies. These results may aid the design of immunogens that elicit antibodies to the trimer apex. PMID:28978711

Slow Photoelectron Spectroscopy and State-Selected Unimolecular Decomposition of Ionized DNA Bases Analogues

NASA Astrophysics Data System (ADS)

Mahjoub, Ahmed; Hochlaf, Majdi; Poisson, Lionel; Garcia, Gustavo A.; Nahon, Laurent

2013-06-01

We studied the single-photon ionization of gas-phase 2-Piperidone (DNA basis analogue) and of its dimer using vacuum-ultraviolet (VUV) synchrotron radiation coupled to a velocity map imaging electron/ion coincidence spectrometer The slow photoelectron spectrum (SPES) of the monomer is dominated by the vibrational transitions to the ground state. These spectra are assigned with the help of theoretical calculations dealing with the equilibrium geometries, electronic-state patterns and evolutions, harmonic and anharmonic wavenumbers. After its formation, dimer is subject of intramolecular isomerization, H transfer and then unimolecular fragmentation processes. The near threshold photofragmentation pattern of the cationic 2-Piperidone cation and its dimer has been recorded. The experimental method yields the fragment intensity as a function of the internal energy deposited into the parent cation. In parallel, ab initio studies on ionic and neutral fragmentation products have been performed with the aim of determining the isomers of the ionic products observed experimentally as well as of their neutral counterparts. L. Nahon, N. De Oliveria,J. F. Gil,B. Pilette,O. Marcouillé, B. La garde and F. Polack Journal of Synchrotron Radiation {19}(4), 508-520; 2012

Genetic basis of adaptation in Arabidopsis thaliana: local adaptation at the seed dormancy QTL DOG1.

PubMed

Kronholm, Ilkka; Picó, F Xavier; Alonso-Blanco, Carlos; Goudet, Jérôme; de Meaux, Juliette

2012-07-01

Local adaptation provides an opportunity to study the genetic basis of adaptation and investigate the allelic architecture of adaptive genes. We study delay of germination 1 (DOG1), a gene controlling natural variation in seed dormancy in Arabidopsis thaliana and investigate evolution of dormancy in 41 populations distributed in four regions separated by natural barriers. Using F(ST) and Q(ST) comparisons, we compare variation at DOG1 with neutral markers and quantitative variation in seed dormancy. Patterns of genetic differentiation among populations suggest that the gene DOG1 contributes to local adaptation. Although Q(ST) for seed dormancy is not different from F(ST) for neutral markers, a correlation with variation in summer precipitation supports that seed dormancy is adaptive. We characterize dormancy variation in several F(2) -populations and show that a series of functionally distinct alleles segregate at the DOG1 locus. Theoretical models have shown that the number and effect of alleles segregatin at quantitative trait loci (QTL) have important consequences for adaptation. Our results provide support to models postulating a large number of alleles at quantitative trait loci involved in adaptation. © 2012 The Author(s).

Evolution, Development and Function of Vertebrate Cone Oil Droplets

PubMed Central

Toomey, Matthew B.; Corbo, Joseph C.

2017-01-01

To distinguish colors, the nervous system must compare the activity of distinct subtypes of photoreceptors that are maximally sensitive to different portions of the light spectrum. In vertebrates, a variety of adaptations have arisen to refine the spectral sensitivity of cone photoreceptors and improve color vision. In this review article, we focus on one such adaptation, the oil droplet, a unique optical organelle found within the inner segment of cone photoreceptors of a diverse array of vertebrate species, from fish to mammals. These droplets, which consist of neutral lipids and carotenoid pigments, are interposed in the path of light through the photoreceptor and modify the intensity and spectrum of light reaching the photosensitive outer segment. In the course of evolution, the optical function of oil droplets has been fine-tuned through changes in carotenoid content. Species active in dim light reduce or eliminate carotenoids to enhance sensitivity, whereas species active in bright light precisely modulate carotenoid double bond conjugation and concentration among cone subtypes to optimize color discrimination and color constancy. Cone oil droplets have sparked the curiosity of vision scientists for more than a century. Accordingly, we begin by briefly reviewing the history of research on oil droplets. We then discuss what is known about the developmental origins of oil droplets. Next, we describe recent advances in understanding the function of oil droplets based on biochemical and optical analyses. Finally, we survey the occurrence and properties of oil droplets across the diversity of vertebrate species and discuss what these patterns indicate about the evolutionary history and function of this intriguing organelle. PMID:29276475

Something old, something borrowed: admixture and adaptation in human evolution.

PubMed

Dannemann, Michael; Racimo, Fernando

2018-06-09

The sequencing of ancient DNA from archaic humans-Neanderthals and Denisovans-has revealed that modern and archaic humans interbred at least twice during the Pleistocene. The field of human paleogenomics has now turned its attention towards understanding the nature of this genetic legacy in the gene pool of present-day humans. What exactly did modern humans obtain from interbreeding with Neanderthals and Denisovans? Was the introgressed genetic material beneficial, neutral or maladaptive? Can differences in phenotypes among present-day human populations be explained by archaic human introgression? These questions are of prime importance for our understanding of recent human evolution, but will require careful computational modeling and extensive functional assays before they can be answered in full. Here, we review the recent literature characterizing introgressed DNA and the likely biological consequences for their modern human carriers. We focus particularly on archaic human haplotypes that were beneficial to modern humans as they expanded across the globe, and on ways to understand how populations harboring these haplotypes evolved over time. Copyright © 2018 Elsevier Ltd. All rights reserved.

Effects of topology on network evolution

NASA Astrophysics Data System (ADS)

Oikonomou, Panos; Cluzel, Philippe

2006-08-01

The ubiquity of scale-free topology in nature raises the question of whether this particular network design confers an evolutionary advantage. A series of studies has identified key principles controlling the growth and the dynamics of scale-free networks. Here, we use neuron-based networks of boolean components as a framework for modelling a large class of dynamical behaviours in both natural and artificial systems. Applying a training algorithm, we characterize how networks with distinct topologies evolve towards a pre-established target function through a process of random mutations and selection. We find that homogeneous random networks and scale-free networks exhibit drastically different evolutionary paths. Whereas homogeneous random networks accumulate neutral mutations and evolve by sparse punctuated steps, scale-free networks evolve rapidly and continuously. Remarkably, this latter property is robust to variations of the degree exponent. In contrast, homogeneous random networks require a specific tuning of their connectivity to optimize their ability to evolve. These results highlight an organizing principle that governs the evolution of complex networks and that can improve the design of engineered systems.

The Stochastic Evolutionary Game for a Population of Biological Networks Under Natural Selection

PubMed Central

Chen, Bor-Sen; Ho, Shih-Ju

2014-01-01

In this study, a population of evolutionary biological networks is described by a stochastic dynamic system with intrinsic random parameter fluctuations due to genetic variations and external disturbances caused by environmental changes in the evolutionary process. Since information on environmental changes is unavailable and their occurrence is unpredictable, they can be considered as a game player with the potential to destroy phenotypic stability. The biological network needs to develop an evolutionary strategy to improve phenotypic stability as much as possible, so it can be considered as another game player in the evolutionary process, ie, a stochastic Nash game of minimizing the maximum network evolution level caused by the worst environmental disturbances. Based on the nonlinear stochastic evolutionary game strategy, we find that some genetic variations can be used in natural selection to construct negative feedback loops, efficiently improving network robustness. This provides larger genetic robustness as a buffer against neutral genetic variations, as well as larger environmental robustness to resist environmental disturbances and maintain a network phenotypic traits in the evolutionary process. In this situation, the robust phenotypic traits of stochastic biological networks can be more frequently selected by natural selection in evolution. However, if the harbored neutral genetic variations are accumulated to a sufficiently large degree, and environmental disturbances are strong enough that the network robustness can no longer confer enough genetic robustness and environmental robustness, then the phenotype robustness might break down. In this case, a network phenotypic trait may be pushed from one equilibrium point to another, changing the phenotypic trait and starting a new phase of network evolution through the hidden neutral genetic variations harbored in network robustness by adaptive evolution. Further, the proposed evolutionary game is extended to an n-tuple evolutionary game of stochastic biological networks with m players (competitive populations) and k environmental dynamics. PMID:24558296

Dissociative recombination in interstellar clouds

NASA Technical Reports Server (NTRS)

Black, John H.; Van Dishoeck, Ewine F.

1989-01-01

Molecular ions play a significant role in the chemistry and evolution of interstellar molecular clouds, even though these regions are overwhelmingly neutral. The dissociative recombination (DR) process governs the abundances of many of these ions and of related neutral species. The gas-phase ion-molecule chemistry of the simplest species is summarized, with emphasis on those problems which are most sensitive to uncertain rates or product branching ratios of DR processes. Examples of the kinds of information needed about DR processes are presented. The importance of the H3(+) ion and prospects for its direct observation are discussed.

Evolutionary constraints and the neutral theory. [mutation-caused nucleotide substitutions in DNA

NASA Technical Reports Server (NTRS)

Jukes, T. H.; Kimura, M.

1984-01-01

The neutral theory of molecular evolution postulates that nucleotide substitutions inherently take place in DNA as a result of point mutations followed by random genetic drift. In the absence of selective constraints, the substitution rate reaches the maximum value set by the mutation rate. The rate in globin pseudogenes is about 5 x 10 to the -9th substitutions per site per year in mammals. Rates slower than this indicate the presence of constraints imposed by negative (natural) selection, which rejects and discards deleterious mutations.

The early universe history from contraction-deformation of the Standard Model

NASA Astrophysics Data System (ADS)

Gromov, N. A.

2017-03-01

The elementary particles evolution in the early Universe from Plank time up to several milliseconds is presented. The developed theory is based on the high-temperature (high-energy) limit of the Standard Model which is generated by the contractions of its gauge groups. At the infinite temperature all particles lose masses. Only massless neutral -bosons, massless Z-quarks, neutrinos and photons are survived in this limit. The weak interactions become long-range and are mediated by neutral currents, quarks have only one color degree of freedom.

Neutral changes during divergent evolution of hemoglobins

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1978-01-01

A comparison of the mRNAs for rabbit and human beta-hemoglobins shows that synonymous changes in codons have accumulated three times as rapidly as nucleotide replacements that produced changes in amino acids. This agrees with predictions based on the so-called neutral theory. In addition, seven codon changes that appear to be single-base changes (according to maximum parsimony) are actually two-base changes. This indicates that the construction of primordial sequences is of limited significance when based on inferences that assume minimum base changes for amino acid replacements.

Using geometric morphometric visualizations of directional selection gradients to investigate morphological differentiation.

PubMed

Weaver, Timothy D; Gunz, Philipp

2018-04-01

Researchers studying extant and extinct taxa are often interested in identifying the evolutionary processes that have lead to the morphological differences among the taxa. Ideally, one could distinguish the influences of neutral evolutionary processes (genetic drift, mutation) from natural selection, and in situations for which selection is implicated, identify the targets of selection. The directional selection gradient is an effective tool for investigating evolutionary process, because it can relate form (size and shape) differences between taxa to the variation and covariation found within taxa. However, although most modern morphometric analyses use the tools of geometric morphometrics (GM) to analyze landmark data, to date, selection gradients have mainly been calculated from linear measurements. To address this methodological gap, here we present a GM approach for visualizing and comparing between-taxon selection gradients with each other, associated difference vectors, and "selection" gradients from neutral simulations. To exemplify our approach, we use a dataset of 347 three-dimensional landmarks and semilandmarks recorded on the crania of 260 primate specimens (112 humans, 67 common chimpanzees, 36 bonobos, 45 gorillas). Results on this example dataset show how incorporating geometric information can provide important insights into the evolution of the human braincase, and serve to demonstrate the utility of our approach for understanding morphological evolution. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

The Nonisothermal Stage of Magnetic Star Formation. I. Formulation of the Problem and Method of Solution

NASA Astrophysics Data System (ADS)

Kunz, Matthew W.; Mouschovias, Telemachos Ch.

2009-03-01

We formulate the problem of the formation and subsequent evolution of fragments (or cores) in magnetically supported, self-gravitating molecular clouds in two spatial dimensions. The six-fluid (neutrals, electrons, molecular and atomic ions, positively charged, negatively charged, and neutral grains) physical system is governed by the radiation, nonideal magnetohydrodynamic equations. The magnetic flux is not assumed to be frozen in any of the charged species. Its evolution is determined by a newly derived generalized Ohm's law, which accounts for the contributions of both elastic and inelastic collisions to ambipolar diffusion and Ohmic dissipation. The species abundances are calculated using an extensive chemical-equilibrium network. Both MRN and uniform grain size distributions are considered. The thermal evolution of the protostellar core and its effect on the dynamics are followed by employing the gray flux-limited diffusion approximation. Realistic temperature-dependent grain opacities are used that account for a variety of grain compositions. We have augmented the publicly available Zeus-MP code to take into consideration all these effects and have modified several of its algorithms to improve convergence, accuracy, and efficiency. Results of magnetic star formation simulations that accurately track the evolution of a protostellar fragment from a density sime103 cm-3 to a density sime1015 cm-3, while rigorously accounting for both nonideal MHD processes and radiative transfer, are presented in a separate paper.

Random genetic drift, natural selection, and noise in human cranial evolution.

PubMed

Roseman, Charles C

2016-08-01

This study assesses the extent to which relationships among groups complicate comparative studies of adaptation in recent human cranial variation and the extent to which departures from neutral additive models of evolution hinder the reconstruction of population relationships among groups using cranial morphology. Using a maximum likelihood evolutionary model fitting approach and a mixed population genomic and cranial data set, I evaluate the relative fits of several widely used models of human cranial evolution. Moreover, I compare the goodness of fit of models of cranial evolution constrained by genomic variation to test hypotheses about population specific departures from neutrality. Models from population genomics are much better fits to cranial variation than are traditional models from comparative human biology. There is not enough evolutionary information in the cranium to reconstruct much of recent human evolution but the influence of population history on cranial variation is strong enough to cause comparative studies of adaptation serious difficulties. Deviations from a model of random genetic drift along a tree-like population history show the importance of environmental effects, gene flow, and/or natural selection on human cranial variation. Moreover, there is a strong signal of the effect of natural selection or an environmental factor on a group of humans from Siberia. The evolution of the human cranium is complex and no one evolutionary process has prevailed at the expense of all others. A holistic unification of phenome, genome, and environmental context, gives us a strong point of purchase on these problems, which is unavailable to any one traditional approach alone. Am J Phys Anthropol 160:582-592, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Emergence and Evolution of Hominidae-Specific Coding and Noncoding Genomic Sequences

PubMed Central

Saber, Morteza Mahmoudi; Adeyemi Babarinde, Isaac; Hettiarachchi, Nilmini; Saitou, Naruya

2016-01-01

Family Hominidae, which includes humans and great apes, is recognized for unique complex social behavior and intellectual abilities. Despite the increasing genome data, however, the genomic origin of its phenotypic uniqueness has remained elusive. Clade-specific genes and highly conserved noncoding sequences (HCNSs) are among the high-potential evolutionary candidates involved in driving clade-specific characters and phenotypes. On this premise, we analyzed whole genome sequences along with gene orthology data retrieved from major DNA databases to find Hominidae-specific (HS) genes and HCNSs. We discovered that Down syndrome critical region 4 (DSCR4) is the only experimentally verified gene uniquely present in Hominidae. DSCR4 has no structural homology to any known protein and was inferred to have emerged in several steps through LTR/ERV1, LTR/ERVL retrotransposition, and transversion. Using the genomic distance as neutral evolution threshold, we identified 1,658 HS HCNSs. Polymorphism coverage and derived allele frequency analysis of HS HCNSs showed that these HCNSs are under purifying selection, indicating that they may harbor important functions. They are overrepresented in promoters/untranslated regions, in close proximity of genes involved in sensory perception of sound and developmental process, and also showed a significantly lower nucleosome occupancy probability. Interestingly, many ancestral sequences of the HS HCNSs showed very high evolutionary rates. This suggests that new functions emerged through some kind of positive selection, and then purifying selection started to operate to keep these functions. PMID:27289096

Ultimate boundedness stability and controllability of hereditary systems

NASA Technical Reports Server (NTRS)

Chukwu, E. N.

1979-01-01

By generalizing the Liapunov-Yoshizawa techniques, necessary and sufficient conditions are given for uniform boundedness and uniform ultimate boundedness of a rather general class of nonlinear differential equations of neutral type. Among the applications treated by the methods are the Lienard equation of neutral type and hereditary systems of Lurie type. The absolute stability of this later equation is also investigated. A certain existence result of a solution of a neutral functional differential inclusion with two point boundary values is applied to study the exact function space controllability of a nonlinear neutral functional differential control system. A geometric growth condition is used to characterize both the function space and Euclidean controllability of another nonlinear delay system which has a compact and convex control set. This yields conditions under which perturbed nonlinear delay controllable systems are controllable.

Dynamics of ion beam charge neutralization by ferroelectric plasma sources

DOE PAGES

Stepanov, Anton D.; Gilson, Erik P.; Grisham, Larry R.; ...

2016-04-27

Ferroelectric Plasma Sources (FEPSs) can generate plasma that provides effective space-charge neutralization of intense high-perveance ion beams, as has been demonstrated on the Neutralized Drift Compression Experiment NDCX-I and NDCX-II. This article presents experimental results on charge neutralization of a high-perveance 38 keV Ar + beam by a plasma produced in a FEPS discharge. By comparing the measured beam radius with the envelope model for space-charge expansion, it is shown that a charge neutralization fraction of 98% is attainable with sufficiently dense FEPS plasma. The transverse electrostatic potential of the ion beam is reduced from 15V before neutralization to 0.3more » V, implying that the energy of the neutralizing electrons is below 0.3 eV. Measurements of the time-evolution of beam radius show that near-complete charge neutralization is established similar to –5 μs after the driving pulse is applied to the FEPS and can last for 35 μs. It is argued that the duration of neutralization is much longer than a reasonable lifetime of the plasma produced in the sub-mu s surface discharge. Measurements of current flow in the driving circuit of the FEPS show the existence of electron emission into vacuum, which lasts for tens of mu s after the high voltage pulse is applied. Lastly, it is argued that the beam is neutralized by the plasma produced by this process and not by a surface discharge plasma that is produced at the instant the high-voltage pulse is applied.« less

A facility to study the particles released by ion sputtering process

NASA Astrophysics Data System (ADS)

de Angelis, E.; di Lellis, A. M.; Vannaroni, G.; Orsini, S.; Mangano, V.; Milillo, A.; Massetti, S.; Mura, A.; Vertolli, N.

2007-08-01

Research on the planetary surface erosion and planetary evolution could be enriched with the detection of the escaping material, in terms of energy and direction, caused by ions sputtering. A complete study of emitted neutral distribution from which infers the processes occurring on the impacted surface requires dedicated instrumentation, tailored on the peculiarity on the low energy profile of the sputtered signal. We propose a comprehensive facility at INAF/IFSI in Rome intended to provide the opportunity to investigate the interaction of selectable ion beam with planetary analogues through the detection of sputtered neutral atoms. The laboratory is equipped with a high volume UHV chamber, ion selectable sources in the range 0 to 10 keV, a set of 3D sample/sensor orientation motion actuation motors down to 1/100 deg resolution. The laboratory will support a set of neutral sensor heads sets derived from the Emitted for Low Energetic Neutral Atoms (ELENA) instrument under development for the ESA BepiColombo Mercury mission able to detect neutral atoms (few eV-up to 5 keV).

Current disruptions in the near-earth neutral sheet region

NASA Technical Reports Server (NTRS)

Lui, A. T. Y.; Lopez, R. E.; Anderson, B. J.; Takahashi, K.; Zanetti, L. J.; Mcentire, R. W.; Potemra, T. A.; Klumpar, D. M.; Greene, E. M.; Strangeway, R.

1992-01-01

Current disruption events observed by the Charge Composition Explorer during 1985 and 1986 are examined. Occurrence of current disruption was accompanied by large magnetic field turbulence and frequently with reversal in the sign of the field component normal to the neutral sheet. Current disruptions in the near-earth region are found to be typically shortlived (about 1-5 min), and their onsets coincide well with the ground onsets of substorm expansion or intensification in the local time sector of the footpoint of the spacecraft. These events are found almost exclusively close to the field reversal plane of the neutral sheet (within about 0.5 RE). Prior to current disruption the field strength can be reduced to as low as one seventh of the dipole field value and can recover to nearly the dipole value after disruption. The temporal evolution of particle pressure in the near-earth neutral sheet during the onset of current disruption indicates that the current buildup during the substorm growth phase is associated with enhancement in the particle pressure at the neutral sheet.

Social evolution. Genomic signatures of evolutionary transitions from solitary to group living.

PubMed

Kapheim, Karen M; Pan, Hailin; Li, Cai; Salzberg, Steven L; Puiu, Daniela; Magoc, Tanja; Robertson, Hugh M; Hudson, Matthew E; Venkat, Aarti; Fischman, Brielle J; Hernandez, Alvaro; Yandell, Mark; Ence, Daniel; Holt, Carson; Yocum, George D; Kemp, William P; Bosch, Jordi; Waterhouse, Robert M; Zdobnov, Evgeny M; Stolle, Eckart; Kraus, F Bernhard; Helbing, Sophie; Moritz, Robin F A; Glastad, Karl M; Hunt, Brendan G; Goodisman, Michael A D; Hauser, Frank; Grimmelikhuijzen, Cornelis J P; Pinheiro, Daniel Guariz; Nunes, Francis Morais Franco; Soares, Michelle Prioli Miranda; Tanaka, Érica Donato; Simões, Zilá Luz Paulino; Hartfelder, Klaus; Evans, Jay D; Barribeau, Seth M; Johnson, Reed M; Massey, Jonathan H; Southey, Bruce R; Hasselmann, Martin; Hamacher, Daniel; Biewer, Matthias; Kent, Clement F; Zayed, Amro; Blatti, Charles; Sinha, Saurabh; Johnston, J Spencer; Hanrahan, Shawn J; Kocher, Sarah D; Wang, Jun; Robinson, Gene E; Zhang, Guojie

2015-06-05

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks. Copyright © 2015, American Association for the Advancement of Science.

A Study of Neutral B Meson Time Evolution Using Exclusively Reconstructed Semileptonic Decays

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meyer, T

2003-11-05

The Standard Model of particle physics describes the fundamental building blocks of the Universe and their basic interactions. The model naturally describes the time evolution of the basic particles, of which lifetime and mixing are two examples. The neutral B meson, consisting of a bottom quark and an oppositely charged down quark, enjoys a lifetime of about 1.5 ps and the special property of mixing with its antiparticle partner, the {bar B}{sup 0}. That is, due to second order weak interactions, the B{sup 0} meson can change into a {bar B}{sup 0} meson and back again as it evolves throughmore » time. The details of this behavior offer an opportunity to closely examine the Standard Model. In this dissertation, I report on a measurement of the lifetime and mixing frequency of the neutral B meson. Using the semileptonic decay channel B{sup 0} {yields} D*{sup -}{ell}{sup +}{bar {nu}}{sub {ell}}, we select more than 68,000 signal and background candidates from about 23 million B{bar B} pairs collected in 1999-2000 with the BABAR detector located at the Stanford Linear Accelerator Center. The other B in the event is reconstructed inclusively. By constructing a master probability density function that describes the distribution of decay time differences in the sample, we use a maximum likelihood technique to simultaneously extract the B{sup 0} lifetime and mixing parameters with precision comparable to the year 2000 world average. The results are {tau}{sub B{sup 0}} = (1.523{sub -0.023}{sup +0.024} {+-} 0.022) ps and {Delta}m{sub d} = (0.492 {+-} 0.018 {+-} 0.013) ps{sup -1}. The statistical correlation coefficient between {tau}{sub B{sup 0}} and {Delta}m{sub d} is -0.22. I describe in detail several cutting-edge strategies this analysis uses to study these phenomena, laying important groundwork for the future. I also discuss several extensions of this work to include possible measurements of higher order parameters such as {Delta}{Lambda}{sub d}.« less

Preferential amygdala reactivity to the negative assessment of neutral faces.

PubMed

Blasi, Giuseppe; Hariri, Ahmad R; Alce, Guilna; Taurisano, Paolo; Sambataro, Fabio; Das, Saumitra; Bertolino, Alessandro; Weinberger, Daniel R; Mattay, Venkata S

2009-11-01

Prior studies suggest that the amygdala shapes complex behavioral responses to socially ambiguous cues. We explored human amygdala function during explicit behavioral decision making about discrete emotional facial expressions that can represent socially unambiguous and ambiguous cues. During functional magnetic resonance imaging, 43 healthy adults were required to make complex social decisions (i.e., approach or avoid) about either relatively unambiguous (i.e., angry, fearful, happy) or ambiguous (i.e., neutral) facial expressions. Amygdala activation during this task was compared with that elicited by simple, perceptual decisions (sex discrimination) about the identical facial stimuli. Angry and fearful expressions were more frequently judged as avoidable and happy expressions most often as approachable. Neutral expressions were equally judged as avoidable and approachable. Reaction times to neutral expressions were longer than those to angry, fearful, and happy expressions during social judgment only. Imaging data on stimuli judged to be avoided revealed a significant task by emotion interaction in the amygdala. Here, only neutral facial expressions elicited greater activity during social judgment than during sex discrimination. Furthermore, during social judgment only, neutral faces judged to be avoided were associated with greater amygdala activity relative to neutral faces that were judged as approachable. Moreover, functional coupling between the amygdala and both dorsolateral prefrontal (social judgment > sex discrimination) and cingulate (sex discrimination > social judgment) cortices was differentially modulated by task during processing of neutral faces. Our results suggest that increased amygdala reactivity and differential functional coupling with prefrontal circuitries may shape complex decisions and behavioral responses to socially ambiguous cues.

Preferential Amygdala Reactivity to the Negative Assessment of Neutral Faces

PubMed Central

Blasi, Giuseppe; Hariri, Ahmad R.; Alce, Guilna; Taurisano, Paolo; Sambataro, Fabio; Das, Saumitra; Bertolino, Alessandro; Weinberger, Daniel R.; Mattay, Venkata S.

2010-01-01

Background Prior studies suggest that the amygdala shapes complex behavioral responses to socially ambiguous cues. We explored human amygdala function during explicit behavioral decision making about discrete emotional facial expressions that can represent socially unambiguous and ambiguous cues. Methods During functional magnetic resonance imaging, 43 healthy adults were required to make complex social decisions (i.e., approach or avoid) about either relatively unambiguous (i.e., angry, fearful, happy) or ambiguous (i.e., neutral) facial expressions. Amygdala activation during this task was compared with that elicited by simple, perceptual decisions (sex discrimination) about the identical facial stimuli. Results Angry and fearful expressions were more frequently judged as avoidable and happy expressions most often as approachable. Neutral expressions were equally judged as avoidable and approachable. Reaction times to neutral expressions were longer than those to angry, fearful, and happy expressions during social judgment only. Imaging data on stimuli judged to be avoided revealed a significant task by emotion interaction in the amygdala. Here, only neutral facial expressions elicited greater activity during social judgment than during sex discrimination. Furthermore, during social judgment only, neutral faces judged to be avoided were associated with greater amygdala activity relative to neutral faces that were judged as approachable. Moreover, functional coupling between the amygdala and both dorsolateral prefrontal (social judgment > sex discrimination) and cingulate (sex discrimination > social judgment) cortices was differentially modulated by task during processing of neutral faces. Conclusions Our results suggest that increased amygdala reactivity and differential functional coupling with prefrontal circuitries may shape complex decisions and behavioral responses to socially ambiguous cues. PMID:19709644

Re-Evaluating Clonal Dominance in Cancer Evolution.

PubMed

Burrell, Rebecca A; Swanton, Charles

2016-05-01

Tumours are composed of genetically heterogeneous subclones which may diverge early during tumour growth. However, our strategies for treating and assessing outcome for patients are overwhelmingly based upon the classical linear paradigm for cancer evolution. Increasing numbers of studies are finding that minor subclones can determine clinical disease course, and that temporal and spatial heterogeneity needs to be considered in disease management. In this article we review evidence for cancer clonal heterogeneity, evaluating the importance of tumour subclones and their growth through both Darwinian and neutral evolution. Major shifts in current clinical practice and trial designs, aimed at understanding cancer evolution on a patient-by-patient basis, may be necessary to achieve more successful treatment of heterogeneous metastatic disease. Copyright © 2016 Elsevier Inc. All rights reserved.

Drift-Induced Selection Between Male and Female Heterogamety.

PubMed

Veller, Carl; Muralidhar, Pavitra; Constable, George W A; Nowak, Martin A

2017-10-01

Evolutionary transitions between male and female heterogamety are common in both vertebrates and invertebrates. Theoretical studies of these transitions have found that, when all genotypes are equally fit, continuous paths of intermediate equilibria link the two sex chromosome systems. This observation has led to a belief that neutral evolution along these paths can drive transitions, and that arbitrarily small fitness differences among sex chromosome genotypes can determine the system to which evolution leads. Here, we study stochastic evolutionary dynamics along these equilibrium paths. We find non-neutrality, both in transitions retaining the ancestral pair of sex chromosomes, and in those creating a new pair. In fact, substitution rates are biased in favor of dominant sex determining chromosomes, which fix with higher probabilities than mutations of no effect. Using diffusion approximations, we show that this non-neutrality is a result of "drift-induced selection" operating at every point along the equilibrium paths: stochastic jumps off the paths return with, on average, a directional bias in favor of the dominant segregating sex chromosome. Our results offer a novel explanation for the observed preponderance of dominant sex determining genes, and hint that drift-induced selection may be a common force in standard population genetic systems. Copyright © 2017 by the Genetics Society of America.

Evolution of the observed Lyα luminosity function from z = 6.5 to z = 7.7: evidence for the epoch of reionization?

NASA Astrophysics Data System (ADS)

Clément, B.; Cuby, J.-G.; Courbin, F.; Fontana, A.; Freudling, W.; Fynbo, J.; Gallego, J.; Hibon, P.; Kneib, J.-P.; Le Fèvre, O.; Lidman, C.; McMahon, R.; Milvang-Jensen, B.; Moller, P.; Moorwood, A.; Nilsson, K. K.; Pentericci, L.; Venemans, B.; Villar, V.; Willis, J.

2012-02-01

Aims: Lyα emitters (LAEs) can be detected out to very high redshifts during the epoch of reionization. The evolution of the LAE luminosity function with redshift is a direct probe of the Lyα transmission of the intergalactic medium (IGM), and therefore of the IGM neutral-hydrogen fraction. Measuring the Lyα luminosity function (LF) of Lyα emitters at redshift z = 7.7 therefore allows us to constrain the ionizing state of the Universe at this redshift. Methods: We observed three 7'.5 × 7'.5 fields with the HAWK-I instrument at the VLT with a narrow band filter centred at 1.06 μm and targeting Lyα emitters at redshift z ~ 7.7. The fields were chosen for the availability of multiwavelength data. One field is a galaxy cluster, the Bullet Cluster, which allowed us to use gravitational amplification to probe luminosities that are fainter than in the field. The two other fields are subareas of the GOODS Chandra Deep Field South and CFHTLS-D4 deep field. We selected z = 7.7 LAE candidates from a variety of colour criteria, in particular from the absence of detection in the optical bands. Results: We do not find any LAE candidates at z = 7.7 in ~2.4 × 104 Mpc3 down to a narrow band AB magnitude of ~26, which allows us to infer robust constraints on the Lyα LAE luminosity function at this redshift. Conclusions: The predicted mean number of objects at z = 6.5, derived from somewhat different luminosity functions of Hu et al. (2010, ApJ, 725, 394), Ouchi et al. (2010, ApJ, 723, 869), and Kashikawa et al. (2011, ApJ, 734, 119) are 2.5, 13.7, and 11.6, respectively. Depending on which of these luminosity functions we refer to, we exclude a scenario with no evolution from z = 6.5 to z = 7.7 at 85% confidence without requiring a strong change in the IGM Lyα transmission, or at 99% confidence with a significant quenching of the IGM Lyα transmission, possibly from a strong increase in the high neutral-hydrogen fraction between these two redshifts. Based on observations collected at the European Organisation for Astronomical Research in the Southern Hemisphere (ESO), Chile, Prog-Id 181.A-0485, 181.A-0717, 60.A-9284, 084.A-0749. Based on observations obtained at the Canada-France-Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Sciences de l'Univers of the Centre National de la Recherche Scientifique of France (CNRS), and the University of Hawaii. This work is based in part on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/DAPNIA and in part on data products produced at TERAPIX and the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. This paper includes data gathered with the 6.5 m Magellan Telescopes located at Las Campanas Observatory, Chile.

Carbon-armored Co9S8 nanoparticles as all-pH efficient and durable H2-evolving electrocatalysts.

PubMed

Feng, Liang-Liang; Li, Guo-Dong; Liu, Yipu; Wu, Yuanyuan; Chen, Hui; Wang, Yun; Zou, Yong-Cun; Wang, Dejun; Zou, Xiaoxin

2015-01-14

Splitting water to produce hydrogen requires the development of non-noble-metal catalysts that are able to make this reaction feasible and energy efficient. Herein, we show that cobalt pentlandite (Co9S8) nanoparticles can serve as an electrochemically active, noble-metal-free material toward hydrogen evolution reaction, and they work stably in neutral solution (pH 7) but not in acidic (pH 0) and basic (pH 14) media. We, therefore, further present a carbon-armoring strategy to increase the durability and activity of Co9S8 over a wider pH range. In particular, carbon-armored Co9S8 nanoparticles (Co9S8@C) are prepared by direct thermal treatment of a mixture of cobalt nitrate and trithiocyanuric acid at 700 °C in N2 atmosphere. Trithiocyanuric acid functions as both sulfur and carbon sources in the reaction system. The resulting Co9S8@C material operates well with high activity over a broad pH range, from pH 0 to 14, and gives nearly 100% Faradaic yield during hydrogen evolution reaction under acidic (pH 0), neutral (pH 7), and basic (pH 14) media. To the best of our knowledge, this is the first time that a transition-metal chalcogenide material is shown to have all-pH efficient and durable electrocatalytic activity. Identifying Co9S8 as the catalytically active phase and developing carbon-armoring as the improvement strategy are anticipated to give a fresh impetus to rational design of high-performance noble-metal-free water splitting catalysts.

Population dynamics in the presence of quasispecies effects and changing environments

NASA Astrophysics Data System (ADS)

Forster, Robert Burke

2006-12-01

This thesis explores how natural selection acts on organisms such as viruses that have either highly error-prone reproduction or face variable environmental conditions or both. By modeling population dynamics under these conditions, we gain a better understanding of the selective forces at work, both in our simulations and hopefully also in real organisms. With an understanding of the important factors in natural selection we can forecast not only the immediate fate of an existing population but also in what directions such a population might evolve in the future. We demonstrate that the concept of a quasispecies is relevant to evolution in a neutral fitness landscape. Motivated by RNA viruses such as HIV, we use RNA secondary structure as our model system and find that quasispecies effects arise both rapidly and in realistically small populations. We discover that the evolutionary effects of neutral drift, punctuated equilibrium and the selection for mutational robustness extend to the concept of a quasispecies. In our study of periodic environments, we consider the tradeoffs faced by quasispecies in adapting to environmental change. We develop an analytical model to predict whether evolution favors short-term or long-term adaptation and validate our model through simulation. Our results bear directly on the population dynamics of viruses such as West Nile that alternate between two host species. More generally, we discover that a selective pressure exists under these conditions to fuse or split genes with complementary environmental functions. Lastly, we study the general effects of frequency-dependent selection on two strains competing in a periodic environment. Under very general assumptions, we prove that stable coexistence rather than extinction is the likely outcome. The population dynamics of this system may be as simple as stable equilibrium or as complex as deterministic chaos.

Redox-Active Hydrogel Polymer Electrolytes with Different pH Values for Enhancing the Energy Density of the Hybrid Solid-State Supercapacitor.

PubMed

Tang, Xiaohui; Lui, Yu Hui; Merhi, Abdul Rahman; Chen, Bolin; Ding, Shaowei; Zhang, Bowei; Hu, Shan

2017-12-27

To enhance the energy density of solid-state supercapacitors, a novel solid-state cell, made of redox-active poly(vinyl alcohol) (PVA) hydrogel electrolytes and functionalized carbon nanotube-coated cellulose paper electrodes, was investigated in this work. Briefly, acidic PVA-[BMIM]Cl-lactic acid-LiBr and neutral PVA-[BMIM]Cl-sodium acetate-LiBr hydrogel polymer electrolytes are used as catholyte and anolyte, respectively. The acidic condition of the catholyte contributes to suppression of the undesired irreversible reaction of Br - and extension of the oxygen evolution reaction potential to a higher value than that of the redox potential of Br - /Br 3 - reaction. The observed Br - /Br 3 - redox activity at the cathode contributes to enhance the cathode capacitance. The neutral condition of the anolyte helps extend the operating voltage window of the supercapacitor by introducing hydrogen evolution reaction overpotential to the anode. The electrosorption of nascent H on the negative electrode also increases the anode capacitance. As a result, the prepared solid-state hybrid supercapacitor shows a broad voltage window of 1.6 V, with a high Coulombic efficiency of 97.6% and the highest energy density of 16.3 Wh/kg with power density of 932.6 W/kg at 2 A/g obtained. After 10 000 cycles of galvanostatic charge and discharge tests at the current density of 10 A/g, it exhibits great cyclic stability with 93.4% retention of the initial capacitance. In addition, a robust capacitive performance can also be observed from the solid-state supercapacitor at different bending angles, indicating its great potential as a flexible energy storage device.

Kinetic Behavior of Leucine and Other Amino Acids Modulating Cognitive Performance via mTOR Pathway

DTIC Science & Technology

2011-12-02

is a potential target for modulation with leucine (or other therapeutic agents), to maintain/enhance normal functioning under stress conditions. Such... functioning under stress conditions. Such an effect has potential for optimizing warfighter cognitive performance under high demand conditions. The... Isoleucine L1 Essential Neutral Non-polar Branched chain Lysine Basic Y+ Essential Basic Polar Proline L1? Neutral Non-polar Aromatic Asparagine Neutral

Multiple scattered radiation emerging from Rayleigh and continental haze layers. 1: Radiance, polarization, and neutral points.

PubMed

Kattawar, G W; Plass, G N; Hitzfelder, S J

1976-03-01

The complete radiation field including polarization is calculated by the matrix operator method for scattering layers of various optical thicknesses. Results obtained for Rayleigh scattering are compared with those for scattering from a continental haze. Radiances calculated using Stokes vectors show differences as large as 23% compared to the approximate scalar theory of radiative transfer, while the same differences are only of the order of 0.1% for a continental haze phase function. The polarization of the reflected and transmitted radiation is given for a wide range of optical thicknesses of the scattering layer, for various solar zenith angles, and various surface albedos. Two entirely different types of neutral points occur for aerosol phase functions. Rayleigh-like neutral points (RNP) arise from the zero polarization in single scattering that occurs for all phase functions at scattering angles of 0 degrees and 180 degrees . For Rayleigh phase functions, the position of the RNP varies appreciably with the optical thickness of the scattering layer. At low solar elevations there may be four RNP. For a continental haze phase function the position of the RNP in the reflected radiation shows only a small variation with the optical thickness, and the RNP exists in the transmitted radiation only for extremely small optical thicknesses. Another type of neutral point (NRNP) exists for aerosol phase functions. It is associated with the zeros of the single scattered polarization, which occur between the end points of the curve; these are called non-Rayleigh neutral points (NRNP). There may be from zero to four of these neutral points associated with each zero of the single scattering curve. They occur over a range of azimuthal angles, unlike the RNP that are in the principal plane only. The position of these neutral points is given as a function of solar angle and optical thickness.

Dynamic Evolution Model Based on Social Network Services

NASA Astrophysics Data System (ADS)

Xiong, Xi; Gou, Zhi-Jian; Zhang, Shi-Bin; Zhao, Wen

2013-11-01

Based on the analysis of evolutionary characteristics of public opinion in social networking services (SNS), in the paper we propose a dynamic evolution model, in which opinions are coupled with topology. This model shows the clustering phenomenon of opinions in dynamic network evolution. The simulation results show that the model can fit the data from a social network site. The dynamic evolution of networks accelerates the opinion, separation and aggregation. The scale and the number of clusters are influenced by confidence limit and rewiring probability. Dynamic changes of the topology reduce the number of isolated nodes, while the increased confidence limit allows nodes to communicate more sufficiently. The two effects make the distribution of opinion more neutral. The dynamic evolution of networks generates central clusters with high connectivity and high betweenness, which make it difficult to control public opinions in SNS.

Cryptic genetic variation: evolution's hidden substrate.

PubMed

Paaby, Annalise B; Rockman, Matthew V

2014-04-01

Cryptic genetic variation (CGV) is invisible under normal conditions, but it can fuel evolution when circumstances change. In theory, CGV can represent a massive cache of adaptive potential or a pool of deleterious alleles that are in need of constant suppression. CGV emerges from both neutral and selective processes, and it may inform about how human populations respond to change. CGV facilitates adaptation in experimental settings, but does it have an important role in the real world? Here, we review the empirical support for widespread CGV in natural populations, including its potential role in emerging human diseases and the growing evidence of its contribution to evolution.

Neutralization of Plasmodium falciparum merozoites by antibodies against PfRH5

PubMed Central

Douglas, Alexander D.; Williams, Andrew R.; Knuepfer, Ellen; Illingworth, Joseph J.; Furze, Julie M.; Crosnier, Cécile; Choudhary, Prateek; Bustamante, Leyla Y.; Zakutansky, Sara E.; Awuah, Dennis K.; Alanine, Daniel G. W.; Theron, Michel; Worth, Andrew; Shimkets, Richard; Rayner, Julian C.; Holder, Anthony A.; Wright, Gavin J.; Draper, Simon J.

2013-01-01

There is intense interest in induction and characterization of strain-transcending neutralizing antibody against antigenically variable human pathogens. We have recently identified the human malaria parasite Plasmodium falciparum reticulocyte-binding protein homologue 5 (PfRH5) as a target of broadly-neutralizing antibodies, but there is little information regarding the functional mechanism(s) of antibody-mediated neutralization. Here, we report that vaccine-induced polyclonal anti-PfRH5 antibodies inhibit the tight attachment of merozoites to erythrocytes, and are capable of blocking the interaction of PfRH5 with its receptor basigin. Furthermore, by developing anti-PfRH5 monoclonal antibodies (mAbs), we provide evidence that i) the ability to block the PfRH5-basigin interaction in vitro is predictive of functional activity, but absence of blockade does not predict absence of functional activity; ii) neutralizing mAbs bind spatially-related epitopes on the folded protein, involving at least two defined regions of the PfRH5 primary sequence; iii) a brief exposure window of PfRH5 is likely to necessitate rapid binding of antibody to neutralize parasites; and iv) intact bivalent IgG contributes to but is not necessary for parasite neutralization. These data provide important insight into the mechanisms of broadly-neutralizing anti-malaria antibodies and further encourage anti-PfRH5 based malaria prevention efforts. PMID:24293631

DNA aptamers as a novel approach to neutralize Staphylococcus aureus α-toxin.

PubMed

Vivekananda, Jeevalatha; Salgado, Christi; Millenbaugh, Nancy J

2014-02-14

Staphylococcus aureus is a versatile pathogen capable of causing a broad spectrum of diseases ranging from superficial skin infections to life threatening conditions such as endocarditis, septicemia, pneumonia and toxic shock syndrome. In vitro and in vivo studies identified an exotoxin, α-toxin, as a major cause of S. aureus toxicity. Because S. aureus has rapidly evolved resistance to a number of antibiotics, including methicillin, it is important to identify new therapeutic strategies, other than antibiotics, for inhibiting the harmful effects of this pathogen. Aptamers are single-stranded DNA or RNA oligonucleotides with three-dimensional folded conformations that bind with high affinity and selectivity to targets and modulate their biological functions. The goal of this study was to isolate DNA aptamers that specifically inhibit the cytotoxic activity of α-toxin. After 10 rounds of Systematic Evolution of Ligands by EXponential Enrichment (SELEX), 49 potential anti-α-toxin aptamers were identified. In vitro neutralization assays demonstrated that 4 of these 49 aptamers, AT-27, AT-33, AT-36, and AT-49, significantly inhibited α-toxin-mediated cell death in Jurkat T cells. Furthermore, RT-PCR analysis revealed that α-toxin increased the transcription of the inflammatory cytokines TNF-α and IL-17 and that anti-α-toxin aptamers AT-33 and AT-36 inhibited the upregulation of these genes. Collectively, the data suggest the feasibility of generating functionally effective aptamers against α-toxin for treatment of S. aureus infections. Published by Elsevier Inc.

Mineral induced phosphorylation of glycolate ion--a metaphor in chemical evolution

NASA Technical Reports Server (NTRS)

Kolb, V.; Zhang, S.; Xu, Y.; Arrhenius, G.

1997-01-01

Bilateral surface-active minerals with excess positive charge concentrate glycolate and trimetaphosphate ion from l0(-3) m aqueous solution to half-saturation of the internal surface sites, and induce phosphorylation of glycolate ion in the mineral with trimetaphosphate, sorbed from l0(-2) m solution. By utilizing reactants from dilute solution at near-neutral pH, and eliminating the need for participating organic nitrogen compounds, the reaction comprises several elements considered necessary for geochemical realism in models for molecular evolution.

Extraction of the gluon density of the proton at x

NASA Astrophysics Data System (ADS)

Derrick, M.; Krakauer, D.; Magill, S.; Musgrave, B.; Repond, J.; Schlereth, J.; Stanek, R.; Talaga, R. L.; Thron, J.; Arzarello, F.; Ayad, R.; Bari, G.; Basile, M.; Bellagamba, L.; Boscherini, D.; Bruni, A.; Bruni, G.; Bruni, P.; Cara Romeo, G.; Castellini, G.; Chiarini, M.; Cifarelli, L.; Cindolo, F.; Ciralli, F.; Contin, A.; D'Auria, S.; Frasconi, F.; Gialas, I.; Giusti, P.; Iacobucci, G.; Laurenti, G.; Levi, G.; Margotti, A.; Massam, T.; Nania, R.; Nemoz, C.; Palmonari, F.; Polini, A.; Sartorelli, G.; Timellini, R.; Zamora Garcia, Y.; Zichichi, A.; Bargende, A.; Crittenden, J.; Desch, K.; Diekmann, B.; Doeker, T.; Eckert, M.; Feld, L.; Frey, A.; Geerts, M.; Geitz, G.; Grothe, M.; Hartmann, H.; Haun, D.; Heinloth, K.; Hilger, E.; Jakob, H.-P.; Katz, U. F.; Mari, S. M.; Mass, A.; Mengel, S.; Mollen, J.; Paul, E.; Rembser, Ch.; Schattevoy, R.; Schramm, D.; Stamm, J.; Wedemeyer, R.; Campbell-Robson, S.; Cassidy, A.; Dyce, N.; Foster, B.; George, S.; Gilmore, R.; Heath, G. P.; Heath, H. F.; Llewellyn, T. J.; Morgado, C. J. S.; Norman, D. J. P.; O'Mara, J. A.; Tapper, R. J.; Wilson, S. S.; Yoshida, R.; Rau, R. R.; Arneodo, M.; Iannotti, L.; Schioppa, M.; Susinno, G.; Bernstein, A.; Caldwell, A.; Parsons, J. A.; Ritz, S.; Sciulli, F.; Straub, P. B.; Wai, L.; Yang, S.; Borzemski, P.; Chwastowski, J.; Eskreys, A.; Piotrzkowski, K.; Zachara, M.; Zawiejski, L.; Adamczyk, L.; Bednarek, B.; Eskreys, K.; Jelén, K.; Kisielewska, D.; Kowalski, T.; Rulikowska-Zarȩbska, E.; Suszycki, L.; Zajaç, J.; Kȩdzierski, T.; Kotański, A.; Przybycień, M.; Bauerdick, L. A. T.; Behrens, U.; Bienlein, J. K.; Böttcher, S.; Coldewey, C.; Drews, G.; Flasiński, M.; Gilkinson, D. J.; Göttlicher, P.; Gutjahr, B.; Haas, T.; Hain, W.; Hasell, D.; Heβling, H.; Hultschig, H.; Iga, Y.; Joos, P.; Kasemann, M.; Klanner, R.; Koch, W.; Köpke, L.; Kötz, U.; Kowalski, H.; Kröger, W.; Krüger, J.; Labs, J.; Ladage, A.; Löhr, B.; Löwe, M.; Lüke, D.; Mańczak, O.; Ng, J. S. T.; Nickel, S.; Notz, D.; Ohrenberg, K.; Roco, M.; Rohde, M.; Roldán, J.; Schneekloth, U.; Schulz, W.; Selonke, F.; Stiliaris, E.; Voβ, T.; Westphal, D.; Wolf, G.; Youngman, C.; Grabosch, H. J.; Leich, A.; Meyer, A.; Rethfeldt, C.; Schlenstedt, S.; Barbagli, G.; Pelfer, P.; Anzivino, G.; Maccarrone, G.; De Pasquale, S.; Qian, S.; Votano, L.; Bamberger, A.; Freidhof, A.; Poser, T.; Söldner-Rembold, S.; Schroeder, J.; Theisen, G.; Trefzger, T.; Brook, N. H.; Bussey, P. J.; Doyle, A. T.; Fleck, I.; Jamieson, V. A.; Saxon, D. H.; Utley, M. L.; Wilson, A. S.; Dannemann, A.; Holm, U.; Horstmann, D.; Kammerlocher, H.; Krebs, B.; Neumann, T.; Sinkus, R.; Wick, K.; Badura, E.; Burow, B. D.; Fürtjes, A.; Hagge, L.; Lohrmann, E.; Mainusch, J.; Milewski, J.; Nakahata, M.; Pavel, N.; Poelz, G.; Schott, W.; Terron, J.; Zetsche, F.; Bacon, T. C.; Beuselinck, R.; Butterworth, I.; Gallo, E.; Harris, V. L.; Hung, B. H.; Long, K. R.; Miller, D. B.; Morawitz, P. P. O.; Prinias, A.; Sedgbeer, J. K.; Whitfield, A. F.; Mallik, U.; McCliment, E.; Wang, M. Z.; Wang, S. M.; Wu, J. T.; Zhang, Y.; Cloth, P.; Filges, D.; An, S. H.; Hong, S. M.; Nam, S. W.; Park, S. K.; Suh, M. H.; Yon, S. H.; Imlay, R.; Kartik, S.; Kim, H.-J.; McNeil, R. R.; Metcalf, W.; Nadendla, V. K.; Barreiro, F.; Cases, G.; Graciani, R.; Hernández, J. M.; Hervás, L.; Labarga, L.; del Peso, J.; Puga, J.; de Trocóniz, J. F.; Ikraiam, F.; Mayer, J. K.; Smith, G. R.; Corriveau, F.; Hanna, D. S.; Hartmann, J.; Hung, L. W.; Lim, J. N.; Matthews, C. G.; Patel, P. M.; Sinclair, L. E.; Stairs, D. G.; St. Laurent, M.; Ullmann, R.; Zacek, G.; Bashkirov, V.; Dolgoshein, B. A.; Stifutkin, A.; Bashindzhagyan, G. L.; Ermolov, P. F.; Gladilin, L. K.; Golubkov, Y. A.; Kobrin, V. D.; Kuzmin, V. A.; Proskuryakov, A. S.; Savin, A. A.; Shcheglova, L. M.; Solomin, A. N.; Zotov, N. P.; Bentvelsen, S.; Botje, M.; Chlebana, F.; Dake, A.; Engelen, J.; de Jong, P.; de Kamps, M.; Kooijman, P.; Kruse, A.; O'Dell, V.; Tenner, A.; Tiecke, H.; Verkerke, W.; Vreeswijk, M.; Wiggers, L.; de Wolf, E.; van Woudenberg, R.; Acosta, D.; Bylsma, B.; Durkin, L. S.; Honscheid, K.; Li, C.; Ling, T. Y.; McLean, K. W.; Murray, W. N.; Park, I. H.; Romanowski, T. A.; Seidlein, R.; Bailey, D. S.; Blair, G. A.; Byrne, A.; Cashmore, R. J.; Cooper-Sarkar, A. M.; Daniels, D.; Devenish, R. C. E.; Harnew, N.; Lancaster, M.; Luffman, P. E.; Lindemann, L.; McFall, J.; Nath, C.; Quadt, A.; Uijterwaal, H.; Walczak, R.; Wilson, F. F.; Yip, T.; Abbiendi, G.; Bertolin, A.; Brugnera, R.; Carlin, R.; Dal Corso, F.; De Giorgi, M.; Dosselli, U.; Limentani, S.; Morandin, M.; Posocco, M.; Stanco, L.; Stroili, R.; Voci, C.; Bulmahn, J.; Butterworth, J. M.; Feild, R. G.; Oh, B. Y.; Whitmore, J. J.; D'Agostini, G.; Iori, M.; Marini, G.; Mattioli, M.; Nigro, A.; Tassi, E.; Hart, J. C.; McCubbin, N. A.; Prytz, K.; Shah, T. P.; Short, T. L.; Barberis, E.; Cartiglia, N.; Dubbs, T.; Heusch, C.; Van Hook, M.; Hubbard, B.; Lockman, W.; Rahn, J. T.; Sadrozinski, H. F.-W.; Seiden, A.; Biltzinger, J.; Seifert, R. J.; Walenta, A. H.; Zech, G.; Abramowicz, H.; Briskin, G.; Dagan, S.; Levy, A.; Hasegawa, T.; Hazumi, M.; Ishii, T.; Kuze, M.; Mine, S.; Nagasawa, Y.; Nagira, T.; Nakao, M.; Suzuki, I.; Tokushuku, K.; Yamada, S.; Yamazaki, Y.; Chiba, M.; Hamatsu, R.; Hirose, T.; Homma, K.; Kitamura, S.; Nagayama, S.; Nakamitsu, Y.; Cirio, R.; Costa, M.; Ferrero, M. I.; Lamberti, L.; Maselli, S.; Peroni, C.; Sacchi, R.; Solano, A.; Staiano, A.; Dardo, M.; Bailey, D. C.; Bandyopadhyay, D.; Benard, F.; Brkic, M.; Crombie, M. B.; Gingrich, D. M.; Hartner, G. F.; Joo, K. K.; Levman, G. M.; Martin, J. F.; Orr, R. S.; Sampson, C. R.; Teuscher, R. J.; Catterall, C. D.; Jones, T. W.; Kaziewicz, P. B.; Lane, J. B.; Saunders, R. L.; Shulman, J.; Blankenship, K.; Kochocki, J.; Lu, B.; Mo, L. W.; Bogusz, W.; Charchuł; a, K.; Ciborowski, J.; Gajewski, J.; Grzelak, G.; Kasprzak, M.; Krzyżanowski, M.; Muchorowski, K.; Nowak, R. J.; Pawlak, J. M.; Tymieniecka, T.; Wróblewski, A. K.; Zakrzewski, J. A.; Zarnecki, A. F.; Adamus, M.; Eisenberg, Y.; Glasman, C.; Karshon, U.; Revel, D.; Shapira, A.; Ali, I.; Behrens, B.; Dasu, S.; Fordham, C.; Foudas, C.; Goussiou, A.; Loveless, R. J.; Reeder, D. D.; Silverstein, S.; Smith, W. H.; Tsurugai, T.; Bhadra, S.; Frisken, W. R.; Furutani, K. M.; Zeus Collaboration

1995-02-01

The gluon momentum density xg( x, Q2) of the proton was extracted at Q2 = 20 GeV 2 for small values of x between 4 × 10 -4 and 10 -2 from the scaling violations of the proton structure function F2 measured recently by ZEUS in deep inelastic neutral current ep scattering at HERA. The extraction was performed in two ways. Firstly, using a global NLO fit to the ZEUS data on F2 at low x constrained by measurementsfrom NMC at larger x; and secondly using published approximate methods for the solution of the GLAP QCD evolution equations. Consistent results are obtained. A substantial increase of the gluon density is found at small x in comparison with the NMC result obtained at larger values of x.

Brownian model of transcriptome evolution and phylogenetic network visualization between tissues.

PubMed

Gu, Xun; Ruan, Hang; Su, Zhixi; Zou, Yangyun

2017-09-01

While phylogenetic analysis of transcriptomes of the same tissue is usually congruent with the species tree, the controversy emerges when multiple tissues are included, that is, whether species from the same tissue are clustered together, or different tissues from the same species are clustered together. Recent studies have suggested that phylogenetic network approach may shed some lights on our understanding of multi-tissue transcriptome evolution; yet the underlying evolutionary mechanism remains unclear. In this paper we develop a Brownian-based model of transcriptome evolution under the phylogenetic network that can statistically distinguish between the patterns of species-clustering and tissue-clustering. Our model can be used as a null hypothesis (neutral transcriptome evolution) for testing any correlation in tissue evolution, can be applied to cancer transcriptome evolution to study whether two tumors of an individual appeared independently or via metastasis, and can be useful to detect convergent evolution at the transcriptional level. Copyright © 2017. Published by Elsevier Inc.

Quantifying evolutionary dynamics from variant-frequency time series

NASA Astrophysics Data System (ADS)

Khatri, Bhavin S.

2016-09-01

From Kimura’s neutral theory of protein evolution to Hubbell’s neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher’s angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.

Quantifying evolutionary dynamics from variant-frequency time series.

PubMed

Khatri, Bhavin S

2016-09-12

From Kimura's neutral theory of protein evolution to Hubbell's neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher's angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series.

A Directed Molecular Evolution Approach to Improved Immunogenicity of the HIV-1 Envelope Glycoprotein

PubMed Central

Du, Sean X.; Xu, Li; Zhang, Wenge; Tang, Susan; Boenig, Rebecca I.; Chen, Helen; Mariano, Ellaine B.; Zwick, Michael B.; Parren, Paul W. H. I.; Burton, Dennis R.; Wrin, Terri; Petropoulos, Christos J.; Ballantyne, John A.; Chambers, Michael; Whalen, Robert G.

2011-01-01

A prophylactic vaccine is needed to slow the spread of HIV-1 infection. Optimization of the wild-type envelope glycoproteins to create immunogens that can elicit effective neutralizing antibodies is a high priority. Starting with ten genes encoding subtype B HIV-1 gp120 envelope glycoproteins and using in vitro homologous DNA recombination, we created chimeric gp120 variants that were screened for their ability to bind neutralizing monoclonal antibodies. Hundreds of variants were identified with novel antigenic phenotypes that exhibit considerable sequence diversity. Immunization of rabbits with these gp120 variants demonstrated that the majority can induce neutralizing antibodies to HIV-1. One novel variant, called ST-008, induced significantly improved neutralizing antibody responses when assayed against a large panel of primary HIV-1 isolates. Further study of various deletion constructs of ST-008 showed that the enhanced immunogenicity results from a combination of effective DNA priming, an enhanced V3-based response, and an improved response to the constant backbone sequences. PMID:21738594

Functional interplay of top-down attention with affective codes during visual short-term memory maintenance.

PubMed

Kuo, Bo-Cheng; Lin, Szu-Hung; Yeh, Yei-Yu

2018-06-01

Visual short-term memory (VSTM) allows individuals to briefly maintain information over time for guiding behaviours. Because the contents of VSTM can be neutral or emotional, top-down influence in VSTM may vary with the affective codes of maintained representations. Here we investigated the neural mechanisms underlying the functional interplay of top-down attention with affective codes in VSTM using functional magnetic resonance imaging. Participants were instructed to remember both threatening and neutral objects in a cued VSTM task. Retrospective cues (retro-cues) were presented to direct attention to the hemifield of a threatening object (i.e., cue-to-threat) or a neutral object (i.e., cue-to-neutral) during VSTM maintenance. We showed stronger activity in the ventral occipitotemporal cortex and amygdala for attending threatening relative to neutral representations. Using multivoxel pattern analysis, we found better classification performance for cue-to-threat versus cue-to-neutral objects in early visual areas and in the amygdala. Importantly, retro-cues modulated the strength of functional connectivity between the frontoparietal and early visual areas. Activity in the frontoparietal areas became strongly correlated with the activity in V3a-V4 coding the threatening representations instructed to be relevant for the task. Together, these findings provide the first demonstration of top-down modulation of activation patterns in early visual areas and functional connectivity between the frontoparietal network and early visual areas for regulating threatening representations during VSTM maintenance. Copyright © 2018 Elsevier Ltd. All rights reserved.

Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy.

PubMed

Lan, Xiaoyang; Jörg, David J; Cavalli, Florence M G; Richards, Laura M; Nguyen, Long V; Vanner, Robert J; Guilhamon, Paul; Lee, Lilian; Kushida, Michelle M; Pellacani, Davide; Park, Nicole I; Coutinho, Fiona J; Whetstone, Heather; Selvadurai, Hayden J; Che, Clare; Luu, Betty; Carles, Annaick; Moksa, Michelle; Rastegar, Naghmeh; Head, Renee; Dolma, Sonam; Prinos, Panagiotis; Cusimano, Michael D; Das, Sunit; Bernstein, Mark; Arrowsmith, Cheryl H; Mungall, Andrew J; Moore, Richard A; Ma, Yussanne; Gallo, Marco; Lupien, Mathieu; Pugh, Trevor J; Taylor, Michael D; Hirst, Martin; Eaves, Connie J; Simons, Benjamin D; Dirks, Peter B

2017-09-14

Human glioblastomas harbour a subpopulation of glioblastoma stem cells that drive tumorigenesis. However, the origin of intratumoural functional heterogeneity between glioblastoma cells remains poorly understood. Here we study the clonal evolution of barcoded glioblastoma cells in an unbiased way following serial xenotransplantation to define their individual fate behaviours. Independent of an evolving mutational signature, we show that the growth of glioblastoma clones in vivo is consistent with a remarkably neutral process involving a conserved proliferative hierarchy rooted in glioblastoma stem cells. In this model, slow-cycling stem-like cells give rise to a more rapidly cycling progenitor population with extensive self-maintenance capacity, which in turn generates non-proliferative cells. We also identify rare 'outlier' clones that deviate from these dynamics, and further show that chemotherapy facilitates the expansion of pre-existing drug-resistant glioblastoma stem cells. Finally, we show that functionally distinct glioblastoma stem cells can be separately targeted using epigenetic compounds, suggesting new avenues for glioblastoma-targeted therapy.

Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy

PubMed Central

Lan, Xiaoyang; Jörg, David J.; Cavalli, Florence M. G.; Richards, Laura M.; Nguyen, Long V.; Vanner, Robert J.; Guilhamon, Paul; Lee, Lilian; Kushida, Michelle; Pellacani, Davide; Park, Nicole I.; Coutinho, Fiona J.; Whetstone, Heather; Selvadurai, Hayden J.; Che, Clare; Luu, Betty; Carles, Annaick; Moksa, Michelle; Rastegar, Naghmeh; Head, Renee; Dolma, Sonam; Prinos, Panagiotis; Cusimano, Michael D.; Das, Sunit; Bernstein, Mark; Arrowsmith, Cheryl H.; Mungall, Andrew J.; Moore, Richard A.; Ma, Yussanne; Gallo, Marco; Lupien, Mathieu; Pugh, Trevor J.; Taylor, Michael D.; Hirst, Martin; Eaves, Connie J.; Simons, Benjamin D.; Dirks, Peter B.

2017-01-01

Summary Human glioblastomas (GBMs) harbour a subpopulation of glioblastoma stem cells (GSCs) that drive tumourigenesis. However, the origin of intra-tumoural functional heterogeneity between GBM cells remains poorly understood. Here we study the clonal evolution of barcoded GBM cells in an unbiased way following serial xenotransplantation to define their individual fate behaviours. Independent of an evolving mutational signature, we show that the growth of GBM clones in vivo is consistent with a remarkably neutral process involving a conserved proliferative hierarchy rooted in GSCs. In this model, slow-cycling stem-like cells give rise to a more rapidly cycling progenitor population with extensive self-maintenance capacity, that in turn generates non-proliferative cells. We also identify rare “outlier” clones that deviate from these dynamics, and further show that chemotherapy facilitates the expansion of pre-existing drug-resistant GSCs. Finally, we show that functionally distinct GSCs can be separately targeted using epigenetic compounds, suggesting new avenues for GBM targeted therapy. PMID:28854171

The Evolution of the Third Reich.

ERIC Educational Resources Information Center

McCleary, George F., Jr.

1995-01-01

Presents a set of four maps illustrating changing German political borders. Includes the time period from 1933, when Hitler came to power, until the division of Germany in 1945. Includes a map showing the Allied Powers against Germany, nations allied with Germany, and neutral nations. (CFR)

Propagation of Interplanetary Disturbances in the Outer Heliosphere

NASA Technical Reports Server (NTRS)

Wang, Chi

2002-01-01

Work finished during 2002 included: (1) Finished a multi-fluid solar wind model; (2) Determined the solar wind slowdown and interstellar neutral density; (3) Studied shock propagation and evolution in the outer heliosphere; (4) Investigated statistical properties of the solar wind in the outer heliosphere.

The diffuse interstellar bands: a tracer for organics in the diffuse interstellar medium?

NASA Technical Reports Server (NTRS)

Salama, F.

1998-01-01

The diffuse interstellar bands (DIBs) are absorption bands seen in the spectra of stars obscured by interstellar dust. DIBs are recognized as a tracer for free, organic molecules in the diffuse interstellar medium (ISM). The potential molecular carriers for the DIBs are discussed with an emphasis on neutral and ionized polycyclic aromatic hydrocarbons (PAHs) for which the most focused effort has been made to date. From the combined astronomical, laboratory and theoretical study, it is concluded that a distribution of free neutral and ionized complex organics (PAHs, fullerenes, unsaturated hydrocarbons) represents the most promising class of candidates to account for the DIBs. The case for aromatic hydrocarbons appears particularly strong. The implied widespread distribution of complex organics in the diffuse ISM bears profound implications for our understanding of the chemical complexity of the ISM, the evolution of prebiotic molecules and its impact on the origin and the evolution of life on early Earth through the exogenous delivery (cometary encounters and metoritic bombardments) of prebiotic organics.

Body mass evolution and diversification within horses (family Equidae).

PubMed

Shoemaker, Lauren; Clauset, Aaron

2014-02-01

Horses (family Equidae) are a classic example of adaptive radiation, exhibiting a nearly 60-fold increase in maximum body mass and a peak taxonomic diversity of nearly 100 species across four continents. Such patterns are commonly attributed to niche competition, in which increased taxonomic diversity drives increased size disparity. However, neutral processes, such as macroevolutionary 'diffusion', can produce similar increases in disparity without increased diversity. Using a comprehensive database of Equidae species size estimates and a common mathematical framework, we measure the contributions of diversity-driven and diffusion-driven mechanisms for increased disparity during the Equidae radiation. We find that more than 90% of changes in size disparity are attributable to diffusion alone. These results clarify the role of species competition in body size evolution, indicate that morphological disparity and species diversity may be only weakly coupled in general, and demonstrate that large species may evolve from neutral macroevolutionary diffusion processes alone. © 2013 John Wiley & Sons Ltd/CNRS.

The effect of recombination and attachment on meteor radar diffusion coefficient profiles

NASA Astrophysics Data System (ADS)

Lee, C. S.; Younger, J. P.; Reid, I. M.; Kim, Y. H.; Kim, J.-H.

2013-04-01

Estimates of the ambipolar diffusion coefficient producedusing meteor radar echo decay times display an increasing trend below 80-85 km, which is inconsistent with a diffusion-only theory of the evolution of meteor trails. Data from the 33 MHz meteor radar at King Sejong Station, Antarctica, have been compared with observations from the Aura Earth Observing System Microwave Limb Sounder satellite instrument. It has been found that the height at which the diffusion coefficient gradient reverses follows the height of a constant neutral atmospheric density surface. Numerical simulations of meteor trail diffusion including dissociative recombination with atmospheric ions and three-body attachment of free electrons to neutral molecules indicate that three-body attachment is responsible for the distortion of meteor radar diffusion coefficient profiles at heights below 90 km, including the gradient reversal below 80-85 km. Further investigation has revealed that meteor trails with low initial electron line density produce decay times more consistent with a diffusion-only model of meteor trail evolution.

Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ovchinnikov, Victor; Louveau, Joy E.; Barton, John P.

Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutationsmore » increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed.« less

Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

DOE PAGES

Ovchinnikov, Victor; Louveau, Joy E.; Barton, John P.; ...

2018-02-14

Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutationsmore » increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed.« less

Role of framework mutations and antibody flexibility in the evolution of broadly neutralizing antibodies

PubMed Central

2018-01-01

Eliciting antibodies that are cross reactive with surface proteins of diverse strains of highly mutable pathogens (e.g., HIV, influenza) could be key for developing effective universal vaccines. Mutations in the framework regions of such broadly neutralizing antibodies (bnAbs) have been reported to play a role in determining their properties. We used molecular dynamics simulations and models of affinity maturation to study specific bnAbs against HIV. Our results suggest that there are different classes of evolutionary lineages for the bnAbs. If germline B cells that initiate affinity maturation have high affinity for the conserved residues of the targeted epitope, framework mutations increase antibody rigidity as affinity maturation progresses to evolve bnAbs. If the germline B cells exhibit weak/moderate affinity for conserved residues, an initial increase in flexibility via framework mutations may be required for the evolution of bnAbs. Subsequent mutations that increase rigidity result in highly potent bnAbs. Implications of our results for immunogen design are discussed. PMID:29442996

Physics-based Control-oriented Modeling of the Current Profile Evolution in NSTX-Upgrade

NASA Astrophysics Data System (ADS)

Ilhan, Zeki; Barton, Justin; Shi, Wenyu; Schuster, Eugenio; Gates, David; Gerhardt, Stefan; Kolemen, Egemen; Menard, Jonathan

2013-10-01

The operational goals for the NSTX-Upgrade device include non-inductive sustainment of high- β plasmas, realization of the high performance equilibrium scenarios with neutral beam heating, and achievement of longer pulse durations. Active feedback control of the current profile is proposed to enable these goals. Motivated by the coupled, nonlinear, multivariable, distributed-parameter plasma dynamics, the first step towards feedback control design is the development of a physics-based, control-oriented model for the current profile evolution in response to non-inductive current drives and heating systems. For this purpose, the nonlinear magnetic-diffusion equation is coupled with empirical models for the electron density, electron temperature, and non-inductive current drives (neutral beams). The resulting first-principles-driven, control-oriented model is tailored for NSTX-U based on the PTRANSP predictions. Main objectives and possible challenges associated with the use of the developed model for control design are discussed. This work was supported by PPPL.

Evolution of organo-cyanometallate cages: supramolecular architectures and new Cs+-specific receptors.

PubMed

Boyer, Julie L; Kuhlman, Matthew L; Rauchfuss, Thomas B

2007-04-01

The ability of inorganic cyanometallate polymers to form interesting and useful complexes is well-known. This Account summarizes work, especially in our laboratories, aimed at replicating aspects of this inorganic chemistry in homogeneous solution using organometallic building blocks. A library of molecular organometallic cyanides and Lewis acids, with varying charges and labilities, are shown to give families of neutral and charged cages. Neutral and anionic cages, often molecular boxes, bind larger alkali metals tightly. Cubic frameworks show an unparalleled affinity for cesium cations over potassium cations. Noncubic cages are described including tetrahedranes, defect boxes, trigonal prisms, and hexagonal prisms.

How Germinal Centers Evolve Broadly Neutralizing Antibodies: the Breadth of the Follicular Helper T Cell Response

DOE PAGES

De Boer, Rob J.; Perelson, Alan S.

2017-09-06

Many HIV-1-infected patients evolve broadly neutralizing antibodies (bnAbs). This evolutionary process typically takes several years and is poorly understood as selection taking place in germinal centers occurs on the basis of antibody affinity. B cells with the highest-affinity receptors tend to acquire the most antigen from the follicular dendritic cell (FDC) network and present the highest density of cognate peptides to follicular helper T (Tfh) cells, which provide survival signals to the B cell. bnAbs are therefore expected to evolve only when the B cell lineage evolving breadth is consistently capturing and presenting more peptides to Tfh cells than othermore » lineages of more specific B cells. Here we develop mathematical models of Tfh cells in germinal centers to explicitly define the mechanisms of selection in this complex evolutionary process. Our results suggest that broadly reactive B cells presenting a high density of peptides bound to major histocompatibility complex class II molecules (pMHC) are readily outcompeted by B cells responding to lineages of HIV-1 that transiently dominate the within host viral population. Conversely, if broadly reactive B cells acquire a large variety of several HIV-1 proteins from the FDC network and present a high diversity of several pMHC, they can be rescued by a large fraction of the Tfh cell repertoire in the germinal center. Under such circumstances the evolution of bnAbs is much more consistent. Increasing either the magnitude of the Tfh cell response or the breadth of the Tfh cell repertoire markedly facilitates the evolution of bnAbs. Because both the magnitude and breadth can be increased by vaccination with several HIV-1 proteins, this calls for experimental testing. Many HIV-infected patients slowly evolve antibodies that can neutralize a large variety of viruses. Such broadly neutralizing antibodies (bnAbs) could in the future become therapeutic agents. bnAbs appear very late, and patients are typically not protected by them. At the moment, we fail to understand why this takes so long and how the immune system selects for broadly neutralizing capacity. Typically, antibodies are selected based on affinity and not on breadth. We developed mathematical models to study two different mechanisms by which the immune system can select for broadly neutralizing capacity. One of these is based upon the repertoire of different follicular helper T (Tfh) cells in germinal centers. In conclusion, we suggest that broadly reactive B cells may interact with a larger fraction of this repertoire and demonstrate that this would select for bnAbs. Intriguingly, this suggests that broadening the Tfh cell repertoire by vaccination may speed up the evolution of bnAbs.« less

How Germinal Centers Evolve Broadly Neutralizing Antibodies: the Breadth of the Follicular Helper T Cell Response

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Boer, Rob J.; Perelson, Alan S.

Many HIV-1-infected patients evolve broadly neutralizing antibodies (bnAbs). This evolutionary process typically takes several years and is poorly understood as selection taking place in germinal centers occurs on the basis of antibody affinity. B cells with the highest-affinity receptors tend to acquire the most antigen from the follicular dendritic cell (FDC) network and present the highest density of cognate peptides to follicular helper T (Tfh) cells, which provide survival signals to the B cell. bnAbs are therefore expected to evolve only when the B cell lineage evolving breadth is consistently capturing and presenting more peptides to Tfh cells than othermore » lineages of more specific B cells. Here we develop mathematical models of Tfh cells in germinal centers to explicitly define the mechanisms of selection in this complex evolutionary process. Our results suggest that broadly reactive B cells presenting a high density of peptides bound to major histocompatibility complex class II molecules (pMHC) are readily outcompeted by B cells responding to lineages of HIV-1 that transiently dominate the within host viral population. Conversely, if broadly reactive B cells acquire a large variety of several HIV-1 proteins from the FDC network and present a high diversity of several pMHC, they can be rescued by a large fraction of the Tfh cell repertoire in the germinal center. Under such circumstances the evolution of bnAbs is much more consistent. Increasing either the magnitude of the Tfh cell response or the breadth of the Tfh cell repertoire markedly facilitates the evolution of bnAbs. Because both the magnitude and breadth can be increased by vaccination with several HIV-1 proteins, this calls for experimental testing. Many HIV-infected patients slowly evolve antibodies that can neutralize a large variety of viruses. Such broadly neutralizing antibodies (bnAbs) could in the future become therapeutic agents. bnAbs appear very late, and patients are typically not protected by them. At the moment, we fail to understand why this takes so long and how the immune system selects for broadly neutralizing capacity. Typically, antibodies are selected based on affinity and not on breadth. We developed mathematical models to study two different mechanisms by which the immune system can select for broadly neutralizing capacity. One of these is based upon the repertoire of different follicular helper T (Tfh) cells in germinal centers. In conclusion, we suggest that broadly reactive B cells may interact with a larger fraction of this repertoire and demonstrate that this would select for bnAbs. Intriguingly, this suggests that broadening the Tfh cell repertoire by vaccination may speed up the evolution of bnAbs.« less

Molecular evolution of calcification genes in morphologically similar but phylogenetically unrelated scleractinian corals.

PubMed

Wirshing, Herman H; Baker, Andrew C

2014-08-01

Molecular phylogenies of scleractinian corals often fail to agree with traditional phylogenies derived from morphological characters. These discrepancies are generally attributed to non-homologous or morphologically plastic characters used in taxonomic descriptions. Consequently, morphological convergence of coral skeletons among phylogenetically unrelated groups is considered to be the major evolutionary process confounding molecular and morphological hypotheses. A strategy that may help identify cases of convergence and/or diversification in coral morphology is to compare phylogenies of existing "neutral" genetic markers used to estimate genealogic phylogenetic history with phylogenies generated from non-neutral genes involved in calcification (biomineralization). We tested the hypothesis that differences among calcification gene phylogenies with respect to the "neutral" trees may represent convergent or divergent functional strategies among calcification gene proteins that may correlate to aspects of coral skeletal morphology. Partial sequences of two nuclear genes previously determined to be involved in the calcification process in corals, "Cnidaria-III" membrane-bound/secreted α-carbonic anhydrase (CIII-MBSα-CA) and bone morphogenic protein (BMP) 2/4, were PCR-amplified, cloned and sequenced from 31 scleractinian coral species in 26 genera and 9 families. For comparison, "neutral" gene phylogenies were generated from sequences from two protein-coding "non-calcification" genes, one nuclear (β-tubulin) and one mitochondrial (cytochrome b), from the same individuals. Cloned CIII-MBSα-CA sequences were found to be non-neutral, and phylogenetic analyses revealed CIII-MBSα-CAs to exhibit a complex evolutionary history with clones distributed between at least 2 putative gene copies. However, for several coral taxa only one gene copy was recovered. With CIII-MBSα-CA, several recovered clades grouped taxa that differed from the "non-calcification" loci. In some cases, these taxa shared aspects of their skeletal morphology (i.e., convergence or diversification relative to the "non-calcification" loci), but in other cases they did not. For example, the "non-calcification" loci recovered Atlantic and Pacific mussids as separate evolutionary lineages, whereas with CIII-MBSα-CA, clones of two species of Atlantic mussids (Isophyllia sinuosa and Mycetophyllia sp.) and two species of Pacific mussids (Acanthastrea echinata and Lobophyllia hemprichii) were united in a distinct clade (except for one individual of Mycetophyllia). However, this clade also contained other taxa which were not unambiguously correlated with morphological features. BMP2/4 also contained clones that likely represent different gene copies. However, many of the sequences showed no significant deviation from neutrality, and reconstructed phylogenies were similar to the "non-calcification" tree topologies with a few exceptions. Although individual calcification genes are unlikely to precisely explain the diverse morphological features exhibited by scleractinian corals, this study demonstrates an approach for identifying cases where morphological taxonomy may have been misled by convergent and/or divergent molecular evolutionary processes in corals. Studies such as this may help illuminate our understanding of the likely complex evolution of genes involved in the calcification process, and enhance our knowledge of the natural history and biodiversity within this central ecological group. Published by Elsevier Inc.

The evolvability of programmable hardware.

PubMed

Raman, Karthik; Wagner, Andreas

2011-02-06

In biological systems, individual phenotypes are typically adopted by multiple genotypes. Examples include protein structure phenotypes, where each structure can be adopted by a myriad individual amino acid sequence genotypes. These genotypes form vast connected 'neutral networks' in genotype space. The size of such neutral networks endows biological systems not only with robustness to genetic change, but also with the ability to evolve a vast number of novel phenotypes that occur near any one neutral network. Whether technological systems can be designed to have similar properties is poorly understood. Here we ask this question for a class of programmable electronic circuits that compute digital logic functions. The functional flexibility of such circuits is important in many applications, including applications of evolutionary principles to circuit design. The functions they compute are at the heart of all digital computation. We explore a vast space of 10(45) logic circuits ('genotypes') and 10(19) logic functions ('phenotypes'). We demonstrate that circuits that compute the same logic function are connected in large neutral networks that span circuit space. Their robustness or fault-tolerance varies very widely. The vicinity of each neutral network contains circuits with a broad range of novel functions. Two circuits computing different functions can usually be converted into one another via few changes in their architecture. These observations show that properties important for the evolvability of biological systems exist in a commercially important class of electronic circuitry. They also point to generic ways to generate fault-tolerant, adaptable and evolvable electronic circuitry.

The evolvability of programmable hardware

PubMed Central

Raman, Karthik; Wagner, Andreas

2011-01-01

In biological systems, individual phenotypes are typically adopted by multiple genotypes. Examples include protein structure phenotypes, where each structure can be adopted by a myriad individual amino acid sequence genotypes. These genotypes form vast connected ‘neutral networks’ in genotype space. The size of such neutral networks endows biological systems not only with robustness to genetic change, but also with the ability to evolve a vast number of novel phenotypes that occur near any one neutral network. Whether technological systems can be designed to have similar properties is poorly understood. Here we ask this question for a class of programmable electronic circuits that compute digital logic functions. The functional flexibility of such circuits is important in many applications, including applications of evolutionary principles to circuit design. The functions they compute are at the heart of all digital computation. We explore a vast space of 1045 logic circuits (‘genotypes’) and 1019 logic functions (‘phenotypes’). We demonstrate that circuits that compute the same logic function are connected in large neutral networks that span circuit space. Their robustness or fault-tolerance varies very widely. The vicinity of each neutral network contains circuits with a broad range of novel functions. Two circuits computing different functions can usually be converted into one another via few changes in their architecture. These observations show that properties important for the evolvability of biological systems exist in a commercially important class of electronic circuitry. They also point to generic ways to generate fault-tolerant, adaptable and evolvable electronic circuitry. PMID:20534598

New paradigms in clonal evolution: punctuated equilibrium in cancer.

PubMed

Cross, William Ch; Graham, Trevor A; Wright, Nicholas A

2016-10-01

Evolutionary theories are themselves subject to evolution. Clonal evolution - the model that describes the initiation and progression of cancer - is entering a period of profound change, brought about largely by technological developments in genome analysis. A flurry of recent publications, using modern mathematical and bioinformatics techniques, have revealed both punctuated and neutral evolution phenomena that are poorly explained by the conventional graduated perspectives. In this review, we propose that a hybrid model, inspired by the evolutionary model of punctuated equilibrium, could better explain these recent observations. We also discuss the conceptual changes and clinical implications of variable evolutionary tempos. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Bridging the gap between chemistry, physiology, and evolution: quantifying the functionality of sperm whale myoglobin mutants.

PubMed

Dasmeh, Pouria; Kepp, Kasper P

2012-01-01

This work merges a large set of previously reported thermochemical data for myoglobin (Mb) mutants with a physiological model of O(2)-transport and -storage. The model allows a quantification of the functional proficiency of myoglobin (Mb) mutants under various physiological conditions, i.e. O(2)-consumption rate resembling workload, O(2) partial pressure resembling hypoxic stress, muscle cell size, and Mb concentration, resembling different organism-specific and compensatory variables. We find that O(2)-storage and -transport are distinct functions that rank mutants and wild type differently depending on O(2) partial pressure. Specifically, the wild type is near-optimal for storage at all conditions, but for transport only at severely hypoxic conditions. At normoxic conditions, low-affinity mutants are in fact better O(2)-transporters because they still have empty sites for O(2), giving rise to a larger [MbO(2)] gradient (more varying saturation curve). The distributions of functionality reveal that many mutants are near-neutral with respect to function, whereas only a few are strongly affected, and the variation in functionality increases dramatically at lower O(2) pressure. These results together show that conserved residues in wild type (WT) Mb were fixated under a selection pressure of low P(O2). Copyright © 2011 Elsevier Inc. All rights reserved.

Measurement of argon neutral velocity distribution functions near an absorbing boundary in a plasma

NASA Astrophysics Data System (ADS)

Short, Zachary; Thompson, Derek; Good, Timothy; Scime, Earl

2016-10-01

Neutral particle distributions are critical to the study of plasma boundary interactions, where ion-neutral collisions, e.g. via charge exchange, may modify energetic particle populations impacting the boundary surface. Neutral particle behavior at absorbing boundaries thus underlies a number of important plasma physics issues, such as wall loading in fusion devices and anomalous erosion in Hall thruster channels. Neutral velocity distribution functions (NVDFs) are measured using laser-induced fluorescence (LIF). Our LIF scheme excites the 1s4 non-metastable state of neutral argon with 667.913 nm photons. The subsequent decay emission at 750.590 nm is recorded synchronously with injection laser frequency. Measurements are performed near a grounded boundary immersed in a cylindrical helicon plasma, with the boundary plate oriented at an oblique angle to the magnetic field. NVDFs are recorded in multiple velocity dimensions and in a three-dimensional volume, enabling point-to-point comparisons with NVDF predictions from particle-in-cell models as well as comparisons with ion velocity distribution function measurements obtained in the same regions through Ar-II LIF. This work is supported by US National Science Foundation Grant Number PHYS-1360278.

Endangered Species Hold Clues to Human Evolution

PubMed Central

Bejerano, Gill; Salama, Sofie R.; Haussler, David

2010-01-01

We report that 18 conserved, and by extension functional, elements in the human genome are the result of retroposon insertions that are evolving under purifying selection in mammals. We show evidence that 1 of the 18 elements regulates the expression of ASXL3 during development by encoding an alternatively spliced exon that causes nonsense-mediated decay of the transcript. The retroposon that gave rise to these functional elements was quickly inactivated in the mammalian ancestor, and all traces of it have been lost due to neutral decay. However, the tuatara has maintained a near-ancestral version of this retroposon in its extant genome, which allows us to connect the 18 human elements to the evolutionary events that created them. We propose that conservation efforts over more than 100 years may not have only prevented the tuatara from going extinct but could have preserved our ability to understand the evolutionary history of functional elements in the human genome. Through simulations, we argue that species with historically low population sizes are more likely to harbor ancient mobile elements for long periods of time and in near-ancestral states, making these species indispensable in understanding the evolutionary origin of functional elements in the human genome. PMID:20332163

Mate choice for neutral and MHC genetic characteristics in Alpine marmots: different targets in different contexts?

PubMed

Ferrandiz-Rovira, Mariona; Allainé, Dominique; Callait-Cardinal, Marie-Pierre; Cohas, Aurélie

2016-07-01

Sexual selection through female mate choice for genetic characteristics has been suggested to be an important evolutionary force maintaining genetic variation in animal populations. However, the genetic targets of female mate choice are not clearly identified and whether female mate choice is based on neutral genetic characteristics or on particular functional loci remains an open question. Here, we investigated the genetic targets of female mate choice in Alpine marmots (Marmota marmota), a socially monogamous mammal where extra-pair paternity (EPP) occurs. We used 16 microsatellites to describe neutral genetic characteristics and two MHC loci belonging to MHC class I and II as functional genetic characteristics. Our results reveal that (1) neutral and MHC genetic characteristics convey different information in this species, (2) social pairs show a higher MHC class II dissimilarity than expected under random mate choice, and (3) the occurrence of EPP increases when social pairs present a high neutral genetic similarity or dissimilarity but also when they present low MHC class II dissimilarity. Thus, female mate choice is based on both neutral and MHC genetic characteristics, and the genetic characteristics targeted seem to be context dependent (i.e., the genes involved in social mate choice and genetic mate choice differ). We emphasize the need for empirical studies of mate choice in the wild using both neutral and MHC genetic characteristics because whether neutral and functional genetic characteristics convey similar information is not universal.

Evolution of nano-rheological properties of Nafion¯ thin films during pH modification by strong base treatment: A static and dynamic force spectroscopy study

NASA Astrophysics Data System (ADS)

Eslami, Babak; López-Guerra, Enrique A.; Raftari, Maryam; Solares, Santiago D.

2016-04-01

Addition of a strong base to Nafion® proton exchange membranes is a common practice in industry to increase their overall performance in fuel cells. Here, we investigate the evolution of the nano-rheological properties of Nafion thin films as a function of the casting pH, via characterization with static and dynamic, contact and intermittent-contact atomic force microscopy (AFM) techniques. The addition of KOH causes non-monotonic changes in the viscoelastic properties of the films, which behave as highly dissipative, softer materials near neutral pH values, and as harder, more elastic materials at extreme pH values. We quantify this behavior through calculation of the temporal evolution of the compliance and the glassy compliance under static AFM measurements. We complement these observations with dynamic AFM metrics, including dissipated power and virial (for intermittent-contact-mode measurements), and contact resonance frequency and quality factor (for dynamic contact-mode measurements). We explain the non-monotonic material property behavior in terms of the degree of ionic crosslinking and moisture content of the films, which vary with the addition of KOH. This work focuses on the special case study of the addition of strong bases, but the observed mechanical property changes are broadly related to water plasticizing effects and ionic crosslinking, which are also important in other types of films.

Measurements of neutral and ion velocity distribution functions in a Hall thruster

NASA Astrophysics Data System (ADS)

Svarnas, Panagiotis; Romadanov, Iavn; Diallo, Ahmed; Raitses, Yevgeny

2015-11-01

Hall thruster is a plasma device for space propulsion. It utilizes a cross-field discharge to generate a partially ionized weakly collisional plasma with magnetized electrons and non-magnetized ions. The ions are accelerated by the electric field to produce the thrust. There is a relatively large number of studies devoted to characterization of accelerated ions, including measurements of ion velocity distribution function using laser-induced fluorescence diagnostic. Interactions of these accelerated ions with neutral atoms in the thruster and the thruster plume is a subject of on-going studies, which require combined monitoring of ion and neutral velocity distributions. Herein, laser-induced fluorescence technique has been employed to study neutral and single-charged ion velocity distribution functions in a 200 W cylindrical Hall thruster operating with xenon propellant. An optical system is installed in the vacuum chamber enabling spatially resolved axial velocity measurements. The fluorescence signals are well separated from the plasma background emission by modulating the laser beam and using lock-in detectors. Measured velocity distribution functions of neutral atoms and ions at different operating parameters of the thruster are reported and analyzed. This work was supported by DOE contract DE-AC02-09CH11466.

Genomic signatures of evolutionary transitions from solitary to group living

PubMed Central

Kapheim, Karen M.; Pan, Hailin; Li, Cai; Salzberg, Steven L.; Puiu, Daniela; Magoc, Tanja; Robertson, Hugh M.; Hudson, Matthew E.; Venkat, Aarti; Fischman, Brielle J.; Hernandez, Alvaro; Yandell, Mark; Ence, Daniel; Holt, Carson; Yocum, George D.; Kemp, William P.; Bosch, Jordi; Waterhouse, Robert M.; Zdobnov, Evgeny M.; Stolle, Eckart; Kraus, F. Bernhard; Helbing, Sophie; Moritz, Robin F. A.; Glastad, Karl M.; Hunt, Brendan G.; Goodisman, Michael A. D.; Hauser, Frank; Grimmelikhuijzen, Cornelis J. P.; Pinheiro, Daniel Guariz; Nunes, Francis Morais Franco; Soares, Michelle Prioli Miranda; Tanaka, Érica Donato; Simões, Zilá Luz Paulino; Hartfelder, Klaus; Evans, Jay D.; Barribeau, Seth M.; Johnson, Reed M.; Massey, Jonathan H.; Southey, Bruce R.; Hasselmann, Martin; Hamacher, Daniel; Biewer, Matthias; Kent, Clement F.; Zayed, Amro; Blatti, Charles; Sinha, Saurabh; Johnston, J. Spencer; Hanrahan, Shawn J.; Kocher, Sarah D.; Wang, Jun; Robinson, Gene E.; Zhang, Guojie

2017-01-01

The evolution of eusociality is one of the major transitions in evolution, but the underlying genomic changes are unknown. We compared the genomes of 10 bee species that vary in social complexity, representing multiple independent transitions in social evolution, and report three major findings. First, many important genes show evidence of neutral evolution as a consequence of relaxed selection with increasing social complexity. Second, there is no single road map to eusociality; independent evolutionary transitions in sociality have independent genetic underpinnings. Third, though clearly independent in detail, these transitions do have similar general features, including an increase in constrained protein evolution accompanied by increases in the potential for gene regulation and decreases in diversity and abundance of transposable elements. Eusociality may arise through different mechanisms each time, but would likely always involve an increase in the complexity of gene networks. PMID:25977371

Oscillation of certain higher-order neutral partial functional differential equations.

PubMed

Li, Wei Nian; Sheng, Weihong

2016-01-01

In this paper, we study the oscillation of certain higher-order neutral partial functional differential equations with the Robin boundary conditions. Some oscillation criteria are established. Two examples are given to illustrate the main results in the end of this paper.

Neutron measurements from beam-target reactions at the ELISE neutral beam test facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xufei, X., E-mail: xiexufei@pku.edu.cn; Fan, T.; Nocente, M.

2014-11-15

Measurements of 2.5 MeV neutron emission from beam-target reactions performed at the ELISE neutral beam test facility are presented in this paper. The measurements are used to study the penetration of a deuterium beam in a copper dump, based on the observation of the time evolution of the neutron counting rate from beam-target reactions with a liquid scintillation detector. A calculation based on a local mixing model of deuterium deposition in the target up to a concentration of 20% at saturation is used to evaluate the expected neutron yield for comparison with data. The results are of relevance to understandmore » neutron emission associated to beam penetration in a solid target, with applications to diagnostic systems for the SPIDER and MITICA Neutral Beam Injection prototypes.« less

TRANSP-based Trajectory Optimization of the Current Profile Evolution to Facilitate Robust Non-inductive Ramp-up in NSTX-U

NASA Astrophysics Data System (ADS)

Wehner, William; Schuster, Eugenio; Poli, Francesca

2016-10-01

Initial progress towards the design of non-inductive current ramp-up scenarios in the National Spherical Torus Experiment Upgrade (NSTX-U) has been made through the use of TRANSP predictive simulations. The strategy involves, first, ramping the plasma current with high harmonic fast waves (HHFW) to about 400 kA, and then further ramping to 900 kA with neutral beam injection (NBI). However, the early ramping of neutral beams and application of HHFW leads to an undesirably peaked current profile making the plasma unstable to ballooning modes. We present an optimization-based control approach to improve on the non-inductive ramp-up strategy. We combine the TRANSP code with an optimization algorithm based on sequential quadratic programming to search for time evolutions of the NBI powers, the HHFW powers, and the line averaged density that define an open-loop actuator strategy that maximizes the non-inductive current while satisfying constraints associated with the current profile evolution for MHD stable plasmas. This technique has the potential of playing a critical role in achieving robustly stable non-inductive ramp-up, which will ultimately be necessary to demonstrate applicability of the spherical torus concept to larger devices without sufficient room for a central coil. Supported by the US DOE under the SCGSR Program.

Characterization of isolated fractions of dissolved organic matter derived from municipal solid waste compost.

PubMed

Yu, Minda; He, Xiaosong; Liu, Jiaomei; Wang, Yuefeng; Xi, Beidou; Li, Dan; Zhang, Hui; Yang, Chao

2018-04-14

Understanding the heterogeneous evolution characteristics of dissolved organic matter fractions derived from compost is crucial to exploring the composting biodegradation process and the possible applications of compost products. Herein, two-dimensional correlation spectroscopy integrated with reversed-phase high performance liquid chromatography and size exclusion chromatography were utilized to obtain the molecular weight (MW) and polarity evolution characteristics of humic acid (HA), fulvic acid (FA), and the hydrophilic (HyI) fractions during composting. The high-MW humic substances and building blocks in the HA fraction degraded faster during composting than polymers, proteins, and organic colloids. Similarly, the low MW acid FA factions transformed faster than the low weight neutral fractions, followed by building blocks, and finally polymers, proteins, and organic colloids. The evolutions of HyI fractions during composting occurred first for building blocks, followed by low MW acids, and finally low weight neutrals. With the progress of composting, the hydrophobic properties of the HA and FA fractions were enhanced. The degradation/humification process of the hydrophilic and transphilic components was faster than that of the hydrophobic component. Compared with the FA and HyI fractions, the HA fraction exhibited a higher MW and increased hydrophobicity. Copyright © 2018 Elsevier B.V. All rights reserved.

Studies of the pedestal structure and inter-ELM pedestal evolution in JET with the ITER-like wall

NASA Astrophysics Data System (ADS)

Maggi, C. F.; Frassinetti, L.; Horvath, L.; Lunniss, A.; Saarelma, S.; Wilson, H.; Flanagan, J.; Leyland, M.; Lupelli, I.; Pamela, S.; Urano, H.; Garzotti, L.; Lerche, E.; Nunes, I.; Rimini, F.; Contributors, JET

2017-11-01

The pedestal structure of type I ELMy H-modes has been analysed for JET with the ITER-like Wall (JET-ILW). The electron pressure pedestal width is independent of ρ * and increases proportionally to  √β pol,PED. Additional broadening of the width is observed, at constant β pol, PED, with increasing ν * and/or neutral gas injection and the contribution of atomic physics effects in setting the pedestal width cannot as yet be ruled out. Neutral penetration alone does not determine the shape of the edge density profile in JET-ILW. The ratio of electron density to electron temperature scale lengths in the edge transport barrier region, η e, is of order 2-3 within experimental uncertainties. Existing understanding, represented in the stationary linear peeling-ballooning mode stability and the EPED pedestal structure models, is extended to the dynamic evolution between ELM crashes in JET-ILW, in order to test the assumptions underlying these two models. The inter-ELM temporal evolution of the pedestal structure in JET-ILW is not unique, but depends on discharge conditions, such as heating power and gas injection levels. The strong reduction in p e,PED with increasing D 2 gas injection at high power is primarily due to clamping of \

A nebula of gases from Io surrounding Jupiter.

PubMed

Krimigis, Stamatios M; Mitchell, Donald G; Hamilton, Douglas C; Dandouras, Jannis; Armstrong, Thomas P; Bolton, Scott J; Cheng, Andrew F; Gloeckler, George; Hsieh, K C; Keath, Edwin P; Krupp, Norbert; Lagg, Andreas; Lanzerotti, Louis J; Livi, Stefano; Mauk, Barry H; McEntire, Richard W; Roelof, Edmond C; Wilken, Berend; Williams, Donald J

2002-02-28

Several planetary missions have reported the presence of substantial numbers of energetic ions and electrons surrounding Jupiter; relativistic electrons are observable up to several astronomical units (au) from the planet. A population of energetic (>30[?]keV) neutral particles also has been reported, but the instrumentation was not able to determine the mass or charge state of the particles, which were subsequently labelled energetic neutral atoms. Although images showing the presence of the trace element sodium were obtained, the source and identity of the neutral atoms---and their overall significance relative to the loss of charged particles from Jupiter's magnetosphere---were unknown. Here we report the discovery by the Cassini spacecraft of a fast (>103[?]km[?]s-1) and hot magnetospheric neutral wind extending more than 0.5[?]au from Jupiter, and the presence of energetic neutral atoms (both hot and cold) that have been accelerated by the electric field in the solar wind. We suggest that these atoms originate in volcanic gases from Io, undergo significant evolution through various electromagnetic interactions, escape Jupiter's magnetosphere and then populate the environment around the planet. Thus a 'nebula' is created that extends outwards over hundreds of jovian radii.

Calibration of an advanced neutral particle analyzer for the Madison Symmetric Torus reversed-field pinch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reusch, J. A.; Anderson, J. K.; Eilerman, S.

2012-10-15

A new E Parallel-To B neutral particle analyzer, which has recently been installed on Madison Symmetric Torus (MST) reversed-field pinch (RFP), has now been calibrated, allowing the measurement of the fast ion density and energy distribution. This diagnostic, dubbed the advanced neutral particle analyzer (ANPA), can simultaneously produce time resolved measurements of the efflux of both hydrogen and deuterium ions from the plasma over a 35 keV energy range with an energy resolution of 2-4 keV and a time resolution of 10 {mu}s. These capabilities are needed to measure both majority ion heating that occurs during magnetic reconnection events inmore » MST and the behavior of the fast ions from the 1 MW hydrogen neutral beam injector on MST. Calibration of the ANPA was performed using a custom ion source that resides in the flight tube between the MST and the ANPA. In this work, the ANPA will be described, the calibration procedure and results will be discussed, and initial measurements of the time evolution of 25 keV neutral beam injection-born fast ions will be presented.« less

Antigenic properties of the human immunodeficiency virus envelope glycoprotein gp120 on virions bound to target cells.

PubMed

Mengistu, Meron; Ray, Krishanu; Lewis, George K; DeVico, Anthony L

2015-03-01

The HIV-1 envelope glycoprotein, gp120, undergoes multiple molecular interactions and structural rearrangements during the course of host cell attachment and viral entry, which are being increasingly defined at the atomic level using isolated proteins. In comparison, antigenic markers of these dynamic changes are essentially unknown for single HIV-1 particles bound to target cells. Such markers should indicate how neutralizing and/or non-neutralizing antibodies might interdict infection by either blocking infection or sensitizing host cells for elimination by Fc-mediated effector function. Here we address this deficit by imaging fluorescently labeled CCR5-tropic HIV-1 pseudoviruses using confocal and superresolution microscopy to track the exposure of neutralizing and non-neutralizing epitopes as they appear on single HIV-1 particles bound to target cells. Epitope exposure was followed under conditions permissive or non-permissive for viral entry to delimit changes associated with virion binding from those associated with post-attachment events. We find that a previously unexpected array of gp120 epitopes is exposed rapidly upon target cell binding. This array comprises both neutralizing and non-neutralizing epitopes, the latter being hidden on free virions yet capable of serving as potent targets for Fc-mediated effector function. Under non-permissive conditions for viral entry, both neutralizing and non-neutralizing epitope exposures were relatively static over time for the majority of bound virions. Under entry-permissive conditions, epitope exposure patterns changed over time on subsets of virions that exhibited concurrent variations in virion contents. These studies reveal that bound virions are distinguished by a broad array of both neutralizing and non-neutralizing gp120 epitopes that potentially sensitize a freshly engaged target cell for destruction by Fc-mediated effector function and/or for direct neutralization at a post-binding step. The elucidation of these epitope exposure patterns during viral entry will help clarify antibody-mediated inhibition of HIV-1 as it is measured in vitro and in vivo.

Fluorescence Adherence Inhibition Assay: A Novel Functional Assessment of Blocking Virus Attachment by Vaccine-Induced Antibodies

PubMed Central

Asati, Atul; Kachurina, Olga; Karol, Alex; Dhir, Vipra; Nguyen, Michael; Parkhill, Robert; Kouiavskaia, Diana; Chumakov, Konstantin; Warren, William; Kachurin, Anatoly

2016-01-01

Neutralizing antibodies induced by vaccination or natural infection play a critically important role in protection against the viral diseases. In general, neutralization of the viral infection occurs via two major pathways: pre- and post-attachment modes, the first being the most important for such infections as influenza and polio, the latter being significant for filoviruses. Neutralizing capacity of antibodies is typically evaluated by virus neutralization assays that assess reduction of viral infectivity to the target cells in the presence of functional antibodies. Plaque reduction neutralization test, microneutralization and immunofluorescent assays are often used as gold standard virus neutralization assays. However, these methods are associated with several important prerequisites such as use of live virus requiring safety precautions, tedious evaluation procedure and long assessment time. Hence, there is a need for a robust, inexpensive high throughput functional assay that can be performed rapidly using inactivated virus, without extensive safety precautions. Herein, we report a novel high throughput Fluorescence Adherence Inhibition assay (fADI) using inactivated virus labeled with fluorescent secondary antibodies virus and Vero cells or erythrocytes as targets. It requires only few hours to assess pre-attachment neutralizing capacity of donor sera. fADI assay was tested successfully on donors immunized with polio, yellow fever and influenza vaccines. To further simplify and improve the throughput of the assay, we have developed a mathematical approach for calculating the 50% titers from a single sample dilution, without the need to analyze multi-point titration curves. Assessment of pre- and post-vaccination human sera from subjects immunized with IPOL®, YF-VAX® and 2013–2014 Fluzone® vaccines demonstrated high efficiency of the assay. The results correlated very well with microneutralization assay performed independently by the FDA Center of Biologics Evaluation and Research, with plaque reduction neutralization test performed by Focus Diagnostics, and with hemaglutination inhibition assay performed in-house at Sanofi Pasteur. Taken together, fADI assay appears to be a useful high throughput functional immunoassay for assessment of antibody-related neutralization of the viral infections for which pre-attachment neutralization pathway is predominant, such as polio, influenza, yellow fever and dengue. PMID:26863313

Cosmic Ray Flux in the Presence of a Neutral Background

NASA Technical Reports Server (NTRS)

Wilson, Thomas L.; Lodhi, Arfin; Diaz, Abel

2007-01-01

The study of cosmic rays (CRs) is a very mature subject developed around the concept of radiative particle flux phi as a mono-variant function of energy E, that is phi = phi(E). This is based on the notion of the cosmos as being filled with cosmic radiation in the form of a collisionless exosphere of plasma. Neutrals, however, are likewise ubiquitous in space and planetary trapped-radiation belts. It will be shown that in the presence of a neutral background of density rho, flux phi is actually bivariant in energy E and rho, creating a surface phi(E,rho). This is an intrinsic property of charged-particle flux, that flux is not merely a function of E but is dependent upon density rho when a background of neutrals is present. The effect is produced by multiple scattering of charged particles off neutral and ionized atoms along with ionization loss where charged and neutral populations interact. For the harder portion of CR spectra, flux is mono-variant but at nonrelativistic energies (below approx, 350 MeV) it becomes sensitive to the presence of neutral backgrounds. The dependence of phi(E,rho) upon background neutrals is helpful in discussing the anomalous CR (ACR) flux made up of ionized components of the heliospheric neutral atmosphere.

Probing Mechanism of Evolution of Simple Genomes

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; Ditzler, Mark; Popovic, Milena; Wei, Chenyu

2016-01-01

Our overarching goal is to discover how the structure of the genotypic space of RNA polymers affects their ability to evolve. Specifically, we will address several fundamental questions that, so far, have remained largely unanswered. Was the genotypic space explored globally or only locally? Was the outcome of early evolution predictable or was it, instead, govern by chance? What was the role of neutral mutations in the evolution of increasing complex systems? As the first step, we study the problem in the example of RNA ligases. We obtain the complete, empirical fitness landscapes for short ligases and examine possible evolutionary paths for RNA molecules that are sufficiently long to preclude exhaustive search of the genotypic space.

Parametric resonant triad interactions in a free shear layer

NASA Technical Reports Server (NTRS)

Mallier, R.; Maslowe, S. A.

1993-01-01

We investigate the weakly nonlinear evolution of a triad of nearly-neutral modes superimposed on a mixing layer with velocity profile u bar equals Um + tanh y. The perturbation consists of a plane wave and a pair of oblique waves each inclined at approximately 60 degrees to the mean flow direction. Because the evolution occurs on a relatively fast time scale, the critical layer dynamics dominate the process and the amplitude evolution of the oblique waves is governed by an integro-differential equation. The long-time solution of this equation predicts very rapid (exponential of an exponential) amplification and we discuss the pertinence of this result to vortex pairing phenomena in mixing layers.

Star formation induced by cloud-cloud collisions and galactic giant molecular cloud evolution

NASA Astrophysics Data System (ADS)

Kobayashi, Masato I. N.; Kobayashi, Hiroshi; Inutsuka, Shu-ichiro; Fukui, Yasuo

2018-05-01

Recent millimeter/submillimeter observations towards nearby galaxies have started to map the whole disk and to identify giant molecular clouds (GMCs) even in the regions between galactic spiral structures. Observed variations of GMC mass functions in different galactic environments indicates that massive GMCs preferentially reside along galactic spiral structures whereas inter-arm regions have many small GMCs. Based on the phase transition dynamics from magnetized warm neutral medium to molecular clouds, Kobayashi et al. (2017, ApJ, 836, 175) proposes a semi-analytical evolutionary description for GMC mass functions including a cloud-cloud collision (CCC) process. Their results show that CCC is less dominant in shaping the mass function of GMCs than the accretion of dense H I gas driven by the propagation of supersonic shock waves. However, their formulation does not take into account the possible enhancement of star formation by CCC. Millimeter/submillimeter observations within the Milky Way indicate the importance of CCC in the formation of star clusters and massive stars. In this article, we reformulate the time-evolution equation largely modified from Kobayashi et al. (2017, ApJ, 836, 175) so that we additionally compute star formation subsequently taking place in CCC clouds. Our results suggest that, although CCC events between smaller clouds are more frequent than the ones between massive GMCs, CCC-driven star formation is mostly driven by massive GMCs ≳ 10^{5.5} M_{⊙} (where M⊙ is the solar mass). The resultant cumulative CCC-driven star formation may amount to a few 10 percent of the total star formation in the Milky Way and nearby galaxies.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

PubMed Central

Thybert, David; Roller, Maša; Navarro, Fábio C.P.; Fiddes, Ian; Streeter, Ian; Feig, Christine; Martin-Galvez, David; Kolmogorov, Mikhail; Janoušek, Václav; Akanni, Wasiu; Aken, Bronwen; Aldridge, Sarah; Chakrapani, Varshith; Chow, William; Clarke, Laura; Cummins, Carla; Doran, Anthony; Dunn, Matthew; Goodstadt, Leo; Howe, Kerstin; Howell, Matthew; Josselin, Ambre-Aurore; Karn, Robert C.; Laukaitis, Christina M.; Jingtao, Lilue; Martin, Fergal; Muffato, Matthieu; Nachtweide, Stefanie; Quail, Michael A.; Sisu, Cristina; Stanke, Mario; Stefflova, Klara; Van Oosterhout, Cock; Veyrunes, Frederic; Ward, Ben; Yang, Fengtang; Yazdanifar, Golbahar; Zadissa, Amonida; Adams, David J.; Brazma, Alvis; Gerstein, Mark; Paten, Benedict; Pham, Son; Keane, Thomas M.; Odom, Duncan T.; Flicek, Paul

2018-01-01

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology. PMID:29563166

Spectroscopic observation of Lyα emitters at z ∼ 7.7 and implications on re-ionization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Faisst, A. L.; Carollo, C. M.; Capak, P.

2014-06-10

We present spectroscopic follow-up observations on two bright Lyα emitter (LAE) candidates originally found by Krug et al. at a redshift of z ∼ 7.7 using the Multi-Object Spectrometer for Infra-Red Exploration at Keck. We rule out any line emission at the >5σ level for both objects, putting on solid ground a previous null result for one of the objects. The limits inferred from the non-detections rule out the previous claim of no or even reversed evolution between 5.7 < z < 7.7 in the Lyα luminosity function (LF) and suggest a drop in the Lyα LF consistent with thatmore » seen in Lyman break galaxy (LBG) samples. We model the redshift evolution of the LAE LF using the LBG UV-continuum LF and the observed rest-frame equivalent width distribution. From the comparison of our empirical model with the observed LAE distribution, we estimate lower limits of the neutral hydrogen fraction to be 50%-70% at z ∼ 7.7. Together with this, we find a strong evolution in the Lyα optical depth characterized by (1 + z){sup 2.2} {sup ±} {sup 0.5} beyond z = 6, indicative of a strong evolution of the intergalactic medium. Finally, we extrapolate the LAE LF to z ∼ 9 using our model and show that it is unlikely that large area surveys, like UltraVISTA or Euclid, pick up LAEs at this redshift assuming the current depths and area.« less

Efficient Means of Detecting Neutral Atoms in Space

NASA Astrophysics Data System (ADS)

Zinicola, W. N.

2006-12-01

This summer, The Society of Physics Students granted me the opportunity to participate in an internship for The National Aeronautics and Space Administration (NASA) and The University of Maryland. Our chief interest was analyzing low energy neutral atoms that were created from random interactions of ions in space plasma. From detecting these neutrals one can project a image of what the plasma's composition is, and how this plasma changes through interactions with the solar wind. Presently, low energy neutral atom detectors have poor efficiency, typically in the range of 1%. Our goal was to increase this efficiency. To detect low energy neutrals we must first convert them from neutral molecules to negatively charged ions. Once converted, these "new" negatively charged ions can be easily detected and completely analyzed giving us information about their energy, mass, and instantaneous direction. The efficiency of the detector is drastically affected by the surface used for converting these neutrals. My job was first to create thin metal conversion surfaces. Then, using an X-ray photoelectron spectrometer, analyze atomic surface composition and gather work function values. Once the work function values were known we placed the surfaces in our neutral detector and measured their conversion efficiencies. Finally, a relation between the work function of the metal surface an its conversion efficiency was generated. With this relationship accurately measured one could use this information to help give suggestions on what surface would be the best to increase our detection efficiency. If we could increase the efficiency of these low energy neutral atom detectors by even 1% we would be able to decrease the size of the detector therefore making it cheaper and more applicable for space exploration.* * A special thanks to Dr. Michael Coplan of the University of Maryland for his support and guidance through all my research.

The impact of exospheric neutral dynamics on ring current decay

NASA Astrophysics Data System (ADS)

Ilie, R.; Liemohn, M. W.; Skoug, R. M.; Funsten, H. O.; Gruntman, M.; Bailey, J. J.; Toth, G.

2015-12-01

The geocorona plays an important role in the energy budget of the Earth's inner magnetosphere since charge exchange of energetic ions with exospheric neutrals makes the exosphere act as an energy sink for ring current particles. Long-term ring current decay following a magnetic storm is mainly due to these electron transfer reactions, leading to the formation energetic neutral atoms (ENAs) that leave the ring current system on ballistic trajectories. The number of ENAs emitted from a given region of space depends on several factors, such as the energy and species of the energetic ion population in that region and the density of the neutral gas with which the ions undergo charge exchange. However, the density and structure of the exosphere are strongly dependent on changes in atmospheric temperature and density as well as charge exchange with the ions of plasmaspheric origin, which depletes the geocorona (by having a neutral removed from the system). Moreover, the radiation pressure exerted by solar far-ultraviolet photons pushes the geocoronal hydrogen away from the Earth in an anti-sunward direction to form a tail of neutral hydrogen. TWINS ENA images provide a direct measurement of these ENA losses and therefore insight into the dynamics of the ring current decay through interactions with the geocorona. We assess the influence of geocoronal neutrals on ring current formation and decay by analysis of the predicted ENA emissions using 6 different geocoronal models and simulations from the HEIDI ring current model during storm time. Comparison with TWINS ENA images shows that the location of the peak ENA enhancements is highly dependent on the distribution of geocoronal hydrogen density. We show that the neutral dynamics has a strong influence on the time evolution of the ring current populations as well as on the formation of energetic neutral atoms.

Graphene quantum dots as the electrolyte for solid state supercapacitors

PubMed Central

Zhang, Su; Li, Yutong; Song, Huaihe; Chen, Xiaohong; Zhou, Jisheng; Hong, Song; Huang, Minglu

2016-01-01

We propose that graphene quantum dots (GQDs) with a sufficient number of acidic oxygen-bearing functional groups such as -COOH and -OH can serve as solution- and solid- type electrolytes for supercapacitors. Moreover, we found that the ionic conductivity and ion-donating ability of the GQDs could be markedly improved by simply neutralizing their acidic functional groups by using KOH. These neutralized GQDs as the solution- or solid-type electrolytes greatly enhanced the capacitive performance and rate capability of the supercapacitors. The reason for the enhancement can be ascribed to the fully ionization of the weak acidic oxygen-bearing functional groups after neutralization. PMID:26763275

Dissolved Divalent Metal and pH Effects on Amino Acid Polymerization: A Thermodynamic Evaluation.

PubMed

Kitadai, Norio

2017-03-01

Polymerization of amino acids is a fundamentally important step for the chemical evolution of life. Nevertheless, its response to changing environmental conditions has not yet been well understood because of the lack of reliable quantitative information. For thermodynamics, detailed prediction over diverse combinations of temperature and pH has been made only for a few amino acid-peptide systems. This study used recently reported thermodynamic dataset for the polymerization of the simplest amino acid "glycine (Gly)" to its short peptides (di-glycine and tri-glycine) to examine chemical and structural characteristics of amino acids and peptides that control the temperature and pH dependence of polymerization. Results showed that the dependency is strongly controlled by the intramolecular distance between the amino and carboxyl groups in an amino acid structure, although the side-chain group role is minor. The polymerization behavior of Gly reported earlier in the literature is therefore expected to be a typical feature for those of α-amino acids. Equilibrium calculations were conducted to examine effects of dissolved metals as a function of pH on the monomer-polymer equilibria of Gly. Results showed that metals shift the equilibria toward the monomer side, particularly at neutral and alkaline pH. Metals that form weak interaction with Gly (e.g., Mg 2+ ) have no noticeable influence on the polymerization, although strong interaction engenders significant decrease of the equilibrium concentrations of Gly peptides. Considering chemical and structural characteristics of Gly and Gly peptides that control their interactions with metals, it can be expected that similar responses to the addition of metals are applicable in the polymerization of neutral α-amino acids. Neutral and alkaline aqueous environments with dissolved metals having high affinity with neutral α-amino acids (e.g., Cu 2+ ) are therefore not beneficial places for peptide bond formation on the primitive Earth.

Clusters of Point Defects Near Dislocations as a Tool to Control CdZnTe Electrical Parameters by Ultrasound

NASA Astrophysics Data System (ADS)

Olikh, Ya. M.; Tymochko, M. D.; Olikh, O. Ya.; Shenderovsky, V. A.

2018-05-01

We studied the temperature dependence (77-300 K) of the electron concentration and mobility using the Hall method under ultrasound (the acoustic Hall method) to determine the mechanisms by which ultrasound influences the electrical activity of near-dislocation clusters in n-type low-ohmic Cd1-x Zn x Te single crystals (N Cl ≈ 1024 m-3; x = 0; 0.04) with different dislocation density (0.4-5.1) × 1010 m-2. Changes in electrophysical parameters were found to occur as a function of temperature and ultrasound intensity. To evaluate the relative contribution of different charge carrier scattering mechanisms (lattice scattering, ionized impurity scattering, neutral impurity scattering, and dislocation scattering) and their change under ultrasound, a differential evolution method was used. This method made it possible to analyze experimental mobility μ H(T) by its nonlinear approximation with characteristic temperature dependence for each mechanism. An increase in neutral impurity scattering and a decrease in ionized impurity and dislocation scattering components were observed under ultrasound. The character and the amount of these acoustically induced changes correlate with particular sample dislocation characteristics. It was concluded that the observed effects are related to the acoustically induced transformation of the point-defect structure, mainly in the near dislocation crystal regions.

Universality in a Neutral Evolution Model

NASA Astrophysics Data System (ADS)

King, Dawn; Scott, Adam; Maric, Nevena; Bahar, Sonya

2013-03-01

Agent-based models are ideal for investigating the complex problems of biodiversity and speciation because they allow for complex interactions between individuals and between individuals and the environment. Presented here is a ``null'' model that investigates three mating types - assortative, bacterial, and random - in phenotype space, as a function of the percentage of random death δ. Previous work has shown phase transition behavior in an assortative mating model with variable fitness landscapes as the maximum mutation size (μ) was varied (Dees and Bahar, 2010). Similarly, this behavior was recently presented in the work of Scott et al. (submitted), on a completely neutral landscape, for bacterial-like fission as well as for assortative mating. Here, in order to achieve an appropriate ``null'' hypothesis, the random death process was changed so each individual, in each generation, has the same probability of death. Results show a continuous nonequilibrium phase transition for the order parameters of the population size and the number of clusters (analogue of species) as δ is varied for three different mutation sizes of the system. The system shows increasing robustness as μ increases. Universality classes and percolation properties of this system are also explored. This research was supported by funding from: University of Missouri Research Board and James S. McDonnell Foundation

Reconstructing the Phylogenetic History of Long-Term Effective Population Size and Life-History Traits Using Patterns of Amino Acid Replacement in Mitochondrial Genomes of Mammals and Birds

PubMed Central

Nabholz, Benoit; Lartillot, Nicolas

2013-01-01

The nearly neutral theory, which proposes that most mutations are deleterious or close to neutral, predicts that the ratio of nonsynonymous over synonymous substitution rates (dN/dS), and potentially also the ratio of radical over conservative amino acid replacement rates (Kr/Kc), are negatively correlated with effective population size. Previous empirical tests, using life-history traits (LHT) such as body-size or generation-time as proxies for population size, have been consistent with these predictions. This suggests that large-scale phylogenetic reconstructions of dN/dS or Kr/Kc might reveal interesting macroevolutionary patterns in the variation in effective population size among lineages. In this work, we further develop an integrative probabilistic framework for phylogenetic covariance analysis introduced previously, so as to estimate the correlation patterns between dN/dS, Kr/Kc, and three LHT, in mitochondrial genomes of birds and mammals. Kr/Kc displays stronger and more stable correlations with LHT than does dN/dS, which we interpret as a greater robustness of Kr/Kc, compared with dN/dS, the latter being confounded by the high saturation of the synonymous substitution rate in mitochondrial genomes. The correlation of Kr/Kc with LHT was robust when controlling for the potentially confounding effects of nucleotide compositional variation between taxa. The positive correlation of the mitochondrial Kr/Kc with LHT is compatible with previous reports, and with a nearly neutral interpretation, although alternative explanations are also possible. The Kr/Kc model was finally used for reconstructing life-history evolution in birds and mammals. This analysis suggests a fairly large-bodied ancestor in both groups. In birds, life-history evolution seems to have occurred mainly through size reduction in Neoavian birds, whereas in placental mammals, body mass evolution shows disparate trends across subclades. Altogether, our work represents a further step toward a more comprehensive phylogenetic reconstruction of the evolution of life-history and of the population-genetics environment. PMID:23711670

Multiple scattered radiation emerging from continental haze layers. 1: Radiance, polarization, and neutral points

NASA Technical Reports Server (NTRS)

Kattawar, G. W.; Plass, G. N.; Hitzfelder, S. J.

1975-01-01

The complete radiation field is calculated for scattering layers of various optical thicknesses. Results obtained for Rayleigh and haze scattering are compared. Calculated radiances show differences as large as 23% compared to the approximate scalar theory of radiative transfer, while the same differences are approximately 0.1% for a continental haze phase function. The polarization of reflected and transmitted radiation is given for various optical thicknesses, solar zenith angles, and surface albedos. Two types of neutral points occur for aerosol phase functions. Rayleigh-like neutral points arise from zero polarization that occurs at scattering angles of 0 deg and 180 deg. For Rayleigh phase functions, the position of these points varies with the optical thickness of the scattering layer. Non-Rayleigh neutral points are associated with the zeros of polarization which occur between the end points of the single scattering curve, and are found over a wide range of azimuthal angles.

Mn-doped NiP2 nanosheets as an efficient electrocatalyst for enhanced hydrogen evolution reaction at all pH values

NASA Astrophysics Data System (ADS)

Wang, Xiaodeng; Zhou, Hongpeng; Zhang, Dingke; Pi, Mingyu; Feng, Jiajia; Chen, Shijian

2018-05-01

Developing stable and high-efficiency hydrogen generation electrocatalysts, particularly for the cathode hydrogen evolution reaction (HER), is an urgent challenge in energy conversion technologies. In this work, we have successfully synthesized Mn-doped NiP2 nanosheets on carbon cloth (Mn-NiP2 NSs/CC), which behaves as a higher efficient three dimensional HER electrocatalyst with better stability at all pH values than pure NiP2. Electrochemical tests demonstrate that the catalytic activity of NiP2 is enhanced by Mn doping. In 0.5 M H2SO4, this Mn-NiP2 NSs/CC catalyst drives 10 mA cm-2 at an overpotential of 69 mV, which is 20 mV smaller than pure NiP2. To achieve the same current density, it demands overpotentials of 97 and 107 mV in 1.0 M KOH and phosphate-buffered saline (PBS), respectively. Compared with pure NiP2, higher HER electrocatalytic performance for Mn-NiP2 NSs/CC can be attributed to its lower thermo-neutral hydrogen adsorption free energy, which is supported by density functional theory calculations.

LADUMA: Looking At the Distant Universe with the MeerKAT Array

NASA Astrophysics Data System (ADS)

Baker, Andrew J.; Blyth, Sarah; Holwerda, Benne W.; LADUMA team

2018-01-01

The cosmic evolution of galaxies' neutral atomic gas content is a major science driver for the Square Kilometre Array (SKA), as well as for its Australian (ASKAP) and South African (MeerKAT) precursors. Among the HI surveys planned for ASKAP and MeerKAT, the deepest and narrowest tier of the "wedding cake" will be defined by the approved 3424-hour Looking At the Distant Universe with the MeerKAT Array (LADUMA) survey, which will probe HI in emission within a single "cosmic vuvuzela" that extends to z = 1.4, when the universe was only a third of its present age. Through a combination of individual and stacked detections (the latter relying on extensive multiwavelength studies of the survey's target field), LADUMA will study the redshift evolution of the baryonic Tully-Fisher relation and the cosmic HI density, the variation of the HI mass function with redshift and environment, and the connection between HI content and the properties of galaxies' stars (mass, age, etc.). The survey will also build a sample of OH megamaser detections that can be used to trace the cosmic merger history. This talk will introduce the science potential of LADUMA and plans for its execution starting in 2018.

RNAmutants: a web server to explore the mutational landscape of RNA secondary structures

PubMed Central

Waldispühl, Jerome; Devadas, Srinivas; Berger, Bonnie; Clote, Peter

2009-01-01

The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics—indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provide the foundation for modern population genetics. In contrast to DNA, the function of most noncoding RNA depends on tertiary structure, experimentally known to be largely determined by secondary structure, for which dynamic programming can efficiently compute the minimum free energy secondary structure. For this reason, understanding the effect of pointwise mutations in RNA secondary structure could reveal fundamental properties of structural RNA molecules and improve our understanding of molecular evolution of RNA. The web server RNAmutants provides several efficient tools to compute the ensemble of low-energy secondary structures for all k-mutants of a given RNA sequence, where k is bounded by a user-specified upper bound. As we have previously shown, these tools can be used to predict putative deleterious mutations and to analyze regulatory sequences from the hepatitis C and human immunodeficiency genomes. Web server is available at http://bioinformatics.bc.edu/clotelab/RNAmutants/, and downloadable binaries at http://rnamutants.csail.mit.edu/. PMID:19531740

Neutralizer Characterization of a NEXT Multi-Thruster Array With Electrostatic Probes

NASA Technical Reports Server (NTRS)

Foster, John E.; Patterson, Michael; Pencil, Eric; McEwen, Heather; Diaz, Esther

2006-01-01

Neutralizers in a multi-thruster array configuration were characterized using conventional diagnostics such as peak-to-peak keeper oscillation amplitude as well as unconventional methods which featured the application of electrostatic probes. The response of the array local plasma environment to neutralizer flow rate changes were documented using Langmuir probes and retarding potential analyzers. Such characterization is necessary for system efficiency and stability optimization. Because the local plasma environment was measured in conjunction with the neutralizer characterization, particle fluxes at the array and thus array lifetime impacts associated with neutralizer operating mode could also be investigated. Neutralizer operating condition was documented for a number of multithruster array configurations ranging from three-engines, three-neutralizers to a single engine, one-neutralizer all as a function of neutralizer flow rate.

Hierarchical cobalt-based hydroxide microspheres for water oxidation.

PubMed

Zhang, Ye; Cui, Bai; Derr, Olivia; Yao, Zhibo; Qin, Zhaotong; Deng, Xiangyun; Li, Jianbao; Lin, Hong

2014-03-21

3D hierarchical cobalt hydroxide carbonate hydrate (Co(CO3)0.5(OH)·0.11H2O) has been synthesized featuring a hollow urchin-like structure by a one-step hydrothermal method at modest temperature on FTO glass substrates. The functionalities of precursor surfactants were isolated and analyzed. A plausible formation mechanism of the spherical urchin-like microclusters has been furnished through time-dependent investigations. Introduction of other transitional metal doping (Cu, Ni) would give rise to a substantial morphological change associated with a surface area drop. The directly grown cobalt-based hydroxide composite electrodes were found to be capable of catalyzing oxygen evolution reaction (OER) under both neutral pH and alkaline conditions. The favorable 3D dendritic morphology and porous structure provide large surface areas and possible defect sites that are likely responsible for their robust electrochemical activity.

Comparison of the analytical and simulation results of the equilibrium beam profile

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Z. J.; Zhu Shaoping; Cao, L. H.

2007-10-15

The evolution of high current electron beams in dense plasmas has been investigated by using two-dimensional particle-in-cell (PIC) simulations with immobile ions. It is shown that electron beams are split into many filaments at the beginning due to the Weibel instability, and then different filamentation beams attract each other and coalesce. The profile of the filaments can be described by formulas. Hammer et al. [Phys. Fluids 13, 1831 (1970)] developed a self-consistent relativistic electron beam model that allows the propagation of relativistic electron fluxes in excess of the Alfven-Lawson critical-current limit for a fully neutralized beam. The equilibrium solution hasmore » been observed in the simulation results, but the electron distribution function assumed by Hammer et al. is different from the simulation results.« less

Genetics and the making of Homo sapiens.

PubMed

Carroll, Sean B

2003-04-24

Understanding the genetic basis of the physical and behavioural traits that distinguish humans from other primates presents one of the great new challenges in biology. Of the millions of base-pair differences between humans and chimpanzees, which particular changes contributed to the evolution of human features after the separation of the Pan and Homo lineages 5-7 million years ago? How can we identify the 'smoking guns' of human genetic evolution from neutral ticks of the molecular evolutionary clock? The magnitude and rate of morphological evolution in hominids suggests that many independent and incremental developmental changes have occurred that, on the basis of recent findings in model animals, are expected to be polygenic and regulatory in nature. Comparative genomics, population genetics, gene-expression analyses and medical genetics have begun to make complementary inroads into the complex genetic architecture of human evolution.

Biological evolution and statistical physics

NASA Astrophysics Data System (ADS)

Drossel, Barbara

2001-03-01

This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications have appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. Throughout the review, attention is paid to giving the necessary biological information, and to pointing out the assumptions underlying the models, and their limits of validity.

Evolution of complex adaptations in molecular systems

PubMed Central

Pál, Csaba; Papp, Balázs

2017-01-01

A central challenge in evolutionary biology concerns the mechanisms by which complex adaptations arise. Such adaptations depend on the fixation of multiple, highly specific mutations, where intermediate stages of evolution seemingly provide little or no benefit. It is generally assumed that the establishment of complex adaptations is very slow in nature, as evolution of such traits demands special population genetic or environmental circumstances. However, blueprints of complex adaptations in molecular systems are pervasive, indicating that they can readily evolve. We discuss the prospects and limitations of non-adaptive scenarios, which assume multiple neutral or deleterious steps in the evolution of complex adaptations. Next, we examine how complex adaptations can evolve by natural selection in changing environment. Finally, we argue that molecular ’springboards’, such as phenotypic heterogeneity and promiscuous interactions facilitate this process by providing access to new adaptive paths. PMID:28782044

Identification of Prostate Cancer-Specific Circular RNAs

DTIC Science & Technology

2016-12-01

they often have regulatory functions. For example, circRNAs can serve as endogenous microRNA sponges to neutralize the microRNA function. However, it...circRNAs is the capability to serve as sponges to neutralize the endogenous microRNAs. In this regard, all of these circRNAs had the potential to

Evolution of Cometary Activity at 67P/Churyumov-Gerasimenko as seen by ROSINA/Rosetta

NASA Astrophysics Data System (ADS)

Jäckel, A.; Altwegg, K.; Balsiger, H.; Calmonte, U.; Gasc, S.; Le Roy, L.; Rubin, M.; Tzou, C. Y.; Wurz, P.; Bieler, A.; Berthelier, J.-J.; Fiethe, B.; Hässig, M.; deKeyser, J.; Mall, U.; Rème, H.

2015-10-01

Since nine months the European Space Agency's spacecraft Rosetta, with the Rosetta Orbiter Spectrometer for Ion and Neutral Analysis (ROSINA) onboard, is in the comet escort phase. ROSINA is a suite of three instruments, consisting of the COmetary Pressure Sensor (COPS), the Double Focusing Mass Spectrometer (DFMS), and the Reflectron-type Time-Of-Flight (RTOF) mass spectrometer [1]. The two mass spectrometers measure in situ the neutral and ionized volatile material in the coma of comet 67P/Churyumov- Gerasimenko (67P/C-G). With COPS we are able to derive the total gas density, bulk velocities and temperatures of the coma.

Radiative decay lifetime of neutrinos and the evolution of the universe after the recombination era

NASA Astrophysics Data System (ADS)

Rephaeli, Yoel; Szalay, Alexander S.

1981-10-01

If the radiative decay lifetime τ of massive neutrinos is less than 1025 s, but exceeding present constraints, the epoch of neutral hydrogen in the history of the universe could have been short or altogether absent. Erasure of small scale fluctuations in the cosmic microwave background radiation and other consequences of such lifetimes are discussed. From observations of neutral hydrogen in the nearby galaxy M 31 a lower limit τ >= 1024 s is obtained (for neutrino masses in the range 30 eV <= m <= 150 eV). Permanent address: Department of Atomic Physics, R. Eotvos University, 1088 Budapest, Hungary.

Neutrality and Robustness in Evo-Devo: Emergence of Lateral Inhibition

PubMed Central

Munteanu, Andreea; Solé, Ricard V.

2008-01-01

Embryonic development is defined by the hierarchical dynamical process that translates genetic information (genotype) into a spatial gene expression pattern (phenotype) providing the positional information for the correct unfolding of the organism. The nature and evolutionary implications of genotype–phenotype mapping still remain key topics in evolutionary developmental biology (evo-devo). We have explored here issues of neutrality, robustness, and diversity in evo-devo by means of a simple model of gene regulatory networks. The small size of the system allowed an exhaustive analysis of the entire fitness landscape and the extent of its neutrality. This analysis shows that evolution leads to a class of robust genetic networks with an expression pattern characteristic of lateral inhibition. This class is a repertoire of distinct implementations of this key developmental process, the diversity of which provides valuable clues about its underlying causal principles. PMID:19023404

Spatial constraints govern competition of mutant clones in human epidermis.

PubMed

Lynch, M D; Lynch, C N S; Craythorne, E; Liakath-Ali, K; Mallipeddi, R; Barker, J N; Watt, F M

2017-10-24

Deep sequencing can detect somatic DNA mutations in tissues permitting inference of clonal relationships. This has been applied to human epidermis, where sun exposure leads to the accumulation of mutations and an increased risk of skin cancer. However, previous studies have yielded conflicting conclusions about the relative importance of positive selection and neutral drift in clonal evolution. Here, we sequenced larger areas of skin than previously, focusing on cancer-prone skin spanning five decades of life. The mutant clones identified were too large to be accounted for solely by neutral drift. Rather, using mathematical modelling and computational lattice-based simulations, we show that observed clone size distributions can be explained by a combination of neutral drift and stochastic nucleation of mutations at the boundary of expanding mutant clones that have a competitive advantage. These findings demonstrate that spatial context and cell competition cooperate to determine the fate of a mutant stem cell.

Distinguishing Positive Selection From Neutral Evolution: Boosting the Performance of Summary Statistics

PubMed Central

Lin, Kao; Li, Haipeng; Schlötterer, Christian; Futschik, Andreas

2011-01-01

Summary statistics are widely used in population genetics, but they suffer from the drawback that no simple sufficient summary statistic exists, which captures all information required to distinguish different evolutionary hypotheses. Here, we apply boosting, a recent statistical method that combines simple classification rules to maximize their joint predictive performance. We show that our implementation of boosting has a high power to detect selective sweeps. Demographic events, such as bottlenecks, do not result in a large excess of false positives. A comparison to other neutrality tests shows that our boosting implementation performs well compared to other neutrality tests. Furthermore, we evaluated the relative contribution of different summary statistics to the identification of selection and found that for recent sweeps integrated haplotype homozygosity is very informative whereas older sweeps are better detected by Tajima's π. Overall, Watterson's θ was found to contribute the most information for distinguishing between bottlenecks and selection. PMID:21041556

Early Antibody Lineage Diversification and Independent Limb Maturation Lead to Broad HIV-1 Neutralization Targeting the Env High-Mannose Patch.

PubMed

MacLeod, Daniel T; Choi, Nancy M; Briney, Bryan; Garces, Fernando; Ver, Lorena S; Landais, Elise; Murrell, Ben; Wrin, Terri; Kilembe, William; Liang, Chi-Hui; Ramos, Alejandra; Bian, Chaoran B; Wickramasinghe, Lalinda; Kong, Leopold; Eren, Kemal; Wu, Chung-Yi; Wong, Chi-Huey; Kosakovsky Pond, Sergei L; Wilson, Ian A; Burton, Dennis R; Poignard, Pascal

2016-05-17

The high-mannose patch on HIV Env is a preferred target for broadly neutralizing antibodies (bnAbs), but to date, no vaccination regimen has elicited bnAbs against this region. Here, we present the development of a bnAb lineage targeting the high-mannose patch in an HIV-1 subtype-C-infected donor from sub-Saharan Africa. The Abs first acquired autologous neutralization, then gradually matured to achieve breadth. One Ab neutralized >47% of HIV-1 strains with only ∼11% somatic hypermutation and no insertions or deletions. By sequencing autologous env, we determined key residues that triggered the lineage and participated in Ab-Env coevolution. Next-generation sequencing of the Ab repertoire showed an early expansive diversification of the lineage followed by independent maturation of individual limbs, several of them developing notable breadth and potency. Overall, the findings are encouraging from a vaccine standpoint and suggest immunization strategies mimicking the evolution of the entire high-mannose patch and promoting maturation of multiple diverse Ab pathways. Copyright © 2016 Elsevier Inc. All rights reserved.

2 years with comet 67P/Churyumov-Gerasimenko: H2O, CO2, CO as seen by ROSINA RTOF

NASA Astrophysics Data System (ADS)

Hoang, M.; Garnier, P.; Lasue, J.; Reme, H.; Altwegg, K.; Balsiger, H. R.; Bieler, A. M.; Calmonte, U.; Capria, M. T.; Combi, M. R.; De Keyser, J. M.; Fiethe, B.; Fougere, N.; Fuselier, S. A.; Galli, A.; Gasc, S.; Gombosi, T. I.; Hansen, K. C.; Jäckel, A.; Korth, A.; Mall, U.; Migliorini, A.; Rubin, M.; Sémon, T.; Tzou, C. Y.; Waite, J. H., Jr.; Wurz, P.

2017-12-01

The Rosetta space mission investigated comet 67P/Churyumov-Gerasimenko (67P) over two years from August 2014 to September 2016. Onboard the spacecraft, the ROSINA experiment included two mass spectrometers to derive the composition of neutrals and ions, and a COmet Pressure Sensor (COPS) to monitor the density and velocity of the neutrals in the coma. We will here analyse and discuss data from the Reflectron-type Time-Of-Flight instrument during the comet escort phase. The RTOF mass spectrometer possessed a wide mass range and a high temporal resolution (Balsiger et al., 2007). The analysis of 67P/C-G's coma major molecules over the mission showed strong variability of the comet coma's main volatiles concentrations (H2O, CO2, CO) and their relative abundances. The 2 years long Rosetta mission allowed us to observe the seasonal evolution in the atmosphere of 67P, in particular the change occurring during the equinoxes and at perihelion. In this work, we analyze the asymmetry in the outgassing rate before and after the perihelion (13/08/2015), the evolution of abundance ratios through the whole mission, and in particular the behavior of the very volatile CO molecules. Density maps projected on the surface of 67P demonstrate the evolution of the three main coma species after the outbound equinox. We will present first results of our comet nucleus thermal modelling used to simulate the internal structure and temperature evolution of 67P at characteristic surface areas. These results will be compared with the coma composition measurements obtained by ROSINA.

Accelerated Evolution of the Lyα Luminosity Function at z >~ 7 Revealed by the Subaru Ultra-deep Survey for Lyα Emitters at z = 7.3

NASA Astrophysics Data System (ADS)

Konno, Akira; Ouchi, Masami; Ono, Yoshiaki; Shimasaku, Kazuhiro; Shibuya, Takatoshi; Furusawa, Hisanori; Nakajima, Kimihiko; Naito, Yoshiaki; Momose, Rieko; Yuma, Suraphong; Iye, Masanori

2014-12-01

We present the ultra-deep Subaru narrowband imaging survey for Lyα emitters (LAEs) at z = 7.3 in the Subaru/XMM-Newton Deep Survey (SXDS) and Cosmic Evolution Survey (COSMOS) fields (~0.5 deg2) with a total integration time of 106 hr. Exploiting our new sharp bandwidth filter, NB101, installed on the Suprime-Cam, we have reached L(Lyα) = 2.4 × 1042 erg s-1 (5σ) for z = 7.3 LAEs, about four times deeper than previous Subaru z >~ 7 studies, which allows us to reliably investigate the evolution of the Lyα luminosity function (LF) for the first time down to the luminosity limit same as those of Subaru z = 3.1-6.6 LAE samples. Surprisingly, we only find three and four LAEs in the SXDS and COSMOS fields, respectively, while one expects a total of ~65 LAEs by our survey in the case of no Lyα LF evolution from z = 6.6 to 7.3. We identify a decrease of the Lyα LF from z = 6.6 to 7.3 at the >90% confidence level from our z = 7.3 Lyα LF with the best-fit Schechter parameters of L*{Lyα } = 2.7+8.0-1.2 × 1042 {erg} {s}-1 and φ * = 3.7+17.6-3.3 × 10-4 {Mpc}-3 for a fixed α = -1.5. Moreover, the evolution of the Lyα LF is clearly accelerated at z > 6.6 beyond the measurement uncertainties including cosmic variance. Because no such accelerated evolution of the UV-continuum LF or the cosmic star formation rate (SFR) is found at z ~ 7, but suggested only at z > 8, this accelerated Lyα LF evolution is explained by physical mechanisms different from a pure SFR decrease but related to the Lyα production and escape in the process of cosmic reionization. Because a simple accelerating increase of intergalactic medium neutral hydrogen absorbing Lyα cannot be reconciled with Thomson scattering of optical depth measurements from WMAP and Planck, our findings may support new physical pictures suggested by recent theoretical studies, such as the existence of HI clumpy clouds within cosmic ionized bubbles that are selectively absorbing Lyα and the large ionizing photon escape fraction of galaxies causing weak Lyα emission.

Evolutionary advantage via common action of recombination and neutrality

NASA Astrophysics Data System (ADS)

Saakian, David B.; Hu, Chin-Kun

2013-11-01

We investigate evolution models with recombination and neutrality. We consider the Crow-Kimura (parallel) mutation-selection model with the neutral fitness landscape, in which there is a central peak with high fitness A, and some of 1-point mutants have the same high fitness A, while the fitness of other sequences is 0. We find that the effect of recombination and neutrality depends on the concrete version of both neutrality and recombination. We consider three versions of neutrality: (a) all the nearest neighbor sequences of the peak sequence have the same high fitness A; (b) all the l-point mutations in a piece of genome of length l≥1 are neutral; (c) the neutral sequences are randomly distributed among the nearest neighbors of the peak sequences. We also consider three versions of recombination: (I) the simple horizontal gene transfer (HGT) of one nucleotide; (II) the exchange of a piece of genome of length l, HGT-l; (III) two-point crossover recombination (2CR). For the case of (a), the 2CR gives a rather strong contribution to the mean fitness, much stronger than that of HGT for a large genome length L. For the random distribution of neutral sequences there is a critical degree of neutrality νc, and for μ<μc and (μc-μ) is not large, the 2CR suppresses the mean fitness while HGT increases it; for ν much larger than νc, the 2CR and HGT-l increase the mean fitness larger than that of the HGT. We also consider the recombination in the case of smooth fitness landscapes. The recombination gives some advantage in the evolutionary dynamics, where recombination distinguishes clearly the mean-field-like evolutionary factors from the fluctuation-like ones. By contrast, mutations affect the mean-field-like and fluctuation-like factors similarly. Consequently, recombination can accelerate the non-mean-field (fluctuation) type dynamics without considerably affecting the mean-field-like factors.

Respiratory Syncytial Virus (RSV): Neutralizing Antibody, a Correlate of Immune Protection.

PubMed

Piedra, Pedro A; Hause, Anne M; Aideyan, Letisha

2016-01-01

Assays that measure RSV-specific neutralizing antibody activity are very useful for evaluating vaccine candidates, performing seroprevalence studies, and detecting infection. Neutralizing antibody activity is normally measured by a plaque reduction neutralization assay or by a microneutralization assay with or without complement. These assays measure the functional capacity of serum (or other fluids) to neutralize virus infectivity in cells as compared to ELISA assays that only measure the binding capacity against an antigen. This chapter discusses important elements in standardization of the RSV-specific microneutralization assay for use in the laboratory.

Man and the chimaera. Selective versus neutral oxytocin evolution.

PubMed

Acher, R; Chauvet, J; Chauvet, M T

1995-01-01

The oxytocin/vasopressin superfamily encompasses vertebrate and invertebrate peptides and therefore the ancestral gene encoding the precursor protein antedates the divergence between the two groups, about 700 million years ago. The preserved nonapeptide pattern indicates that both the precursor structures and the processing enzymatic machinery were greatly conserved to ensure the building of a specific conformation. Substitutions, which may be neutral or selective, occurred in precise positions. Virtually all vertebrate species possess an oxytocin-like and a vasopressin-like peptide so that two evolutionary lineages can be traced. Because a single peptide, vasotocin ([Ile3]-vasopressin or [Arg8]-oxytocin) has been found in the most primitive Cyclostomata, a primordial gene duplication and subsequent mutations are assumed to have given rise to the two lineages. They started with vasotocin and isotocin ([Ser4,Ile8]-oxytocin) in bony fishes and culminated with vasopressin and oxytocin in placental mammals. Mesotocin ([Ile3]-oxytocin), found in lungfishes, amphibians, reptiles, birds and marsupials, appears as an evolutionary intermediate. The change from isotocin ([Ser4,Ile8]-oxytocin) into mesotocin ([Ile8]-oxytocin), can be observed in African and Australian lungfishes, species making the transition from bony fishes to land vertebrates. On the other hand the replacement of mesotocin by oxytocin can be detected in marsupials, particularly in the North-American opossum and the Australian Northern bandicoot that have both mesotocin and oxytocin whereas placental mammals possess only oxytocin. The invariability of this peptide in placentals can be explained by receptor-fitting selective pressure. In contrast to bony vertebrates in which neurohypophysial hormones revealed a remarkable structural stability, cartilaginous fishes displayed an unique oxytocin-like hormone evolution with variability and duality. Aside from vasotocin, in the subclass Selachii, rays have glumitocin ([Gln8-oxytocin]) and sharks possess two peptides: aspargtocin ([Asn4-oxytocin]) and valitocin ([Val8-oxytocin]) for the spiny dogfish, asvatocin ([Asn4,Val8]-oxytocin) and phasvatocin ([Phe3,Asn4,Val8]-oxytocin) for the spotted dogfish. In the other subclass Holocephali, the chimaera (ratfish) has oxytocin, the typical hormone of placental mammals. Cartilaginous fishes used urea rather than salts for their osmoregulation and oxytocin-like hormones could have been relieved from osmoregulatory functions and able to accept many neutral variations.

Antigenic Properties of the HIV Envelope on Virions in Solution

PubMed Central

Mengistu, Meron; Lewis, George K.; Lakowicz, Joseph R.

2014-01-01

The structural flexibility found in human immunodeficiency virus (HIV) envelope glycoproteins creates a complex relationship between antigenicity and sensitivity to antiviral antibodies. The study of this issue in the context of viral particles is particularly problematic as conventional virus capture approaches can perturb antigenicity profiles. Here, we employed a unique analytical system based on fluorescence correlation spectroscopy (FCS), which measures antibody-virion binding with all reactants continuously in solution. Panels of nine anti-envelope monoclonal antibodies (MAbs) and five virus types were used to connect antibody binding profiles with neutralizing activities. Anti-gp120 MAbs against the 2G12 or b12 epitope, which marks functional envelope structures, neutralized viruses expressing CCR5-tropic envelopes and exhibited efficient virion binding in solution. MAbs against CD4-induced (CD4i) epitopes considered hidden on functional envelope structures poorly bound these viruses and were not neutralizing. Anti-gp41 MAb 2F5 was neutralizing despite limited virion binding. Similar antigenicity patterns occurred on CXCR4-tropic viruses, except that anti-CD4i MAbs 17b and 19e were neutralizing despite little or no virion binding. Notably, anti-gp120 MAb PG9 and anti-gp41 MAb F240 bound to both CCR5-tropic and CXCR4-tropic viruses without exerting neutralizing activity. Differences in the virus production system altered the binding efficiencies of some antibodies but did not enhance antigenicity of aberrant gp120 structures. Of all viruses tested, only JRFL pseudoviruses showed a direct relationship between MAb binding efficiency and neutralizing potency. Collectively, these data indicate that the antigenic profiles of free HIV particles generally favor the exposure of functional over aberrant gp120 structures. However, the efficiency of virion-antibody interactions in solution inconsistently predicts neutralizing activity in vitro. PMID:24284318

Two photon absorption laser induced fluorescence measurements of neutral density in a helicon plasma

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galante, M. E.; Magee, R. M.; Scime, E. E.

2014-05-15

We have developed a new diagnostic based on two-photon absorption laser induced fluorescence (TALIF). We use a high intensity (5 MW/cm{sup 2}), narrow bandwidth (0.1 cm{sup −1}) laser to probe the ground state of neutral hydrogen, deuterium and krypton with spatial resolution better than 0.2 cm, a time resolution of 10 ns, and a measurement cadence of 20 Hz. Here, we describe proof-of-principle measurements in a helicon plasma source that demonstrate the TALIF diagnostic is capable of measuring neutral densities spanning four orders of magnitude; comparable to the edge neutral gradients predicted in the DIII-D tokamak pedestal. The measurements are performed in hydrogen and deuteriummore » plasmas and absolute calibration is accomplished through TALIF measurements in neutral krypton. The optical configuration employed is confocal, i.e., both light injection and collection are accomplished with a single lens through a single optical port in the vacuum vessel. The wavelength resolution of the diagnostic is sufficient to separate hydrogen and deuterium spectra and we present measurements from mixed hydrogen and deuterium plasmas that demonstrate isotopic abundance measurements are feasible. Time resolved measurements also allow us to explore the evolution of the neutral hydrogen density and temperature and effects of wall recycling. We find that the atomic neutral density grows rapidly at the initiation of the discharge, reaching the steady-state value within 1 ms. Additionally, we find that neutral hydrogen atoms are born with 0.08 eV temperatures, not 2 eV as is typically assumed.« less

Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization.

PubMed

Gout, Jean-Francois; Lynch, Michael

2015-08-01

Whole-genome duplications (WGDs) have contributed to gene-repertoire enrichment in many eukaryotic lineages. However, most duplicated genes are eventually lost and it is still unclear why some duplicated genes are evolutionary successful whereas others quickly turn to pseudogenes. Here, we show that dosage constraints are major factors opposing post-WGD gene loss in several Paramecium species that share a common ancestral WGD. We propose a model where a majority of WGD-derived duplicates preserve their ancestral function and are retained to produce enough of the proteins performing this same ancestral function. Under this model, the expression level of individual duplicated genes can evolve neutrally as long as they maintain a roughly constant summed expression, and this allows random genetic drift toward uneven contributions of the two copies to total expression. Our analysis suggests that once a high level of imbalance is reached, which can require substantial lengths of time, the copy with the lowest expression level contributes a small enough fraction of the total expression that selection no longer opposes its loss. Extension of our analysis to yeast species sharing a common ancestral WGD yields similar results, suggesting that duplicated-gene retention for dosage constraints followed by divergence in expression level and eventual deterministic gene loss might be a universal feature of post-WGD evolution. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Control of power, torque, and instability drive using in-shot variable neutral beam energy in tokamaks

DOE PAGES

Pace, D. C.; Collins, C. S.; Crowley, B.; ...

2016-09-28

A first-ever demonstration of controlling power and torque injection through time evolution of neutral beam energy has been achieved in recent experiments at the DIII-D tokamak. Pre-programmed waveforms for the neutral beam energy produce power and torque inputs that can be separately and continuously controlled. Previously, these inputs were tailored using on/off modulation of neutral beams resulting in large perturbations (e.g. power swings of over 1 MW). The new method includes, importantly for experiments, the ability to maintain a fixed injected power while varying the torque. In another case, different beam energy waveforms (in the same plasma conditions) produce significantmore » changes in the observed spectrum of beam ion-driven instabilities. Measurements of beam ion loss show that one energy waveform results in the complete avoidance of coherent losses due to Alfvénic instabilities. This new method of neutral beam operation is intended for further application in a variety of DIII-D experiments including those concerned with high-performance steady state scenarios, fast particle effects, and transport in the low torque regime. As a result, developing this capability would provide similar benefits and improved plasma control for other magnetic confinement fusion facilities.« less

Control of power, torque, and instability drive using in-shot variable neutral beam energy in tokamaks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pace, D. C.; Collins, C. S.; Crowley, B.

A first-ever demonstration of controlling power and torque injection through time evolution of neutral beam energy has been achieved in recent experiments at the DIII-D tokamak. Pre-programmed waveforms for the neutral beam energy produce power and torque inputs that can be separately and continuously controlled. Previously, these inputs were tailored using on/off modulation of neutral beams resulting in large perturbations (e.g. power swings of over 1 MW). The new method includes, importantly for experiments, the ability to maintain a fixed injected power while varying the torque. In another case, different beam energy waveforms (in the same plasma conditions) produce significantmore » changes in the observed spectrum of beam ion-driven instabilities. Measurements of beam ion loss show that one energy waveform results in the complete avoidance of coherent losses due to Alfvénic instabilities. This new method of neutral beam operation is intended for further application in a variety of DIII-D experiments including those concerned with high-performance steady state scenarios, fast particle effects, and transport in the low torque regime. As a result, developing this capability would provide similar benefits and improved plasma control for other magnetic confinement fusion facilities.« less

Control of power, torque, and instability drive using in-shot variable neutral beam energy in tokamaks

NASA Astrophysics Data System (ADS)

Pace, D. C.; Collins, C. S.; Crowley, B.; Grierson, B. A.; Heidbrink, W. W.; Pawley, C.; Rauch, J.; Scoville, J. T.; Van Zeeland, M. A.; Zhu, Y. B.; The DIII-D Team

2017-01-01

A first-ever demonstration of controlling power and torque injection through time evolution of neutral beam energy has been achieved in recent experiments at the DIII-D tokamak (Luxon 2002 Nucl. Fusion 42 614). Pre-programmed waveforms for the neutral beam energy produce power and torque inputs that can be separately and continuously controlled. Previously, these inputs were tailored using on/off modulation of neutral beams resulting in large perturbations (e.g. power swings of over 1 MW). The new method includes, importantly for experiments, the ability to maintain a fixed injected power while varying the torque. In another case, different beam energy waveforms (in the same plasma conditions) produce significant changes in the observed spectrum of beam ion-driven instabilities. Measurements of beam ion loss show that one energy waveform results in the complete avoidance of coherent losses due to Alfvénic instabilities. This new method of neutral beam operation is intended for further application in a variety of DIII-D experiments including those concerned with high-performance steady state scenarios, fast particle effects, and transport in the low torque regime. Developing this capability would provide similar benefits and improved plasma control for other magnetic confinement fusion facilities.

Cyber Charter Schools: Evolution, Issues, and Opportunities in Funding and Localized Oversight

ERIC Educational Resources Information Center

Ellis, Kathleen

2008-01-01

Cyber schools, also known as virtual schools, are noteworthy charter school developments that provide viable options for education. Charter schools in general and cyber charter schools in particular are not "revenue neutral" to local school districts. Nationwide, hundreds of millions of dollars allocated for education are being routed…

The evolution of newcastle disease virus of low virulence

USDA-ARS?s Scientific Manuscript database

Newcastle disease viruses (NDVs) are also known as avian paramyxoviruses of serotype-1 (APMV-1). All NDVs (or APMV-1) are in one serotype and, by definition, antibodies produced from an exposure to any NDV will neutralize any other NDV. However, not all NDV (or APMV-1) cause Newcastle disease (ND)...

Electrical conductivity of In2O3 and Ga2O3 after low temperature ion irradiation; implications for instrinsic defect formation and charge neutrality level.

PubMed

Vines, L; Bhoodoo, C; von Wenckstern, H; Grundmann, M

2017-12-13

The evolution of sheet resistance of n-type In 2 O 3 and Ga 2 O 3 exposed to bombardment with MeV 12 C and 28 Si ions at 35 K is studied in situ. While the sheet resistance of Ga 2 O 3 increased by more than eight orders of magnitude as a result of ion irradiation, In 2 O 3 showed a more complex defect evolution and became more conductive when irradiated at the highest doses. Heating up to room temperature reduced the sheet resistivity somewhat, but Ga 2 O 3 remained highly resistive, while In 2 O 3 showed a lower resistance than as deposited samples. Thermal admittance spectroscopy and deep level transient spectroscopy did not reveal new defect levels for irradiation up to [Formula: see text] cm -2 . A model where larger defect complexes preferentially produce donor like defects in In 2 O 3 is proposed, and may reveal a microscopic view of a charge neutrality level within the conduction band, as previously proposed.

Electrical conductivity of In2O3 and Ga2O3 after low temperature ion irradiation; implications for instrinsic defect formation and charge neutrality level

NASA Astrophysics Data System (ADS)

Vines, L.; Bhoodoo, C.; von Wenckstern, H.; Grundmann, M.

2018-01-01

The evolution of sheet resistance of n-type In2O3 and Ga2O3 exposed to bombardment with MeV 12C and 28Si ions at 35 K is studied in situ. While the sheet resistance of Ga2O3 increased by more than eight orders of magnitude as a result of ion irradiation, In2O3 showed a more complex defect evolution and became more conductive when irradiated at the highest doses. Heating up to room temperature reduced the sheet resistivity somewhat, but Ga2O3 remained highly resistive, while In2O3 showed a lower resistance than as deposited samples. Thermal admittance spectroscopy and deep level transient spectroscopy did not reveal new defect levels for irradiation up to 2 × 1012 cm-2. A model where larger defect complexes preferentially produce donor like defects in In2O3 is proposed, and may reveal a microscopic view of a charge neutrality level within the conduction band, as previously proposed.

MCMC genome rearrangement.

PubMed

Miklós, István

2003-10-01

As more and more genomes have been sequenced, genomic data is rapidly accumulating. Genome-wide mutations are believed more neutral than local mutations such as substitutions, insertions and deletions, therefore phylogenetic investigations based on inversions, transpositions and inverted transpositions are less biased by the hypothesis on neutral evolution. Although efficient algorithms exist for obtaining the inversion distance of two signed permutations, there is no reliable algorithm when both inversions and transpositions are considered. Moreover, different type of mutations happen with different rates, and it is not clear how to weight them in a distance based approach. We introduce a Markov Chain Monte Carlo method to genome rearrangement based on a stochastic model of evolution, which can estimate the number of different evolutionary events needed to sort a signed permutation. The performance of the method was tested on simulated data, and the estimated numbers of different types of mutations were reliable. Human and Drosophila mitochondrial data were also analysed with the new method. The mixing time of the Markov Chain is short both in terms of CPU times and number of proposals. The source code in C is available on request from the author.

Bacterial evolution through the selective loss of beneficial Genes. Trade-offs in expression involving two loci.

PubMed Central

Zinser, Erik R; Schneider, Dominique; Blot, Michel; Kolter, Roberto

2003-01-01

The loss of preexisting genes or gene activities during evolution is a major mechanism of ecological specialization. Evolutionary processes that can account for gene loss or inactivation have so far been restricted to one of two mechanisms: direct selection for the loss of gene activities that are disadvantageous under the conditions of selection (i.e., antagonistic pleiotropy) and selection-independent genetic drift of neutral (or nearly neutral) mutations (i.e., mutation accumulation). In this study we demonstrate with an evolved strain of Escherichia coli that a third, distinct mechanism exists by which gene activities can be lost. This selection-dependent mechanism involves the expropriation of one gene's upstream regulatory element by a second gene via a homologous recombination event. Resulting from this genetic exchange is the activation of the second gene and a concomitant inactivation of the first gene. This gene-for-gene expression tradeoff provides a net fitness gain, even if the forfeited activity of the first gene can play a positive role in fitness under the conditions of selection. PMID:12930738

3D ordered porous MoxC (x = 1 or 2) for advanced hydrogen evolution and Li storage.

PubMed

Yu, Hong; Fan, Haosen; Wang, Jiong; Zheng, Yun; Dai, Zhengfei; Lu, Yizhong; Kong, Junhua; Wang, Xin; Kim, Young Jin; Yan, Qingyu; Lee, Jong-Min

2017-06-01

3D ordered porous structures of Mo x C are prepared with different Mo to C ratios and tested for two possible promising applications: hydrogen evolution reaction (HER) through water splitting and lithium ion batteries (LIBs). Mo 2 C and MoC with 3D periodic ordered structures are prepared with a similar process but different precursors. The 3D ordered porous MoC exhibits excellent cycling stability and rate performance as an anode material for LIBs. A discharge capacity of 450.9 mA h g -1 is maintained up to 3000 cycles at 10.0 A g -1 . The Mo 2 C with a similar ordered porous structure shows impressive electrocatalytic activity for the HER in neutral, alkaline and acidic pH solutions. In particular, Mo 2 C shows an onset potential of only 33 mV versus a reversible hydrogen electrode (RHE) and a Tafel slope of 42.5 mV dec -1 in a neutral aqueous solution (1.0 M phosphate buffer solution), which is approaching that of the commercial Pt/C catalyst.

Chloroplast DNA analysis of Tunisian cork oak populations (Quercus suber L.): sequence variations and molecular evolution of the trnL (UAA)-trnF (GAA) region.

PubMed

Abdessamad, A; Baraket, G; Sakka, H; Ammari, Y; Ksontini, M; Hannachi, A Salhi

2016-10-24

Sequences of the trnL-trnF spacer and combined trnL-trnF region in chloroplast DNA of cork oak (Quercus suber L.) were analyzed to detect polymorphisms and to elucidate molecular evolution and demographic history. The aligned sequences varied in length and nucleotide composition. The overall ratio of transition/transversion (ti/tv) of 0.724 for the intergenic spacer and 0.258 for the pooled sequences were estimated, and indicated that transversions are more frequent than transitions. The molecular evolution and demographic history of Q. suber were investigated. Neutrality tests (Tajima's D and Fu and Li) ruled out the null hypothesis of a strictly neutral model, and Fu's Fs and Ramos-Onsins and Rozas' R2 confirmed the recent expansion of cork oak trees, validating its persistency in North Africa since the last glaciation during the Quaternary. The observed uni-modal mismatch distribution and the Harpending's raggedness index confirmed the demographic history model for cork oak. A phylogenetic dendrogram showed that the distribution of Q. suber trees occurs independently of geographical origin, the relief of the population site, and the bioclimatic stages. The molecular history and cytoplasmic diversity suggest that in situ and ex situ conservation strategies can be recommended for preserving landscape value and facing predictable future climatic changes.

The evolution of the competition-dispersal trade-off affects α- and β-diversity in a heterogeneous metacommunity.

PubMed

Laroche, Fabien; Jarne, Philippe; Perrot, Thomas; Massol, Francois

2016-04-27

Difference in dispersal ability is a key driver of species coexistence in metacommunities. However, the available frameworks for interpreting species diversity patterns in natura often overlook trade-offs and evolutionary constraints associated with dispersal. Here, we build a metacommunity model accounting for dispersal evolution and a competition-dispersal trade-off. Depending on the distribution of carrying capacities among communities, species dispersal values are distributed either around a single strategy (evolutionarily stable strategy, ESS), or around distinct strategies (evolutionary branching, EB). We show that limited dispersal generates spatial aggregation of dispersal traits in ESS and EB scenarios, and that the competition-dispersal trade-off strengthens the pattern in the EB scenario. Importantly, individuals in larger (respectively (resp.) smaller) communities tend to harbour lower (resp. higher) dispersal, especially under the EB scenario. We explore how dispersal evolution affects species diversity patterns by comparing those from our model to the predictions of a neutral metacommunity model. The most marked difference is detected under EB, with distinctive values of both α- and β-diversity (e.g. the dissimilarity in species composition between small and large communities was significantly larger than neutral predictions). We conclude that, from an empirical perspective, jointly assessing community carrying capacity with species dispersal strategies should improve our understanding of diversity patterns in metacommunities. © 2016 The Author(s).

Ionized and Neutral Outflows in the QUEST QSOs

NASA Astrophysics Data System (ADS)

Veilleux, Sylvain

2011-10-01

The role of galactic winds in gas-rich mergers is of crucial importance to understand galaxy and SMBH evolution. In recent months, our group has had three major scientific breakthroughs in this area: {1} The discovery with Herschel of massive molecular {OH-absorbing} outflows in several ULIRGs, including the nearest quasar, Mrk 231. {2} The independent discovery from mm-wave interferometric observations in the same object of a spatially resolved molecular {CO-emitting} wind with estimated mass outflow rate 3x larger than the star formation rate and spatially coincident with blueshifted neutral {Na ID-absorbing} gas in optical long-slit spectra. {3} The unambiguous determination from recent Gemini/IFU observations that the Na ID outflow in this object is wide-angle, thus driven by a QSO wind rather than a jet. This powerful outflow may be the long-sought "smoking gun" of quasar mechanical feedback purported to transform gas-rich mergers. However, our Herschel survey excludes all FIR-faint {UV-bright} "classic" QSOs by necessity. So here we propose a complementary FUV absorption-line survey of all FIR-bright -and- FIR-faint QSOs from the same parent sample. New {19 targets} and archival {11} spectra will be used to study, for the first time, the gaseous environments of QSOs as a function of host properties and age across the merger sequence ULIRG -> QSO. These data will allow us to distinguish between ionized & neutral quasar-driven outflows, starburst-driven winds, and tidal debris around the mergers. They will also be uniquely suited for a shallow but broad study of the warm & warm-hot intergalactic media, complementary to on-going surveys that are deeper but narrower.

Selective intra-dinucleotide interactions and periodicities of bases separated by K sites: a new vision and tool for phylogeny analyses.

PubMed

Valenzuela, Carlos Y

2017-02-13

Direct tests of the random or non-random distribution of nucleotides on genomes have been devised to test the hypothesis of neutral, nearly-neutral or selective evolution. These tests are based on the direct base distribution and are independent of the functional (coding or non-coding) or structural (repeated or unique sequences) properties of the DNA. The first approach described the longitudinal distribution of bases in tandem repeats under the Bose-Einstein statistics. A huge deviation from randomness was found. A second approach was the study of the base distribution within dinucleotides whose bases were separated by 0, 1, 2… K nucleotides. Again an enormous difference from the random distribution was found with significances out of tables and programs. These test values were periodical and included the 16 dinucleotides. For example a high "positive" (more observed than expected dinucleotides) value, found in dinucleotides whose bases were separated by (3K + 2) sites, was preceded by two smaller "negative" (less observed than expected dinucleotides) values, whose bases were separated by (3K) or (3K + 1) sites. We examined mtDNAs, prokaryote genomes and some eukaryote chromosomes and found that the significant non-random interactions and periodicities were present up to 1000 or more sites of base separation and in human chromosome 21 until separations of more than 10 millions sites. Each nucleotide has its own significant value of its distance to neutrality; this yields 16 hierarchical significances. A three dimensional table with the number of sites of separation between the bases and the 16 significances (the third dimension is the dinucleotide, individual or taxon involved) gives directly an evolutionary state of the analyzed genome that can be used to obtain phylogenies. An example is provided.

How the charge-neutrality level of interface states controls energy level alignment in cathode contacts of organic bulk-heterojunction solar cells.

PubMed

Guerrero, Antonio; Marchesi, Luís F; Boix, Pablo P; Ruiz-Raga, Sonia; Ripolles-Sanchis, Teresa; Garcia-Belmonte, Germà; Bisquert, Juan

2012-04-24

Electronic equilibration at the metal-organic interface, leading to equalization of the Fermi levels, is a key process in organic optoelectronic devices. How the energy levels are set across the interface determines carrier extraction at the contact and also limits the achievable open-circuit voltage under illumination. Here, we report an extensive investigation of the cathode energy equilibration of organic bulk-heterojunction solar cells. We show that the potential to balance the mismatch between the cathode metal and the organic layer Fermi levels is divided into two contributions: spatially extended band bending in the organic bulk and voltage drop at the interface dipole layer caused by a net charge transfer. We scan the operation of the cathode under a varied set of conditions, using metals of different work functions in the range of ∼2 eV, different fullerene acceptors, and several cathode interlayers. The measurements allow us to locate the charge-neutrality level within the interface density of sates and calculate the corresponding dipole layer strength. The dipole layer withstands a large part of the total Fermi level mismatch when the polymer:fullerene blend ratio approaches ∼1:1, producing the practical alignment between the metal Fermi level and the charge-neutrality level. Origin of the interface states is linked with fullerene reduced molecules covering the metal contact. The dipole contribution, and consequently the band bending, is highly sensitive to the nature and amount of fullerene molecules forming the interface density of states. Our analysis provides a detailed picture of the evolution of the potentials in the bulk and the interface of the solar cell when forward voltage is applied or when photogeneration takes place.

Troubling Neutrality: Toward a Philosophy of Teacher Ambiguity

ERIC Educational Resources Information Center

Heybach, Jessica A.

2014-01-01

Who is keeping watch to warn when policies and practices become essentially the same as those used in previous eras to justify the destruction of human beings? This question is asked by author Jessica Heybach, as she describes the etymological roots of the word "neutrality," the social function of teacher as neutral, and its relationship…

On the pair correlations of neutral K, D, B and BS mesons with close momenta produced in inclusive multiparticle processes

NASA Astrophysics Data System (ADS)

Lyuboshitz, Valery V.; Lyuboshitz, Vladimir L.

2016-04-01

The phenomenological structure of inclusive cross-sections of the production of two neutral K mesons in collisions of hadrons and nuclei is investigated taking into account the strangeness conservation in strong and electromagnetic interactions. Relations describing the dependenceof the correlations of two short-lived and two long-lived neutral kaons KS∘ KS∘, KL∘ KL∘ and the correlations of ;mixed; pairs KS∘ KL∘ at small relative momenta upon the space-time parameters of the generation region of K∘ and Kbar∘ mesons have been obtained. It is shown that under the strangeness conservation the correlation functions of the pairs KS∘ KS∘ and KL∘ KL∘, produced in the same inclusive process, coincide, and the difference between the correlation functions of the pairs KS∘ KS∘ and KS∘ KL∘ is conditioned exclusively by the production of the pairs of non-identical neutral kaons K∘Kbar∘. Analogous correlations for the pairs of neutral heavy mesons D∘ ,B∘ and BS∘, generated in multiple processes with the charm (beauty) conservation, are analyzed, and differences from the case of neutral K mesons are discussed.

Sex reduces genetic variation: a multidisciplinary review.

PubMed

Gorelick, Root; Heng, Henry H Q

2011-04-01

For over a century, the paradigm has been that sex invariably increases genetic variation, despite many renowned biologists asserting that sex decreases most genetic variation. Sex is usually perceived as the source of additive genetic variance that drives eukaryotic evolution vis-à-vis adaptation and Fisher's fundamental theorem. However, evidence for sex decreasing genetic variation appears in ecology, paleontology, population genetics, and cancer biology. The common thread among many of these disciplines is that sex acts like a coarse filter, weeding out major changes, such as chromosomal rearrangements (that are almost always deleterious), but letting minor variation, such as changes at the nucleotide or gene level (that are often neutral), flow through the sexual sieve. Sex acts as a constraint on genomic and epigenetic variation, thereby limiting adaptive evolution. The diverse reasons for sex reducing genetic variation (especially at the genome level) and slowing down evolution may provide a sufficient benefit to offset the famed costs of sex. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Integrated Multiregional Analysis Proposing a New Model of Colorectal Cancer Evolution.

PubMed

Uchi, Ryutaro; Takahashi, Yusuke; Niida, Atsushi; Shimamura, Teppei; Hirata, Hidenari; Sugimachi, Keishi; Sawada, Genta; Iwaya, Takeshi; Kurashige, Junji; Shinden, Yoshiaki; Iguchi, Tomohiro; Eguchi, Hidetoshi; Chiba, Kenichi; Shiraishi, Yuichi; Nagae, Genta; Yoshida, Kenichi; Nagata, Yasunobu; Haeno, Hiroshi; Yamamoto, Hirofumi; Ishii, Hideshi; Doki, Yuichiro; Iinuma, Hisae; Sasaki, Shin; Nagayama, Satoshi; Yamada, Kazutaka; Yachida, Shinichi; Kato, Mamoru; Shibata, Tatsuhiro; Oki, Eiji; Saeki, Hiroshi; Shirabe, Ken; Oda, Yoshinao; Maehara, Yoshihiko; Komune, Shizuo; Mori, Masaki; Suzuki, Yutaka; Yamamoto, Ken; Aburatani, Hiroyuki; Ogawa, Seishi; Miyano, Satoru; Mimori, Koshi

2016-02-01

Understanding intratumor heterogeneity is clinically important because it could cause therapeutic failure by fostering evolutionary adaptation. To this end, we profiled the genome and epigenome in multiple regions within each of nine colorectal tumors. Extensive intertumor heterogeneity is observed, from which we inferred the evolutionary history of the tumors. First, clonally shared alterations appeared, in which C>T transitions at CpG site and CpG island hypermethylation were relatively enriched. Correlation between mutation counts and patients' ages suggests that the early-acquired alterations resulted from aging. In the late phase, a parental clone was branched into numerous subclones. Known driver alterations were observed frequently in the early-acquired alterations, but rarely in the late-acquired alterations. Consistently, our computational simulation of the branching evolution suggests that extensive intratumor heterogeneity could be generated by neutral evolution. Collectively, we propose a new model of colorectal cancer evolution, which is useful for understanding and confronting this heterogeneous disease.

Physical Model for the Evolution of the Genetic Code

NASA Astrophysics Data System (ADS)

Yamashita, Tatsuro; Narikiyo, Osamu

2011-12-01

Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our description, a physical quantity, codon level is introduced. In terms of the codon levels two scenarios are typically classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform an evolutional simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario. In the case of the codon capture scenario the survival against mutations under the mutational pressure minimizing GC content in genomes is simulated and it is demonstrated that cells which experience only neutral mutations survive.

Benchmark study on glyphosate-resistant cropping systems in the United States. Part 6: Timeliness of economic decision-making in implementing weed resistance management strategies.

PubMed

Weirich, Jason W; Shaw, David R; Coble, Keith H; Owen, Micheal D K; Dixon, Philip M; Weller, Stephen C; Young, Bryan G; Wilson, Robert G; Jordan, David L

2011-07-01

The introduction of glyphosate-resistant (GR) crops in the late 1990s made weed control in maize, cotton and soybean simple. With the rapid adoption of GR crops, many growers began to rely solely on glyphosate for weed control. This eventually led to the evolution of GR weeds. Growers are often reluctant to adopt a weed resistance best management practice (BMP) because of the added cost of additional herbicides to weed control programs which would reduce short-term revenue. This study was designed to evaluate when a grower that is risk neutral (profit maximizing) or risk averse should adopt a weed resistance BMP. Whether a grower is risk neutral or risk averse, the optimal decision would be to adopt a weed resistance BMP when the expected loss in revenue is greater than 30% and the probability of resistance evolution is 0.1 or greater. However, if the probability of developing resistance increases to 0.3, then the best decision would be to adopt a weed resistance BMP when the expected loss is 10% or greater. Given the scenarios analyzed, risk-neutral or risk-averse growers should implement a weed resistance BMP with confidence that they have made the right decision economically and avoided the risk of lost revenue from resistance. If the grower wants to continue to see the same level of return, adoption of BMP is required. Copyright © 2011 Society of Chemical Industry.

Contrasting patterns of diversity and population differentiation at the innate immunity gene toll-like receptor 2 (TLR2) in two sympatric rodent species.

PubMed

Tschirren, Barbara; Andersson, Martin; Scherman, Kristin; Westerdahl, Helena; Råberg, Lars

2012-03-01

Comparing patterns of diversity and divergence between populations at immune genes and neutral markers can give insights into the nature and geographic scale of parasite-mediated selection. To date, studies investigating such patterns of selection in vertebrates have primarily focused on the acquired branch of the immune system, whereas it remains largely unknown how parasite-mediated selection shapes innate immune genes both within and across vertebrate populations. Here, we present a study on the diversity and population differentiation at the innate immune gene Toll-like receptor 2 (TLR2) across nine populations of yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) in southern Sweden. In yellow-necked mice, TLR2 diversity was very low, as was TLR2 population differentiation compared to neutral loci. In contrast, several TLR2 haplotypes co-occurred at intermediate frequencies within and across bank vole populations, and pronounced isolation by distance between populations was observed. The diversity and differentiation at neutral loci was similar in the two species. These results indicate that parasite-mediated selection has been acting in dramatically different ways on a given immune gene in ecologically similar and sympatric species. Furthermore, the finding of TLR2 population differentiation at a small geographical scale in bank voles highlights that vertebrate innate immune defense may be evolutionarily more dynamic than has previously been appreciated. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Dust cloud evolution in sub-stellar atmospheres via plasma deposition and plasma sputtering

NASA Astrophysics Data System (ADS)

Stark, C. R.; Diver, D. A.

2018-04-01

Context. In contemporary sub-stellar model atmospheres, dust growth occurs through neutral gas-phase surface chemistry. Recently, there has been a growing body of theoretical and observational evidence suggesting that ionisation processes can also occur. As a result, atmospheres are populated by regions composed of plasma, gas and dust, and the consequent influence of plasma processes on dust evolution is enhanced. Aim. This paper aims to introduce a new model of dust growth and destruction in sub-stellar atmospheres via plasma deposition and plasma sputtering. Methods: Using example sub-stellar atmospheres from DRIFT-PHOENIX, we have compared plasma deposition and sputtering timescales to those from neutral gas-phase surface chemistry to ascertain their regimes of influence. We calculated the plasma sputtering yield and discuss the circumstances where plasma sputtering dominates over deposition. Results: Within the highest dust density cloud regions, plasma deposition and sputtering dominates over neutral gas-phase surface chemistry if the degree of ionisation is ≳10-4. Loosely bound grains with surface binding energies of the order of 0.1-1 eV are susceptible to destruction through plasma sputtering for feasible degrees of ionisation and electron temperatures; whereas, strong crystalline grains with binding energies of the order 10 eV are resistant to sputtering. Conclusions: The mathematical framework outlined sets the foundation for the inclusion of plasma deposition and plasma sputtering in global dust cloud formation models of sub-stellar atmospheres.

Does population size affect genetic diversity? A test with sympatric lizard species.

PubMed

Hague, M T J; Routman, E J

2016-01-01

Genetic diversity is a fundamental requirement for evolution and adaptation. Nonetheless, the forces that maintain patterns of genetic variation in wild populations are not completely understood. Neutral theory posits that genetic diversity will increase with a larger effective population size and the decreasing effects of drift. However, the lack of compelling evidence for a relationship between genetic diversity and population size in comparative studies has generated some skepticism over the degree that neutral sequence evolution drives overall patterns of diversity. The goal of this study was to measure genetic diversity among sympatric populations of related lizard species that differ in population size and other ecological factors. By sampling related species from a single geographic location, we aimed to reduce nuisance variance in genetic diversity owing to species differences, for example, in mutation rates or historical biogeography. We compared populations of zebra-tailed lizards and western banded geckos, which are abundant and short-lived, to chuckwallas and desert iguanas, which are less common and long-lived. We assessed population genetic diversity at three protein-coding loci for each species. Our results were consistent with the predictions of neutral theory, as the abundant species almost always had higher levels of haplotype diversity than the less common species. Higher population genetic diversity in the abundant species is likely due to a combination of demographic factors, including larger local population sizes (and presumably effective population sizes), faster generation times and high rates of gene flow with other populations.

Lineage-specific expansions of retroviral insertions within the genomes of African great apes but not humans and orangutans.

PubMed

Yohn, Chris T; Jiang, Zhaoshi; McGrath, Sean D; Hayden, Karen E; Khaitovich, Philipp; Johnson, Matthew E; Eichler, Marla Y; McPherson, John D; Zhao, Shaying; Pääbo, Svante; Eichler, Evan E

2005-04-01

Retroviral infections of the germline have the potential to episodically alter gene function and genome structure during the course of evolution. Horizontal transmissions between species have been proposed, but little evidence exists for such events in the human/great ape lineage of evolution. Based on analysis of finished BAC chimpanzee genome sequence, we characterize a retroviral element (Pan troglodytes endogenous retrovirus 1 [PTERV1]) that has become integrated in the germline of African great ape and Old World monkey species but is absent from humans and Asian ape genomes. We unambiguously map 287 retroviral integration sites and determine that approximately 95.8% of the insertions occur at non-orthologous regions between closely related species. Phylogenetic analysis of the endogenous retrovirus reveals that the gorilla and chimpanzee elements share a monophyletic origin with a subset of the Old World monkey retroviral elements, but that the average sequence divergence exceeds neutral expectation for a strictly nuclear inherited DNA molecule. Within the chimpanzee, there is a significant integration bias against genes, with only 14 of these insertions mapping within intronic regions. Six out of ten of these genes, for which there are expression data, show significant differences in transcript expression between human and chimpanzee. Our data are consistent with a retroviral infection that bombarded the genomes of chimpanzees and gorillas independently and concurrently, 3-4 million years ago. We speculate on the potential impact of such recent events on the evolution of humans and great apes.

Where is the Most Likely Location Where the Secondary Interstellar Oxygen Atoms Are Created Around the Heliosheath?

NASA Astrophysics Data System (ADS)

Park, J.; Kucharek, H.; Szabo, A.; Paschalidis, N.; Grocer, A.; Jones, S.

2017-12-01

The secondary component of the interstellar neutral gas flow is originated from charge exchange between the undisturbed primary interstellar neutrals and the ions that have been deflected as they approach the heliopause. The secondary neutrals that are emitted from the interstellar ion flow through charge exchange carry information on the diverted flow and a fraction of them can travel to the Sun. Therefore, the secondary component of the interstellar neutrals is an excellent diagnostic tool to provide important information to constrain the shape of the heliopause. The presence of the secondary neutrals was predicted in the global heliospheric models and they are observed by Interstellar Boundary Explorer (IBEX) at Earth's orbit. Using the IBEX observations of neutral helium atoms, Kubiak et al. (2016, ApJS, 223, 25) approximated the parent distribution of the secondary interstellar He atoms (so-called Warm Breeze) with a homogeneous Maxwellian distribution function. Park et al. (2016, ApJ, 833, 130) analyzed IBEX observations of secondary interstellar helium and oxygen distributions at Earth's orbit. Lee et al. (2012, ApJS, 198, 10) constructed the heliospheric phase-space distribution function of an interstellar gas species in the Earth frame as a function of solar longitude. In this distribution, the authors assume that the distribution is a drifting Maxwellian at large distances from the Sun. In this study, we assume that a fraction of the secondary neutral atoms has a velocity vector toward the Sun and they can be described as a flow with a drifting Maxwellian distribution near the heliopause. Unlike the primary interstellar gas flow, the distribution of the secondary neutrals is expected to have a wide width and their bulk speeds are slower than the bulk speed of the primary interstellar gas flow. We compare Lee's distribution and IBEX observations of neutral oxygen atoms and then estimate the most likely direction where the secondary interstellar oxygen atoms are created near the heliopause.

Dynamical Casimir-Polder force on a partially dressed atom near a conducting wall

DOE Office of Scientific and Technical Information (OSTI.GOV)

Messina, Riccardo; Vasile, Ruggero; Passante, Roberto

2010-12-15

We study the time evolution of the Casimir-Polder force acting on a neutral atom in front of a perfectly conducting plate, when the system starts its unitary evolution from a partially dressed state. We solve the Heisenberg equations for both atomic and field quantum operators, exploiting a series expansion with respect to the electric charge and an iterative technique. After discussing the behavior of the time-dependent force on an initially partially dressed atom, we analyze a possible experimental scheme to prepare the partially dressed state and the observability of this new dynamical effect.

Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion

DOE PAGES

Wang, Peng; Chang, Angela Y.; Novosad, Valentyn; ...

2017-06-11

We report on entirely man-made nanobio hybrid fabricated through assembly of cell-free expressed transmembrane proton pump and semiconductor nanoparticles as an efficient nanocatalysis for photocatalytic H 2 evolution. The system produces H 2 at a turnover rate of 239 (μmole protein) -1 h -1 under green and 17742 (μmole protein) -1 h -1 under white light at ambient conditions, in water at neutral pH with methanol as a sacrificial electron donor. Robustness and flexibility of this approach allows for systemic manipulation at nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.

Cell-Free Synthetic Biology Chassis for Nanocatalytic Photon-to-Hydrogen Conversion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Peng; Chang, Angela Y.; Novosad, Valentyn

We report on entirely man-made nanobio hybrid fabricated through assembly of cell-free expressed transmembrane proton pump and semiconductor nanoparticles as an efficient nanocatalysis for photocatalytic H 2 evolution. The system produces H 2 at a turnover rate of 239 (μmole protein) -1 h -1 under green and 17742 (μmole protein) -1 h -1 under white light at ambient conditions, in water at neutral pH with methanol as a sacrificial electron donor. Robustness and flexibility of this approach allows for systemic manipulation at nanoparticle-bio interface toward directed evolution of energy transformation materials and artificial systems.

Is a neutral expression also a neutral stimulus? A study with functional magnetic resonance.

PubMed

Carvajal, Fernando; Rubio, Sandra; Serrano, Juan M; Ríos-Lago, Marcos; Alvarez-Linera, Juan; Pacheco, Lara; Martín, Pilar

2013-08-01

Although neutral faces do not initially convey an explicit emotional message, it has been found that individuals tend to assign them an affective content. Moreover, previous research has shown that affective judgments are mediated by the task they have to perform. Using functional magnetic resonance imaging in 21 healthy participants, we focus this study on the cerebral activity patterns triggered by neutral and emotional faces in two different tasks (social or gender judgments). Results obtained, using conjunction analyses, indicated that viewing both emotional and neutral faces evokes activity in several similar brain areas indicating a common neural substrate. Moreover, neutral faces specifically elicit activation of cerebellum, frontal and temporal areas, while emotional faces involve the cuneus, anterior cingulated gyrus, medial orbitofrontal cortex, posterior superior temporal gyrus, precentral/postcentral gyrus and insula. The task selected was also found to influence brain activity, in that the social task recruited frontal areas while the gender task involved the posterior cingulated, inferior parietal lobule and middle temporal gyrus to a greater extent. Specifically, in the social task viewing neutral faces was associated with longer reaction times and increased activity of left dorsolateral frontal cortex compared with viewing facial expressions of emotions. In contrast, in the same task emotional expressions distinctively activated the left amygdale. The results are discussed taking into consideration the fact that, like other facial expressions, neutral expressions are usually assigned some emotional significance. However, neutral faces evoke a greater activation of circuits probably involved in more elaborate cognitive processing.

Work function measurements during plasma exposition at conditions relevant in negative ion sources for the ITER neutral beam injection.

PubMed

Gutser, R; Wimmer, C; Fantz, U

2011-02-01

Cesium seeded sources for surface generated negative hydrogen ions are major components of neutral beam injection systems in future large-scale fusion experiments such as ITER. The stability and delivered current density depend highly on the work function during vacuum and plasma phases of the ion source. One of the most important quantities that affect the source performance is the work function. A modified photocurrent method was developed to measure the temporal behavior of the work function during and after cesium evaporation. The investigation of cesium exposed Mo and MoLa samples under ITER negative hydrogen ion based neutral beam injection relevant surface and plasma conditions showed the influence of impurities which result in a fast degradation when the plasma exposure or the cesium flux onto the sample is stopped. A minimum work function close to that of bulk cesium was obtained under the influence of the plasma exposition, while a significantly higher work function was observed under ITER-like vacuum conditions.

Dissipative instability in a partially ionised prominence plasma slab

NASA Astrophysics Data System (ADS)

Ballai, I.; Pintér, B.; Oliver, R.; Alexandrou, M.

2017-07-01

Aims: We aim to investigate the nature of dissipative instability appearing in a prominence planar thread filled with partially ionised plasma in the incompressible limit. The importance of partial ionisation is investigated in terms of the ionisation factor and the wavelength of sausage and kink waves propagating in the slab. Methods: In order to highlight the role of partial ionisation, we have constructed models describing various situations we can meet in solar prominence fine structure. Matching the solutions for the transversal component of the velocity and total pressure at the interfaces between the prominence slab and surrounding plasmas, we derived a dispersion relation whose imaginary part describes the evolution of the instability. Results were obtained in the limit of weak dissipation. We have investigated the appearance of instabilities in prominence dark plumes using single and two-fluid approximations. Results: Using simple analytical methods, we show that dissipative instabilities appear for flow speeds that are less than the Kelvin-Helmholtz instability threshold. The onset of instability is determined by the equilibrium flow strength, the ionisation factor of the plasma, the wavelength of waves and the ion-neutral collisional rate. For a given wavelength and for ionisation degrees closer to a neutral gas, the propagating waves become unstable for a narrow band of flow speeds, meaning that neutrals have a stabilising effect. Our results show that the partially ionised plasma describing prominence dark plumes becomes unstable only in a two-fluid (charged particles-neutrals) model, that is for periods that are smaller than the ion-neutral collision time. Conclusions: The present study improves our understanding of the complexity of dynamical processes and stability of solar prominences and the role partial ionisation in destabilising the plasma. We showed the necessity of two-fluid approximation when discussing the nature of instabilities: waves in a single fluid approximation show a great deal of stability. Our results clearly show that the problem of partial ionisation introduces new aspects of plasma stability with consequences on the evolution of partially ionised plasmas and solar prominences, in particular.

A neutral functional differential equation of Lurie type. [on asymptotic stability of feedback control

NASA Technical Reports Server (NTRS)

Chukwu, E. N.

1980-01-01

The problem of Lurie is posed for systems described by a functional differential equation of neutral type. Sufficient conditions are obtained for absolute stability for the controlled system if it is assumed that the uncontrolled plant equation is uniformly asymptotically stable. Both the direct and indirect control cases are treated.

Global asymptotic stability to a generalized Cohen-Grossberg BAM neural networks of neutral type delays.

PubMed

Zhang, Zhengqiu; Liu, Wenbin; Zhou, Dongming

2012-01-01

In this paper, we first discuss the existence of a unique equilibrium point of a generalized Cohen-Grossberg BAM neural networks of neutral type delays by means of the Homeomorphism theory and inequality technique. Then, by applying the existence result of an equilibrium point and constructing a Lyapunov functional, we study the global asymptotic stability of the equilibrium solution to the above Cohen-Grossberg BAM neural networks of neutral type. In our results, the hypothesis for boundedness in the existing paper, which discussed Cohen-Grossberg neural networks of neutral type on the activation functions, are removed. Finally, we give an example to demonstrate the validity of our global asymptotic stability result for the above neural networks. Copyright © 2011 Elsevier Ltd. All rights reserved.

A functional magnetic resonance imaging investigation of short-term source and item memory for negative pictures.

PubMed

Mitchell, Karen J; Mather, Mara; Johnson, Marcia K; Raye, Carol L; Greene, Erich J

2006-10-02

We investigated the hypothesis that arousal recruits attention to item information, thereby disrupting working memory processes that help bind items to context. Using functional magnetic resonance imaging, we compared brain activity when participants remembered negative or neutral picture-location conjunctions (source memory) versus pictures only. Behaviorally, negative trials showed disruption of short-term source, but not picture, memory; long-term picture recognition memory was better for negative than for neutral pictures. Activity in areas involved in working memory and feature integration (precentral gyrus and its intersect with superior temporal gyrus) was attenuated on negative compared with neutral source trials relative to picture-only trials. Visual processing areas (middle occipital and lingual gyri) showed greater activity for negative than for neutral trials, especially on picture-only trials.

Discharge Characterization of 40 cm-Microwave ECR Ion Source and Neutralizer

NASA Technical Reports Server (NTRS)

Foster, John E.; Patterson, Michael J.; Britton, Melissa

2003-01-01

Discharge characteristics of a 40 cm, 2.45 GHz Electron Cyclotron Resonance (ECR) ion thruster discharge chamber and neutralizer were acquired. Thruster bulk discharge plasma characteristics were assessed using a single Langmuir probe. Total extractable ion current was measured as a function of input microwave power and flow rate. Additionally, radial ion current density profiles at the thruster.s exit plane were characterized using five equally spaced Faraday probes. Distinct low and high density operating modes were observed as discharge input power was varied from 0 to 200 W. In the high mode, extractable ion currents as high as 0.82 A were measured. Neutralizer emission current was characterized as a function of flow rate and microwave power. Neutralizer extraction currents as high as 0.6 A were measured.

Assessment of effects of neutrals on the power threshold for L to H transitions in DIII-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Owen, L.W.; Carreras, B.A.; Maingi, R.

1998-11-01

To assess the effect of edge neutrals on the low-to-high confinement transition threshold, a broad range of plasma discharges has been analyzed. From this analysis, the transition power divided by the density, at constant magnetic field, appears to be a function of a single parameter measuring the neutrals` effect. This results suggest that there is a missing parameter linked to the neutrals in the power threshold scaling laws.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

PubMed

Thybert, David; Roller, Maša; Navarro, Fábio C P; Fiddes, Ian; Streeter, Ian; Feig, Christine; Martin-Galvez, David; Kolmogorov, Mikhail; Janoušek, Václav; Akanni, Wasiu; Aken, Bronwen; Aldridge, Sarah; Chakrapani, Varshith; Chow, William; Clarke, Laura; Cummins, Carla; Doran, Anthony; Dunn, Matthew; Goodstadt, Leo; Howe, Kerstin; Howell, Matthew; Josselin, Ambre-Aurore; Karn, Robert C; Laukaitis, Christina M; Jingtao, Lilue; Martin, Fergal; Muffato, Matthieu; Nachtweide, Stefanie; Quail, Michael A; Sisu, Cristina; Stanke, Mario; Stefflova, Klara; Van Oosterhout, Cock; Veyrunes, Frederic; Ward, Ben; Yang, Fengtang; Yazdanifar, Golbahar; Zadissa, Amonida; Adams, David J; Brazma, Alvis; Gerstein, Mark; Paten, Benedict; Pham, Son; Keane, Thomas M; Odom, Duncan T; Flicek, Paul

2018-04-01

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroli and Mus pahari genomes. Together with the Mus musculus and Rattus norvegicus genomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculus and Mus caroli between 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli , which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology. © 2018 Thybert et al.; Published by Cold Spring Harbor Laboratory Press.

Analysis of Serine Codon Conservation Reveals Diverse Phenotypic Constraints on Hepatitis C Virus Glycoprotein Evolution

PubMed Central

Koutsoudakis, George; Urbanowicz, Richard A.; Mirza, Deeman; Ginkel, Corinne; Riebesehl, Nina; Calland, Noémie; Albecka, Anna; Price, Louisa; Hudson, Natalia; Descamps, Véronique; Backx, Matthijs; McClure, C. Patrick; Duverlie, Gilles; Pecheur, Eve-Isabelle; Dubuisson, Jean; Perez-del-Pulgar, Sofia; Forns, Xavier; Steinmann, Eike; Tarr, Alexander W.; Pietschmann, Thomas

2014-01-01

Serine is encoded by two divergent codon types, UCN and AGY, which are not interchangeable by a single nucleotide substitution. Switching between codon types therefore occurs via intermediates (threonine or cysteine) or via simultaneous tandem substitutions. Hepatitis C virus (HCV) chronically infects 2 to 3% of the global population. The highly variable glycoproteins E1 and E2 decorate the surface of the viral envelope, facilitate cellular entry, and are targets for host immunity. Comparative sequence analysis of globally sampled E1E2 genes, coupled with phylogenetic analysis, reveals the signatures of multiple archaic codon-switching events at seven highly conserved serine residues. Limited detection of intermediate phenotypes indicates that associated fitness costs restrict their fixation in divergent HCV lineages. Mutational pathways underlying codon switching were probed via reverse genetics, assessing glycoprotein functionality using multiple in vitro systems. These data demonstrate selection against intermediate phenotypes can act at the structural/functional level, with some intermediates displaying impaired virion assembly and/or decreased capacity for target cell entry. These effects act in residue/isolate-specific manner. Selection against intermediates is also provided by humoral targeting, with some intermediates exhibiting increased epitope exposure and enhanced neutralization sensitivity, despite maintaining a capacity for target cell entry. Thus, purifying selection against intermediates limits their frequencies in globally sampled strains, with divergent functional constraints at the protein level restricting the fixation of deleterious mutations. Overall our study provides an experimental framework for identification of barriers limiting viral substitutional evolution and indicates that serine codon-switching represents a genomic “fossil record” of historical purifying selection against E1E2 intermediate phenotypes. PMID:24173227

Enhanced vulnerability of human proteins towards disease-associated inactivation through divergent evolution.

PubMed

Medina-Carmona, Encarnación; Fuchs, Julian E; Gavira, Jose A; Mesa-Torres, Noel; Neira, Jose L; Salido, Eduardo; Palomino-Morales, Rogelio; Burgos, Miguel; Timson, David J; Pey, Angel L

2017-09-15

Human proteins are vulnerable towards disease-associated single amino acid replacements affecting protein stability and function. Interestingly, a few studies have shown that consensus amino acids from mammals or vertebrates can enhance protein stability when incorporated into human proteins. Here, we investigate yet unexplored relationships between the high vulnerability of human proteins towards disease-associated inactivation and recent evolutionary site-specific divergence of stabilizing amino acids. Using phylogenetic, structural and experimental analyses, we show that divergence from the consensus amino acids at several sites during mammalian evolution has caused local protein destabilization in two human proteins linked to disease: cancer-associated NQO1 and alanine:glyoxylate aminotransferase, mutated in primary hyperoxaluria type I. We demonstrate that a single consensus mutation (H80R) acts as a disease suppressor on the most common cancer-associated polymorphism in NQO1 (P187S). The H80R mutation reactivates P187S by enhancing FAD binding affinity through local and dynamic stabilization of its binding site. Furthermore, we show how a second suppressor mutation (E247Q) cooperates with H80R in protecting the P187S polymorphism towards inactivation through long-range allosteric communication within the structural ensemble of the protein. Our results support that recent divergence of consensus amino acids may have occurred with neutral effects on many functional and regulatory traits of wild-type human proteins. However, divergence at certain sites may have increased the propensity of some human proteins towards inactivation due to disease-associated mutations and polymorphisms. Consensus mutations also emerge as a potential strategy to identify structural hot-spots in proteins as targets for pharmacological rescue in loss-of-function genetic diseases. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Non-neutralized Electric Currents in Solar Active Regions and Flare Productivity

NASA Astrophysics Data System (ADS)

Kontogiannis, Ioannis; Georgoulis, Manolis K.; Park, Sung-Hong; Guerra, Jordan A.

2017-11-01

We explore the association of non-neutralized currents with solar flare occurrence in a sizable sample of observations, aiming to show the potential of such currents in solar flare prediction. We used the high-quality vector magnetograms that are regularly produced by the Helioseismic Magnetic Imager, and more specifically, the Space weather HMI Active Region Patches (SHARP). Through a newly established method that incorporates detailed error analysis, we calculated the non-neutralized currents contained in active regions (AR). Two predictors were produced, namely the total and the maximum unsigned non-neutralized current. Both were tested in AR time-series and a representative sample of point-in-time observations during the interval 2012 - 2016. The average values of non-neutralized currents in flaring active regions are higher by more than an order of magnitude than in non-flaring regions and correlate very well with the corresponding flare index. The temporal evolution of these parameters appears to be connected to physical processes, such as flux emergence and/or magnetic polarity inversion line formation, that are associated with increased solar flare activity. Using Bayesian inference of flaring probabilities, we show that the total unsigned non-neutralized current significantly outperforms the total unsigned magnetic flux and other well-established current-related predictors. It therefore shows good prospects for inclusion in an operational flare-forecasting service. We plan to use the new predictor in the framework of the FLARECAST project along with other highly performing predictors.

Genomic Regions in Local Endangered Sheep Encode Potentially Favorable Genes.

PubMed

Moioli, Bianca; Steri, Roberto; Catillo, Gennaro

2018-01-02

The economic evaluation of farm animal genetic resources plays a key role in developing conservation programs. However, to date, the link between diversity as assessed by neutral genetic markers and the functional diversity is not yet understood. Two genome-wide comparisons, using over 44,000 Single Nucleotide Polymorphisms, identified the markers with the highest difference in allele frequency between the Alpago endangered breed and two clusters, composed of four specialized dairy sheep, and four meat breeds respectively. The genes in proximity of these markers were mapped to known pathways of the Gene Ontology to determine which ones were most represented. Our results indicated that the differences of the Alpago breed from the more productive sheep rely upon genes involved in cellular defense and repair mechanisms. A higher number of different markers and genes were detected in the comparison with the specialized dairy sheep. These genes play a role in complex biological processes: metabolic, homeostatic, neurological system, and macromolecular organization; such processes may possibly explain the evolution of gene function as a result of selection to improve milk yield.

The limits to biocatalysis: pushing the envelope.

PubMed

Sheldon, Roger A; Brady, Dean

2018-06-12

In the period 1985 to 1995 applications of biocatalysis, driven by the need for more sustainable manufacture of chemicals and catalytic, (enantio)selective methods for the synthesis of pharmaceutical intermediates, largely involved the available hydrolases. This was followed, in the next two decades, by revolutionary developments in protein engineering and directed evolution for the optimisation of enzyme function and performance that totally changed the biocatalysis landscape. In the same period, metabolic engineering and synthetic biology revolutionised the use of whole cell biocatalysis in the synthesis of commodity chemicals by fermentation. In particular, developments in the enzymatic enantioselective synthesis of chiral alcohols and amines are highlighted. Progress in enzyme immobilisation facilitated applications under harsh industrial conditions, such as in organic solvents. The emergence of biocatalytic or chemoenzymatic cascade processes, often with co-immobilised enzymes, has enabled telescoping of multi-step processes. Discovering and inventing new biocatalytic processes, based on (meta)genomic sequencing, evolving enzyme promiscuity, chemomimetic biocatalysis, artificial metalloenzymes, and the introduction of non-canonical amino acids into proteins, are pushing back the limits of biocatalysis function. Finally, the integral role of biocatalysis in developing a biobased carbon-neutral economy is discussed.

Feedback between neutral winds and auroral arc electrodynamics

NASA Technical Reports Server (NTRS)

Lyons, L. R.; Walterscheid, R. L.

1986-01-01

The feedback between neutral atmospheric winds and the electrodynamics of a stable, discrete auroral arc is analyzed. The ionospheric current continuity equation and the equation for neutral gas acceleration by ion drag are solved simultaneously, as a function of time. The results show that, in general, the electric field in the ionosphere adjusts to neutral wind acceleration so as to keep auroral field-aligned currents and electron acceleration approximately independent of time. It is thus concluded that the neutral winds that develop as a result of the electrodynamical forcing associated with an arc do not significantly affect the intensity of the arc.

Functional flexibility of infant vocalization and the emergence of language

PubMed Central

Oller, D. Kimbrough; Buder, Eugene H.; Ramsdell, Heather L.; Warlaumont, Anne S.; Chorna, Lesya; Bakeman, Roger

2013-01-01

We report on the emergence of functional flexibility in vocalizations of human infants. This vastly underappreciated capability becomes apparent when prelinguistic vocalizations express a full range of emotional content—positive, neutral, and negative. The data show that at least three types of infant vocalizations (squeals, vowel-like sounds, and growls) occur with this full range of expression by 3–4 mo of age. In contrast, infant cry and laughter, which are species-specific signals apparently homologous to vocal calls in other primates, show functional stability, with cry overwhelmingly expressing negative and laughter positive emotional states. Functional flexibility is a sine qua non in spoken language, because all words or sentences can be produced as expressions of varying emotional states and because learning conventional “meanings” requires the ability to produce sounds that are free of any predetermined function. Functional flexibility is a defining characteristic of language, and empirically it appears before syntax, word learning, and even earlier-developing features presumed to be critical to language (e.g., joint attention, syllable imitation, and canonical babbling). The appearance of functional flexibility early in the first year of human life is a critical step in the development of vocal language and may have been a critical step in the evolution of human language, preceding protosyntax and even primitive single words. Such flexible affect expression of vocalizations has not yet been reported for any nonhuman primate but if found to occur would suggest deep roots for functional flexibility of vocalization in our primate heritage. PMID:23550164

50th Anniversary Perspective: A Perspective on Polyelectrolyte Solutions

PubMed Central

2017-01-01

From the beginning of life with the information-containing polymers until the present era of a plethora of water-based materials in health care industry and biotechnology, polyelectrolytes are ubiquitous with a broad range of structural and functional properties. The main attribute of polyelectrolyte solutions is that all molecules are strongly correlated both topologically and electrostatically in their neutralizing background of charged ions in highly polarizable solvent. These strong correlations and the necessary use of numerous variables in experiments on polyelectrolytes have presented immense challenges toward fundamental understanding of the various behaviors of charged polymeric systems. This Perspective presents the author’s subjective summary of several conceptual advances and the remaining persistent challenges in the contexts of charge and size of polymers, structures in homogeneous solutions, thermodynamic instability and phase transitions, structural evolution with oppositely charged polymers, dynamics in polyelectrolyte solutions, kinetics of phase separation, mobility of charged macromolecules between compartments, and implications to biological systems. PMID:29296029

Computational analysis and functional expression of ancestral copepod luciferase.

PubMed

Takenaka, Yasuhiro; Noda-Ogura, Akiko; Imanishi, Tadashi; Yamaguchi, Atsushi; Gojobori, Takashi; Shigeri, Yasushi

2013-10-10

We recently reported the cDNA sequences of 11 copepod luciferases from the superfamily Augaptiloidea in the order Calanoida. They were classified into two groups, Metridinidae and Heterorhabdidae/Lucicutiidae families, by phylogenetic analyses. To elucidate the evolutionary processes, we have now further isolated 12 copepod luciferases from Augaptiloidea species (Metridia asymmetrica, Metridia curticauda, Pleuromamma scutullata, Pleuromamma xiphias, Lucicutia ovaliformis and Heterorhabdus tanneri). Codon-based synonymous/nonsynonymous tests of positive selection for 25 identified copepod luciferases suggested that positive Darwinian selection operated in the evolution of Heterorhabdidae luciferases, whereas two types of Metridinidae luciferases had diversified via neutral mechanism. By in silico analysis of the decoded amino acid sequences of 25 copepod luciferases, we inferred two protein sequences as ancestral copepod luciferases. They were expressed in HEK293 cells where they exhibited notable luciferase activity both in intracellular lysates and cultured media, indicating that the luciferase activity was established before evolutionary diversification of these copepod species. © 2013.

Solar wind structure out of the ecliptic plane over solar cycles

NASA Astrophysics Data System (ADS)

Sokol, J. M.; Bzowski, M.; Tokumaru, M.

2017-12-01

Sun constantly emits a stream of plasma known as solar wind. Ground-based observations of the solar wind speed through the interplanetary scintillations (IPS) of radio flux from distant point sources and in-situ measurements by Ulysses mission revealed that the solar wind flow has different characteristics depending on the latitude. This latitudinal structure evolves with the cycle of solar activity. The knowledge on the evolution of solar wind structure is important for understanding the interaction between the interstellar medium surrounding the Sun and the solar wind, which is responsible for creation of the heliosphere. The solar wind structure must be taken into account in interpretation of most of the observations of heliospheric energetic neutral atoms, interstellar neutral atoms, pickup ions, and heliospheric backscatter glow. The information on the solar wind structure is not any longer available from direct measurements after the termination of Ulysses mission and the only source of the solar wind out of the ecliptic plane is the IPS observations. However, the solar wind structure obtained from this method contains inevitable gaps in the time- and heliolatitude coverage. Sokół et al 2015 used the solar wind speed data out of the ecliptic plane retrieved from the IPS observations performed by Institute for Space-Earth Environmental Research (Nagoya University, Japan) and developed a methodology to construct a model of evolution of solar wind speed and density from 1985 to 2013 that fills the data gaps. In this paper we will present a refined model of the solar wind speed and density structure as a function of heliographic latitude updated by the most recent data from IPS observations. And we will discuss methods of extrapolation of the solar wind structure out of the ecliptic plane for the past solar cycles, when the data were not available, as well as forecasting for few years upward.

Age-Neutrality of a Brief Assessment of the Section III Alternative Model for Personality Disorders in Older Adults.

PubMed

Debast, Inge; Rossi, Gina; van Alphen, S P J

2018-04-01

The alternative model for personality disorders in the fifth edition of the Diagnostic and Statistical Manual of Mental Disorders ( DSM-5) is considered an important step toward a possibly better conceptualization of personality pathology in older adulthood, by the introduction of levels of personality functioning (Criterion A) and trait dimensions (Criterion B). Our main aim was to examine age-neutrality of the Short Form of the Severity Indices of Personality Problems (SIPP-SF; Criterion A) and Personality Inventory for DSM-5-Brief Form (PID-5-BF; Criterion B). Differential item functioning (DIF) analyses and more specifically the impact on scale level through differential test functioning (DTF) analyses made clear that the SIPP-SF was more age-neutral (6% DIF, only one of four domains showed DTF) than the PID-5-BF (25% DIF, all four tested domains had DTF) in a community sample of older and younger adults. Age differences in convergent validity also point in the direction of differences in underlying constructs. Concurrent and criterion validity in geriatric psychiatry inpatients suggest that both the SIPP-SF scales measuring levels of personality functioning (especially self-functioning) and the PID-5-BF might be useful screening measures in older adults despite age-neutrality not being confirmed.

The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process.

PubMed

Wu, Chung-I; Wang, Hurng-Yi; Ling, Shaoping; Lu, Xuemei

2016-11-23

Although tumorigenesis has been accepted as an evolutionary process ( 20 , 102 ), many forces may operate differently in cancers than in organisms, as they evolve at vastly different time scales. Among such forces, natural selection, here defined as differential cellular proliferation among distinct somatic cell genotypes, is particularly interesting because its action might be thwarted in multicellular organisms ( 20 , 29 ). In this review, selection is analyzed in two stages of cancer evolution: Stage I is the evolution between tumors and normal tissues, and Stage II is the evolution within tumors. The Cancer Genome Atlas (TCGA) data show a low degree of convergent evolution in Stage I, where genetic changes are not extensively shared among cases. An equally important, albeit much less highlighted, discovery using TCGA data is that there is almost no net selection in cancer evolution. Both positive and negative selection are evident but they neatly cancel each other out, rendering total selection ineffective in the absence of recombination. The efficacy of selection is even lower in Stage II, where neutral (non-Darwinian) evolution is increasingly supported by high-density sampling studies ( 81 , 123 ). Because natural selection is not a strong deterministic force, cancers usually evolve divergently even in similar tissue environments.

Loading Ag nanoparticles on Cd(II) boron imidazolate framework for photocatalysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Min; State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 350002; Zhang, De-Xiang

2016-05-15

An amine-functionalized Cd(II) boron imidazolate framework (BIF-77) with three-dimensional open structure has been successfully synthesized, which can load Ag nanoparticles (NPs) for photocatalytic degradation of methylene blue (MB). - Graphical abstract: An amine-functionalized neutral Cd(II) boron imidazolate framework can load Ag NPs and show excellent photocatalytic degradation behavious for MB. - Highlights: • Amine-functionalization. • Neutral boron imidazolate framework. • Loading Ag nanoparticles (NPs). • Photocatalytic degradation of methylene blue.

Neutralizing antibody and functional mapping of Bacillus anthracis protective antigen-The first step toward a rationally designed anthrax vaccine.

PubMed

McComb, Ryan C; Martchenko, Mikhail

2016-01-02

Anthrax is defined by the Centers for Disease Control and Prevention as a Category A pathogen for its potential use as a bioweapon. Current prevention treatments include Anthrax Vaccine Adsorbed (AVA). AVA is an undefined formulation of Bacillus anthracis culture supernatant adsorbed to aluminum hydroxide. It has an onerous vaccination schedule, is slow and cumbersome to produce and is slightly reactogenic. Next-generation vaccines are focused on producing recombinant forms of anthrax toxin in a well-defined formulation but these vaccines have been shown to lose potency as they are stored. In addition, studies have shown that a proportion of the antibody response against these vaccines is focused on non-functional, non-neutralizing regions of the anthrax toxin while some essential functional regions are shielded from eliciting an antibody response. Rational vaccinology is a developing field that focuses on designing vaccine antigens based on structural information provided by neutralizing antibody epitope mapping, crystal structure analysis, and functional mapping through amino acid mutations. This information provides an opportunity to design antigens that target only functionally important and conserved regions of a pathogen in order to make a more optimal vaccine product. This review provides an overview of the literature related to functional and neutralizing antibody epitope mapping of the Protective Antigen (PA) component of anthrax toxin. Copyright © 2015 Elsevier Ltd. All rights reserved.

Geological Evolution of the Ganiki Planitia Quadrangle (V14) on Venus

NASA Technical Reports Server (NTRS)

Grosfils, E. B.; Drury, D. E.; Hurwitz, D. M.; Kastl, B.; Long, s. M.; Richards, J. W.; Venechuk, E. M.

2005-01-01

The Ganiki Planitia quadrangle (25-50degN, 180-210degE) is located north of Atla Regio, south of Vinmara Planitia, and southeast of Atalanta Planitia. The region contains a diverse array of volcanic-, tectonic- and impact-derived features, and the objectives for the ongoing mapping effort are fivefold: 1) explore the formation and evolution of radiating dike swarms within the region, 2) use the diverse array of volcanic deposits to further test the neutral buoyancy hypothesis proposed to explain the origin of reservoir-derived features, 3&4) unravel the volcanic and tectonic evolution in this area, and 5) explore the implications of 1-4 for resurfacing mechanisms. Here we summarize our onging analysis of the material unit stratigraphy in the quadrangle, data central to meeting the aforementioned objectives successfully.

ACIDIFICATION TRENDS AND THE EVOLUTION OF NEUTRALIZATION MECHANISMS THROUGH TIME AT THE BEAR BROOK WATERSHED IN MAINE (BBWM), U.S.A.

EPA Science Inventory

The paired catchment study at the forested Bear Brook Watershed in Maine (BBWM) U.S.A. documents interactions among short- to long-term processes of acidification. In 1987-1989, runoff from the two catchments was nearly identical in quality and quantity. Ammonium sulfate has been...

Instrument Suite for Vertical Characterization of the Ionosphere-Thermosphere System

NASA Technical Reports Server (NTRS)

Herrero, Federico; Jones, Hollis; Finne, Theodore; Nicholas, Andrew

2012-01-01

A document describes a suite that provides four simultaneous ion and neutral-atom measurements as a function of altitude, with variable sensitivity for neutral atmospheric species. The variable sensitivity makes it possible to extend the measurements over the altitude range of 100 to more than 700 km. The four instruments in the suite are (1) a neutral wind-temperature spectrometer (WTS), (2) an ion-drift ion-temperature spectrometer (IDTS), (3) a neutral mass spectrometer (NMS), and (4) an ion mass spectrometer (IMS).

Arabidopsis lipid droplet-associated protein (LDAP)–interacting protein (LDIP) influences lipid droplet size and neutral lipid homeostasis in both leaves and seeds

USDA-ARS?s Scientific Manuscript database

Cytoplasmic lipid droplets (LDs) are found in all types of plant cells where they are derived from the endoplasmic reticulum and function as a repository for neutral lipids, as well as serving in lipid remodelling and signalling. However, the mechanisms underlying the formation and functioning of pl...

Temporal evolution of a Current Sheet with Initial Finite Perturbations by Three-dimensional MHD Simulations

NASA Astrophysics Data System (ADS)

Yokoyama, Takaaki

Temporal evolution of a current sheet with initial perturbations is studied by using the threedimensional resistive magnetohydrodynamic (MHD) simulations. The magnetic reconnection is considered to be the main engine of the energy rele ase in solar flares. The structure of the diffusion region is, however, not stil l understood under the circumstances with enormously large magnetic Reynolds num ber as the solar corona. In particular, the relationship between the flare's macroscopic physics and the microscopic ones are unclear. It is generally believed that the MHD turbulence s hould play a role in the intermediate scale. The initial current sheet is in an approximately hydromagnetic equilibrium with anti-parallel magnetic field in the y-direction. We imposed a finite-amplitude perturbations (=50ee what happens. Special attention is paid upon the evolution of a three-dimens ional structure in the direction along the initial electric current (z-direction ). Our preliminary results are as follows: (1) In the early phase of the evolut ion, high wavenumber modes in the z-direction are excited and grow. (2) Many "X "-type neutral points (lines) are generated along the magnetic neutral line (pla ne) in the current sheet. When they evolve into the non-linear phase, three-dime nsional structures in the z-direction also evolve. The spatial scale in the z-di rection seems to be almost comparable with that in the xy-plane. (3) The energy release rate is reduced in case of 3D simulations compared with 2D ones probably because of the reduction of the inflow cross sections by the formation of pattc hy structures in the current sheet.

The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster.

PubMed

Chong, Zechen; Zhai, Weiwei; Li, Chunyan; Gao, Min; Gong, Qiang; Ruan, Jue; Li, Juan; Jiang, Lan; Lv, Xuemei; Hungate, Eric; Wu, Chung-I

2013-12-01

Studies of protein evolution have focused on amino acid substitutions with much less systematic analysis on insertion and deletions (indels) in protein coding genes. We hence surveyed 7,500 genes between Drosophila melanogaster and D. simulans, using D. yakuba as an outgroup for this purpose. The evolutionary rate of coding indels is indeed low, at only 3% of that of nonsynonymous substitutions. As coding indels follow a geometric distribution in size and tend to fall in low-complexity regions of proteins, it is unclear whether selection or mutation underlies this low rate. To resolve the issue, we collected genomic sequences from an isogenic African line of D. melanogaster (ZS30) at a high coverage of 70× and analyzed indel polymorphism between ZS30 and the reference genome. In comparing polymorphism and divergence, we found that the divergence to polymorphism ratio (i.e., fixation index) for smaller indels (size ≤ 10 bp) is very similar to that for synonymous changes, suggesting that most of the within-species polymorphism and between-species divergence for indels are selectively neutral. Interestingly, deletions of larger sizes (size ≥ 11 bp and ≤ 30 bp) have a much higher fixation index than synonymous mutations and 44.4% of fixed middle-sized deletions are estimated to be adaptive. To our surprise, this pattern is not found for insertions. Protein indel evolution appear to be in a dynamic flux of neutrally driven expansion (insertions) together with adaptive-driven contraction (deletions), and these observations provide important insights for understanding the fitness of new mutations as well as the evolutionary driving forces for genomic evolution in Drosophila species.

To determine and compare the position of neutral zone in relation to crest of mandibular alveolar ridge with different duration of edentulousness: A clinico–radiographic study

PubMed Central

Jain, Ajay; Shetty, N. Sridhar; Ugrappa, Sridevi

2015-01-01

Purpose: The purpose of this study was to establish a relation between the crest of alveolar ridge and functionally obtained neutral zone and to determine the effect of duration of edentulousness on the location of neutral zone in relation to the crest of residual alveolar ridge. Materials and Methods: The study included three groups: Group I–15 subjects edentulous for 0 months to 2 years; Group 2–15 subjects edentulous for 2–5 years; and Group 3–15 subjects edentulous for more than 5 years. Neutral zone recording was performed for each subject and the buccolingual relationship of the crest of the mandibular alveolar ridge and position of the neutral zone was examined. The results were analyzed by the Kruskal–Wallis H test and the Chi-square test. Results: The results suggested that the location of the neutral zone varies from individual to individual depending on their musculature and that there is a significant relation to the duration of edentulousness. As edentulousness increases, there is more lingual positioning of the neutral zone at the molar region of both sides of the arch. At the premolar region, there is no change in position of the neutral zone; it remains constant as resorption of the alveolar ridge is directly under the buttress. In the anterior region, there is more labial positioning of the neutral zone as edentulousness increases. Conclusions: This technique proves itself to be an easy and inexpensive way to determine the relationship between the crest of alveolar ridge and neutral zone. Incorporating this technique into practice will be a great aid that can be exploited by the clinicians for functional and psychological comfort of the patients. PMID:25767354

The cosmic evolution of dust-corrected metallicity in the neutral gas

NASA Astrophysics Data System (ADS)

De Cia, Annalisa; Ledoux, Cédric; Petitjean, Patrick; Savaglio, Sandra

2018-04-01

Interpreting abundances of damped Ly-α absorbers (DLAs) from absorption-line spectroscopy has typically been a challenge because of the presence of dust. Nevertheless, because DLAs trace distant gas-rich galaxies regardless of their luminosity, they provide an attractive way of measuring the evolution of the metallicity of the neutral gas with cosmic time. This has been done extensively so far, but typically not taking proper dust corrections into account. The aims of this paper are to: (i) provide a simplified way of calculating dust corrections, based on a single observed [X/Fe], (ii) assess the importance of dust corrections for DLA metallicities and their evolution, and (iii) investigate the cosmic evolution of iron for a large DLA sample. We have derived dust corrections based on the observed [Zn/Fe], [Si/Fe], or [S/Fe], and confirmed their robustness. We present dust-corrected metallicities in a scale of [Fe/H]tot for 236 DLAs over a broad range of z, and assess the extent of dust corrections for different metals at different metallicities. Dust corrections in DLAs are important even for Zn (typically of 0.1-0.2, and up to 0.5 dex), which is often neglected. Finally, we study the evolution of the dust-corrected metallicity with z. The DLA metallicities decrease with redshift, by a factor of 50-100 from today to 12.6 billion years ago (z = 5). When including dust corrections, the average DLA metallicities are 0.4-0.5 dex higher than without corrections. The upper envelope of the relation between metallicity and z reaches solar metallicity at z ≲ 0.5, although some systems can have solar metallicity already out to z 3. Based on observations carried out at the European Organisation for Astronomical Research in the Southern Hemisphere under ESO programmes 065.P-0038, 065.O-0063, 066.A-0624, 067.A-0078, and 068.A-0600.

Sediment Suspension by Straining-Induced Convection at the Head of Salinity Intrusion

NASA Astrophysics Data System (ADS)

Zhang, Qianjiang; Wu, Jiaxue

2018-01-01

The tidal straining can generate convective motions and exert a periodic modification of turbulence and sediment transport in estuarine and coastal bottom boundary layers. However, the evidence and physics of convection and sediment suspension induced by tidal straining have not been straightforward. To examine these questions, mooring and transect surveys have been conducted in September 2015 in the region of the Yangtze River plume influence. Field observations and scaling analyses indicate an occurrence of convective motions at the head of saline wedge. Theoretical analyses of stratification evolution in the saline wedge show that unstable stratification and resultant convection are induced by tidal straining. Vertical turbulent velocity and eddy viscosity at the head of saline wedge are both larger than their neutral counterparts in the main body, largely enhancing sediment suspension at the head of saline wedge. Moreover, sediment suspension in both neutral and convection-affected flows is supported by the variance of vertical turbulent velocity, rather than the shearing stress. Finally, the stability correction functions in the Monin-Obukhov similarity theory can be simply derived from the local turbulent kinetic energy balance to successfully describe the effects of tidal straining on turbulent length scale, eddy viscosity, and sediment diffusivity in the convection-affected flow. These recognitions may provide novel understanding of estuarine turbidity maxima, and the dynamical structure and processes for coastal hypoxia.

Energy Deposition and Escape Fluxes Induced by Energetic Solar Wind Ions and ENAs Precipitating into Mars Atmosphere: Accurate Consideration of Energy Transfer Collisions

NASA Astrophysics Data System (ADS)

Kharchenko, V. A.; Lewkow, N.; Gacesa, M.

2014-12-01

Formation and evolution of neutral fluxes of atoms and molecules escaping from the Mars atmosphere have been investigated for the sputtering and photo-chemical mechanisms. Energy and momentum transfer in collisions between the atmospheric gas and fast atoms and molecules have been considered using our recently obtained angular and energy dependent cross sections[1]. We have showed that accurate angular dependent collision cross sections are critical for the description of the energy relaxation of precipitating keV energetic ions/ENAs and for computations of altitude profiles of the fast atom and molecule production rates in recoil collisions. Upward and escape fluxes of the secondary energetic He and O atoms and H2, N2, CO and CO2 molecules, induced by precipitating ENAs, have been determined and their non-thermal energy distribution functions have been computed at different altitudes for different solar conditions. Precipitation and energy deposition of the energetic H2O molecules and products of their dissociations into the Mars atmosphere in the Comet C/2013 A1 (Siding Spring) - Mars interaction have been modeled using accurate cross sections. Reflection of precipitating ENAs by the Mars atmosphere has been analyzed in detail. [1] N. Lewkow and V. Kharchenko, "Precipitation of Energetic Neutral Atoms and Escape Fluxes induced from the Mars Atmosphere, ApJ, v.790, p.98 (2014).

Structural and dynamical properties of recombining ultracold neutral plasma

NASA Astrophysics Data System (ADS)

Tiwari, Sanat Kumar; Shaffer, Nathaniel R.; Baalrud, Scott D.

2017-10-01

An ultracold plasma (UCP) is an evolving collection of free charges and bound charges (Rydberg atoms). Over time, bound species concentration increases due to recombination. We present the structural and dynamical properties of an evolving UCP using classical molecular dynamics simulation. Coulomb collapse is avoided using a repulsive core with the attractive Coulomb potential. The repulsive core size controls the concentration of bound states, as it determines the depth of the potential well between opposite charges. We vary the repulsive core size to emulate the quasi-static state of plasma at different time during the evolution. Binary, chain and ring-like bound states are observed in the simulation carried out at different coupling strengths and repulsive core size. The effect of bound states can be seen as molecular peaks in the radial distribution function (RDF). The thermodynamic properties associated with the free charges can be analyzed from RDF by separating free from bound states. These bound states also change the dynamical properties of the plasma. The electron velocity auto-correlation displays oscillations due to the orbital motion in bound states. These bound states act like a neutral species, damping electron plasmon modes and broadening the ion acoustic mode. This work is supported by AFOSR Grant Number FA9550-16-1-0221. It used computational resources by XSEDE, which is supported by NSF Grant Number ACI-1053575.

Effects of Darwinian Selection and Mutability on Rate of Broadly Neutralizing Antibody Evolution during HIV-1 Infection

PubMed Central

Sheng, Zizhang; Schramm, Chaim A.; Connors, Mark; Morris, Lynn; Mascola, John R.; Kwong, Peter D.; Shapiro, Lawrence

2016-01-01

Accumulation of somatic mutations in antibody variable regions is critical for antibody affinity maturation, with HIV-1 broadly neutralizing antibodies (bnAbs) generally requiring years to develop. We recently found that the rate at which mutations accumulate decreases over time, but the mechanism governing this slowing is unclear. In this study, we investigated whether natural selection and/or mutability of the antibody variable region contributed significantly to observed decrease in rate. We used longitudinally sampled sequences of immunoglobulin transcripts of single lineages from each of 3 donors, as determined by next generation sequencing. We estimated the evolutionary rates of the complementarity determining regions (CDRs), which are most significant for functional selection, and found they evolved about 1.5- to 2- fold faster than the framework regions. We also analyzed the presence of AID hotspots and coldspots at different points in lineage development and observed an average decrease in mutability of less than 10 percent over time. Altogether, the correlation between Darwinian selection strength and evolutionary rate trended toward significance, especially for CDRs, but cannot fully explain the observed changes in evolutionary rate. The mutability modulated by AID hotspots and coldspots changes correlated only weakly with evolutionary rates. The combined effects of Darwinian selection and mutability contribute substantially to, but do not fully explain, evolutionary rate change for HIV-1-targeting bnAb lineages. PMID:27191167

Theoretical studies on the electronic structures and photoelectron spectra of tri-rhenium oxide clusters: Re3O(n)(-) and Re3O(n) (n=1-6).

PubMed

Zhou, Qi; Gong, Wei-Chao; Xie, Lu; Zheng, Cun-Gong; Zhang, Wei; Wang, Bin; Zhang, Yong-Fan; Huang, Xin

2014-01-03

Density functional theory (DFT) calculations are performed to study the structural and electronic properties of tri-rhenium oxide clusters Re3On(-/0) (n=1-6). Generalized Koopmans' theorem is applied to predict the vertical detachment energies (VDEs) and simulate the photoelectron spectra (PES). Theoretical calculations at the B3LYP level are carried out to search for the global minima for both the anions and the neutrals. For the anions, the first two O atoms prefer the same corner position of a Re3 triangle. Whereas, Re3O3(-) possesses a C2v symmetry with one bridging and two terminal O atoms. The next three O atoms (n=4-6) are adding sequentially on the basis of Re3O3(-) motif, i.e., adding one terminal O atom for Re3O4(-), one terminal and one bridging O atoms for Re3O5(-), and one terminal and two bridging O atoms for Re3O6(-), respectively. Their corresponding neutral species are similar to the anions in geometry except Re3O4 and Re3O5. Molecular orbital analyses are employed to investigate the chemical bonding and structural evolution in these tri-rhenium oxide clusters. Copyright © 2013 Elsevier B.V. All rights reserved.

Genetic adaptation of the antibacterial human innate immunity network.

PubMed

Casals, Ferran; Sikora, Martin; Laayouni, Hafid; Montanucci, Ludovica; Muntasell, Aura; Lazarus, Ross; Calafell, Francesc; Awadalla, Philip; Netea, Mihai G; Bertranpetit, Jaume

2011-07-11

Pathogens have represented an important selective force during the adaptation of modern human populations to changing social and other environmental conditions. The evolution of the immune system has therefore been influenced by these pressures. Genomic scans have revealed that immune system is one of the functions enriched with genes under adaptive selection. Here, we describe how the innate immune system has responded to these challenges, through the analysis of resequencing data for 132 innate immunity genes in two human populations. Results are interpreted in the context of the functional and interaction networks defined by these genes. Nucleotide diversity is lower in the adaptors and modulators functional classes, and is negatively correlated with the centrality of the proteins within the interaction network. We also produced a list of candidate genes under positive or balancing selection in each population detected by neutrality tests and showed that some functional classes are preferential targets for selection. We found evidence that the role of each gene in the network conditions the capacity to evolve or their evolvability: genes at the core of the network are more constrained, while adaptation mostly occurred at particular positions at the network edges. Interestingly, the functional classes containing most of the genes with signatures of balancing selection are involved in autoinflammatory and autoimmune diseases, suggesting a counterbalance between the beneficial and deleterious effects of the immune response.

Genetic adaptation of the antibacterial human innate immunity network

PubMed Central

2011-01-01

Background Pathogens have represented an important selective force during the adaptation of modern human populations to changing social and other environmental conditions. The evolution of the immune system has therefore been influenced by these pressures. Genomic scans have revealed that immune system is one of the functions enriched with genes under adaptive selection. Results Here, we describe how the innate immune system has responded to these challenges, through the analysis of resequencing data for 132 innate immunity genes in two human populations. Results are interpreted in the context of the functional and interaction networks defined by these genes. Nucleotide diversity is lower in the adaptors and modulators functional classes, and is negatively correlated with the centrality of the proteins within the interaction network. We also produced a list of candidate genes under positive or balancing selection in each population detected by neutrality tests and showed that some functional classes are preferential targets for selection. Conclusions We found evidence that the role of each gene in the network conditions the capacity to evolve or their evolvability: genes at the core of the network are more constrained, while adaptation mostly occurred at particular positions at the network edges. Interestingly, the functional classes containing most of the genes with signatures of balancing selection are involved in autoinflammatory and autoimmune diseases, suggesting a counterbalance between the beneficial and deleterious effects of the immune response. PMID:21745391

An Evolutionary Classification of Genomic Function

PubMed Central

Graur, Dan; Zheng, Yichen; Azevedo, Ricardo B.R.

2015-01-01

The pronouncements of the ENCODE Project Consortium regarding “junk DNA” exposed the need for an evolutionary classification of genomic elements according to their selected-effect function. In the classification scheme presented here, we divide the genome into “functional DNA,” that is, DNA sequences that have a selected-effect function, and “rubbish DNA,” that is, sequences that do not. Functional DNA is further subdivided into “literal DNA” and “indifferent DNA.” In literal DNA, the order of nucleotides is under selection; in indifferent DNA, only the presence or absence of the sequence is under selection. Rubbish DNA is further subdivided into “junk DNA” and “garbage DNA.” Junk DNA neither contributes to nor detracts from the fitness of the organism and, hence, evolves under selective neutrality. Garbage DNA, on the other hand, decreases the fitness of its carriers. Garbage DNA exists in the genome only because natural selection is neither omnipotent nor instantaneous. Each of these four functional categories can be 1) transcribed and translated, 2) transcribed but not translated, or 3) not transcribed. The affiliation of a DNA segment to a particular functional category may change during evolution: Functional DNA may become junk DNA, junk DNA may become garbage DNA, rubbish DNA may become functional DNA, and so on; however, determining the functionality or nonfunctionality of a genomic sequence must be based on its present status rather than on its potential to change (or not to change) in the future. Changes in functional affiliation are divided into pseudogenes, Lazarus DNA, zombie DNA, and Jekyll-to-Hyde DNA. PMID:25635041

Regulatory networks and connected components of the neutral space. A look at functional islands

NASA Astrophysics Data System (ADS)

Boldhaus, G.; Klemm, K.

2010-09-01

The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory systems is neutrality - typically a large number of alternative network structures give rise to the necessary dynamics. Here we study the discretized regulatory dynamics of the yeast cell cycle [Li et al., PNAS, 2004] and the set of networks capable of reproducing it, which we call functional. Among these, the empirical yeast wildtype network is close to optimal with respect to sparse wiring. Under point mutations, which establish or delete single interactions, the neutral space of functional networks is fragmented into ≈ 4.7 × 108 components. One of the smaller ones contains the wildtype network. On average, functional networks reachable from the wildtype by mutations are sparser, have higher noise resilience and fewer fixed point attractors as compared with networks outside of this wildtype component.

Serum virus neutralization assay for detection and quantitation of serum neutralizing antibodies to influenza A virus in swine

USDA-ARS?s Scientific Manuscript database

The serum virus neutralization (SVN) assay is a serological test to detect the presence and magnitude of functional systemic antibodies that prevent infectivity of a virus. The SVN assay is a highly sensitive and specific test that may be applied to influenza A viruses (IAV) in swine to measure the ...

Dynamics of HIV neutralization by a microbicide formulation layer: biophysical fundamentals and transport theory.

PubMed

Geonnotti, Anthony R; Katz, David F

2006-09-15

Topical microbicides are an emerging HIV/AIDS prevention modality. Microbicide biofunctionality requires creation of a chemical-physical barrier against HIV transmission. Barrier effectiveness derives from properties of the active compound and its delivery system, but little is known about how these properties translate into microbicide functionality. We developed a mathematical model simulating biologically relevant transport and HIV-neutralization processes occurring when semen-borne virus interacts with a microbicide delivery vehicle coating epithelium. The model enables analysis of how vehicle-related variables, and anti-HIV compound characteristics, affect microbicide performance. Results suggest HIV neutralization is achievable with postcoital coating thicknesses approximately 100 mum. Increased microbicide concentration and potency hasten viral neutralization and diminish penetration of infectious virus through the coating layer. Durable vehicle structures that restrict viral diffusion could provide significant protection. Our findings demonstrate the need to pair potent active ingredients with well-engineered formulation vehicles, and highlight the importance of the dosage form in microbicide effectiveness. Microbicide formulations can function not only as drug delivery vehicles, but also as physical barriers to viral penetration. Total viral neutralization with 100-mum-thin coating layers supports future microbicide use against HIV transmission. This model can be used as a tool to analyze diverse factors that govern microbicide functionality.

Investigating the Predictive Value of Functional MRI to Appetitive and Aversive Stimuli: A Pattern Classification Approach.

PubMed

McCabe, Ciara; Rocha-Rego, Vanessa

2016-01-01

Dysfunctional neural responses to appetitive and aversive stimuli have been investigated as possible biomarkers for psychiatric disorders. However it is not clear to what degree these are separate processes across the brain or in fact overlapping systems. To help clarify this issue we used Gaussian process classifier (GPC) analysis to examine appetitive and aversive processing in the brain. 25 healthy controls underwent functional MRI whilst seeing pictures and receiving tastes of pleasant and unpleasant food. We applied GPCs to discriminate between the appetitive and aversive sights and tastes using functional activity patterns. The diagnostic accuracy of the GPC for the accuracy to discriminate appetitive taste from neutral condition was 86.5% (specificity = 81%, sensitivity = 92%, p = 0.001). If a participant experienced neutral taste stimuli the probability of correct classification was 92. The accuracy to discriminate aversive from neutral taste stimuli was 82.5% (specificity = 73%, sensitivity = 92%, p = 0.001) and appetitive from aversive taste stimuli was 73% (specificity = 77%, sensitivity = 69%, p = 0.001). In the sight modality, the accuracy to discriminate appetitive from neutral condition was 88.5% (specificity = 85%, sensitivity = 92%, p = 0.001), to discriminate aversive from neutral sight stimuli was 92% (specificity = 92%, sensitivity = 92%, p = 0.001), and to discriminate aversive from appetitive sight stimuli was 63.5% (specificity = 73%, sensitivity = 54%, p = 0.009). Our results demonstrate the predictive value of neurofunctional data in discriminating emotional and neutral networks of activity in the healthy human brain. It would be of interest to use pattern recognition techniques and fMRI to examine network dysfunction in the processing of appetitive, aversive and neutral stimuli in psychiatric disorders. Especially where problems with reward and punishment processing have been implicated in the pathophysiology of the disorder.

Inertia-Centric Stability Analysis of a Planar Uniform Dust Molecular Cloud with Weak Neutral-Charged Dust Frictional Coupling

NASA Astrophysics Data System (ADS)

K. Karmakar, P.; Borah, B.

2014-05-01

This paper adopts an inertia-centric evolutionary model to study the excitation mechanism of new gravito-electrostatic eigenmode structures in a one-dimensional (1-D) planar self-gravitating dust molecular cloud (DMC) on the Jeans scale. A quasi-neutral multi-fluid consisting of warm electrons, warm ions, neutral gas and identical inertial cold dust grains with partial ionization is considered. The grain-charge is assumed not to vary at the fluctuation evolution time scale. The neutral gas particles form the background, which is weakly coupled with the collapsing grainy plasma mass. The gravitational decoupling of the background neutral particles is justifiable for a higher inertial mass of the grains with higher neutral population density so that the Jeans mode frequency becomes reasonably large. Its physical basis is the Jeans assumption of a self-gravitating uniform medium adopted for fiducially analytical simplification by neglecting the zero-order field. So, the equilibrium is justifiably treated initially as “homogeneous”. The efficacious inertial role of the thermal species amidst weak collisions of the neutral-charged grains is taken into account. A standard multiscale technique over the gravito-electrostatic equilibrium yields a unique pair of Korteweg-de Vries (KdV) equations. It is integrated numerically by the fourth-order Runge-Kutta method with multi-parameter variation for exact shape analyses. Interestingly, the model is conducive for the propagation of new conservative solitary spectral patterns. Their basic physics, parametric features and unique characteristics are discussed. The results go qualitatively in good correspondence with the earlier observations made by others. Tentative applications relevant to space and astrophysical environments are concisely highlighted.

Semiclassical neutral atom as a reference system in density functional theory.

PubMed

Constantin, Lucian A; Fabiano, E; Laricchia, S; Della Sala, F

2011-05-06

We use the asymptotic expansions of the semiclassical neutral atom as a reference system in density functional theory to construct accurate generalized gradient approximations (GGAs) for the exchange-correlation and kinetic energies without any empiricism. These asymptotic functionals are among the most accurate GGAs for molecular systems, perform well for solid state, and overcome current GGA state of the art in frozen density embedding calculations. Our results also provide evidence for the conjointness conjecture between exchange and kinetic energies of atomic systems.

Structural comparison of four different antibodies interacting with human papillomavirus 16 and mechanisms of neutralization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Guan, Jian; Bywaters, Stephanie M.; Brendle, Sarah A.

2015-09-15

Cryo-electron microscopy (cryo-EM) was used to solve the structures of human papillomavirus type 16 (HPV16) complexed with fragments of antibody (Fab) from three different neutralizing monoclonals (mAbs): H16.1A, H16.14J, and H263.A2. The structure-function analysis revealed predominantly monovalent binding of each Fab with capsid interactions that involved multiple loops from symmetry related copies of the major capsid protein. The residues identified in each Fab-virus interface map to a conformational groove on the surface of the capsomer. In addition to the known involvement of the FG and HI loops, the DE loop was also found to constitute the core of each epitope.more » Surprisingly, the epitope mapping also identified minor contributions by EF and BC loops. Complementary immunological assays included mAb and Fab neutralization. The specific binding characteristics of mAbs correlated with different neutralizing behaviors in pre- and post-attachment neutralization assays. - Highlights: • We present HPV16-Fab complexes from neutralizing mAbs: H16.1A, H16.14J, and H263.A2. • The structure-function analysis revealed predominantly monovalent binding of each mAb. • Capsid–Fab interactions involved multiple loops from symmetry related L1 proteins. • Besides the known FG and HI loops, epitope mapping also identified DE, EF, and BC loops. • Neutralizing assays complement the structures to show multiple neutralization mechanisms.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eslami, Babak; López-Guerra, Enrique A.; Raftari, Maryam

Addition of a strong base to Nafion{sup ®} proton exchange membranes is a common practice in industry to increase their overall performance in fuel cells. Here, we investigate the evolution of the nano-rheological properties of Nafion thin films as a function of the casting pH, via characterization with static and dynamic, contact and intermittent-contact atomic force microscopy (AFM) techniques. The addition of KOH causes non-monotonic changes in the viscoelastic properties of the films, which behave as highly dissipative, softer materials near neutral pH values, and as harder, more elastic materials at extreme pH values. We quantify this behavior through calculationmore » of the temporal evolution of the compliance and the glassy compliance under static AFM measurements. We complement these observations with dynamic AFM metrics, including dissipated power and virial (for intermittent-contact-mode measurements), and contact resonance frequency and quality factor (for dynamic contact-mode measurements). We explain the non-monotonic material property behavior in terms of the degree of ionic crosslinking and moisture content of the films, which vary with the addition of KOH. This work focuses on the special case study of the addition of strong bases, but the observed mechanical property changes are broadly related to water plasticizing effects and ionic crosslinking, which are also important in other types of films.« less

Evolution subverting essentiality: Dispensability of the cell attachment Arg-Gly-Asp motif in multiply passaged foot-and-mouth disease virus

PubMed Central

Martínez, Miguel A.; Verdaguer, Nuria; Mateu, Mauricio G.; Domingo, Esteban

1997-01-01

Aphthoviruses use a conserved Arg-Gly-Asp triplet for attachment to host cells and this motif is believed to be essential for virus viability. Here we report that this triplet—which is also a widespread motif involved in cell-to-cell adhesion—can become dispensable upon short-term evolution of the virus harboring it. Foot-and-mouth disease virus (FMDV), which was multiply passaged in cell culture, showed an altered repertoire of antigenic variants resistant to a neutralizing monoclonal antibody. The altered repertoire includes variants with substitutions at the Arg-Gly-Asp motif. Mutants lacking this sequence replicated normally in cell culture and were indistinguishable from the parental virus. Studies with individual FMDV clones indicate that amino acid replacements on the capsid surface located around the loop harboring the Arg-Gly-Asp triplet may mediate in the dispensability of this motif. The results show that FMDV quasispecies evolving in a constant biological environment have the capability of rendering totally dispensable a receptor recognition motif previously invariant, and to ensure an alternative pathway for normal viral replication. Thus, variability of highly conserved motifs, even those that viruses have adapted from functional cellular motifs, can contribute to phenotypic flexibility of RNA viruses in nature. PMID:9192645