WorldWideScience

Sample records for epochal evolution insights

  1. Epochs of radioactivity in historical evolution of the earth with reference to evolution of biosphere

    International Nuclear Information System (INIS)

    Neruchev, S.G.

    1976-01-01

    Periodic epochs of intense contamination of the medium by uranium in the course of the Earth's evolution and the biogene mechanism of uranium accumulation in sediments during the lifetime are established. Global differentiation of the radioactivity epochs and essential effect of periodic radiation on the evolution of biosphere are shown. Radiational-mutational mechanism in shown to be extremely nonuniform during the evolution of the organic kingdom. It has been found that the intermittency in radioactive epochs is responsible for peculiarities in the stratigraphic distribution of sedimentary uranium, sapropelic shales, phosphorites, oil-producing rocks and other minerals

  2. Late Globalization and Evolution, Episodes and Epochs of Industries

    DEFF Research Database (Denmark)

    Turcan, Romeo V.; Boujarzadeh, Behnam; Dholakia, Nikhilesh

    While the empirical focus of this paper is the Danish Textile and Fashion Industry (DTFI) – specifically the episodes and epochs in the emergence and evolution of DTFI, in essence the micro and macro time-slices – the theoretical intent is wider. We aim to explore the conceptual terrain of what we...... for further exploration of the late globalization phenomenon. To get to the empirical case study, we follow a macro-conceptual to a micro-empirical path. We discuss the multidisciplinary and multifaceted field of late globalization and employing the historic-analytic approach to study DTFI we draw out very...... specific, empirically derived, conceptual themes about the patterns of global interactions that characterized the evolutionary trajectory of DTFI. We return to a final macro-conceptual section on late globalization where the particular DTFI case study advances the knowledge register only slightly; and we...

  3. Episodes and Epochs in the Evolution of Danish Textile and Fashion Industry

    DEFF Research Database (Denmark)

    Boujarzadeh, Behnam; Turcan, Romeo V.; Dholakia, Nikhilesh

    2016-01-01

    In this paper we explore the emergence and evolution of industries. Specifically we investigate the episodes and epochs in the emergence and evolution of Danish Textile and Fashion Industry. We collected historical data on Danish Textile and Fashion Industry between 1945 and 2015. We employ radar...

  4. THE TIME EVOLUTION OF HH 1 FROM FOUR EPOCHS OF HST IMAGES

    Energy Technology Data Exchange (ETDEWEB)

    Raga, A. C.; Esquivel, A. [Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Ap. 70-543, 04510 D.F., México (Mexico); Reipurth, B. [Institute for Astronomy, University of Hawaii at Manoa, Hilo, HI 96720 (United States); Bally, J., E-mail: raga@nucleares.unam.mx [Center for Astrophysics and Space Astronomy, University of Colorado, UCB 389, Boulder, CO 80309 (United States)

    2016-05-15

    We present an analysis of four epochs of Hα and [S ii] λλ 6716/6731 Hubble Space Telescope (HST) images of HH 1. For determining proper motions, we explore a new method based on the analysis of spatially degraded images obtained convolving the images with wavelet functions of chosen widths. With this procedure, we are able to generate maps of proper motion velocities along and across the outflow axis, as well as (angularly integrated) proper motion velocity distributions. From the four available epochs, we find the time evolution of the velocities, intensities, and spatial distribution of the line emission. We find that over the last two decades HH 1 shows a clear acceleration. Also, the Hα and [S ii] intensities first dropped and then recovered in the more recent (2014) images. Finally, we show a comparison between the two available HST epochs of [O iii] λ 5007 (1994 and 2014), in which we see a clear drop in the value of the [O iii]/Hα ratio.

  5. Evolution, Insight and Truth?

    Science.gov (United States)

    Newall, Emma

    2017-01-01

    Evolution has been positioned at the centre of conflict between scientific and religious explanations of the workings of the world. However, little research has examined other possible reasons for some people rejecting scientific explanations. The author's research indicates that for some people, irrespective of faith, the ideas associated with…

  6. Evolution of the intergalactic medium - What happened during the epoch z = 3-10?

    Science.gov (United States)

    Ikeuchi, S.; Ostriker, J. P.

    1986-01-01

    An attempt is made to model consistently the thermal and dynamic history of the intergalactic medium (IGM) from the era of reheating (z = 10-5) to the present, and to provide a unified explanation for the origin of ordinary galaxies, blue compact objects, and Lyman-alpha clouds. The evolution of the intergalactic gas is analyzed, treating the IGM as perfectly homogeneous at every epoch and taking into account radiative and Compton cooling, adiabatic cooling, shock heating, and heating produced by the diffuse UV flux. It is suggested that the IGM must have been heated to higher than a 10 to the 6th K by shock heasting caused either by explosions of pregalactic objects or expanding voids. The formation of intergalactic clouds by fragmentation of the resulting shells and the subsequent collapse of the shells to form galaxies are studied. An attempt is made to determine model parameters on the basis of an analysis of Lyman-alpha absorption lines.

  7. Sub-horizon evolution of cold dark matter perturbations through dark matter-dark energy equivalence epoch

    International Nuclear Information System (INIS)

    Piattella, O.F.; Martins, D.L.A.; Casarini, L.

    2014-01-01

    We consider a cosmological model of the late universe constituted by standard cold dark matter plus a dark energy component with constant equation of state w and constant effective speed of sound. By neglecting fluctuations in the dark energy component, we obtain an equation describing the evolution of sub-horizon cold dark matter perturbations through the epoch of dark matter-dark energy equality. We explore its analytic solutions and calculate an exact w-dependent correction for the dark matter growth function, logarithmic growth function and growth index parameter through the epoch considered. We test our analytic approximation with the numerical solution and find that the discrepancy is less than 1% for 0k = during the cosmic evolution up to a = 100

  8. On the spin-temperature evolution during the epoch of reionization

    NARCIS (Netherlands)

    Thomas, Rajat M.; Zaroubi, Saleem

    Simulations estimating the brightness temperature (delta T-b) of the redshifted 21 cm from the epoch of reionization (EoR) often assume that the spin temperature (T-s) is decoupled from the background cosmic microwave background (CMB) temperature and is much larger than it, i.e. T-s T-CMB. Although

  9. Phylogenomic Insights into Animal Evolution.

    Science.gov (United States)

    Telford, Maximilian J; Budd, Graham E; Philippe, Hervé

    2015-10-05

    Animals make up only a small fraction of the eukaryotic tree of life, yet, from our vantage point as members of the animal kingdom, the evolution of the bewildering diversity of animal forms is endlessly fascinating. In the century following the publication of Darwin's Origin of Species, hypotheses regarding the evolution of the major branches of the animal kingdom - their relationships to each other and the evolution of their body plans - was based on a consideration of the morphological and developmental characteristics of the different animal groups. This morphology-based approach had many successes but important aspects of the evolutionary tree remained disputed. In the past three decades, molecular data, most obviously primary sequences of DNA and proteins, have provided an estimate of animal phylogeny largely independent of the morphological evolution we would ultimately like to understand. The molecular tree that has evolved over the past three decades has drastically altered our view of animal phylogeny and many aspects of the tree are no longer contentious. The focus of molecular studies on relationships between animal groups means, however, that the discipline has become somewhat divorced from the underlying biology and from the morphological characteristics whose evolution we aim to understand. Here, we consider what we currently know of animal phylogeny; what aspects we are still uncertain about and what our improved understanding of animal phylogeny can tell us about the evolution of the great diversity of animal life. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. Principles of evolution from the Planck epoch to complex multicellular life

    CERN Document Server

    Meyer-Ortmanns, Hildegard

    2011-01-01

    With contributions from a team of leading experts, this volume provides a comprehensive survey of recent achievements in our scientific understanding of evolution. The questions it asks concern the beginnings of the universe, the origin of life and the chances of its arising at all, the role of contingency, and the search for universal features in the plethora of evolutionary phenomena. Rather than oversimplified or premature answers, the chapters provide a clear picture of how these essential problems are being tackled, enabling the reader to understand current thinking and open questions.  The tools employed stem from a range of disciplines including mathematics, physics, biochemistry and cell biology. Self-organization as an overarching concept is demonstrated in the most diverse areas: from galaxy formation in the universe to spindle and aster formation in the cell. Chemical master equations, population dynamics, and evolutionary game theory are presented as suitable frameworks for understanding the univ...

  11. LOFAR insights into the epoch of reionization from the cross-power spectrum of 21 cm emission and galaxies

    NARCIS (Netherlands)

    Wiersma, R. P. C.; Ciardi, B.; Thomas, R. M.; Harker, G. J. A.; Zaroubi, S.; Bernardi, G.; Brentjens, M.; de Bruyn, A. G.; Daiboo, S.; Jelic, V.; Kazemi, S.; Koopmans, L. V. E.; Labropoulos, P.; Martinez, O.; Offringa, A.; Pandey, V. N.; Schaye, J.; Veligatla, V.; Vedantham, H.; Yatawatta, S.; Mellema, G.

    2013-01-01

    Using a combination of N-body simulations, semi-analytic models and radiative transfer calculations, we have estimated the theoretical cross-power spectrum between galaxies and the 21 cm emission from neutral hydrogen during the epoch of reionization. In accordance with previous studies, we find

  12. Carbonate landscapes evolution: Insights from 36Cl

    Science.gov (United States)

    Godard, Vincent; Thomas, Franck; Ollivier, Vincent; Bellier, Olivier; Shabanian, Esmaeil; Miramont, Cécile; Fleury, Jules; Benedetti, Lucilla; Guillou, Valéry; Aster Team

    2017-04-01

    Carbonate landscapes cover a significant fraction of the Earth surface, but their long-term dynamics is still poorly understood. When comparing with the situation in areas underlain by quartz-rich lithologies, where the routine use of 10Be-derived denudation rates has delivered fundamental insights on landscape evolution processes, this knowledge gap is particularly notable. Recent advances in the measurement of 36Cl and better understanding of its production pathways has opened the way to the development of a similar physically-based and quantitative analysis of landscape evolution in carbonate settings. However, beyond these methodological considerations, we still face fundamental geomorphological open questions, as for example the assessment of the importance of congruent carbonate dissolution in long-wavelength topographic evolution. Such unresolved problems concerning the relative importance of physical and chemical weathering processes lead to question the applicability of standard slope-dependent Geomorphic Transport Laws in carbonate settings. These issues have been addressed studying the geomorphological evolution of selected limestone ranges in Provence, SE France, where 36Cl concentration measurements in bedrock and stream sediment samples allow constraining denudation over 10 ka time-scale. We first identify a significant denudation contrast between the summit surface and the flanks of the ranges, pointing to a substantial contribution of gravity-driven processes to the landscape evolution, in addition to dissolution. Furthermore, a detailed analysis of the relationships between hillslope morphology and hilltop denudation allow to identify a fundamental transition between two regimes: (1) a dynamics where hillslope evolution is controlled by linear diffusive downslope regolith transport; and, (2) a domain where denudation is limited by the rate at which physical and chemical weathering processes can produce clasts and lower the hilltop. Such an abrupt

  13. Astrobiology, Evolution, and Society: Public Engagement Insights

    Science.gov (United States)

    Bertka, C. M.

    2009-12-01

    frequently was “my religious beliefs.” A review of religious identification in this country will be presented in the context of offering insights for public engagement on the topic of evolution, and the contribution that astrobiology could make to encouraging a positive relationship between science and religion. A widespread acceptance of evolution in the United States may require that the scientific community go beyond a simple contrast approach to science and religion and be willing to encourage, and participate in, a program of in-depth and long-term engagement with theologians and religious community leaders. Astrobiology as a discipline is particularly burdened, perhaps blessed, with the responsibility to engage this issue. After all, humanity itself may be inherently defined by the ability we collectively posses to ask “Where did we come from?,” “Are we alone?,” and “Where are we going?”

  14. EVOLUTION IN THE H I GAS CONTENT OF GALAXY GROUPS: PRE-PROCESSING AND MASS ASSEMBLY IN THE CURRENT EPOCH

    Energy Technology Data Exchange (ETDEWEB)

    Hess, Kelley M. [Astrophysics, Cosmology and Gravity Centre (ACGC), Department of Astronomy, University of Cape Town, Rondebosch 7701 (South Africa); Wilcots, Eric M., E-mail: hess@ast.uct.ac.za, E-mail: ewilcots@astro.wisc.edu [Department of Astronomy, University of Wisconsin-Madison, Madison, WI 53706 (United States)

    2013-11-01

    We present an analysis of the neutral hydrogen (H I) content and distribution of galaxies in groups as a function of their parent dark matter halo mass. The Arecibo Legacy Fast ALFA survey α.40 data release allows us, for the first time, to study the H I properties of over 740 galaxy groups in the volume of sky common to the Sloan Digital Sky Survey (SDSS) and ALFALFA surveys. We assigned ALFALFA H I detections a group membership based on an existing magnitude/volume-limited SDSS Data Release 7 group/cluster catalog. Additionally, we assigned group ''proximity' membership to H I detected objects whose optical counterpart falls below the limiting optical magnitude—thereby not contributing substantially to the estimate of the group stellar mass, but significantly to the total group H I mass. We find that only 25% of the H I detected galaxies reside in groups or clusters, in contrast to approximately half of all optically detected galaxies. Further, we plot the relative positions of optical and H I detections in groups as a function of parent dark matter halo mass to reveal strong evidence that H I is being processed in galaxies as a result of the group environment: as optical membership increases, groups become increasingly deficient of H I rich galaxies at their center and the H I distribution of galaxies in the most massive groups starts to resemble the distribution observed in comparatively more extreme cluster environments. We find that the lowest H I mass objects lose their gas first as they are processed in the group environment, and it is evident that the infall of gas rich objects is important to the continuing growth of large scale structure at the present epoch, replenishing the neutral gas supply of groups. Finally, we compare our results to those of cosmological simulations and find that current models cannot simultaneously predict the H I selected halo occupation distribution for both low and high mass halos.

  15. Reading the metal diaries of the universe : tracing cosmic chemical evolution from the reionization epoch till the present

    NARCIS (Netherlands)

    Vink, J.

    2009-01-01

    Metals are essential for star formation and their subsequent evolution, and ultimately the formation of planets and the development of life, as we know it. Reconstructing the cosmic history of metals, reaching from the first population of stars to the processes involved in the formation of galaxies

  16. THE INNER DISK STRUCTURE, DISK-PLANET INTERACTIONS, AND TEMPORAL EVOLUTION IN THE β PICTORIS SYSTEM: A TWO-EPOCH HST/STIS CORONAGRAPHIC STUDY

    Energy Technology Data Exchange (ETDEWEB)

    Apai, Dániel; Schneider, Glenn [Department of Astronomy and Steward Observatory, The University of Arizona, Tucson, AZ 85721 (United States); Grady, Carol A. [Eureka Scientific, 2452 Delmer, Suite 100, Oakland CA 96002 (United States); Wyatt, Mark C. [Institute of Astronomy, University of Cambridge, Madingley Road, Cambridge CB3 0HA (United Kingdom); Lagrange, Anne-Marie [Université Grenoble Alpes, IPAG, F-38000, Grenoble (France); Kuchner, Marc J.; Stark, Christopher J. [NASA Goddard Space Flight Center, Exoplanets and Stellar Astrophysics Laboratory, Code 667, Greenbelt, MD 20771 (United States); Lubow, Stephen H., E-mail: apai@arizona.edu [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States)

    2015-02-20

    We present deep Hubble Space Telescope/Space Telescope Imaging Spectrograph coronagraphic images of the β Pic debris disk obtained at two epochs separated by 15 yr. The new images and the re-reduction of the 1997 data provide the most sensitive and detailed views of the disk at optical wavelengths as well as the yet smallest inner working angle optical coronagraphic image of the disk. Our observations characterize the large-scale and inner-disk asymmetries and we identify multiple breaks in the disk radial surface brightness profile. We study in detail the radial and vertical disk structure and show that the disk is warped. We explore the disk at the location of the β Pic b super-Jupiter and find that the disk surface brightness slope is continuous between 0.''5 and 2.''0, arguing for no change at the separations where β Pic b orbits. The two epoch images constrain the disk's surface brightness evolution on orbital and radiation pressure blow-out timescales. We place an upper limit of 3% on the disk surface brightness change between 3'' and 5'', including the locations of the disk warp, and the CO and dust clumps. We discuss the new observations in the context of high-resolution multi-wavelength images and divide the disk asymmetries in two groups: axisymmetric and non-axisymmetric. The axisymmetric structures (warp, large-scale butterfly, etc.) are consistent with disk structure models that include interactions of a planetesimal belt and a non-coplanar giant planet. The non-axisymmetric features, however, require a different explanation.

  17. Archeological insights into hominin cognitive evolution.

    Science.gov (United States)

    Wynn, Thomas; Coolidge, Frederick L

    2016-07-01

    How did the human mind evolve? How and when did we come to think in the ways we do? The last thirty years have seen an explosion in research related to the brain and cognition. This research has encompassed a range of biological and social sciences, from epigenetics and cognitive neuroscience to social and developmental psychology. Following naturally on this efflorescence has been a heightened interest in the evolution of the brain and cognition. Evolutionary scholars, including paleoanthropologists, have deployed the standard array of evolutionary methods. Ethological and experimental evidence has added significantly to our understanding of nonhuman brains and cognition, especially those of nonhuman primates. Studies of fossil brains through endocasts and sophisticated imaging techniques have revealed evolutionary changes in gross neural anatomy. Psychologists have also gotten into the game through application of reverse engineering to experimentally based descriptions of cognitive functions. For hominin evolution, there is another rich source of evidence of cognition, the archeological record. Using the methods of Paleolithic archeology and the theories and models of cognitive science, evolutionary cognitive archeology documents developments in the hominin mind that would otherwise be inaccessible. © 2016 Wiley Periodicals, Inc.

  18. Constraining the Evolution of the Ionizing Background and the Epoch of Reionization with z~6 Quasars. II. A Sample of 19 Quasars

    Science.gov (United States)

    Fan, Xiaohui; Strauss, Michael A.; Becker, Robert H.; White, Richard L.; Gunn, James E.; Knapp, Gillian R.; Richards, Gordon T.; Schneider, Donald P.; Brinkmann, J.; Fukugita, Masataka

    2006-07-01

    We study the evolution of the ionization state of the intergalactic medium (IGM) at the end of the reionization epoch using moderate-resolution spectra of a sample of 19 quasars at 5.745.7: the GP optical depth evolution changes from τeffGP~(1+z)4.3 to (1+z)>~11, and the average length of dark gaps with τ>3.5 increases from 80 comoving Mpc. The dispersion of IGM properties along different lines of sight also increases rapidly, implying fluctuations by a factor of >~4 in the UV background at z>6, when the mean free path of UV photons is comparable to the correlation length of the star-forming galaxies that are thought to have caused reionization. The mean length of dark gaps shows the most dramatic increase at z~6, as well as the largest line-of-sight variations. We suggest using dark gap statistics as a powerful probe of the ionization state of the IGM at yet higher redshift. The sizes of H II regions around luminous quasars decrease rapidly toward higher redshift, suggesting that the neutral fraction of the IGM has increased by a factor of >~10 from z=5.7 to 6.4, consistent with the value derived from the GP optical depth. The mass-averaged neutral fraction is 1%-4% at z~6.2 based on the GP optical depth and H II region size measurements. The observations suggest that z~6 is the end of the overlapping stage of reionization and are inconsistent with a mostly neutral IGM at z~6, as indicated by the finite length of the dark absorption gaps. Based on observations obtained with the Sloan Digital Sky Survey at the W. M. Keck Observatory, which is operated as a scientific partnership among the California Institute of Technology, the University of California, and the National Aeronautics and Space Administration, made possible by the generous financial support of the W. M. Keck Foundation, with the MMT Observatory, a joint facility of the University of Arizona and the Smithsonian Institution, and with the Kitt Peak National Observatory 4 m Mayall Telescope. This paper

  19. Arthropod evolution and development: recent insights from chelicerates and myriapods.

    Science.gov (United States)

    Leite, Daniel J; McGregor, Alistair P

    2016-08-01

    Research on arthropod genetics and development has added much to our understanding of animal evolution. While this work has mainly focused on insects, a growing body of research on the less studied myriapods and chelicerates is providing important new insights into arthropod genomics and development. Multiple chelicerate lineages have a high incidence of gene duplication, which is suggestive of large-scale and even whole genome duplications. Furthermore, the duplication and divergence of genes is associated with the evolution of appendage morphology and other phenotypes in chelicerates and myriapods. Recent studies of these arthropods have also helped to understand the evolution and development of segmented bodies. Further research on chelicerate and myriapod models as well as species from other orders of these subphyla has great potential to expand our understanding of the evolution of animal genomes and development. Copyright © 2016 Elsevier Ltd. All rights reserved.

  20. The Evolution of the Faint End of the UV Luminosity Function during the Peak Epoch of Star Formation (1 < z < 3)

    Science.gov (United States)

    Alavi, Anahita; Siana, Brian; Richard, Johan; Rafelski, Marc; Jauzac, Mathilde; Limousin, Marceau; Freeman, William R.; Scarlata, Claudia; Robertson, Brant; Stark, Daniel P.; Teplitz, Harry I.; Desai, Vandana

    2016-11-01

    We present a robust measurement of the rest-frame UV luminosity function (LF) and its evolution during the peak epoch of cosmic star formation at 1\\lt z\\lt 3. We use our deep near-ultraviolet imaging from WFC3/UVIS on the Hubble Space Telescope and existing Advanced Camera for Surveys (ACS)/WFC and WFC3/IR imaging of three lensing galaxy clusters, Abell 2744 and MACS J0717 from the Hubble Frontier Field survey and Abell 1689. Combining deep UV imaging and high magnification from strong gravitational lensing, we use photometric redshifts to identify 780 ultra-faint galaxies with {M}{UV}\\lt -12.5 AB mag at 1\\lt z\\lt 3. From these samples, we identified five new, faint, multiply imaged systems in A1689. We run a Monte Carlo simulation to estimate the completeness correction and effective volume for each cluster using the latest published lensing models. We compute the rest-frame UV LF and find the best-fit faint-end slopes of α =-1.56+/- 0.04, α =-1.72+/- 0.04, and α =-1.94+/- 0.06 at 1.0\\lt z\\lt 1.6, 1.6\\lt z\\lt 2.2, and 2.2\\lt z\\lt 3.0, respectively. Our results demonstrate that the UV LF becomes steeper from z˜ 1.3 to z˜ 2.6 with no sign of a turnover down to {M}{UV}=-14 AB mag. We further derive the UV LFs using the Lyman break “dropout” selection and confirm the robustness of our conclusions against different selection methodologies. Because the sample sizes are so large and extend to such faint luminosities, the statistical uncertainties are quite small, and systematic uncertainties (due to the assumed size distribution, for example) likely dominate. If we restrict our analysis to galaxies and volumes above \\gt 50 % completeness in order to minimize these systematics, we still find that the faint-end slope is steep and getting steeper with redshift, though with slightly shallower (less negative) values (α =-1.55+/- 0.06, -1.69 ± 0.07, and -1.79 ± 0.08 for z˜ 1.3, 1.9, and 2.6, respectively). Finally, we conclude that the faint star

  1. Senescence gives insights into the morphogenetic evolution of anamniotes

    Directory of Open Access Journals (Sweden)

    Éric Villiard

    2017-06-01

    Full Text Available Senescence represents a mechanism to avoid undesired cell proliferation that plays a role in tumor suppression, wound healing and embryonic development. In order to gain insight on the evolution of senescence, we looked at its presence in developing axolotls (urodele amphibians and in zebrafish (teleost fish, which are both anamniotes. Our data indicate that cellular senescence is present in various developing structures in axolotls (pronephros, olfactory epithelium of nerve fascicles, lateral organs, gums and in zebrafish (epithelium of the yolk sac and in the lower part of the gut. Senescence was particularly associated with transient structures (pronephros in axolotls and yolk sac in zebrafish suggesting that it may play a role in the elimination of these tissues. Our data supports the notion that cellular senescence evolved early in vertebrate evolution to influence embryonic development.

  2. Comparative genomics provide insights into evolution of trichoderma nutrition style.

    Science.gov (United States)

    Xie, Bin-Bin; Qin, Qi-Long; Shi, Mei; Chen, Lei-Lei; Shu, Yan-Li; Luo, Yan; Wang, Xiao-Wei; Rong, Jin-Cheng; Gong, Zhi-Ting; Li, Dan; Sun, Cai-Yun; Liu, Gui-Ming; Dong, Xiao-Wei; Pang, Xiu-Hua; Huang, Feng; Liu, Weifeng; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Song, Xiao-Yan

    2014-02-01

    Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma. However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum, an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei (Tr), including glycoside hydrolases and nonribosomal peptide synthetase-polyketide synthase. Homology and phylogenetic analyses suggest that a large number of nutrition-related genes, including GH18 chitinases, β-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum (Tl) and Tr. dN/dS (ω) calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in Tl and Tr, suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma.

  3. Observing the epoch of galaxy formation.

    Science.gov (United States)

    Steidel, C C

    1999-04-13

    Significant observational progress in addressing the question of the origin and early evolution of galaxies has been made in the past few years, allowing for direct comparison of the epoch when most of the stars in the universe were forming to prevailing theoretical models. There is currently broad consistency between theoretical expectations and the observations, but rapid improvement in the data will provide much more critical tests of theory in the coming years.

  4. Pliocene geomagnetic polarity epochs

    Science.gov (United States)

    Dalrymple, G.B.; Cox, A.; Doell, Richard R.; Gromme, C.S.

    1967-01-01

    A paleomagnetic and K-Ar dating study of 44 upper Miocene and Pliocene volcanic units from the western United States suggests that the frequency of reversals of the earth's magnetic field during Pliocene time may have been comparable with that of the last 3.6 m.y. Although the data are too limited to permit the formal naming of any new polarity epochs or events, four polarity transitions have been identified: the W10 R/N boundary at 3.7 ?? 0.1 m.y., the A12 N/R boundary at 4.9 ?? 0.1 m.y., the W32 N/R boundary at 9.0 ?? 0.2m.y., and the W36 R/N boundary at 10.8 ?? 0.3 - 1.0 m.y. The loss of absolute resolution of K-Ar dating in older rocks indicates that the use of well defined stratigraphic successions to identify and date polarity transitions will be important in the study of Pliocene and older reversals. ?? 1967.

  5. Eggshell Porosity Provides Insight on Evolution of Nesting in Dinosaurs.

    Directory of Open Access Journals (Sweden)

    Kohei Tanaka

    Full Text Available Knowledge about the types of nests built by dinosaurs can provide insight into the evolution of nesting and reproductive behaviors among archosaurs. However, the low preservation potential of their nesting materials and nesting structures means that most information can only be gleaned indirectly through comparison with extant archosaurs. Two general nest types are recognized among living archosaurs: 1 covered nests, in which eggs are incubated while fully covered by nesting material (as in crocodylians and megapodes, and 2 open nests, in which eggs are exposed in the nest and brooded (as in most birds. Previously, dinosaur nest types had been inferred by estimating the water vapor conductance (i.e., diffusive capacity of their eggs, based on the premise that high conductance corresponds to covered nests and low conductance to open nests. However, a lack of statistical rigor and inconsistencies in this method render its application problematic and its validity questionable. As an alternative we propose a statistically rigorous approach to infer nest type based on large datasets of eggshell porosity and egg mass compiled for over 120 extant archosaur species and 29 archosaur extinct taxa/ootaxa. The presence of a strong correlation between eggshell porosity and nest type among extant archosaurs indicates that eggshell porosity can be used as a proxy for nest type, and thus discriminant analyses can help predict nest type in extinct taxa. Our results suggest that: 1 covered nests are likely the primitive condition for dinosaurs (and probably archosaurs, and 2 open nests first evolved among non-avian theropods more derived than Lourinhanosaurus and were likely widespread in non-avian maniraptorans, well before the appearance of birds. Although taphonomic evidence suggests that basal open nesters (i.e., oviraptorosaurs and troodontids were potentially the first dinosaurs to brood their clutches, they still partially buried their eggs in sediment

  6. Eggshell Porosity Provides Insight on Evolution of Nesting in Dinosaurs.

    Science.gov (United States)

    Tanaka, Kohei; Zelenitsky, Darla K; Therrien, François

    2015-01-01

    Knowledge about the types of nests built by dinosaurs can provide insight into the evolution of nesting and reproductive behaviors among archosaurs. However, the low preservation potential of their nesting materials and nesting structures means that most information can only be gleaned indirectly through comparison with extant archosaurs. Two general nest types are recognized among living archosaurs: 1) covered nests, in which eggs are incubated while fully covered by nesting material (as in crocodylians and megapodes), and 2) open nests, in which eggs are exposed in the nest and brooded (as in most birds). Previously, dinosaur nest types had been inferred by estimating the water vapor conductance (i.e., diffusive capacity) of their eggs, based on the premise that high conductance corresponds to covered nests and low conductance to open nests. However, a lack of statistical rigor and inconsistencies in this method render its application problematic and its validity questionable. As an alternative we propose a statistically rigorous approach to infer nest type based on large datasets of eggshell porosity and egg mass compiled for over 120 extant archosaur species and 29 archosaur extinct taxa/ootaxa. The presence of a strong correlation between eggshell porosity and nest type among extant archosaurs indicates that eggshell porosity can be used as a proxy for nest type, and thus discriminant analyses can help predict nest type in extinct taxa. Our results suggest that: 1) covered nests are likely the primitive condition for dinosaurs (and probably archosaurs), and 2) open nests first evolved among non-avian theropods more derived than Lourinhanosaurus and were likely widespread in non-avian maniraptorans, well before the appearance of birds. Although taphonomic evidence suggests that basal open nesters (i.e., oviraptorosaurs and troodontids) were potentially the first dinosaurs to brood their clutches, they still partially buried their eggs in sediment. Open nests

  7. Plasmids and rickettsial evolution: insight from Rickettsia felis.

    Directory of Open Access Journals (Sweden)

    Joseph J Gillespie

    2007-03-01

    Full Text Available The genome sequence of Rickettsia felis revealed a number of rickettsial genetic anomalies that likely contribute not only to a large genome size relative to other rickettsiae, but also to phenotypic oddities that have confounded the categorization of R. felis as either typhus group (TG or spotted fever group (SFG rickettsiae. Most intriguing was the first report from rickettsiae of a conjugative plasmid (pRF that contains 68 putative open reading frames, several of which are predicted to encode proteins with high similarity to conjugative machinery in other plasmid-containing bacteria.Using phylogeny estimation, we determined the mode of inheritance of pRF genes relative to conserved rickettsial chromosomal genes. Phylogenies of chromosomal genes were in agreement with other published rickettsial trees. However, phylogenies including pRF genes yielded different topologies and suggest a close relationship between pRF and ancestral group (AG rickettsiae, including the recently completed genome of R. bellii str. RML369-C. This relatedness is further supported by the distribution of pRF genes across other rickettsiae, as 10 pRF genes (or inactive derivatives also occur in AG (but not SFG rickettsiae, with five of these genes characteristic of typical plasmids. Detailed characterization of pRF genes resulted in two novel findings: the identification of oriV and replication termination regions, and the likelihood that a second proposed plasmid, pRFdelta, is an artifact of the original genome assembly.Altogether, we propose a new rickettsial classification scheme with the addition of a fourth lineage, transitional group (TRG rickettsiae, that is unique from TG and SFG rickettsiae and harbors genes from possible exchanges with AG rickettsiae via conjugation. We offer insight into the evolution of a plastic plasmid system in rickettsiae, including the role plasmids may have played in the acquirement of virulence traits in pathogenic strains, and the

  8. Insights into hominid evolution from the gorilla genome sequence

    Science.gov (United States)

    Scally, Aylwyn; Dutheil, Julien Y.; Hillier, LaDeana W.; Jordan, Greg E.; Goodhead, Ian; Herrero, Javier; Hobolth, Asger; Lappalainen, Tuuli; Mailund, Thomas; Marques-Bonet, Tomas; McCarthy, Shane; Montgomery, Stephen H.; Schwalie, Petra C.; Tang, Y. Amy; Ward, Michelle C.; Xue, Yali; Yngvadottir, Bryndis; Alkan, Can; Andersen, Lars N.; Ayub, Qasim; Ball, Edward V.; Beal, Kathryn; Bradley, Brenda J.; Chen, Yuan; Clee, Chris M.; Fitzgerald, Stephen; Graves, Tina A.; Gu, Yong; Heath, Paul; Heger, Andreas; Karakoc, Emre; Kolb-Kokocinski, Anja; Laird, Gavin K.; Lunter, Gerton; Meader, Stephen; Mort, Matthew; Mullikin, James C.; Munch, Kasper; O’Connor, Timothy D.; Phillips, Andrew D.; Prado-Martinez, Javier; Rogers, Anthony S.; Sajjadian, Saba; Schmidt, Dominic; Shaw, Katy; Simpson, Jared T.; Stenson, Peter D.; Turner, Daniel J.; Vigilant, Linda; Vilella, Albert J.; Whitener, Weldon; Zhu, Baoli; Cooper, David N.; de Jong, Pieter; Dermitzakis, Emmanouil T.; Eichler, Evan E.; Flicek, Paul; Goldman, Nick; Mundy, Nicholas I.; Ning, Zemin; Odom, Duncan T.; Ponting, Chris P.; Quail, Michael A.; Ryder, Oliver A.; Searle, Stephen M.; Warren, Wesley C.; Wilson, Richard K.; Schierup, Mikkel H.; Rogers, Jane; Tyler-Smith, Chris; Durbin, Richard

    2012-01-01

    Summary Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution. PMID:22398555

  9. The quantum epoché.

    Science.gov (United States)

    Pylkkänen, Paavo

    2015-12-01

    The theme of phenomenology and quantum physics is here tackled by examining some basic interpretational issues in quantum physics. One key issue in quantum theory from the very beginning has been whether it is possible to provide a quantum ontology of particles in motion in the same way as in classical physics, or whether we are restricted to stay within a more limited view of quantum systems, in terms of complementary but mutually exclusive phenomena. In phenomenological terms we could describe the situation by saying that according to the usual interpretation of quantum theory (especially Niels Bohr's), quantum phenomena require a kind of epoché (i.e. a suspension of assumptions about reality at the quantum level). However, there are other interpretations (especially David Bohm's) that seem to re-establish the possibility of a mind-independent ontology at the quantum level. We will show that even such ontological interpretations contain novel, non-classical features, which require them to give a special role to "phenomena" or "appearances", a role not encountered in classical physics. We will conclude that while ontological interpretations of quantum theory are possible, quantum theory implies the need of a certain kind of epoché even for this type of interpretations. While different from the epoché connected to phenomenological description, the "quantum epoché" nevertheless points to a potentially interesting parallel between phenomenology and quantum philosophy. Copyright © 2015. Published by Elsevier Ltd.

  10. Insights into bilaterian evolution from three spiralian genomes

    Energy Technology Data Exchange (ETDEWEB)

    Simakov, Oleg; Marletaz, Ferdinand; Cho, Sung-Jin; Edsinger-Gonzales, Eric; Havlak, Paul; Hellsten, Uffe; Kuo, Dian-Han; Larsson, Tomas; Lv, Jie; Arendt, Detlev; Savage, Robert; Osoegawa, Kazutoyo; de Jong, Pieter; Grimwood, Jane; Chapman, Jarrod A.; Shapiro, Harris; Otillar, Robert P.; Terry, Astrid Y.; Boore, Jeffrey L.; Grigoriev, Igor V.; Lindberg, David R.; Seaver, Elaine C.; Weisblat, David A.; Putnam, Nicholas H.; Rokhsar, Daniel S.; Aerts, Andrea

    2012-01-07

    Current genomic perspectives on animal diversity neglect two prominent phyla, the molluscs and annelids, that together account for nearly one-third of known marine species and are important both ecologically and as experimental systems in classical embryology1, 2, 3. Here we describe the draft genomes of the owl limpet (Lottia gigantea), a marine polychaete (Capitella teleta) and a freshwater leech (Helobdella robusta), and compare them with other animal genomes to investigate the origin and diversification of bilaterians from a genomic perspective. We find that the genome organization, gene structure and functional content of these species are more similar to those of some invertebrate deuterostome genomes (for example, amphioxus and sea urchin) than those of other protostomes that have been sequenced to date (flies, nematodes and flatworms). The conservation of these genomic features enables us to expand the inventory of genes present in the last common bilaterian ancestor, establish the tripartite diversification of bilaterians using multiple genomic characteristics and identify ancient conserved long- and short-range genetic linkages across metazoans. Superimposed on this broadly conserved pan-bilaterian background we find examples of lineage-specific genome evolution, including varying rates of rearrangement, intron gain and loss, expansions and contractions of gene families, and the evolution of clade-specific genes that produce the unique content of each genome.

  11. The Value of Change: Surprises and Insights in Stellar Evolution

    Science.gov (United States)

    Bildsten, Lars

    2018-01-01

    Astronomers with large-format cameras regularly scan the sky many times per night to detect what's changing, and telescopes in space such as Kepler and, soon, TESS obtain very accurate brightness measurements of nearly a million stars over time periods of years. These capabilities, in conjunction with theoretical and computational efforts, have yielded surprises and remarkable new insights into the internal properties of stars and how they end their lives. I will show how asteroseismology reveals the properties of the deep interiors of red giants, and highlight how astrophysical transients may be revealing unusual thermonuclear outcomes from exploding white dwarfs and the births of highly magnetic neutron stars. All the while, stellar science has been accelerated by the availability of open source tools, such as Modules for Experiments in Stellar Astrophysics (MESA), and the nearly immediate availability of observational results.

  12. Comparative genomics reveals insights into avian genome evolution and adaptation

    Science.gov (United States)

    Zhang, Guojie; Li, Cai; Li, Qiye; Li, Bo; Larkin, Denis M.; Lee, Chul; Storz, Jay F.; Antunes, Agostinho; Greenwold, Matthew J.; Meredith, Robert W.; Ödeen, Anders; Cui, Jie; Zhou, Qi; Xu, Luohao; Pan, Hailin; Wang, Zongji; Jin, Lijun; Zhang, Pei; Hu, Haofu; Yang, Wei; Hu, Jiang; Xiao, Jin; Yang, Zhikai; Liu, Yang; Xie, Qiaolin; Yu, Hao; Lian, Jinmin; Wen, Ping; Zhang, Fang; Li, Hui; Zeng, Yongli; Xiong, Zijun; Liu, Shiping; Zhou, Long; Huang, Zhiyong; An, Na; Wang, Jie; Zheng, Qiumei; Xiong, Yingqi; Wang, Guangbiao; Wang, Bo; Wang, Jingjing; Fan, Yu; da Fonseca, Rute R.; Alfaro-Núñez, Alonzo; Schubert, Mikkel; Orlando, Ludovic; Mourier, Tobias; Howard, Jason T.; Ganapathy, Ganeshkumar; Pfenning, Andreas; Whitney, Osceola; Rivas, Miriam V.; Hara, Erina; Smith, Julia; Farré, Marta; Narayan, Jitendra; Slavov, Gancho; Romanov, Michael N; Borges, Rui; Machado, João Paulo; Khan, Imran; Springer, Mark S.; Gatesy, John; Hoffmann, Federico G.; Opazo, Juan C.; Håstad, Olle; Sawyer, Roger H.; Kim, Heebal; Kim, Kyu-Won; Kim, Hyeon Jeong; Cho, Seoae; Li, Ning; Huang, Yinhua; Bruford, Michael W.; Zhan, Xiangjiang; Dixon, Andrew; Bertelsen, Mads F.; Derryberry, Elizabeth; Warren, Wesley; Wilson, Richard K; Li, Shengbin; Ray, David A.; Green, Richard E.; O’Brien, Stephen J.; Griffin, Darren; Johnson, Warren E.; Haussler, David; Ryder, Oliver A.; Willerslev, Eske; Graves, Gary R.; Alström, Per; Fjeldså, Jon; Mindell, David P.; Edwards, Scott V.; Braun, Edward L.; Rahbek, Carsten; Burt, David W.; Houde, Peter; Zhang, Yong; Yang, Huanming; Wang, Jian; Jarvis, Erich D.; Gilbert, M. Thomas P.; Wang, Jun

    2015-01-01

    Birds are the most species-rich class of tetrapod vertebrates and have wide relevance across many research fields. We explored bird macroevolution using full genomes from 48 avian species representing all major extant clades. The avian genome is principally characterized by its constrained size, which predominantly arose because of lineage-specific erosion of repetitive elements, large segmental deletions, and gene loss. Avian genomes furthermore show a remarkably high degree of evolutionary stasis at the levels of nucleotide sequence, gene synteny, and chromosomal structure. Despite this pattern of conservation, we detected many non-neutral evolutionary changes in protein-coding genes and noncoding regions. These analyses reveal that pan-avian genomic diversity covaries with adaptations to different lifestyles and convergent evolution of traits. PMID:25504712

  13. Evolution of carbonaceous chondrite parent bodies: Insights into cometary nuclei

    International Nuclear Information System (INIS)

    McSween, H.Y. Jr.

    1989-01-01

    It is thought that cometary samples will comprise the most primitive materials that are able to be sampled. Although parent body alteration of such samples would not necessarily detract from scientists' interest in them, the possibility exists that modification processes may have affected cometary nuclei. Inferences about the kinds of modifications that might be encountered can be drawn from data on the evolution of carbonaceous chondrite parent bodies. Observations suggest that, of all the classes of chondrites, these meteorites are most applicable to the study of comets. If the proportion of possible internal heat sources such as Al-26 in cometary materials are similar to those in chondrites, and if the time scale of comet accretion was fast enough to permit incorporation of live radionuclides, comets might have had early thermal histories somewhat like those of carbonaceous chondrite parent bodies

  14. Insights into metazoan evolution from alvinella pompejana cDNAs

    Directory of Open Access Journals (Sweden)

    Thierry Jean-Claude

    2010-11-01

    Full Text Available Abstract Background Alvinella pompejana is a representative of Annelids, a key phylum for evo-devo studies that is still poorly studied at the sequence level. A. pompejana inhabits deep-sea hydrothermal vents and is currently known as one of the most thermotolerant Eukaryotes in marine environments, withstanding the largest known chemical and thermal ranges (from 5 to 105°C. This tube-dwelling worm forms dense colonies on the surface of hydrothermal chimneys and can withstand long periods of hypo/anoxia and long phases of exposure to hydrogen sulphides. A. pompejana specifically inhabits chimney walls of hydrothermal vents on the East Pacific Rise. To survive, Alvinella has developed numerous adaptations at the physiological and molecular levels, such as an increase in the thermostability of proteins and protein complexes. It represents an outstanding model organism for studying adaptation to harsh physicochemical conditions and for isolating stable macromolecules resistant to high temperatures. Results We have constructed four full length enriched cDNA libraries to investigate the biology and evolution of this intriguing animal. Analysis of more than 75,000 high quality reads led to the identification of 15,858 transcripts and 9,221 putative protein sequences. Our annotation reveals a good coverage of most animal pathways and networks with a prevalence of transcripts involved in oxidative stress resistance, detoxification, anti-bacterial defence, and heat shock protection. Alvinella proteins seem to show a slow evolutionary rate and a higher similarity with proteins from Vertebrates compared to proteins from Arthropods or Nematodes. Their composition shows enrichment in positively charged amino acids that might contribute to their thermostability. The gene content of Alvinella reveals that an important pool of genes previously considered to be specific to Deuterostomes were in fact already present in the last common ancestor of the Bilaterian

  15. Insights into the evolution of sialic acid catabolism among bacteria

    Directory of Open Access Journals (Sweden)

    Almagro-Moreno Salvador

    2009-05-01

    Full Text Available Abstract Background Sialic acids comprise a family of nine-carbon amino sugars that are prevalent in mucus rich environments. Sialic acids from the human host are used by a number of pathogens as an energy source. Here we explore the evolution of the genes involved in the catabolism of sialic acid. Results The cluster of genes encoding the enzymes N-acetylneuraminate lyase (NanA, epimerase (NanE, and kinase (NanK, necessary for the catabolism of sialic acid (the Nan cluster, are confined 46 bacterial species, 42 of which colonize mammals, 33 as pathogens and 9 as gut commensals. We found a putative sialic acid transporter associated with the Nan cluster in most species. We reconstructed the phylogenetic history of the NanA, NanE, and NanK proteins from the 46 species and compared them to the species tree based on 16S rRNA. Within the NanA phylogeny, Gram-negative and Gram-positive bacteria do not form distinct clades. NanA from Yersinia and Vibrio species was most closely related to the NanA clade from eukaryotes. To examine this further, we reconstructed the phylogeny of all NanA homologues in the databases. In this analysis of 83 NanA sequences, Bacteroidetes, a human commensal group formed a distinct clade with Verrucomicrobia, and branched with the Eukaryotes and the Yersinia/Vibrio clades. We speculate that pathogens such as V. cholerae may have acquired NanA from a commensal aiding their colonization of the human gut. Both the NanE and NanK phylogenies more closely represented the species tree but numerous incidences of incongruence are noted. We confirmed the predicted function of the sialic acid catabolism cluster in members the major intestinal pathogens Salmonella enterica, Vibrio cholerae, V. vulnificus, Yersinia enterocolitica and Y. pestis. Conclusion The Nan cluster among bacteria is confined to human pathogens and commensals conferring them the ability to utilize a ubiquitous carbon source in mucus rich surfaces of the human body

  16. Insights from amphioxus into the evolution of vertebrate cartilage.

    Directory of Open Access Journals (Sweden)

    Daniel Meulemans

    2007-08-01

    Full Text Available Central to the story of vertebrate evolution is the origin of the vertebrate head, a problem difficult to approach using paleontology and comparative morphology due to a lack of unambiguous intermediate forms. Embryologically, much of the vertebrate head is derived from two ectodermal tissues, the neural crest and cranial placodes. Recent work in protochordates suggests the first chordates possessed migratory neural tube cells with some features of neural crest cells. However, it is unclear how and when these cells acquired the ability to form cellular cartilage, a cell type unique to vertebrates. It has been variously proposed that the neural crest acquired chondrogenic ability by recruiting proto-chondrogenic gene programs deployed in the neural tube, pharynx, and notochord. To test these hypotheses we examined the expression of 11 amphioxus orthologs of genes involved in neural crest chondrogenesis. Consistent with cellular cartilage as a vertebrate novelty, we find that no single amphioxus tissue co-expresses all or most of these genes. However, most are variously co-expressed in mesodermal derivatives. Our results suggest that neural crest-derived cartilage evolved by serial cooption of genes which functioned primitively in mesoderm.

  17. Farming System Evolution and Adaptive Capacity: Insights for Adaptation Support

    Directory of Open Access Journals (Sweden)

    Jami L. Dixon

    2014-02-01

    Full Text Available Studies of climate impacts on agriculture and adaptation often provide current or future assessments, ignoring the historical contexts farming systems are situated within. We investigate how historical trends have influenced farming system adaptive capacity in Uganda using data from household surveys, semi-structured interviews, focus-group discussions and observations. By comparing two farming systems, we note three major findings: (1 similar trends in farming system evolution have had differential impacts on the diversity of farming systems; (2 trends have contributed to the erosion of informal social and cultural institutions and an increasing dependence on formal institutions; and (3 trade-offs between components of adaptive capacity are made at the farm-scale, thus influencing farming system adaptive capacity. To identify the actual impacts of future climate change and variability, it is important to recognize the dynamic nature of adaptation. In practice, areas identified for further adaptation support include: shift away from one-size-fits-all approach the identification and integration of appropriate modern farming method; a greater focus on building inclusive formal and informal institutions; and a more nuanced understanding regarding the roles and decision-making processes of influential, but external, actors. More research is needed to understand farm-scale trade-offs and the resulting impacts across spatial and temporal scales.

  18. Evolution of external genitalia: insights from reptilian development.

    Science.gov (United States)

    Gredler, Marissa L; Larkins, Christine E; Leal, Francisca; Lewis, A Kelsey; Herrera, Ana M; Perriton, Claire L; Sanger, Thomas J; Cohn, Martin J

    2014-01-01

    External genitalia are found in each of the major clades of amniotes. The phallus is an intromittent organ that functions to deliver sperm into the female reproductive tract for internal fertilization. The cellular and molecular genetic mechanisms of external genital development have begun to be elucidated from studies of the mouse genital tubercle, an embryonic appendage adjacent to the cloaca that is the precursor of the penis and clitoris. Progress in this area has improved our understanding of genitourinary malformations, which are among the most common birth defects in humans, and created new opportunities for comparative studies of other taxa. External genitalia evolve rapidly, which has led to a striking diversity of anatomical forms. Within the past year, studies of external genital development in non-mammalian amniotes, including birds, lizards, snakes, alligators, and turtles, have begun to shed light on the molecular and morphogenetic mechanisms underlying the diversification of phallus morphology. Here, we review recent progress in the comparative developmental biology of external genitalia and discuss the implications of this work for understanding external genital evolution. We address the question of the deep homology (shared common ancestry) of genital structures and of developmental mechanisms, and identify new areas of investigation that can be pursued by taking a comparative approach to studying development of the external genitalia. We propose an evolutionary interpretation of hypospadias, a congenital malformation of the urethra, and discuss how investigations of non-mammalian species can provide novel perspectives on human pathologies.

  19. Evolution and development: some insights from evolutionary theory

    Directory of Open Access Journals (Sweden)

    DAVID JEAN R.

    2001-01-01

    Full Text Available Developmental biology and evolutionary biology are both mature integrative disciplines which started in the 19th century and then followed parallel and independent scientific pathways. Recently, a genetical component has stepped into both disciplines (developmental genetics and evolutionary genetics pointing out the need for future convergent maturation. Indeed, the Evo-Devo approach is becoming popular among developmental biologists, based on the facts that distant groups share a common ancestry, that precise phylogenies can be worked out and that homologous genes often play similar roles during the development of very different organisms. In this essay, I try to show that the real future of Evo-Devo thinking is still broader. The evolutionary theory is a set of diverse concepts which can and should be used in any biological field. Evolutionary thinking trains to ask « why » questions and to provide logical and plausible answers. It can shed some light on a diversity of general problems such as how to distinguish homologies from analogies, the costs and benefits of multicellularity, the origin of novel structures (e.g. the head, or the evolution of sexual reproduction. In the next decade, we may expect a progressive convergence between developmental genetics and quantitative genetics.

  20. Insights on landscape evolution and climatic forcing on Titan

    Science.gov (United States)

    Lucas, A.; Daudon, C.; Rodriguez, S.; Cornet, T.; Perron, J. T.

    2017-12-01

    The landscapes of Titan were observed for nearly 13 years by the Cassini spacecraft and Huygens probe. With dunes, mountains, seas, lakes, rivers..., the great morphological variety observed testifies to the geological richness that Titan shares with the Earth. In this study, we combine analysis of radar and hyperspectral data provided by the Cassini-Huygens mission, with models of valley and river network evolution to better understand the processes at work that sculpt these familiar landscapes. We develop quantitative criteria for comparing 3D morphologies obtained by numerical simulation with those derived for Titan by photogrammetry. These criteria are validated on Earth's landscapes. We simulate morphologies similar to those observed and show that landscapes at the equator and poles are mainly controlled by river incision and mass wasting such as landslides for which we quantify their respective contribution. Subsequently, we relate modeling to precipitation rates of methane and show values that are to be compared with general circulation model predictions (GCM). Our results also show a very young age of formation of the observed morphologies, less than a few million years. Finally, we provide new constraints on current amplitude of the tidal effects and organic precipitation rates from atmosphere chemistry.

  1. LCROSS Impact Conditions and Ejecta Evolution: Insight from Experiments

    Science.gov (United States)

    Hermalyn, B.; Schultz, P. H.; Colaprete, A.

    2009-12-01

    from these experiments is a factor of ~10 less than predicted by methods above (Korycansky, et al 2009). Analysis of the LCROSS ejecta emergence and evolution, when compared with scaled experimental results, will provide an understanding of the impact conditions as well as constraints on the properties of the regolith.

  2. Pulsar slow-down epochs

    International Nuclear Information System (INIS)

    Heintzmann, H.; Novello, M.

    1981-01-01

    The relative importance of magnetospheric currents and low frequency waves for pulsar braking is assessed and a model is developed which tries to account for the available pulsar timing data under the unifying aspect that all pulsars have equal masses and magnetic moments and are born as rapid rotators. Four epochs of slow-down are distinguished which are dominated by different braking mechanisms. According to the model no direct relationship exists between 'slow-down age' and true age of a pulsar and leads to a pulsar birth-rate of one event per hundred years. (Author) [pt

  3. New Insights about Enzyme Evolution from Large Scale Studies of Sequence and Structure Relationships*

    Science.gov (United States)

    Brown, Shoshana D.; Babbitt, Patricia C.

    2014-01-01

    Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes. PMID:25210038

  4. New insights about enzyme evolution from large scale studies of sequence and structure relationships.

    Science.gov (United States)

    Brown, Shoshana D; Babbitt, Patricia C

    2014-10-31

    Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfamilies, each representing a large set of sequences that evolved from a common ancestor and that retain conserved features of their structures and active sites. Using several examples, we describe the different structural strategies nature has used to evolve new reaction and substrate specificities in each unique superfamily. The results provide insight about enzyme evolution that is not easily obtained from studies of one or only a few enzymes. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  5. Description of nighttime cough epochs in patients with stable COPD GOLD II-IV.

    Science.gov (United States)

    Fischer, Patrick; Gross, Volker; Kroenig, Johannes; Weissflog, Andreas; Hildebrandt, Olaf; Sohrabi, Keywan; Koehler, Ulrich

    Chronic cough is one of the main symptoms of COPD. Ambulatory objective monitoring provides novel insights into the determinants and characteristics of nighttime cough in COPD. Nighttime cough was monitored objectively by LEOSound lung sound monitor in patients with stable COPD II-IV. In 30 patients, with 10 patients in each stage group, nighttime cough was analyzed for epoch frequency, epoch severity (epoch length and coughs per epoch), and pattern (productive or nonproductive). Cough was found in all patients ranging from 1 to 294 events over the recording period. In 29 patients, cough epochs were monitored, ranging from 1 to 75 epochs. The highest amount of cough epochs was found in patients with COPD stage III. Active smokers had significantly more productive cough epochs (61%) than nonsmokers (24%). We found a high rate of nighttime cough epochs in patients with COPD, especially in those in stage III. Productive cough was predominantly found in patients with persistent smoking. LEOSound lung sound monitor offers a practical and valuable opportunity to evaluate cough objectively.

  6. FORMATION EPOCHS, STAR FORMATION HISTORIES, AND SIZES OF MASSIVE EARLY-TYPE GALAXIES IN CLUSTER AND FIELD ENVIRONMENTS AT z = 1.2: INSIGHTS FROM THE REST-FRAME ULTRAVIOLET

    International Nuclear Information System (INIS)

    Rettura, Alessandro; Demarco, R.; Ford, H. C.; Rosati, P.; Gobat, R.; Nonino, M.; Fosbury, R. A. E.; Menci, N.; Strazzullo, V.; Mei, S.

    2010-01-01

    We derive stellar masses, ages, and star formation histories (SFHs) of massive early-type galaxies in the z = 1.237 RDCS1252.9-2927 cluster and compare them with those measured in a similarly mass-selected sample of field contemporaries drawn from the Great Observatories Origin Deep Survey South Field. Robust estimates of these parameters are obtained by comparing a large grid of composite stellar population models with 8-9 band photometry in the rest-frame near-ultraviolet, optical, and IR, thus sampling the entire relevant domain of emission of the different stellar populations. Additionally, we present new, deep U-band photometry of both fields, giving access to the critical far-ultraviolet rest frame, in order to empirically constrain the dependence of the most recent star formation processes on the environment. We also analyze the morphological properties of both samples to examine the dependence of their scaling relations on their mass and environment. We find that early-type galaxies, both in the cluster and in the field, show analogous optical morphologies, follow comparable mass versus size relation, have congruent average surface stellar mass densities, and lie on the same Kormendy relation. We also show that a fraction of early-type galaxies in the field employ longer timescales, τ, to assemble their mass than their cluster contemporaries. Hence, we conclude that while the formation epoch of early-type galaxies only depends on their mass, the environment does regulate the timescales of their SFHs. Our deep U-band imaging strongly supports this conclusion. We show that cluster galaxies are at least 0.5 mag fainter than their field contemporaries of similar mass and optical-to-infrared colors, implying that the last episode of star formation must have happened more recently in the field than in the cluster.

  7. The epochs of international law

    CERN Document Server

    Grewe, Wilhelm G

    2000-01-01

    A theoretical overview and detailed analysis of the history of international law from the Middle Ages through to the end of the twentieth century (updated from the 1984 German language edition). Wilhelm Grewe's "Epochen der Völkerrechtsgeschichte" is widely regarded as one of the classic twentieth century works of international law. This revised translation by Michael Byers of Oxford University makes this important book available to non-German readers for the first time. "The Epochs of International Law" provides a theoretical overview and detailed analysis of the history of international law from the Middle Ages, to the Age of Discovery and the Thirty Years War, from Napoleon Bonaparte to the Treaty of Versailles and the Age of the Single Superpower, and does so in a way that reflects Grewe's own experience as one of Germany's leading diplomats and professors of international law. A new chapter, written by Wilhelm Grewe and Michael Byers, updates the book to 1998, making the revised translation of interest ...

  8. The Importance of Lake Overflow Floods for Early Martian Landscape Evolution: Insights From Licus Vallis

    Science.gov (United States)

    Goudge, T. A.; Fassett, C. I.

    2017-01-01

    Open-basin lake outlet valleys are incised when water breaches the basin-confining topography and overflows. Outlet valleys record this flooding event and provide insight into how the lake and surrounding terrain evolved over time. Here we present a study of the paleolake outlet Licus Vallis, a >350 km long, >2 km wide, >100 m deep valley that heads at the outlet breach of an approx.30 km diameter impact crater. Multiple geomorphic features of this valley system suggest it records a more complex evolution than formation from a single lake overflow flood. This provides unique insight into the paleohydrology of lakes on early Mars, as we can make inferences beyond the most recent phase of activity..

  9. Epochality, Global Capitalism and Ecology

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    Wayne Hope

    2018-05-01

    Full Text Available What type of capitalism do we live in today? My answer to this question draws upon two interrelated lines of argument. Firstly, I will argue that we inhabit an epoch of global capitalism. The precursors of this kind of capitalism originated from the late nineteenth century when the development of telegraph networks, modern transport systems and world time zones provided a global template for industrialisation and Western imperialism. From about 1980 a confluence of global events and processes bought a fully-fledged global capitalism into being. These included the collapse of Fordist Keynesianism, national Keynesianism and Soviet Communism along with First, Second and Third World demarcations; the international proliferation of neo-liberal policy regimes; the growth of transnational corporations in all economic sectors; the predominance of financialisation and the reconstitution of global workforces. Secondly, I will argue that the shift from organic surface energy to underground fossil energy intertwined the time of the earth with the time of human history as nature was being instrumentalised as a resource for humanity. Understanding the capitalist relations of power involved here requires that we rethink the emergence of industrial capitalism in the historical context of a world system built upon unequal socio-ecological exchange between core and periphery. Today, global capitalism has intensified the anthropogenic feedback loops associated with CO2 emissions and climate change and universalised the organisational frameworks of profit extraction and socio-ecological destruction. I refer here to the transnational systems of fossil fuel capitalism along with their interlinkages with financialisation and advertising/commodity fetishism. From the preceding lines of argument I will briefly outline the intra-capitalist and planetary-ecological crises out of which transnational coalitions of opposition might emerge.

  10. Linear Covariance Analysis and Epoch State Estimators

    Science.gov (United States)

    Markley, F. Landis; Carpenter, J. Russell

    2014-01-01

    This paper extends in two directions the results of prior work on generalized linear covariance analysis of both batch least-squares and sequential estimators. The first is an improved treatment of process noise in the batch, or epoch state, estimator with an epoch time that may be later than some or all of the measurements in the batch. The second is to account for process noise in specifying the gains in the epoch state estimator. We establish the conditions under which the latter estimator is equivalent to the Kalman filter.

  11. The evolution of Yellowstone's magmatic system over the past 630 kyr: Insights from the crystal record

    Science.gov (United States)

    Stelten, M. E.

    2017-12-01

    The Yellowstone Plateau volcanic field in northwestern Wyoming is one of the world's largest, active silicic volcanic centers, and has produced three caldera-forming "super eruptions" over the past 2.1 Myr. As a result, the petrologic evolution of Yellowstone's magmatic system has been the focus of numerous studies over the past 60 years. Early studies at Yellowstone focused on characterizing whole-rock chemical and isotopic variations observed in magmas erupted over Yellowstone's lifetime. While these have provided important insights into the source of Yellowstone magmas and the processes controlling their compositional evolution though time, whole-rock studies are limited in their ability to identify the mechanisms and timescales of rhyolite generation. In contrast, much of the recent work at Yellowstone has focused on applying micro-analytical techniques to characterize the age and composition of phenocrysts hosted in Yellowstone rhyolites. These studies have greatly advanced our understanding of the magmatic system at Yellowstone and have provided crucial new insights into the mechanisms and timescales of rhyolite generation. In particular, recent work has focused on applying micro-analytical techniques to study the age and origin of the [1] three caldera-forming eruptions that produced the Huckleberry Ridge, Mesa Falls, Lava Creek tuffs and [2] post-Lava Creek tuff intracaldera rhyolites that compose the Plateau Rhyolite. As a result, a wealth of crystal-chemical data now exists for rhyolites erupted throughout Yellowstone's 2.1 Myr history. These data provide a unique opportunity to create a detailed reconstruction of Yellowstone's magmatic system through time. In this contribution, I integrate available age, chemical, and isotopic data for phenocrysts hosted in Yellowstone rhyolites to construct a model for the evolution of Yellowstone's magmatic system from the caldera-forming eruption of the Lava Creek tuff at ca. 0.63 Ma to the present day. In particular

  12. Root evolution at the base of the lycophyte clade: insights from an Early Devonian lycophyte

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    Matsunaga, Kelly K. S.; Tomescu, Alexandru M. F.

    2016-01-01

    Background and Aims The evolution of complex rooting systems during the Devonian had significant impacts on global terrestrial ecosystems and the evolution of plant body plans. However, detailed understanding of the pathways of root evolution and the architecture of early rooting systems is currently lacking. We describe the architecture and resolve the structural homology of the rooting system of an Early Devonian basal lycophyte. Insights gained from these fossils are used to address lycophyte root evolution and homology. Methods Plant fossils are preserved as carbonaceous compressions at Cottonwood Canyon (Wyoming), in the Lochkovian–Pragian (∼411 Ma; Early Devonian) Beartooth Butte Formation. We analysed 177 rock specimens and documented morphology, cuticular anatomy and structural relationships, as well as stratigraphic position and taphonomic conditions. Key Results The rooting system of the Cottonwood Canyon lycophyte is composed of modified stems that bear fine, dichotomously branching lateral roots. These modified stems, referred to as root-bearing axes, are produced at branching points of the above-ground shoot system. Root-bearing axes preserved in growth position exhibit evidence of positive gravitropism, whereas the lateral roots extend horizontally. Consistent recurrence of these features in successive populations of the plant preserved in situ demonstrates that they represent constitutive structural traits and not opportunistic responses of a flexible developmental programme. Conclusions This is the oldest direct evidence for a rooting system preserved in growth position. These rooting systems, which can be traced to a parent plant, include some of the earliest roots known to date and demonstrate that substantial plant–substrate interactions were under way by Early Devonian time. The morphological relationships between stems, root-bearing axes and roots corroborate evidence that positive gravitropism and root identity were evolutionarily

  13. Y-chromosome evolution: emerging insights into processes of Y-chromosome degeneration.

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    Bachtrog, Doris

    2013-02-01

    The human Y chromosome is intriguing not only because it harbours the master-switch gene that determines gender but also because of its unusual evolutionary history. The Y chromosome evolved from an autosome, and its evolution has been characterized by massive gene decay. Recent whole-genome and transcriptome analyses of Y chromosomes in humans and other primates, in Drosophila species and in plants have shed light on the current gene content of the Y chromosome, its origins and its long-term fate. Furthermore, comparative analysis of young and old Y chromosomes has given further insights into the evolutionary and molecular forces triggering Y-chromosome degeneration and into the evolutionary destiny of the Y chromosome.

  14. Spider genomes provide insight into composition and evolution of venom and silk

    Science.gov (United States)

    Sanggaard, Kristian W.; Bechsgaard, Jesper S.; Fang, Xiaodong; Duan, Jinjie; Dyrlund, Thomas F.; Gupta, Vikas; Jiang, Xuanting; Cheng, Ling; Fan, Dingding; Feng, Yue; Han, Lijuan; Huang, Zhiyong; Wu, Zongze; Liao, Li; Settepani, Virginia; Thøgersen, Ida B.; Vanthournout, Bram; Wang, Tobias; Zhu, Yabing; Funch, Peter; Enghild, Jan J.; Schauser, Leif; Andersen, Stig U.; Villesen, Palle; Schierup, Mikkel H; Bilde, Trine; Wang, Jun

    2014-01-01

    Spiders are ecologically important predators with complex venom and extraordinarily tough silk that enables capture of large prey. Here we present the assembled genome of the social velvet spider and a draft assembly of the tarantula genome that represent two major taxonomic groups of spiders. The spider genomes are large with short exons and long introns, reminiscent of mammalian genomes. Phylogenetic analyses place spiders and ticks as sister groups supporting polyphyly of the Acari. Complex sets of venom and silk genes/proteins are identified. We find that venom genes evolved by sequential duplication, and that the toxic effect of venom is most likely activated by proteases present in the venom. The set of silk genes reveals a highly dynamic gene evolution, new types of silk genes and proteins, and a novel use of aciniform silk. These insights create new opportunities for pharmacological applications of venom and biomaterial applications of silk. PMID:24801114

  15. Evolution of the vertebrate claudin gene family: insights from a basal vertebrate, the sea lamprey.

    Science.gov (United States)

    Mukendi, Christian; Dean, Nicholas; Lala, Rushil; Smith, Jeramiah; Bronner, Marianne E; Nikitina, Natalya V

    2016-01-01

    Claudins are major constituents of tight junctions, contributing both to their intercellular sealing and selective permeability properties. While claudins and claudin-like molecules are present in some invertebrates, the association of claudins with tight junctions has been conclusively documented only in vertebrates. Here we report the sequencing, phylogenetic analysis and comprehensive spatiotemporal expression analysis of the entire claudin gene family in the basal extant vertebrate, the sea lamprey. Our results demonstrate that clear orthologues to about half of all mammalian claudins are present in the lamprey, suggesting that at least one round of whole genome duplication contributed to the diversification of this gene family. Expression analysis revealed that claudins are expressed in discrete and specific domains, many of which represent vertebrate-specific innovations, such as in cranial ectodermal placodes and the neural crest; whereas others represent structures characteristic of chordates, e.g. pronephros, notochord, somites, endostyle and pharyngeal arches. By comparing the embryonic expression of claudins in the lamprey to that of other vertebrates, we found that ancestral expression patterns were often preserved in higher vertebrates. Morpholino mediated loss of Cldn3b demonstrated a functional role for this protein in placode and pharyngeal arch morphogenesis. Taken together, our data provide novel insights into the origins and evolution of the claudin gene family and the significance of claudin proteins in the evolution of vertebrates.

  16. Convergent evolution in aquatic tetrapods: insights from an exceptional fossil mosasaur.

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    Johan Lindgren

    Full Text Available Mosasaurs (family Mosasauridae are a diverse group of secondarily aquatic lizards that radiated into marine environments during the Late Cretaceous (98-65 million years ago. For the most part, they have been considered to be simple anguilliform swimmers--i.e., their propulsive force was generated by means of lateral undulations incorporating the greater part of the body--with unremarkable, dorsoventrally narrow tails and long, lizard-like bodies. Convergence with the specialized fusiform body shape and inferred carangiform locomotory style (in which only a portion of the posterior body participates in the thrust-producing flexure of ichthyosaurs and metriorhynchid crocodyliform reptiles, along with cetaceans, has so far only been recognized in Plotosaurus, the most highly derived member of the Mosasauridae. Here we report on an exceptionally complete specimen (LACM 128319 of the moderately derived genus Platecarpus that preserves soft tissues and anatomical details (e.g., large portions of integument, a partial body outline, putative skin color markings, a downturned tail, branching bronchial tubes, and probable visceral traces to an extent that has never been seen previously in any mosasaur. Our study demonstrates that a streamlined body plan and crescent-shaped caudal fin were already well established in Platecarpus, a taxon that preceded Plotosaurus by 20 million years. These new data expand our understanding of convergent evolution among marine reptiles, and provide insights into their evolution's tempo and mode.

  17. Genomes and geography: genomic insights into the evolution and phylogeography of the genus Schistosoma

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    Ironside Joe E

    2011-07-01

    Full Text Available Abstract Blood flukes within the genus Schistosoma still remain a major cause of disease in the tropics and subtropics and the study of their evolution has been an area of major debate and research. With the advent of modern molecular and genomic approaches deeper insights have been attained not only into the divergence and speciation of these worms, but also into the historic movement of these parasites from Asia into Africa, via migration and dispersal of definitive and snail intermediate hosts. This movement was subsequently followed by a radiation of Schistosoma species giving rise to the S. mansoni and S. haematobium groups, as well as the S. indicum group that reinvaded Asia. Each of these major evolutionary events has been marked by distinct changes in genomic structure evident in differences in mitochondrial gene order and nuclear chromosomal architecture between the species associated with Asia and Africa. Data from DNA sequencing, comparative molecular genomics and karyotyping are indicative of major constitutional genomic events which would have become fixed in the ancestral populations of these worms. Here we examine how modern genomic techniques may give a more in depth understanding of the evolution of schistosomes and highlight the complexity of speciation and divergence in this group.

  18. A six-gene phylogeny provides new insights into choanoflagellate evolution.

    Science.gov (United States)

    Carr, Martin; Richter, Daniel J; Fozouni, Parinaz; Smith, Timothy J; Jeuck, Alexandra; Leadbeater, Barry S C; Nitsche, Frank

    2017-02-01

    Recent studies have shown that molecular phylogenies of the choanoflagellates (Class Choanoflagellatea) are in disagreement with their traditional taxonomy, based on morphology, and that Choanoflagellatea requires considerable taxonomic revision. Furthermore, phylogenies suggest that the morphological and ecological evolution of the group is more complex than has previously been recognized. Here we address the taxonomy of the major choanoflagellate order Craspedida, by erecting four new genera. The new genera are shown to be morphologically, ecologically and phylogenetically distinct from other choanoflagellate taxa. Furthermore, we name five novel craspedid species, as well as formally describe ten species that have been shown to be either misidentified or require taxonomic revision. Our revised phylogeny, including 18 new species and sequence data for two additional genes, provides insights into the morphological and ecological evolution of the choanoflagellates. We examine the distribution within choanoflagellates of these two additional genes, EF-1A and EFL, closely related translation GTPases which are required for protein synthesis. Mapping the presence and absence of these genes onto the phylogeny highlights multiple events of gene loss within the choanoflagellates. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  19. Insights into Mercury's Core Evolution from the Thermodynamic Properties of Fe-S-Si

    Science.gov (United States)

    Edgington, A.; Vocadlo, L.; Stixrude, L. P.; Wood, I. G.; Lord, O. T.

    2015-12-01

    The structure, composition and evolution of Mercury, the innermost planet, are puzzling, as its high uncompressed density implies a body highly enriched in metallic iron, whilst the existence of Mercury's magnetic field and observations of its longitude librations [1] suggest at least a partially molten core. This study uses a combination of experimental and ab-initio computer simulation techniques to determine the properties of Fe-S-Si (relative atomic percentages, 80:10:10) throughout the conditions of the interior of the planet Mercury, and evaluates the implications of this material for the structure and evolution of the planet's core. Previous studies have considered the addition of sulphur to the pure iron system, as this can significantly depress the melting curve of iron, and so may possibly allow Mercury's core to remain molten to the present day [2]. However, important constraints placed by the MESSENGER spacecraft on Mercury's surface abundance of iron [3] suggest that the planet formed in highly reduced conditions, in which significant amounts of silicon could have also dissolved into the core [4]. First-principles molecular dynamics simulations of the thermodynamic properties of liquid Fe-S-Si, alongside laser-heated diamond-anvil-cell experiments to determine the melting behaviour of the same composition, reveal the slopes of the adiabatic gradient and melting curve respectively, which together may allow insight into the evolution of our solar system's smallest planet. [1] Margot, J. L. et al. (2007) Science, 316: 710-714[2] Schubert, G. et al. (1988) in 'Mercury' 429-460[3] Nittler, L. R. et al. (2011) Science, 333, 1847-1850[4] Malavergne, V. et al. (2010) Icarus, 206:199-209

  20. Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes.

    Science.gov (United States)

    Johnson, Kim L; Cassin, Andrew M; Lonsdale, Andrew; Wong, Gane Ka-Shu; Soltis, Douglas E; Miles, Nicholas W; Melkonian, Michael; Melkonian, Barbara; Deyholos, Michael K; Leebens-Mack, James; Rothfels, Carl J; Stevenson, Dennis W; Graham, Sean W; Wang, Xumin; Wu, Shuangxiu; Pires, J Chris; Edger, Patrick P; Carpenter, Eric J; Bacic, Antony; Doblin, Monika S; Schultz, Carolyn J

    2017-06-01

    The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall-based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins. Using motif and amino acid bias, a newly developed bioinformatics pipeline, we identified HRGPs in sequences from the 1000 Plants transcriptome project (www.onekp.com). Our analyses provide new insights into the evolution of HRGPs across major evolutionary milestones, including the transition to land and the early radiation of angiosperms. Significantly, data mining reveals the origin of glycosylphosphatidylinositol (GPI)-anchored AGPs in green algae and a 3- to 4-fold increase in GPI-AGPs in liverworts and mosses. The first detection of cross-linking (CL)-EXTs is observed in bryophytes, which suggests that CL-EXTs arose though the juxtaposition of preexisting SP n EXT glycomotifs with refined Y-based motifs. We also detected the loss of CL-EXT in a few lineages, including the grass family (Poaceae), that have a cell wall composition distinct from other monocots and eudicots. A key challenge in HRGP research is tracking individual HRGPs throughout evolution. Using the 1000 Plants output, we were able to find putative orthologs of Arabidopsis pollen-specific GPI-AGPs in basal eudicots. © 2017 American Society of Plant Biologists. All Rights Reserved.

  1. Insights into the Evolution of Hydroxyproline-Rich Glycoproteins from 1000 Plant Transcriptomes1[OPEN

    Science.gov (United States)

    Cassin, Andrew M.; Soltis, Douglas E.; Miles, Nicholas W.; Melkonian, Michael; Melkonian, Barbara; Wu, Shuangxiu; Edger, Patrick P.; Carpenter, Eric J.

    2017-01-01

    The carbohydrate-rich cell walls of land plants and algae have been the focus of much interest given the value of cell wall-based products to our current and future economies. Hydroxyproline-rich glycoproteins (HRGPs), a major group of wall glycoproteins, play important roles in plant growth and development, yet little is known about how they have evolved in parallel with the polysaccharide components of walls. We investigate the origins and evolution of the HRGP superfamily, which is commonly divided into three major multigene families: the arabinogalactan proteins (AGPs), extensins (EXTs), and proline-rich proteins. Using motif and amino acid bias, a newly developed bioinformatics pipeline, we identified HRGPs in sequences from the 1000 Plants transcriptome project (www.onekp.com). Our analyses provide new insights into the evolution of HRGPs across major evolutionary milestones, including the transition to land and the early radiation of angiosperms. Significantly, data mining reveals the origin of glycosylphosphatidylinositol (GPI)-anchored AGPs in green algae and a 3- to 4-fold increase in GPI-AGPs in liverworts and mosses. The first detection of cross-linking (CL)-EXTs is observed in bryophytes, which suggests that CL-EXTs arose though the juxtaposition of preexisting SPn EXT glycomotifs with refined Y-based motifs. We also detected the loss of CL-EXT in a few lineages, including the grass family (Poaceae), that have a cell wall composition distinct from other monocots and eudicots. A key challenge in HRGP research is tracking individual HRGPs throughout evolution. Using the 1000 Plants output, we were able to find putative orthologs of Arabidopsis pollen-specific GPI-AGPs in basal eudicots. PMID:28446636

  2. Geomagnetic Polarity Epochs: Sierra Nevada II.

    Science.gov (United States)

    Cox, A; Doell, R R; Dalrymple, G B

    1963-10-18

    Ten new determinations on volcanic extrusions in the Sierra Nevada with potassium-argon ages of 3.1 million years or less indicate that the remanent magnetizations fall into two groups, a normal group in which the remanent magnetization is directed downward and to the north, and a reversed group magnetized up and to the south. Thermomagnetic experiments and mineralogic studies fail to provide an explanation of the opposing polarities in terms of mineralogic control, but rather suggest that the remanent magnetization reflects reversals of the main dipole field of the earth. All available radiometric ages are consistent with this field-reversal hypothesis and indicate that the present normal polarity epoch (N1) as well as the previous reversed epoch (R1) are 0.9 to 1.0 million years long, whereas the previous normal epoch (N2) was at least 25 percent longer.

  3. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists.

    Science.gov (United States)

    Burki, Fabien; Kudryavtsev, Alexander; Matz, Mikhail V; Aglyamova, Galina V; Bulman, Simon; Fiers, Mark; Keeling, Patrick J; Pawlowski, Jan

    2010-12-02

    work reveals another possible rhizarian signature in the 60S ribosomal protein L10a. Our study provides new insights into the evolution of Rhizaria based on phylogenomic analyses of ESTs from three groups of previously under-sampled protists. It was enabled through the application of a recently developed method of transcriptome analysis, requiring very small amount of starting material. Our study illustrates the potential of this method to elucidate the early evolution of eukaryotes by providing large amount of data for uncultivable free-living and parasitic protists.

  4. Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists

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    Bulman Simon

    2010-12-01

    insertion in Acantharea. Finally, this work reveals another possible rhizarian signature in the 60S ribosomal protein L10a. Conclusions Our study provides new insights into the evolution of Rhizaria based on phylogenomic analyses of ESTs from three groups of previously under-sampled protists. It was enabled through the application of a recently developed method of transcriptome analysis, requiring very small amount of starting material. Our study illustrates the potential of this method to elucidate the early evolution of eukaryotes by providing large amount of data for uncultivable free-living and parasitic protists.

  5. Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity.

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    Jessica N Ricaldi

    Full Text Available The whole genome analysis of two strains of the first intermediately pathogenic leptospiral species to be sequenced (Leptospira licerasiae strains VAR010 and MMD0835 provides insight into their pathogenic potential and deepens our understanding of leptospiral evolution. Comparative analysis of eight leptospiral genomes shows the existence of a core leptospiral genome comprising 1547 genes and 452 conserved genes restricted to infectious species (including L. licerasiae that are likely to be pathogenicity-related. Comparisons of the functional content of the genomes suggests that L. licerasiae retains several proteins related to nitrogen, amino acid and carbohydrate metabolism which might help to explain why these Leptospira grow well in artificial media compared with pathogenic species. L. licerasiae strains VAR010(T and MMD0835 possess two prophage elements. While one element is circular and shares homology with LE1 of L. biflexa, the second is cryptic and homologous to a previously identified but unnamed region in L. interrogans serovars Copenhageni and Lai. We also report a unique O-antigen locus in L. licerasiae comprised of a 6-gene cluster that is unexpectedly short compared with L. interrogans in which analogous regions may include >90 such genes. Sequence homology searches suggest that these genes were acquired by lateral gene transfer (LGT. Furthermore, seven putative genomic islands ranging in size from 5 to 36 kb are present also suggestive of antecedent LGT. How Leptospira become naturally competent remains to be determined, but considering the phylogenetic origins of the genes comprising the O-antigen cluster and other putative laterally transferred genes, L. licerasiae must be able to exchange genetic material with non-invasive environmental bacteria. The data presented here demonstrate that L. licerasiae is genetically more closely related to pathogenic than to saprophytic Leptospira and provide insight into the genomic bases for

  6. Champagne Pool (New Zealand) Thermophiles Yield Insights into the Evolution of Microbial Arsenic Resistance

    Science.gov (United States)

    Hug, K.; Krikowa, F.; Morgan, X.; Maher, W. A.; Stott, M. B.; Moreau, J. W.

    2011-12-01

    Arsenic is a highly toxic metalloid typically enriched in geothermal waters due to aqueous weathering of arsenic-bearing minerals. Investigation of enzymatic pathways by which thermophilic microorganisms cope with toxic arsenic levels may yield insights into the evolution of arsenic resistance mechanisms on the early Earth. At Wai-O-Tapu in the Taupo Volcanic Zone on the North Island of New Zealand, hot springs with temperatures of 30-90°C and elemental sulfur concentrations (expressed as equivalent sulfate) from 340 to 850 mg/l establish a range of environmental conditions. Total arsenic concentrations varied from 0.083 mg/l to 56 mg/l. Arsenic speciation analysis elucidated various biogeochemical arsenic transformations occurring within different springs. For example, in the Alum Cliff spring oxidizing conditions (Eh = 225 mV) were expected to stabilize dissolved arsenate (AsO43-). However, HPLC-ICPMS analyses yielded dissolved arsenate and arsenite (AsO33-) concentrations of 0.25 mg/l versus 43.3 mg/l, respectively, and point towards microbial arsenate reduction as the likely mechanism for arsenic redox transformation. 16S rRNA gene cloning of Alum Cliff DNA showed a predominantly archaeal population with the dominant clone "AC1_A1" most closely related (99% sequence similarity, NCBI BLAST°) to the uncultured Sulfolobus clone "ChP_97P" found in Champagne Pool (Childs et al., 2008). The closest isolated relative to AC1_A1 is Sulfolobus tokodaii str. TW with a sequence similarity of 94%. Arsenic speciation measurements from the Alum Cliff spring suggest that clone AC1_A1 features the arsenate reduction resistance mechanism, and we hypothesize therefore that an arsC (homolog or analog) provides this functionality. The organic arsenic species monomethylarsonic acid (MMA) and dimethylarsinic acid (DMA), detected via HPLC-ICPMS at concentrations ranging from 1 μg/l to 12 μg/l in various springs, may also implicate microbial methyl-group transfers as an active

  7. Aspects of gorgonopsian paleobiology and evolution: insights from the basicranium, occiput, osseous labyrinth, vasculature, and neuroanatomy

    Directory of Open Access Journals (Sweden)

    Ricardo Araújo

    2017-04-01

    Full Text Available Synapsida, the clade including therapsids and thus also mammals, is one of the two major branches of amniotes. Organismal design, with modularity as a concept, offers insights into the evolution of therapsids, a group that experienced profound anatomical transformations throughout the past 270 Ma, eventually leading to the evolution of the mammalian bauplan. However, the anatomy of some therapsid groups remains obscure. Gorgonopsian braincase anatomy is poorly known and many anatomical aspects of the brain, cranial nerves, vasculature, and osseous labyrinth, remain unclear. We analyzed two gorgonopsian specimens, GPIT/RE/7124 and GPIT/RE/7119, using propagation phase contrast synchrotron micro-computed tomography. The lack of fusion between many basicranial and occipital bones in GPIT/RE/7124, which is an immature specimen, allowed us to reconstruct its anatomy and ontogenetic sequence, in comparison with the mature GPIT/RE/7119, in great detail. We explored the braincase and rendered various skull cavities. Notably, we found that there is a separate ossification between what was previously referred to as the “parasphenoid” and the basioccipital. We reinterpreted this element as a posterior ossification of the basisphenoid: the basipostsphenoid. Moreover, we show that the previously called “parasphenoid” is in fact the co-ossification of the dermal parasphenoid and the endochondral basipresphenoid. In line with previous descriptions, the anatomy of the osseous labyrinth is rendered in detail, revealing a unique discoid morphology of the horizontal semicircular canal, rather than toroidal, probably due to architectural constraints of the ossification of the opisthotic and supraoccipital. In addition, the orientation of the horizontal semicircular canal suggests that gorgonopsians had an anteriorly tilted alert head posture. The morphology of the brain endocast is in accordance with the more reptilian endocast shape of other non

  8. Comparison of the Internal Dynamics of Metalloproteases Provides New Insights on Their Function and Evolution.

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    Henrique F Carvalho

    Full Text Available Metalloproteases have evolved in a vast number of biological systems, being one of the most diverse types of proteases and presenting a wide range of folds and catalytic metal ions. Given the increasing understanding of protein internal dynamics and its role in enzyme function, we are interested in assessing how the structural heterogeneity of metalloproteases translates into their dynamics. Therefore, the dynamical profile of the clan MA type protein thermolysin, derived from an Elastic Network Model of protein structure, was evaluated against those obtained from a set of experimental structures and molecular dynamics simulation trajectories. A close correspondence was obtained between modes derived from the coarse-grained model and the subspace of functionally-relevant motions observed experimentally, the later being shown to be encoded in the internal dynamics of the protein. This prompted the use of dynamics-based comparison methods that employ such coarse-grained models in a representative set of clan members, allowing for its quantitative description in terms of structural and dynamical variability. Although members show structural similarity, they nonetheless present distinct dynamical profiles, with no apparent correlation between structural and dynamical relatedness. However, previously unnoticed dynamical similarity was found between the relevant members Carboxypeptidase Pfu, Leishmanolysin, and Botulinum Neurotoxin Type A, despite sharing no structural similarity. Inspection of the respective alignments shows that dynamical similarity has a functional basis, namely the need for maintaining proper intermolecular interactions with the respective substrates. These results suggest that distinct selective pressure mechanisms act on metalloproteases at structural and dynamical levels through the course of their evolution. This work shows how new insights on metalloprotease function and evolution can be assessed with comparison schemes that

  9. New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha

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    Wei-Jen eChen

    2014-10-01

    Full Text Available The Acanthomorpha is the largest group of teleost fishes with about one third of extant vertebrate species. In the course of its evolution this lineage experienced several episodes of radiation, leading to a large number of descendant lineages differing profoundly in morphology, ecology, distribution and behavior. Although Acanthomorpha was recognized decades ago, we are only now beginning to decipher its large-scale, time-calibrated phylogeny, a prerequisite to test various evolutionary hypotheses explaining the tremendous diversity of this group. In this study, we provide new insights into the early evolution of the acanthomorphs and the euteleost allies based on the phylogenetic analysis of a newly developed dataset combining nine nuclear and mitochondrial gene markers. Our inferred tree is time-calibrated using 15 fossils, some of which have not been used before. While our phylogeny strongly supports a monophyletic Neoteleostei, Ctenosquamata (i.e., Acanthomorpha plus Myctophiformes, and Acanthopterygii, we find weak support (bootstrap value < 48% for the traditionally defined Acanthomorpha, as well as evidence of non-monophyly for the traditional Paracanthopterygii, Beryciformes, and Percomorpha. We corroborate the new Paracanthopterygii sensu Miya et al. (2005 including Polymixiiformes, Zeiformes, Gadiformes, Percopsiformes, and likely the enigmatic Stylephorus chordatus. Our timetree largely agrees with other recent studies based on nuclear loci in inferring an Early Cretaceous origin for the acanthomorphs followed by a Late Cretaceous/Early Paleogene radiation of major lineages. This is in contrast to mitogenomic studies mostly inferring Jurassic or even Triassic ages for the origin of the acanthomorphs. We compare our results to those of previous studies, and attempt to address some of the issues that may have led to incongruence between the fossil record and the molecular clock studies, as well as between the different molecular

  10. LEDDB : LOFAR Epoch of Reionization Diagnostic Database

    NARCIS (Netherlands)

    Martinez-Rubi, O.; Veligatla, V. K.; de Bruyn, A. G.; Lampropoulos, P.; Offringa, A. R.; Jelic, V.; Yatawatta, S.; Koopmans, L. V. E.; Zaroubi, S.

    2013-01-01

    One of the key science projects of the Low-Frequency Array (LOFAR) is the detection of the cosmological signal coming from the Epoch of Reionization (EoR). Here we present the LOFAR EoR Diagnostic Database (LEDDB) that is used in the storage, management, processing and analysis of the LOFAR EoR

  11. Galaxy Evolution Insights from Spectral Modeling of Large Data Sets from the Sloan Digital Sky Survey

    Energy Technology Data Exchange (ETDEWEB)

    Hoversten, Erik A. [Johns Hopkins Univ., Baltimore, MD (United States)

    2007-10-01

    This thesis centers on the use of spectral modeling techniques on data from the Sloan Digital Sky Survey (SDSS) to gain new insights into current questions in galaxy evolution. The SDSS provides a large, uniform, high quality data set which can be exploited in a number of ways. One avenue pursued here is to use the large sample size to measure precisely the mean properties of galaxies of increasingly narrow parameter ranges. The other route taken is to look for rare objects which open up for exploration new areas in galaxy parameter space. The crux of this thesis is revisiting the classical Kennicutt method for inferring the stellar initial mass function (IMF) from the integrated light properties of galaxies. A large data set (~ 105 galaxies) from the SDSS DR4 is combined with more in-depth modeling and quantitative statistical analysis to search for systematic IMF variations as a function of galaxy luminosity. Galaxy Hα equivalent widths are compared to a broadband color index to constrain the IMF. It is found that for the sample as a whole the best fitting IMF power law slope above 0.5 M is Γ = 1.5 ± 0.1 with the error dominated by systematics. Galaxies brighter than around Mr,0.1 = -20 (including galaxies like the Milky Way which has Mr,0.1 ~ -21) are well fit by a universal Γ ~ 1.4 IMF, similar to the classical Salpeter slope, and smooth, exponential star formation histories (SFH). Fainter galaxies prefer steeper IMFs and the quality of the fits reveal that for these galaxies a universal IMF with smooth SFHs is actually a poor assumption. Related projects are also pursued. A targeted photometric search is conducted for strongly lensed Lyman break galaxies (LBG) similar to MS1512-cB58. The evolution of the photometric selection technique is described as are the results of spectroscopic follow-up of the best targets. The serendipitous discovery of two interesting blue compact dwarf galaxies is reported. These

  12. Modelling the Course of an HIV Infection: Insights from Ecology and Evolution

    Directory of Open Access Journals (Sweden)

    Carsten Magnus

    2012-10-01

    Full Text Available The Human Immunodeficiency Virus (HIV is one of the most threatening viral agents. This virus infects approximately 33 million people, many of whom are unaware of their status because, except for flu-like symptoms right at the beginning of the infection during the acute phase, the disease progresses more or less symptom-free for 5 to 10 years. During this asymptomatic phase, the virus slowly destroys the immune system until the onset of AIDS when opportunistic infections like pneumonia or Kaposi’s sarcoma can overcome immune defenses. Mathematical models have played a decisive role in estimating important parameters (e.g., virion clearance rate or life-span of infected cells. However, most models only account for the acute and asymptomatic latency phase and cannot explain the progression to AIDS. Models that account for the whole course of the infection rely on different hypotheses to explain the progression to AIDS. The aim of this study is to review these models, present their technical approaches and discuss the robustness of their biological hypotheses. Among the few models capturing all three phases of an HIV infection, we can distinguish between those that mainly rely on population dynamics and those that involve virus evolution. Overall, the modeling quest to capture the dynamics of an HIV infection has improved our understanding of the progression to AIDS but, more generally, it has also led to the insight that population dynamics and evolutionary processes can be necessary to explain the course of an infection.

  13. The sea cucumber genome provides insights into morphological evolution and visceral regeneration.

    Science.gov (United States)

    Zhang, Xiaojun; Sun, Lina; Yuan, Jianbo; Sun, Yamin; Gao, Yi; Zhang, Libin; Li, Shihao; Dai, Hui; Hamel, Jean-François; Liu, Chengzhang; Yu, Yang; Liu, Shilin; Lin, Wenchao; Guo, Kaimin; Jin, Songjun; Xu, Peng; Storey, Kenneth B; Huan, Pin; Zhang, Tao; Zhou, Yi; Zhang, Jiquan; Lin, Chenggang; Li, Xiaoni; Xing, Lili; Huo, Da; Sun, Mingzhe; Wang, Lei; Mercier, Annie; Li, Fuhua; Yang, Hongsheng; Xiang, Jianhai

    2017-10-01

    Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

  14. A primitive endogenous lentivirus in a colugo: insights into the early evolution of lentiviruses.

    Science.gov (United States)

    Han, Guan-Zhu; Worobey, Michael

    2015-01-01

    Lentiviruses infect a wide range of mammal species. Much remains unknown about their deep history and host distribution. Here, we report the discovery of an endogenous lentivirus within the genome of the Sunda flying lemur (Galeopterus variegatus) (which we designate "Galeopterus variegatus endogenous lentivirus" [GvaELV]). We estimate the GvaELV genome invasion to have occurred more than 14 Ma, supporting an ancient origin of the lentivirus clade and an ancient lentiviral infection in colugo. Phylogenetic analyses show that GvaELV is a sister group of all previously known lentiviruses. The GvaELV genome appears to possess some primitive genomic features of a lentivirus, encoding not only a trans-activator of transcription (tat) gene but also two additional putative accessory genes that share no discernible similarity with other lentiviral accessory genes. The discovery of GvaELV provides novel insights into the prehistory and host distribution of lentivirus. © The Author 2014. 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.

  15. Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets (Viola

    Directory of Open Access Journals (Sweden)

    Sungkyu Park

    2017-12-01

    Full Text Available Cyclotides are a family of plant proteins that are characterized by a cyclic backbone and a knotted disulfide topology. Their cyclic cystine knot (CCK motif makes them exceptionally resistant to thermal, chemical, and enzymatic degradation. By disrupting cell membranes, the cyclotides function as host defense peptides by exhibiting insecticidal, anthelmintic, antifouling, and molluscicidal activities. In this work, we provide the first insight into the evolution of this family of plant proteins by studying the Violaceae, in particular species of the genus Viola. We discovered 157 novel precursor sequences by the transcriptomic analysis of six Viola species: V. albida var. takahashii, V. mandshurica, V. orientalis, V. verecunda, V. acuminata, and V. canadensis. By combining these precursor sequences with the phylogenetic classification of Viola, we infer the distribution of cyclotides across 63% of the species in the genus (i.e., ~380 species. Using full precursor sequences from transcriptomes, we show an evolutionary link to the structural diversity of the cyclotides, and further classify the cyclotides by sequence signatures from the non-cyclotide domain. Also, transcriptomes were compared to cyclotide expression on a peptide level determined using liquid chromatography-mass spectrometry. Furthermore, the novel cyclotides discovered were associated with the emergence of new biological functions.

  16. The sea cucumber genome provides insights into morphological evolution and visceral regeneration.

    Directory of Open Access Journals (Sweden)

    Xiaojun Zhang

    2017-10-01

    Full Text Available Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb, with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94-like gene family and a significantly expanded fibrinogen-related protein (FREP gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

  17. Enhanced dewaterability of sludge during anaerobic digestion with thermal hydrolysis pretreatment: New insights through structure evolution.

    Science.gov (United States)

    Zhang, Jingsi; Li, Ning; Dai, Xiaohu; Tao, Wenquan; Jenkinson, Ian R; Li, Zhuo

    2017-12-19

    Comprehensive insights into the sludge digestate dewaterability were gained through porous network structure of sludge. We measured the evolution of digestate dewaterability, represented by the solid content of centrifugally dewatered cake, in high-solids sequencing batch digesters with and without thermal hydrolysis pretreatment (THP). The results show that the dewaterability of the sludge after digestion was improved by 3.5% (±0.5%) for unpretreated sludge and 5.1% (±0.4%) for thermally hydrolyzed sludge. Compared to the unpretreated sludge digestate, thermal hydrolysis pretreatment eventually resulted in an improvement of dewaterability by 4.6% (±0.5%). Smaller particle size and larger surface area of sludge were induced by thermal hydrolysis and anaerobic digestion treatments. The structure strength and compactness of sludge, represented by elastic modulus and fractal dimension respectively, decreased with increase of digestion time. The porous network structure was broken up by thermal hydrolysis pretreatment and was further weakened during anaerobic digestion, which correspondingly improved the dewaterability of digestates. The logarithm of elastic modulus increased linearly with fractal dimension regardless of the pretreatment. Both fractal dimension and elastic modulus showed linear relationship with dewaterability. The rheological characterization combined with the analysis of fractal dimension of sewage sludge porous network structure was found applicable in quantitative evaluation of sludge dewaterability, which depended positively on both thermal hydrolysis and anaerobic digestion. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Expanding the Diversity of Mycobacteriophages: Insights into Genome Architecture and Evolution

    Science.gov (United States)

    Pope, Welkin H.; Jacobs-Sera, Deborah; Russell, Daniel A.; Peebles, Craig L.; Al-Atrache, Zein; Alcoser, Turi A.; Alexander, Lisa M.; Alfano, Matthew B.; Alford, Samantha T.; Amy, Nichols E.; Anderson, Marie D.; Anderson, Alexander G.; Ang, Andrew A. S.; Ares, Manuel; Barber, Amanda J.; Barker, Lucia P.; Barrett, Jonathan M.; Barshop, William D.; Bauerle, Cynthia M.; Bayles, Ian M.; Belfield, Katherine L.; Best, Aaron A.; Borjon, Agustin; Bowman, Charles A.; Boyer, Christine A.; Bradley, Kevin W.; Bradley, Victoria A.; Broadway, Lauren N.; Budwal, Keshav; Busby, Kayla N.; Campbell, Ian W.; Campbell, Anne M.; Carey, Alyssa; Caruso, Steven M.; Chew, Rebekah D.; Cockburn, Chelsea L.; Cohen, Lianne B.; Corajod, Jeffrey M.; Cresawn, Steven G.; Davis, Kimberly R.; Deng, Lisa; Denver, Dee R.; Dixon, Breyon R.; Ekram, Sahrish; Elgin, Sarah C. R.; Engelsen, Angela E.; English, Belle E. V.; Erb, Marcella L.; Estrada, Crystal; Filliger, Laura Z.; Findley, Ann M.; Forbes, Lauren; Forsyth, Mark H.; Fox, Tyler M.; Fritz, Melissa J.; Garcia, Roberto; George, Zindzi D.; Georges, Anne E.; Gissendanner, Christopher R.; Goff, Shannon; Goldstein, Rebecca; Gordon, Kobie C.; Green, Russell D.; Guerra, Stephanie L.; Guiney-Olsen, Krysta R.; Guiza, Bridget G.; Haghighat, Leila; Hagopian, Garrett V.; Harmon, Catherine J.; Harmson, Jeremy S.; Hartzog, Grant A.; Harvey, Samuel E.; He, Siping; He, Kevin J.; Healy, Kaitlin E.; Higinbotham, Ellen R.; Hildebrandt, Erin N.; Ho, Jason H.; Hogan, Gina M.; Hohenstein, Victoria G.; Holz, Nathan A.; Huang, Vincent J.; Hufford, Ericka L.; Hynes, Peter M.; Jackson, Arrykka S.; Jansen, Erica C.; Jarvik, Jonathan; Jasinto, Paul G.; Jordan, Tuajuanda C.; Kasza, Tomas; Katelyn, Murray A.; Kelsey, Jessica S.; Kerrigan, Larisa A.; Khaw, Daryl; Kim, Junghee; Knutter, Justin Z.; Ko, Ching-Chung; Larkin, Gail V.; Laroche, Jennifer R.; Latif, Asma; Leuba, Kohana D.; Leuba, Sequoia I.; Lewis, Lynn O.; Loesser-Casey, Kathryn E.; Long, Courtney A.; Lopez, A. Javier; Lowery, Nicholas; Lu, Tina Q.; Mac, Victor; Masters, Isaac R.; McCloud, Jazmyn J.; McDonough, Molly J.; Medenbach, Andrew J.; Menon, Anjali; Miller, Rachel; Morgan, Brandon K.; Ng, Patrick C.; Nguyen, Elvis; Nguyen, Katrina T.; Nguyen, Emilie T.; Nicholson, Kaylee M.; Parnell, Lindsay A.; Peirce, Caitlin E.; Perz, Allison M.; Peterson, Luke J.; Pferdehirt, Rachel E.; Philip, Seegren V.; Pogliano, Kit; Pogliano, Joe; Polley, Tamsen; Puopolo, Erica J.; Rabinowitz, Hannah S.; Resiss, Michael J.; Rhyan, Corwin N.; Robinson, Yetta M.; Rodriguez, Lauren L.; Rose, Andrew C.; Rubin, Jeffrey D.; Ruby, Jessica A.; Saha, Margaret S.; Sandoz, James W.; Savitskaya, Judith; Schipper, Dale J.; Schnitzler, Christine E.; Schott, Amanda R.; Segal, J. Bradley; Shaffer, Christopher D.; Sheldon, Kathryn E.; Shepard, Erica M.; Shepardson, Jonathan W.; Shroff, Madav K.; Simmons, Jessica M.; Simms, Erika F.; Simpson, Brandy M.; Sinclair, Kathryn M.; Sjoholm, Robert L.; Slette, Ingrid J.; Spaulding, Blaire C.; Straub, Clark L.; Stukey, Joseph; Sughrue, Trevor; Tang, Tin-Yun; Tatyana, Lyons M.; Taylor, Stephen B.; Taylor, Barbara J.; Temple, Louise M.; Thompson, Jasper V.; Tokarz, Michael P.; Trapani, Stephanie E.; Troum, Alexander P.; Tsay, Jonathan; Tubbs, Anthony T.; Walton, Jillian M.; Wang, Danielle H.; Wang, Hannah; Warner, John R.; Weisser, Emilie G.; Wendler, Samantha C.; Weston-Hafer, Kathleen A.; Whelan, Hilary M.; Williamson, Kurt E.; Willis, Angelica N.; Wirtshafter, Hannah S.; Wong, Theresa W.; Wu, Phillip; Yang, Yun jeong; Yee, Brandon C.; Zaidins, David A.; Zhang, Bo; Zúniga, Melina Y.; Hendrix, Roger W.; Hatfull, Graham F.

    2011-01-01

    Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists. PMID:21298013

  19. Expanding the diversity of mycobacteriophages: insights into genome architecture and evolution.

    Directory of Open Access Journals (Sweden)

    Welkin H Pope

    2011-01-01

    Full Text Available Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand our knowledge of mycobacteriophage diversity and enhance our understanding of the roles of mobile elements in viral evolution. Expansion of the number of mycobacteriophages grouped within Cluster A provides insights into the basis of immune specificity in these temperate phages, and we also describe a novel example of apparent immunity theft. The isolation and genomic analysis of bacteriophages by freshman college students provides an example of an authentic research experience for novice scientists.

  20. Insights from the past: incorporating long-term landscape evolution in studies of land degradation

    Science.gov (United States)

    Ferro-Vazquez, Cruz; Lang, Carol; Kabora, Tabitha; Thornton-Barnett, Senna; Richer, Suzi; Gallello, Gianni; Stump, Daryl

    2017-04-01

    Modern approaches for assessing land degradation encompass multidisciplinary studies that have allowed a more realistic understanding of the causes and consequences of land degradation. This incipient perspective includes an increasingly important role of the studies of the past, including human history, to understand modern ecosystems and landscapes. Indeed, the current promotion of indigenous resource-use strategies as models of sustainable development was initially prompted by historical studies. However, systematic studies on whether or not indigenous management practices led to land degradation, and therefore their benefits or constraints for sustained use of natural resources, are not truly known. We argue that a joint approach combining the characterization of current soil properties with the archaeological study of traditional agricultural systems can provide insights on their sustainability. Archaeological excavation enables discerning the order in which sediments are deposited and the sequence in which structures are built. This provides data on coincident cultural and ecological change, and a long-term perspective on how agro-ecological systems operated in pre-modern states and the ways in which they resemble or differ from modern contexts. Simultaneously, these changes would have left a physical, chemical and isotopic imprint in soils that can be detected and interpreted to contribute to the production of a "usable past" (Stump, 2013). The premise is: since ancient agricultural sites may provide information on agronomic conditions after centuries to millennia of use, they can help in understanding the ways in which agroecosystems have survived, failed or adapted in the past. This will contribute to a better holistic understanding of social-ecological systems evolution by including a temporal perspective, and to a more nuanced assessment of land degradation and sustainable use. To illustrate this we present the outcome of our research at two traditional

  1. Geomagnetic reversal in brunhes normal polarity epoch.

    Science.gov (United States)

    Smith, J D; Foster, J H

    1969-02-07

    The magnetic stratigraphly of seven cores of deep-sea sediment established the existence of a short interval of reversed polarity in the upper part of the Brunches epoch of normal polarity. The reversed zone in the cores correlates well with paleontological boundaries and is named the Blake event. Its boundaries are estimated to be 108,000 and 114,000 years ago +/- 10 percent.

  2. Phylogenetic analyses provide insights into the historical biogeography and evolution of Brachyrhaphis fishes.

    Science.gov (United States)

    Ingley, Spencer J; Reina, Ruth G; Bermingham, Eldredge; Johnson, Jerald B

    2015-08-01

    The livebearing fish genus Brachyrhaphis (Poeciliidae) has become an increasingly important model in evolution and ecology research, yet the phylogeny of this group is not well understood, nor has it been examined thoroughly using modern phylogenetic methods. Here, we present the first comprehensive phylogenetic analysis of Brachyrhaphis by using four molecular markers (3mtDNA, 1nucDNA) to infer relationships among species in this genus. We tested the validity of this genus as a monophyletic group using extensive outgroup sampling based on recent phylogenetic hypotheses of Poeciliidae. We also tested the validity of recently described species of Brachyrhaphis that are part of the B. episcopi complex in Panama. Finally, we examined the impact of historical events on diversification of Brachyrhaphis, and made predictions regarding the role of different ecological environments on evolutionary diversification where known historical events apparently fail to explain speciation. Based on our results, we reject the monophyly of Brachyrhaphis, and question the validity of two recently described species (B. hessfeldi and B. roswithae). Historical biogeography of Brachyrhaphis generally agrees with patterns found in other freshwater taxa in Lower Central America, which show that geological barriers frequently predict speciation. Specifically, we find evidence in support of an 'island' model of Lower Central American formation, which posits that the nascent isthmus was partitioned by several marine connections before linking North and South America. In some cases where historic events (e.g., vicariance) fail to explain allopatric species breaks in Brachyrhaphis, ecological processes (e.g., divergent predation environments) offer additional insight into our understanding of phylogenetic diversification in this group. Copyright © 2015 Elsevier Inc. All rights reserved.

  3. New insights on the evolution of Leafy cotyledon1 (LEC1) type genes in vascular plants.

    Science.gov (United States)

    Cagliari, Alexandro; Turchetto-Zolet, Andreia Carina; Korbes, Ana Paula; Maraschin, Felipe Dos Santos; Margis, Rogerio; Margis-Pinheiro, Marcia

    2014-01-01

    NF-Y is a conserved oligomeric transcription factor found in all eukaryotes. In plants, this regulator evolved with a broad diversification of the genes coding for its three subunits (NF-YA, NF-YB and NF-YC). The NF-YB members can be divided into Leafy Cotyledon1 (LEC1) and non-LEC1 types. Here we presented a comparative genomic study using phylogenetic analyses to validate an evolutionary model for the origin of LEC-type genes in plants and their emergence from non-LEC1-type genes. We identified LEC1-type members in all vascular plant genomes, but not in amoebozoa, algae, fungi, metazoa and non-vascular plant representatives, which present exclusively non-LEC1-type genes as constituents of their NF-YB subunits. The non-synonymous to synonymous nucleotide substitution rates (Ka/Ks) between LEC1 and non-LEC1-type genes indicate the presence of positive selection acting on LEC1-type members to the fixation of LEC1-specific amino acid residues. The phylogenetic analyses demonstrated that plant LEC1-type genes are evolutionary divergent from the non-LEC1-type genes of plants, fungi, amoebozoa, algae and animals. Our results point to a scenario in which LEC1-type genes have originated in vascular plants after gene expansion in plants. We suggest that processes of neofunctionalization and/or subfunctionalization were responsible for the emergence of a versatile role for LEC1-type genes in vascular plants, especially in seed plants. LEC1-type genes besides being phylogenetic divergent also present different expression profile when compared with non-LEC1-type genes. Altogether, our data provide new insights about the LEC1 and non-LEC1 evolutionary relationship during the vascular plant evolution. Copyright © 2014 Elsevier Inc. All rights reserved.

  4. The complete chloroplast genome of banana (Musa acuminata, Zingiberales): insight into plastid monocotyledon evolution.

    Science.gov (United States)

    Martin, Guillaume; Baurens, Franc-Christophe; Cardi, Céline; Aury, Jean-Marc; D'Hont, Angélique

    2013-01-01

    Banana (genus Musa) is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-)specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus. The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp) and a Small Single Copy region (SSC, 10,768 bp) separated by Inverted Repeat regions (IRs, 35,433 bp). Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1) and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed. The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas.

  5. The complete chloroplast genome of banana (Musa acuminata, Zingiberales: insight into plastid monocotyledon evolution.

    Directory of Open Access Journals (Sweden)

    Guillaume Martin

    Full Text Available Banana (genus Musa is a crop of major economic importance worldwide. It is a monocotyledonous member of the Zingiberales, a sister group of the widely studied Poales. Most cultivated bananas are natural Musa inter-(sub-specific triploid hybrids. A Musa acuminata reference nuclear genome sequence was recently produced based on sequencing of genomic DNA enriched in nucleus.The Musa acuminata chloroplast genome was assembled with chloroplast reads extracted from whole-genome-shotgun sequence data. The Musa chloroplast genome is a circular molecule of 169,972 bp with a quadripartite structure containing two single copy regions, a Large Single Copy region (LSC, 88,338 bp and a Small Single Copy region (SSC, 10,768 bp separated by Inverted Repeat regions (IRs, 35,433 bp. Two forms of the chloroplast genome relative to the orientation of SSC versus LSC were found. The Musa chloroplast genome shows an extreme IR expansion at the IR/SSC boundary relative to the most common structures found in angiosperms. This expansion consists of the integration of three additional complete genes (rps15, ndhH and ycf1 and part of the ndhA gene. No such expansion has been observed in monocots so far. Simple Sequence Repeats were identified in the Musa chloroplast genome and a new set of Musa chloroplastic markers was designed.The complete sequence of M. acuminata ssp malaccensis chloroplast we reported here is the first one for the Zingiberales order. As such it provides new insight in the evolution of the chloroplast of monocotyledons. In particular, it reinforces that IR/SSC expansion has occurred independently several times within monocotyledons. The discovery of new polymorphic markers within Musa chloroplast opens new perspectives to better understand the origin of cultivated triploid bananas.

  6. Insights on the evolution of mid-ocean basins: the Atlantis Basin of southern Azores

    Science.gov (United States)

    Alves, T.; Bouriak, S.; Volkonskaya, A.; Monteiro, J.; Ivanov, M.

    2003-04-01

    Single-channel seismic reflection and sidescan (OKEAN) data acquired in an unstudied region of the North Atlantic give important insights on the evolution of mid-ocean basins. Located on the eastern flank of the Mid-Atlantic Ridge, south of the Azores Islands, the study area contains more than 1,000 ms two-way travel-time of sediments with a similar seismic stratigraphy to that of ODP sites 950-952 in the Madeira Abyssal Plain. Processed thickness values correspond to a maximum thickness of about 1450 m and an average thickness of more than 500 m based on velocity data from ODP sites 950-952. The structure of the surveyed area and its location in relation to the Madeira Abyssal Plain and Mid-Atlantic Ridge indicate the existence, south of Azores, of two distinct sedimentary basins separated by major structural lineaments (Azores-Gibraltar and Atlantis Fracture Zones) and by seamount chains (Cruiser-Great Meteor Chain, Plato-Atlantis Chain). The basement of the sedimentary basins is irregular, showing multiple dome-shaped volcanic structures identical to those in the Norwegian-Greenland Sea and Madeira Abyssal Plain. However, half-graben/graben basement blocks predominate east of 30ºW underneath a moderately deformed overburden. The complex structure observed most likely reflects changes in the direction and velocity of ocean spreading plus variations in the regional thermal gradients induced by local hot spots. In parallel, some of the sub-surface structures identified next to basin-bounding Fracture Zones may have resulted from transtensional and transpressional tectonism.

  7. BRIGHTEST CLUSTER GALAXIES AT THE PRESENT EPOCH

    Energy Technology Data Exchange (ETDEWEB)

    Lauer, Tod R. [National Optical Astronomy Observatory, P.O. Box 26732, Tucson, AZ 85726 (United States); Postman, Marc [Space Telescope Science Institute, 3700 San Martin Drive, Baltimore, MD 21218 (United States); Strauss, Michael A.; Graves, Genevieve J.; Chisari, Nora E. [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States)

    2014-12-20

    We have obtained photometry and spectroscopy of 433 z ≤ 0.08 brightest cluster galaxies (BCGs) in a full-sky survey of Abell clusters to construct a BCG sample suitable for probing deviations from the local Hubble flow. The BCG Hubble diagram over 0 < z < 0.08 is consistent to within 2% of the Hubble relation specified by a Ω {sub m} = 0.3, Λ = 0.7 cosmology. This sample allows us to explore the structural and photometric properties of BCGs at the present epoch, their location in their hosting galaxy clusters, and the effects of the cluster environment on their structure and evolution. We revisit the L{sub m} -α relation for BCGs, which uses α, the log-slope of the BCG photometric curve of growth, to predict the metric luminosity in an aperture with 14.3 kpc radius, L{sub m} , for use as a distance indicator. Residuals in the relation are 0.27 mag rms. We measure central stellar velocity dispersions, σ, of the BCGs, finding the Faber-Jackson relation to flatten as the metric aperture grows to include an increasing fraction of the total BCG luminosity. A three-parameter ''metric plane'' relation using α and σ together gives the best prediction of L{sub m} , with 0.21 mag residuals. The distribution of projected spatial offsets, r{sub x} of BCGs from the X-ray-defined cluster center is a steep γ = –2.33 power law over 1 < r{sub x} < 10{sup 3} kpc. The median offset is ∼10 kpc, but ∼15% of the BCGs have r{sub x} > 100 kpc. The absolute cluster-dispersion normalized BCG peculiar velocity |ΔV {sub 1}|/σ {sub c} follows an exponential distribution with scale length 0.39 ± 0.03. Both L{sub m} and α increase with σ {sub c}. The α parameter is further moderated by both the spatial and velocity offset from the cluster center, with larger α correlated with the proximity of the BCG to the cluster mean velocity or potential center. At the same time, position in the cluster has little effect on L{sub m} . Likewise, residuals from

  8. Insight as a social identity process in the evolution of psychosocial functioning in the early phase of psychosis.

    Science.gov (United States)

    Klaas, H S; Clémence, A; Marion-Veyron, R; Antonietti, J-P; Alameda, L; Golay, P; Conus, P

    2017-03-01

    Awareness of illness (insight) has been found to have contradictory effects for different functional outcomes after the early course of psychosis. Whereas it is related to psychotic symptom reduction and medication adherence, it is also associated with increased depressive symptoms. In this line, the specific effects of insight on the evolution of functioning over time have not been identified, and social indicators, such as socio-occupational functioning have barely been considered. Drawing from social identity theory we investigated the impact of insight on the development of psychosocial outcomes and the interactions of these variables over time. The participants, 240 patients in early phase of psychosis from the Treatment and Early Intervention in Psychosis Program (TIPP) of the University Hospital of Lausanne, Switzerland, were assessed at eight time points over 3 years. Cross-lagged panel analyses and multilevel analyses were conducted on socio-occupational and general functioning [Social and Occupational Functioning Assessment Scale (SOFAS) and Global Assessment of Functioning (GAF)] with insight, time and depressive symptoms as independent variables. Results from multilevel analyses point to an overall positive impact of insight on psychosocial functioning, which increases over time. Yet the cross-lagged panel analysis did not reveal a systematic positive and causal effect of insight on SOFAS and GAF scores. Depressive symptoms seem only to be relevant in the beginning of the treatment process. Our results point to a complex process in which the positive impact of insight on psychosocial functioning increases over time, even when considering depressive symptoms. Future studies and treatment approaches should consider the procedural aspect of insight.

  9. Administering an epoch initiated for remote memory access

    Science.gov (United States)

    Blocksome, Michael A; Miller, Douglas R

    2012-10-23

    Methods, systems, and products are disclosed for administering an epoch initiated for remote memory access that include: initiating, by an origin application messaging module on an origin compute node, one or more data transfers to a target compute node for the epoch; initiating, by the origin application messaging module after initiating the data transfers, a closing stage for the epoch, including rejecting any new data transfers after initiating the closing stage for the epoch; determining, by the origin application messaging module, whether the data transfers have completed; and closing, by the origin application messaging module, the epoch if the data transfers have completed.

  10. A superposed epoch analysis of geomagnetic storms

    Directory of Open Access Journals (Sweden)

    J. R. Taylor

    1994-06-01

    Full Text Available A superposed epoch analysis of geomagnetic storms has been undertaken. The storms are categorised via their intensity (as defined by the Dst index. Storms have also been classified here as either storm sudden commencements (SSCs or storm gradual commencements (SGCs, that is all storms which did not begin with a sudden commencement. The prevailing solar wind conditions defined by the parameters solar wind speed (vsw, density (ρsw and pressure (Psw and the total field and the components of the interplanetary magnetic field (IMF during the storms in each category have been investigated by a superposed epoch analysis. The southward component of the IMF, appears to be the controlling parameter for the generation of small SGCs (-100 nT< minimum Dst ≤ -50 nT for ≥ 4 h, but for SSCs of the same intensity solar wind pressure is dominant. However, for large SSCs (minimum Dst ≤ -100 nT for ≥ 4 h the solar wind speed is the controlling parameter. It is also demonstrated that for larger storms magnetic activity is not solely driven by the accumulation of substorm activity, but substantial energy is directly input via the dayside. Furthermore, there is evidence that SSCs are caused by the passage of a coronal mass ejection, whereas SGCs result from the passage of a high speed/ slow speed coronal stream interface. Storms are also grouped by the sign of Bz during the first hour epoch after the onset. The sign of Bz at t = +1 h is the dominant sign of the Bz for ~24 h before the onset. The total energy released during storms for which Bz was initially positive is, however, of the same order as for storms where Bz was initially negative.

  11. Widely available active sites on Ni2P for electrochemical hydrogen evolution - insights from first principles calculations

    DEFF Research Database (Denmark)

    Hansen, Martin Hangaard; Stern, Lucas-Alexandre; Feng, Ligang

    2015-01-01

    We present insights into the mechanism and the active site for hydrogen evolution on nickel phosphide (Ni2P). Ni2P was recently discovered to be a very active non-precious hydrogen evolution catalyst. Current literature attributes the activity of Ni2P to a particular site on the (0001) facet....... In the present study, using Density Functional Theory (DFT) calculations, we show that several widely available low index crystal facets on Ni2P have better properties for a high catalytic activity. DFT calculations were used to identify moderately bonding nickel bridge sites and nickel hollow sites for hydrogen...... adsorption and to calculate barriers for the Tafel pathway. The investigated surfaces in this study were the (10 (1) over bar0), ((1) over bar(1) over bar 20), (11 (2) over bar0), (11 (2) over bar1) and (0001) facets of the hexagonal Ni2P crystal. In addition to the DFT results, we present experiments on Ni2...

  12. New insights about enzyme evolution from large scale studies of sequence and structure relationships

    OpenAIRE

    Babbitt, Patricia; Brown, SD; Babbitt, PC

    2014-01-01

    © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.Understanding how enzymes have evolved offers clues about their structure-function relationships and mechanisms. Here, we describe evolution of functionally diverse enzyme superfami

  13. Hydrogen Epoch of Reionization Array (HERA)

    Science.gov (United States)

    DeBoer, David R.; HERA

    2015-01-01

    The Hydrogen Epoch of Reionization Arrays (HERA - reionization.org) roadmap uses the unique properties of the neutral hydrogen (HI) 21cm line to probe our cosmic dawn: from the birth of the first stars and black holes, through the full reionization of the primordial intergalactic medium (IGM). HERA is a collaboration between the Precision Array Probing the Epoch of Reionization (PAPER - eor.berkeley.edu), the US-based Murchison Widefield Array (MWA - mwatelescope.org), and MIT Epoch of Reionization (MITEOR) teams along with the South African SKA-SA, University of KwaZulu Natal and the University of Cambridge Cavendish Laborabory. HERA has recently been awarded a National Science Foundation Mid-Scale Innovation Program grant to begin the next phase.HERA leverages the operation of the PAPER and MWA telescopes to explore techniques and designs required to detect the primordial HI signal in the presence of systematics and radio continuum foreground emission some four orders of magnitude brighter. With this understanding, we are now able to remove foregrounds to the limits of our sensitivity, culminating in the first physically meaningful upper limits. A redundant calibration algorithm from MITEOR improves the sensitivity of the approach.Building on this, the next stage of HERA incorporates a 14m diameter antenna element that is optimized both for sensitivity and for minimizing foreground systematics. Arranging these elements in a compact hexagonal grid yields an array that facilitates calibration, leverages proven foreground removal techniques, and is scalable to large collecting areas. HERA will be located in the radio quiet environment of the SKA site in the Karoo region of South Africa (where PAPER is currently located). It will have a sensitivity close to two orders of magnitude better than PAPER and the MWA to ensure a robust detection. With its sensitivity and broader frequency coverage, HERA can paint an uninterrupted picture through reionization, back to the

  14. Amphioxus photoreceptors insights into the evolution of vertebrate opsins, vision and circadian rhythmicity

    Czech Academy of Sciences Publication Activity Database

    Pergner, Jiří; Kozmik, Zbyněk

    2017-01-01

    Roč. 61, č. 10-12 (2017), s. 665-681 ISSN 0214-6282 R&D Projects: GA ČR GA17-15374S; GA MŠk(CZ) LM2015062; GA MŠk LO1419 Institutional support: RVO:68378050 Keywords : chordate * opsin evolution * photoreceptor * eye evolution * phototransduction Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biology (theoretical, mathematical, thermal, cryobiology, biological rhythm), Evolutionary biology Impact factor: 1.981, year: 2016

  15. Masticatory muscle architecture in the Laotian rock rat Laonastes aenigmamus (Mammalia, Rodentia): new insights into the evolution of hystricognathy.

    Science.gov (United States)

    Hautier, Lionel; Saksiri, Soonchan

    2009-10-01

    We present the first descriptive comparison of the skull, mandible and jaw muscles of the recently recovered Laotian rock rat Laonastes aenigmamus. The gross anatomy of five specimens captured in Laos and internal architecture of the jaw musculature were studied using dissections. The following muscles are described: temporal, masseter, pterygoids, digastric, mylohyoid, geniohyoid and transverse mandibular. The description of the masticatory apparatus of L. aenigmamus offers a rare opportunity to assess the order of establishment of the morphological characters during the evolution of Ctenohystrica. Striking convergences have occurred during the evolution of Diatomyidae and L. aenigmamus presents a unique combination of myological features that corresponds to a mixture of sciurognathous and hystricognathous characters. If L. aenigmamus is a sciurognathous rodent, we have to assume that it independently acquired a pars reflexa of the superficial masseter. We show for the first time that the development of this pars reflexa has occurred several times during the evolution of Ctenohystrica and can no longer be considered a synapomorphic feature of 'Hystricognathi'. These results bring new insights into the evolution of hystricognathy and have profound implications for the interpretation of the fossil record of early hystricognath rodents.

  16. LSST and the Epoch of Reionization Experiments

    Science.gov (United States)

    Ivezić, Željko

    2018-05-01

    The Large Synoptic Survey Telescope (LSST), a next generation astronomical survey, sited on Cerro Pachon in Chile, will provide an unprecedented amount of imaging data for studies of the faint optical sky. The LSST system includes an 8.4m (6.7m effective) primary mirror and a 3.2 Gigapixel camera with a 9.6 sq. deg. field of view. This system will enable about 10,000 sq. deg. of sky to be covered twice per night, every three to four nights on average, with typical 5-sigma depth for point sources of r = 24.5 (AB). With over 800 observations in the ugrizy bands over a 10-year period, these data will enable coadded images reaching r = 27.5 (about 5 magnitudes deeper than SDSS) as well as studies of faint time-domain astronomy. The measured properties of newly discovered and known astrometric and photometric transients will be publicly reported within 60 sec after closing the shutter. The resulting hundreds of petabytes of imaging data for about 40 billion objects will be used for scientific investigations ranging from the properties of near-Earth asteroids to characterizations of dark matter and dark energy. For example, simulations estimate that LSST will discover about 1,000 quasars at redshifts exceeding 7; this sample will place tight constraints on the cosmic environment at the end of the reionization epoch. In addition to a brief introduction to LSST, I review the value of LSST data in support of epoch of reionization experiments and discuss how international participants can join LSST.

  17. Faint galaxies - Bounds on the epoch of galaxy formation and the cosmological deceleration parameter

    International Nuclear Information System (INIS)

    Yoshii, Yuzuru; Peterson, B.A.

    1991-01-01

    Models of galaxy luminosity evolution are used to interpret the observed color distributions, redshift distributions, and number counts of faint galaxies. It is found from the color distributions that the redshift corresponding to the epoch of galaxy formation must be greater than three, and that the number counts of faint galaxies, which are sensitive to the slope of the faint end of the luminosity function, are incompatible with q0 = 1/2 and indicate a smaller value. The models assume that the sequence of galaxy types is due to different star-formation rates, that the period of galaxy formation can be characterized by a single epoch, and that after formation, galaxies change in luminosity by star formation and stellar evolution, maintaining a constant comoving space density. 40 refs

  18. Integrative studies of cultural evolution: crossing disciplinary boundaries to produce new insights.

    Science.gov (United States)

    Kolodny, Oren; Feldman, Marcus W; Creanza, Nicole

    2018-04-05

    Culture evolves according to dynamics on multiple temporal scales, from individuals' minute-by-minute behaviour to millennia of cultural accumulation that give rise to population-level differences. These dynamics act on a range of entities-including behavioural sequences, ideas and artefacts as well as individuals, populations and whole species-and involve mechanisms at multiple levels, from neurons in brains to inter-population interactions. Studying such complex phenomena requires an integration of perspectives from a diverse array of fields, as well as bridging gaps between traditionally disparate areas of study. In this article, which also serves as an introduction to the current special issue, we highlight some specific respects in which the study of cultural evolution has benefited and should continue to benefit from an integrative approach. We showcase a number of pioneering studies of cultural evolution that bring together numerous disciplines. These studies illustrate the value of perspectives from different fields for understanding cultural evolution, such as cognitive science and neuroanatomy, behavioural ecology, population dynamics, and evolutionary genetics. They also underscore the importance of understanding cultural processes when interpreting research about human genetics, neuroscience, behaviour and evolution.This article is part of the theme issue 'Bridging cultural gaps: interdisciplinary studies in human cultural evolution'. © 2018 The Author(s).

  19. Kinematic evolution of fold and thrust belts. Insights from experimental modeling

    International Nuclear Information System (INIS)

    Ueta, Keiichi

    2011-01-01

    Physical experiments were performed to gain a better understanding on the kinematic evolution of fold and thrust belts. The present study focuses on deformation of sedimentary cover caused by thrust and reverse movements along the basement fault. Our physical models comprise dry quartz sand representing brittle sedimentary rock and viscous silicone polymer representing overpressured mudstone. Computerized X-ray tomography was applied to the experiments to analyze the kinematic evolution of fold and thrust belts. In the sand models, the width of deformation zone above thrust was wider than that above reverse fault, because back thrust developed on the hanging wall of reverse fault. Within the physical models composed of dry sand and silicone polymer, minor folds and thrusts with minor displacement developed on the footwall of the major monoclinal flexure. These results compare well with the geometry and kinematic evolution of the fold and thrust belts in Japan. (author)

  20. The Formation and Evolution of Tessera and Insights into the Beginning of Recorded History on Venus: Geology of the Fortuna Tessera Quadrangle (V-2)

    Science.gov (United States)

    Head, J. W.; Ivanov, M. A.

    2010-01-01

    Today, and throughout its recorded history, Venus can be classified as a "one-plate planet." The observable geological record of the planet comprises only the last 1/4 or less of its overall geologic history. As shown by many authors, it started with intensive deformation in broad regions to form tessera [1-6] during the Fortunian period of history [7]. The period of tessera formation quickly changed to numerous zonal deformational belts of ridges and grooves that were followed by emplacement of vast volcanic plains (shield plains, regional plains) [7,8]. During the final epoch of the geologic history of Venus, large but isolated centers of volcanism formed extensive fields of lavas, with tectonics concentrated within fewer very prominent rift zones [8,9]. The observable changes in intensity and character of volcanism and tectonics suggest progressive changes from thin lithosphere early in the geologic history to thick lithosphere during later epochs [6,10]. We have little idea of the character of the first 3/4 of Venus' history. So, what does the earliest period of recorded history tell us about the transition from the Pre-Fortunian to the Fortunian period and what insight does this give us into this earlier period?

  1. Comparative Riftology: Insights into the Evolution of Passive Continental Margins and Continental Rifts from the Failed Midcontinent Rift (MCR)

    Science.gov (United States)

    Elling, R. P.; Stein, C. A.; Stein, S.; Kley, J.; Keller, G. R.; Wysession, M. E.

    2017-12-01

    Continental rifts evolve to seafloor spreading and are preserved in passive margins, or fail and remain as fossil features in continents. Rifts at different stages give insight into these evolutionary paths. Of particular interest is the evolution of volcanic passive margins, which are characterized by seaward dipping reflectors, volcanic rocks yielding magnetic anomalies landward of the oldest spreading anomalies, and are underlain by high-velocity lower crustal bodies. How and when these features form remains unclear. Insights are given by the Midcontinent Rift (MCR), which began to form during the 1.1 Ga rifting of Amazonia from Laurentia, but failed when seafloor spreading was established elsewhere. MCR volcanics are much thicker than other continental flood basalts, due to deposition in a narrow rift rather than a broad region, giving a rift's geometry but a LIP's magma volume. The MCR provides a snapshot of the deposition of a thick and highly magnetized volcanic section during rifting. Surface exposures and reflection seismic data near Lake Superior show a rift basin filled by inward-dipping flood basalt layers. Had the rift evolved to seafloor spreading, the basin would have split into two sets of volcanics with opposite-facing SDRs, each with a magnetic anomaly. Because the rift formed as a series of alternating half-grabens, structural asymmetries between conjugate margins would have naturally occurred had it gone to completion. Hence the MCR implies that many passive margin features form prior to seafloor spreading. Massive inversion of the MCR long after it failed has provided a much clearer picture of its structure compared to failed rifts with lesser degrees of inversion. Seismic imaging as well as gravity and magnetic modeling provide important insight into the effects of inversion on failed rifts. The MCR provides an end member for the evolution of actively extending rifts, characterized by upwelling mantle and negative gravity anomalies, to failed

  2. A Comparative Genomic Survey Provides Novel Insights into Molecular Evolution of l-Aromatic Amino Acid Decarboxylase in Vertebrates

    Directory of Open Access Journals (Sweden)

    Yanping Li

    2018-04-01

    Full Text Available Melatonin is a pleiotropic molecule with various important physiological roles in vertebrates. l-aromatic amino acid decarboxylase (AAAD is the second enzyme for melatonin synthesis. By far, a clear-cut gene function of AAAD in the biosynthesis of melatonin has been unclear in vertebrates. Here, we provide novel insights into the evolution of AAAD based on 77 vertebrate genomes. According to our genome-wide alignments, we extracted a total of 151 aaad nucleotide sequences. A phylogenetic tree was constructed on the basis of these sequences and corresponding protein alignments, indicating that tetrapods and diploid bony fish genomes contained one aaad gene and a new aaad-like gene, which formed a novel AAAD family. However, in tetraploid teleosts, there were two copies of the aaad gene due to whole genome duplication. A subsequent synteny analysis investigated 81 aaad sequences and revealed their collinearity and systematic evolution. Interestingly, we discovered that platypus (Ornithorhynchus anatinus, Atlantic cod (Guadus morhua, Mexican tetra (Astyanax mexicanus, and a Sinocyclocheilus cavefish (S. anshuiensis have long evolutionary branches in the phylogenetic topology. We also performed pseudogene identification and selection pressure analysis; however, the results revealed a deletion of 37 amino acids in Atlantic cod and premature stop codons in the cave-restricted S. anshuiensis and A. mexicanus, suggesting weakening or disappearing rhythms in these cavefishes. Selective pressure analysis of aaad between platypus and other tetrapods showed that rates of nonsynonymous (Ka and synonymous (Ks substitutions were higher when comparing the platypus to other representative tetrapods, indicating that, in this semiaquatic mammal, the aaad gene experienced selection during the process of evolution. In summary, our current work provides novel insights into aaad genes in vertebrates from a genome-wide view.

  3. Parasitism drives host genome evolution: Insights from the Pasteuria ramosa-Daphnia magna system.

    Science.gov (United States)

    Bourgeois, Yann; Roulin, Anne C; Müller, Kristina; Ebert, Dieter

    2017-04-01

    Because parasitism is thought to play a major role in shaping host genomes, it has been predicted that genomic regions associated with resistance to parasites should stand out in genome scans, revealing signals of selection above the genomic background. To test whether parasitism is indeed such a major factor in host evolution and to better understand host-parasite interaction at the molecular level, we studied genome-wide polymorphisms in 97 genotypes of the planktonic crustacean Daphnia magna originating from three localities across Europe. Daphnia magna is known to coevolve with the bacterial pathogen Pasteuria ramosa for which host genotypes (clonal lines) are either resistant or susceptible. Using association mapping, we identified two genomic regions involved in resistance to P. ramosa, one of which was already known from a previous QTL analysis. We then performed a naïve genome scan to test for signatures of positive selection and found that the two regions identified with the association mapping further stood out as outliers. Several other regions with evidence for selection were also found, but no link between these regions and phenotypic variation could be established. Our results are consistent with the hypothesis that parasitism is driving host genome evolution. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  4. Insights into the Diversity of Attitudes Concerning Evolution and Creation: A Multidimensional Approach

    Science.gov (United States)

    Konneman, Christiane; Asshoff, Roman; Hammann, Marcus

    2016-01-01

    The main aim of this paper is to describe high school students' attitudes concerning evolution and creation, with a focus on (1) attitudes toward evolutionary theory, (2) attitudes toward the Biblical accounts of creation, (3) creationist beliefs, and (4) scientistic beliefs. Latent class analyses revealed seven attitude profiles in a sample of…

  5. Radio Evolution of Supernova Remnants Including Nonlinear Particle Acceleration: Insights from Hydrodynamic Simulations

    Science.gov (United States)

    Pavlović, Marko Z.; Urošević, Dejan; Arbutina, Bojan; Orlando, Salvatore; Maxted, Nigel; Filipović, Miroslav D.

    2018-01-01

    We present a model for the radio evolution of supernova remnants (SNRs) obtained by using three-dimensional hydrodynamic simulations coupled with nonlinear kinetic theory of cosmic-ray (CR) acceleration in SNRs. We model the radio evolution of SNRs on a global level by performing simulations for a wide range of the relevant physical parameters, such as the ambient density, supernova (SN) explosion energy, acceleration efficiency, and magnetic field amplification (MFA) efficiency. We attribute the observed spread of radio surface brightnesses for corresponding SNR diameters to the spread of these parameters. In addition to our simulations of Type Ia SNRs, we also considered SNR radio evolution in denser, nonuniform circumstellar environments modified by the progenitor star wind. These simulations start with the mass of the ejecta substantially higher than in the case of a Type Ia SN and presumably lower shock speed. The magnetic field is understandably seen as very important for the radio evolution of SNRs. In terms of MFA, we include both resonant and nonresonant modes in our large-scale simulations by implementing models obtained from first-principles, particle-in-cell simulations and nonlinear magnetohydrodynamical simulations. We test the quality and reliability of our models on a sample consisting of Galactic and extragalactic SNRs. Our simulations give Σ ‑ D slopes between ‑4 and ‑6 for the full Sedov regime. Recent empirical slopes obtained for the Galactic samples are around ‑5, while those for the extragalactic samples are around ‑4.

  6. The origin and evolution of the surfactant system in fish: insights into the evolution of lungs and swim bladders.

    Science.gov (United States)

    Daniels, Christopher B; Orgeig, Sandra; Sullivan, Lucy C; Ling, Nicholas; Bennett, Michael B; Schürch, Samuel; Val, Adalberto Luis; Brauner, Colin J

    2004-01-01

    Several times throughout their radiation fish have evolved either lungs or swim bladders as gas-holding structures. Lungs and swim bladders have different ontogenetic origins and can be used either for buoyancy or as an accessory respiratory organ. Therefore, the presence of air-filled bladders or lungs in different groups of fishes is an example of convergent evolution. We propose that air breathing could not occur without the presence of a surfactant system and suggest that this system may have originated in epithelial cells lining the pharynx. Here we present new data on the surfactant system in swim bladders of three teleost fish (the air-breathing pirarucu Arapaima gigas and tarpon Megalops cyprinoides and the non-air-breathing New Zealand snapper Pagrus auratus). We determined the presence of surfactant using biochemical, biophysical, and morphological analyses and determined homology using immunohistochemical analysis of the surfactant proteins (SPs). We relate the presence and structure of the surfactant system to those previously described in the swim bladders of another teleost, the goldfish, and those of the air-breathing organs of the other members of the Osteichthyes, the more primitive air-breathing Actinopterygii and the Sarcopterygii. Snapper and tarpon swim bladders are lined with squamous and cuboidal epithelial cells, respectively, containing membrane-bound lamellar bodies. Phosphatidylcholine dominates the phospholipid (PL) profile of lavage material from all fish analyzed to date. The presence of the characteristic surfactant lipids in pirarucu and tarpon, lamellar bodies in tarpon and snapper, SP-B in tarpon and pirarucu lavage, and SPs (A, B, and D) in swim bladder tissue of the tarpon provide strong evidence that the surfactant system of teleosts is homologous with that of other fish and of tetrapods. This study is the first demonstration of the presence of SP-D in the air-breathing organs of nonmammalian species and SP-B in actinopterygian

  7. Genome sequence analysis of the model grass Brachypodium distachyon: insights into grass genome evolution

    Energy Technology Data Exchange (ETDEWEB)

    Schulman, Al

    2009-08-09

    Three subfamilies of grasses, the Erhardtoideae (rice), the Panicoideae (maize, sorghum, sugar cane and millet), and the Pooideae (wheat, barley and cool season forage grasses) provide the basis of human nutrition and are poised to become major sources of renewable energy. Here we describe the complete genome sequence of the wild grass Brachypodium distachyon (Brachypodium), the first member of the Pooideae subfamily to be completely sequenced. Comparison of the Brachypodium, rice and sorghum genomes reveals a precise sequence- based history of genome evolution across a broad diversity of the grass family and identifies nested insertions of whole chromosomes into centromeric regions as a predominant mechanism driving chromosome evolution in the grasses. The relatively compact genome of Brachypodium is maintained by a balance of retroelement replication and loss. The complete genome sequence of Brachypodium, coupled to its exceptional promise as a model system for grass research, will support the development of new energy and food crops

  8. Spatiotemporal evolution of Reaumuria (Tamaricaceae) in Central Asia: insights from molecular biogeography

    Science.gov (United States)

    Mingli Zhang; Xiaoli Hao; Stewart C. Sanderson; Byalt V. Vyacheslav; Alexander P. Sukhorukov; Xia Zhang

    2014-01-01

    Reaumuria is an arid adapted genus with a distribution center in Central Asia; its evolution and dispersal is investigated in this paper. Eighteen species of Reaumuria and nine species of two other genera in the Tamaricaceae, Tamarix and Myricaria, were sampled, and four markers ITS, rps16, psbB-psbH, and trnL-trnF were sequenced. The reconstructed phylogenetic tree is...

  9. The origin and evolution of the sexes: Novel insights from a distant eukaryotic linage.

    Science.gov (United States)

    Mignerot, Laure; Coelho, Susana M

    2016-01-01

    Sexual reproduction is an extraordinarily widespread phenomenon that assures the production of new genetic combinations in nearly all eukaryotic lineages. Although the core features of sexual reproduction (meiosis and syngamy) are highly conserved, the control mechanisms that determine whether an individual is male or female are remarkably labile across eukaryotes. In genetically controlled sexual systems, gender is determined by sex chromosomes, which have emerged independently and repeatedly during evolution. Sex chromosomes have been studied in only a handful of classical model organism, and empirical knowledge on the origin and evolution of the sexes is still surprisingly incomplete. With the advent of new generation sequencing, the taxonomic breadth of model systems has been rapidly expanding, bringing new ideas and fresh views on this fundamental aspect of biology. This mini-review provides a quick state of the art of how the remarkable richness of the sexual characteristics of the brown algae is helping to increase our knowledge about the evolution of sex determination. Copyright © 2016 Académie des sciences. Published by Elsevier SAS. All rights reserved.

  10. An insight into the mechanism and evolution of shale reservoir characteristics with over-high maturity

    Directory of Open Access Journals (Sweden)

    Xinjing Li

    2016-10-01

    Full Text Available Over-high maturity is one of the most vital characteristics of marine organic-rich shale reservoirs from the Lower Paleozoic in the south part of China. The organic matter (OM in shale gas reservoirs almost went through the entire thermal evolution. During this wide span, a great amount of hydrocarbon was available and numerous pores were observed within the OM including kerogen and solid bitumen/pyrobitumen. These nanopores in solid bitumen/pyrobitumen can be identified using SEM. The imaging can be dissected and understood better based on the sequence of diagenesis and hydrocarbon charge with the shape of OM and pores. In terms of the maturity process showed by the various typical cases, the main effects of the relationship between the reservoir porosity and organic carbon abundance are interpreted as follows: the change and mechanism of reservoirs properties due to thermal evolution are explored, such as gas carbon isotope from partial to complete rollover zone, wettability alteration from water-wet to oil-wet and then water-wet pore surface again, electrical resistivity reversal from the increasing to decreasing stage, and nonlinearity fluctuation of rock elasticity anisotropy. These indicate a possible evolution pathway for shale gas reservoirs from the Lower Paleozoic in the southern China, as well as the general transformation processes between different shale reservoirs in thermal stages.

  11. Weird mammals provide insights into the evolution of mammalian sex chromosomes and dosage compensation.

    Science.gov (United States)

    Graves, Jennifer A Marshall

    2015-12-01

    The deep divergence of mammalian groups 166 and 190 million years ago (MYA) provide genetic variation to explore the evolution of DNA sequence, gene arrangement and regulation of gene expression in mammals. With encouragement from the founder of the field, Mary Lyon, techniques in cytogenetics and molecular biology were progressively adapted to characterize the sex chromosomes of kangaroos and other marsupials, platypus and echidna-and weird rodent species. Comparative gene mapping reveals the process of sex chromosome evolution from their inception 190 MYA (they are autosomal in platypus) to their inevitable end (the Y has disappeared in two rodent lineages). Our X and Y are relatively young, getting their start with the evolution of the sex-determining SRY gene, which triggered progressive degradation of the Y chromosome. Even more recently, sex chromosomes of placental mammals fused with an autosomal region which now makes up most of the Y. Exploration of gene activity patterns over four decades showed that dosage compensation via X-chromosome inactivation is unique to therian mammals, and that this whole chromosome control process is different in marsupials and absent in monotremes and reptiles, and birds. These differences can be exploited to deduce how mammalian sex chromosomes and epigenetic silencing evolved.

  12. Designing Successful Next-Generation Instruments to Detect the Epoch of Reionization

    Science.gov (United States)

    Thyagarajan, Nithyanandan; Hydrogen Epoch of Reionization Array (HERA) team, Murchison Widefield Array (MWA) team

    2018-01-01

    The Epoch of Reionization (EoR) signifies a period of intense evolution of the Inter-Galactic Medium (IGM) in the early Universe caused by the first generations of stars and galaxies, wherein they turned the neutral IGM to be completely ionized by redshift ≥ 6. This important epoch is poorly explored to date. Measurement of redshifted 21 cm line from neutral Hydrogen during the EoR is promising to provide the most direct constraints of this epoch. Ongoing experiments to detect redshifted 21 cm power spectrum during reionization, including the Murchison Widefield Array (MWA), Precision Array for Probing the Epoch of Reionization (PAPER), and the Low Frequency Array (LOFAR), appear to be severely affected by bright foregrounds and unaccounted instrumental systematics. For example, the spectral structure introduced by wide-field effects, aperture shapes and angular power patterns of the antennas, electrical and geometrical reflections in the antennas and electrical paths, and antenna position errors can be major limiting factors. These mimic the 21 cm signal and severely degrade the instrument performance. It is imperative for the next-generation of experiments to eliminate these systematics at their source via robust instrument design. I will discuss a generic framework to set cosmologically motivated antenna performance specifications and design strategies using the Precision Radio Interferometry Simulator (PRISim) -- a high-precision tool that I have developed for simulations of foregrounds and the instrument transfer function intended primarily for 21 cm EoR studies, but also broadly applicable to interferometer-based intensity mapping experiments. The Hydrogen Epoch of Reionization Array (HERA), designed in-part based on this framework, is expected to detect the 21 cm signal with high significance. I will present this framework and the simulations, and their potential for designing upcoming radio instruments such as HERA and the Square Kilometre Array (SKA).

  13. Insights from the complete chloroplast genome into the evolution of Sesamum indicum L.

    Directory of Open Access Journals (Sweden)

    Haiyang Zhang

    Full Text Available Sesame (Sesamum indicum L. is one of the oldest oilseed crops. In order to investigate the evolutionary characters according to the Sesame Genome Project, apart from sequencing its nuclear genome, we sequenced the complete chloroplast genome of S. indicum cv. Yuzhi 11 (white seeded using Illumina and 454 sequencing. Comparisons of chloroplast genomes between S. indicum and the 18 other higher plants were then analyzed. The chloroplast genome of cv. Yuzhi 11 contains 153,338 bp and a total of 114 unique genes (KC569603. The number of chloroplast genes in sesame is the same as that in Nicotiana tabacum, Vitis vinifera and Platanus occidentalis. The variation in the length of the large single-copy (LSC regions and inverted repeats (IR in sesame compared to 18 other higher plant species was the main contributor to size variation in the cp genome in these species. The 77 functional chloroplast genes, except for ycf1 and ycf2, were highly conserved. The deletion of the cp ycf1 gene sequence in cp genomes may be due either to its transfer to the nuclear genome, as has occurred in sesame, or direct deletion, as has occurred in Panax ginseng and Cucumis sativus. The sesame ycf2 gene is only 5,721 bp in length and has lost about 1,179 bp. Nucleotides 1-585 of ycf2 when queried in BLAST had hits in the sesame draft genome. Five repeats (R10, R12, R13, R14 and R17 were unique to the sesame chloroplast genome. We also found that IR contraction/expansion in the cp genome alters its rate of evolution. Chloroplast genes and repeats display the signature of convergent evolution in sesame and other species. These findings provide a foundation for further investigation of cp genome evolution in Sesamum and other higher plants.

  14. Nematode and arthropod genomes provide new insights into the evolution of class 2 B1 GPCRs.

    Science.gov (United States)

    Cardoso, João C R; Félix, Rute C; Power, Deborah M

    2014-01-01

    Nematodes and arthropods are the most speciose animal groups and possess Class 2 B1 G-protein coupled receptors (GPCRs). Existing models of invertebrate Class 2 B1 GPCR evolution are mainly centered on Caenorhabditis elegans and Drosophila melanogaster and a few other nematode and arthropod representatives. The present study reevaluates the evolution of metazoan Class 2 B1 GPCRs and orthologues by exploring the receptors in several nematode and arthropod genomes and comparing them to the human receptors. Three novel receptor phylogenetic clusters were identified and designated cluster A, cluster B and PDF-R-related cluster. Clusters A and B were identified in several nematode and arthropod genomes but were absent from D. melanogaster and Culicidae genomes, whereas the majority of the members of the PDF-R-related cluster were from nematodes. Cluster A receptors were nematode and arthropod-specific but shared a conserved gene environment with human receptor loci. Cluster B members were orthologous to human GCGR, PTHR and Secretin members with which they probably shared a common origin. PDF-R and PDF-R related clusters were present in representatives of both nematodes and arthropods. The results of comparative analysis of GPCR evolution and diversity in protostomes confirm previous notions that C. elegans and D. melanogaster genomes are not good representatives of nematode and arthropod phyla. We hypothesize that at least four ancestral Class 2 B1 genes emerged early in the metazoan radiation, which after the protostome-deuterostome split underwent distinct selective pressures that resulted in duplication and deletion events that originated the current Class 2 B1 GPCRs in nematode and arthropod genomes.

  15. Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells.

    Science.gov (United States)

    Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U-Ser; Lin, Hao-Wu

    2015-09-04

    The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

  16. Insight into Evolution, Processing and Performance of Multi-length-scale Structures in Planar Heterojunction Perovskite Solar Cells

    Science.gov (United States)

    Huang, Yu-Ching; Tsao, Cheng-Si; Cho, Yi-Ju; Chen, Kuan-Chen; Chiang, Kai-Ming; Hsiao, Sheng-Yi; Chen, Chang-Wen; Su, Chun-Jen; Jeng, U.-Ser; Lin, Hao-Wu

    2015-09-01

    The structural characterization correlated to the processing control of hierarchical structure of planar heterojunction perovskite layer is still incomplete due to the limitations of conventional microscopy and X-ray diffraction. This present study performed the simultaneously grazing-incidence small-angle scattering and wide-angle scattering (GISAXS/GIWAXS) techniques to quantitatively probe the hierarchical structure of the planar heterojunction perovskite solar cells. The result is complementary to the currently microscopic study. Correlation between the crystallization behavior, crystal orientation, nano- and meso-scale internal structure and surface morphology of perovskite film as functions of various processing control parameters is reported for the first time. The structural transition from the fractal pore network to the surface fractal can be tuned by the chloride percentage. The GISAXS/GIWAXS measurement provides the comprehensive understanding of concurrent evolution of the film morphology and crystallization correlated to the high performance. The result can provide the insight into formation mechanism and rational synthesis design.

  17. The evolution of nervous system patterning: insights from sea urchin development

    Science.gov (United States)

    Angerer, Lynne M.; Yaguchi, Shunsuke; Angerer, Robert C.; Burke, Robert D.

    2011-01-01

    Recent studies of the sea urchin embryo have elucidated the mechanisms that localize and pattern its nervous system. These studies have revealed the presence of two overlapping regions of neurogenic potential at the beginning of embryogenesis, each of which becomes progressively restricted by separate, yet linked, signals, including Wnt and subsequently Nodal and BMP. These signals act to specify and localize the embryonic neural fields – the anterior neuroectoderm and the more posterior ciliary band neuroectoderm – during development. Here, we review these conserved nervous system patterning signals and consider how the relationships between them might have changed during deuterostome evolution. PMID:21828090

  18. Empowering insight: The role of collaboration in the evolution of intelligence practice

    Directory of Open Access Journals (Sweden)

    Craig Fleisher

    2016-08-01

    Conclusion: The evidence we have amassed provides substantial evidence of a notable and beneficial shift from doing intelligence work independently, frequently within silos, towards doing it collaboratively and across multiple types of boundaries. Intelligence practitioners are growing in their capabilities by taking advantage of emerging technologies, adapting practices imported from adjacent fields and benefitting from academic and/or scholarly research that helps push ahead the working boundaries of the field and allows it to make progress. In our view, CMI practice has recently entered a third era of evolution, one in which collaboration will continue to feature prominently, if not centrally.

  19. The transcriptome of Nacobbus aberrans reveals insights into the evolution of sedentary endoparasitism in plant-parasitic nematodes.

    Science.gov (United States)

    Eves-van den Akker, Sebastian; Lilley, Catherine J; Danchin, Etienne G J; Rancurel, Corinne; Cock, Peter J A; Urwin, Peter E; Jones, John T

    2014-08-13

    Within the phylum Nematoda, plant-parasitism is hypothesized to have arisen independently on at least four occasions. The most economically damaging plant-parasitic nematode species, and consequently the most widely studied, are those that feed as they migrate destructively through host roots causing necrotic lesions (migratory endoparasites) and those that modify host root tissue to create a nutrient sink from which they feed (sedentary endoparasites). The false root-knot nematode Nacobbus aberrans is the only known species to have both migratory endoparasitic and sedentary endoparasitic stages within its life cycle. Moreover, its sedentary stage appears to have characteristics of both the root-knot and the cyst nematodes. We present the first large-scale genetic resource of any false-root knot nematode species. We use RNAseq to describe relative abundance changes in all expressed genes across the life cycle to provide interesting insights into the biology of this nematode as it transitions between modes of parasitism. A multigene phylogenetic analysis of N. aberrans with respect to plant-parasitic nematodes of all groups confirms its proximity to both cyst and root-knot nematodes. We present a transcriptome-wide analysis of both lateral gene transfer events and the effector complement. Comparing parasitism genes of typical root-knot and cyst nematodes to those of N. aberrans has revealed interesting similarities. Importantly, genes that were believed to be either cyst nematode, or root-knot nematode, "specific" have both been identified in N. aberrans. Our results provide insights into the characteristics of a common ancestor and the evolution of sedentary endoparasitism of plants by nematodes. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  20. The FGGY carbohydrate kinase family: insights into the evolution of functional specificities.

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    Ying Zhang

    2011-12-01

    Full Text Available Function diversification in large protein families is a major mechanism driving expansion of cellular networks, providing organisms with new metabolic capabilities and thus adding to their evolutionary success. However, our understanding of the evolutionary mechanisms of functional diversity in such families is very limited, which, among many other reasons, is due to the lack of functionally well-characterized sets of proteins. Here, using the FGGY carbohydrate kinase family as an example, we built a confidently annotated reference set (CARS of proteins by propagating experimentally verified functional assignments to a limited number of homologous proteins that are supported by their genomic and functional contexts. Then, we analyzed, on both the phylogenetic and the molecular levels, the evolution of different functional specificities in this family. The results show that the different functions (substrate specificities encoded by FGGY kinases have emerged only once in the evolutionary history following an apparently simple divergent evolutionary model. At the same time, on the molecular level, one isofunctional group (L-ribulokinase, AraB evolved at least two independent solutions that employed distinct specificity-determining residues for the recognition of a same substrate (L-ribulose. Our analysis provides a detailed model of the evolution of the FGGY kinase family. It also shows that only combined molecular and phylogenetic approaches can help reconstruct a full picture of functional diversifications in such diverse families.

  1. New insights on equid locomotor evolution from the lumbar region of fossil horses.

    Science.gov (United States)

    Jones, Katrina Elizabeth

    2016-04-27

    The specialization of equid limbs for cursoriality is a classic case of adaptive evolution, but the role of the axial skeleton in this famous transition is not well understood. Extant horses are extremely fast and efficient runners, which use a stiff-backed gallop with reduced bending of the lumbar region relative to other mammals. This study tests the hypothesis that stiff-backed running in horses evolved in response to evolutionary increases in body size by examining lumbar joint shape from a broad sample of fossil equids in a phylogenetic context. Lumbar joint shape scaling suggests that stability of the lumbar region does correlate with size through equid evolution. However, scaling effects were dampened in the posterior lumbar region, near the sacrum, which suggests strong selection for sagittal mobility in association with locomotor-respiratory coupling near the lumbosacral joint. I hypothesize that small-bodied fossil horses may have used a speed-dependent running gait, switching between stiff-backed and flex-backed galloping as speed increased. © 2016 The Author(s).

  2. Genome Sequences of Marine Shrimp Exopalaemon carinicauda Holthuis Provide Insights into Genome Size Evolution of Caridea.

    Science.gov (United States)

    Yuan, Jianbo; Gao, Yi; Zhang, Xiaojun; Wei, Jiankai; Liu, Chengzhang; Li, Fuhua; Xiang, Jianhai

    2017-07-05

    Crustacea, particularly Decapoda, contains many economically important species, such as shrimps and crabs. Crustaceans exhibit enormous (nearly 500-fold) variability in genome size. However, limited genome resources are available for investigating these species. Exopalaemon carinicauda Holthuis, an economical caridean shrimp, is a potential ideal experimental animal for research on crustaceans. In this study, we performed low-coverage sequencing and de novo assembly of the E. carinicauda genome. The assembly covers more than 95% of coding regions. E. carinicauda possesses a large complex genome (5.73 Gb), with size twice higher than those of many decapod shrimps. As such, comparative genomic analyses were implied to investigate factors affecting genome size evolution of decapods. However, clues associated with genome duplication were not identified, and few horizontally transferred sequences were detected. Ultimately, the burst of transposable elements, especially retrotransposons, was determined as the major factor influencing genome expansion. A total of 2 Gb repeats were identified, and RTE-BovB, Jockey, Gypsy, and DIRS were the four major retrotransposons that significantly expanded. Both recent (Jockey and Gypsy) and ancestral (DIRS) originated retrotransposons responsible for the genome evolution. The E. carinicauda genome also exhibited potential for the genomic and experimental research of shrimps.

  3. Sequencing of the sea lamprey (Petromyzon marinus) genome provides insights into vertebrate evolution

    Science.gov (United States)

    Smith, Jeramiah J; Kuraku, Shigehiro; Holt, Carson; Sauka-Spengler, Tatjana; Jiang, Ning; Campbell, Michael S; Yandell, Mark D; Manousaki, Tereza; Meyer, Axel; Bloom, Ona E; Morgan, Jennifer R; Buxbaum, Joseph D; Sachidanandam, Ravi; Sims, Carrie; Garruss, Alexander S; Cook, Malcolm; Krumlauf, Robb; Wiedemann, Leanne M; Sower, Stacia A; Decatur, Wayne A; Hall, Jeffrey A; Amemiya, Chris T; Saha, Nil R; Buckley, Katherine M; Rast, Jonathan P; Das, Sabyasachi; Hirano, Masayuki; McCurley, Nathanael; Guo, Peng; Rohner, Nicolas; Tabin, Clifford J; Piccinelli, Paul; Elgar, Greg; Ruffier, Magali; Aken, Bronwen L; Searle, Stephen MJ; Muffato, Matthieu; Pignatelli, Miguel; Herrero, Javier; Jones, Matthew; Brown, C Titus; Chung-Davidson, Yu-Wen; Nanlohy, Kaben G; Libants, Scot V; Yeh, Chu-Yin; McCauley, David W; Langeland, James A; Pancer, Zeev; Fritzsch, Bernd; de Jong, Pieter J; Zhu, Baoli; Fulton, Lucinda L; Theising, Brenda; Flicek, Paul; Bronner, Marianne E; Warren, Wesley C; Clifton, Sandra W; Wilson, Richard K; Li, Weiming

    2013-01-01

    Lampreys are representatives of an ancient vertebrate lineage that diverged from our own ~500 million years ago. By virtue of this deeply shared ancestry, the sea lamprey (P. marinus) genome is uniquely poised to provide insight into the ancestry of vertebrate genomes and the underlying principles of vertebrate biology. Here, we present the first lamprey whole-genome sequence and assembly. We note challenges faced owing to its high content of repetitive elements and GC bases, as well as the absence of broad-scale sequence information from closely related species. Analyses of the assembly indicate that two whole-genome duplications likely occurred before the divergence of ancestral lamprey and gnathostome lineages. Moreover, the results help define key evolutionary events within vertebrate lineages, including the origin of myelin-associated proteins and the development of appendages. The lamprey genome provides an important resource for reconstructing vertebrate origins and the evolutionary events that have shaped the genomes of extant organisms. PMID:23435085

  4. New insights into the stratigraphic, paleogeographic and tectonic evolution and petroleum potential of Kerkennah Islands, Eastern Tunisia

    Science.gov (United States)

    Elfessi, Maroua

    2017-01-01

    This work presents general insights into the stratigraphic and paleogeographic evolution as well as the structural architecture and the petroleum potential of Kerkennah Islands, located in the Eastern Tunisia Foreland, from Cenomanian to Pliocene times. Available data from twenty wells mostly drilled in Cercina and Chergui fields are used to establish three lithostratigraphic correlations as well as isopach and isobath maps in order to point out thickness and depth variations of different geological formations present within our study area; in addition to a synthetic log and isoporosity map of the main carbonate reservoir (the nummulites enriched Reineche Member). The integrated geological study reveals relatively condensed but generally continuous sedimentation and a rugged substrate with horsts, grabens and tilted blocks due to the initiation and the individualization of Kerkennah arch throughout the studied geological times. Furthermore, a relationship was highlighted between the evolution of our study zone and those of Sirt basin, Western Mediterranean Sea and Pelagian troughs; this relationship is due to the outstanding location of Kerkennah Islands. The main Bou Dabbous source rock is thicker and more mature within the central-east of the Gulf of Gabes indicating therefore the southeast charge of Reineche reservoir which shows NW-SE trending tilted block system surrounded by normal faults representing the hydrocarbon migration pathways. Besides, the thick Oligo-Miocene formations deposited during the collapse of the Pelagian block caused the maturation of the Ypresian source rock, while the Pliocene unconformity allowed basin inversion and hydrocarbon migration.

  5. Genomic and secondary metabolite analyses of Streptomyces sp. 2AW provide insight into the evolution of the cycloheximide pathway

    Directory of Open Access Journals (Sweden)

    Elizabeth eStulberg

    2016-05-01

    Full Text Available The dearth of new antibiotics in the face of widespread antimicrobial resistance makes developing innovative strategies for discovering new antibiotics critical for the future management of infectious disease. Understanding the genetics and evolution of antibiotic producers will help guide the discovery and bioengineering of novel antibiotics. We discovered an isolate in Alaskan boreal forest soil that had broad antimicrobial activity. We elucidated the corresponding antimicrobial natural products and sequenced the genome of this isolate, designated Streptomyces sp. 2AW. This strain illustrates the chemical virtuosity typical of the Streptomyces genus, producing cycloheximide as well as two other biosynthetically unrelated antibiotics, neutramycin and hygromycin A. Combining bioinformatic and chemical analyses, we identified the gene clusters responsible for antibiotic production. Interestingly, 2AW appears dissimilar from other cycloheximide producers in that the gene encoding the polyketide synthase resides on a separate part of the chromosome from the genes responsible for tailoring cycloheximide-specific modifications. This gene arrangement and our phylogenetic analyses of the gene products suggest that 2AW holds an evolutionarily ancestral lineage of the cycloheximide pathway. Our analyses support the hypothesis that the 2AW glutaramide gene cluster is basal to the lineage wherein cycloheximide production diverged from other glutarimide antibiotics. This study illustrates the power of combining modern biochemical and genomic analyses to gain insight into the evolution of antibiotic-producing microorganisms.

  6. A Genomic Survey of SCPP Family Genes in Fishes Provides Novel Insights into the Evolution of Fish Scales.

    Science.gov (United States)

    Lv, Yunyun; Kawasaki, Kazuhiko; Li, Jia; Li, Yanping; Bian, Chao; Huang, Yu; You, Xinxin; Shi, Qiong

    2017-11-16

    The family of secretory calcium-binding phosphoproteins (SCPPs) have been considered vital to skeletal tissue mineralization. However, most previous SCPP studies focused on phylogenetically distant animals but not on those closely related species. Here we provide novel insights into the coevolution of SCPP genes and fish scales in 10 species from Otophysi . According to their scale phenotypes, these fishes can be divided into three groups, i.e., scaled, sparsely scaled, and scaleless. We identified homologous SCPP genes in the genomes of these species and revealed an absence of some SCPP members in some genomes, suggesting an uneven evolutionary history of SCPP genes in fishes. In addition, most of these SCPP genes, with the exception of SPP1 , individually form one or two gene cluster(s) on each corresponding genome. Furthermore, we constructed phylogenetic trees using maximum likelihood method to estimate their evolution. The phylogenetic topology mostly supports two subclasses in some species, such as Cyprinus carpio , Sinocyclocheilus anshuiensis , S. grahamin , and S. rhinocerous , but not in the other examined fishes. By comparing the gene structures of recently reported candidate genes, SCPP1 and SCPP5 , for determining scale phenotypes, we found that the hypothesis is suitable for Astyanax mexicanus , but denied by S. anshuiensis , even though they are both sparsely scaled for cave adaptation. Thus, we conclude that, although different fish species display similar scale phenotypes, the underlying genetic changes however might be diverse. In summary, this paper accelerates the recognition of the SCPP family in teleosts for potential scale evolution.

  7. Insights into recent and ancient trends in the co-evolution of Earth and life as revealed by microbial genomics

    Science.gov (United States)

    Anderson, R. E.; Huber, J. A.; Parsons, C.; Stüeken, E.

    2017-12-01

    tree of life. In contrast, genes related to nitrogen fixation display much more consistent rates of horizontal gene transfer throughout Earth's history. Studies that couple genomics approaches with geochemistry have the potential to reveal insights into the co-evolution of life and Earth both in the recent and distant past.

  8. Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.

    Science.gov (United States)

    Kelleher, Philip; Bottacini, Francesca; Mahony, Jennifer; Kilcawley, Kieran N; van Sinderen, Douwe

    2017-03-29

    Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production. In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon. Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted.

  9. Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

    Directory of Open Access Journals (Sweden)

    McGuire Abigail

    2012-03-01

    Full Text Available Abstract Background The sequence of the pathogen Mycobacterium tuberculosis (Mtb strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of Mtb pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org, including 8 strains of Mtb and M. bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum. Results Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four. Conclusions Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of Mtb in a comparative context, and are available online and through TBDB.org.

  10. Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.

    Science.gov (United States)

    McGuire, Abigail Manson; Weiner, Brian; Park, Sang Tae; Wapinski, Ilan; Raman, Sahadevan; Dolganov, Gregory; Peterson, Matthew; Riley, Robert; Zucker, Jeremy; Abeel, Thomas; White, Jared; Sisk, Peter; Stolte, Christian; Koehrsen, Mike; Yamamoto, Robert T; Iacobelli-Martinez, Milena; Kidd, Matthew J; Maer, Andreia M; Schoolnik, Gary K; Regev, Aviv; Galagan, James

    2012-03-28

    The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of Mtb pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org), including 8 strains of Mtb and M. bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum. Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four. Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of Mtb in a comparative context, and are available online and through TBDB.org.

  11. A novel insight into the cost-benefit model for the evolution of botanical carnivory.

    Science.gov (United States)

    Pavlovič, Andrej; Saganová, Michaela

    2015-06-01

    The cost-benefit model for the evolution of botanical carnivory provides a conceptual framework for interpreting a wide range of comparative and experimental studies on carnivorous plants. This model assumes that the modified leaves called traps represent a significant cost for the plant, and this cost is outweighed by the benefits from increased nutrient uptake from prey, in terms of enhancing the rate of photosynthesis per unit leaf mass or area (AN) in the microsites inhabited by carnivorous plants. This review summarizes results from the classical interpretation of the cost-benefit model for evolution of botanical carnivory and highlights the costs and benefits of active trapping mechanisms, including water pumping, electrical signalling and accumulation of jasmonates. Novel alternative sequestration strategies (utilization of leaf litter and faeces) in carnivorous plants are also discussed in the context of the cost-benefit model. Traps of carnivorous plants have lower AN than leaves, and the leaves have higher AN after feeding. Prey digestion, water pumping and electrical signalling represent a significant carbon cost (as an increased rate of respiration, RD) for carnivorous plants. On the other hand, jasmonate accumulation during the digestive period and reprogramming of gene expression from growth and photosynthesis to prey digestion optimizes enzyme production in comparison with constitutive secretion. This inducibility may have evolved as a cost-saving strategy beneficial for carnivorous plants. The similarities between plant defence mechanisms and botanical carnivory are highlighted. © The Author 2015. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  12. Insight Into the Origin and Evolution of the Vibrio parahaemolyticus Pandemic Strain

    Directory of Open Access Journals (Sweden)

    Romilio T. Espejo

    2017-07-01

    Full Text Available A strain of Vibrio parahaemolyticus that emerged in 1995 caused the first known pandemic involving this species. This strain comprises clonal autochthonous ocean-dwelling bacteria whose evolution has occurred in the ocean environment. The low sequence diversity in this population enabled the discovery of information on its origin and evolution that has been hidden in bacterial clones that have evolved over a long period. Multilocus sequencing and microarray analysis, together with phylogenetic analysis, of pandemic and pre-pandemic isolates has suggested that the founder clone was an O3:K6 non-pathogenic strain that initially acquired a toxRS/new region and subsequently acquired at least seven novel genomic islands. Sequencing and comparison of whole genomes later confirmed these early observations, and it confirmed that most of the genetic changes occurred via gene conversion involving horizontally transmitted DNA. The highly clonal population rapidly diversified, especially in terms of antigenicity, and 27 serotypes have already been reported. Comparisons of the core genomes derived from the founder clone indicate that there are only a few hundred single-nucleotide variations between isolates. However, when the whole genome is considered (the core plus non-core genome and from any clonal frame, the amount of DNA with a different clonal frame can reach up to 4.2% and the number of single-nucleotide variations can reach several hundred thousand. Altogether, these and previous observations based on multilocus sequence typing, microarray analysis, and whole-genome sequencing indicate the large contribution made by DNA with different clonal genealogy to genome diversification. The evidence also indicates that horizontal gene transfer (HGT caused the emergence of new pathogens. Furthermore, the extent of HGT seems to depend on the vicissitudes of the life of each bacterium, as exemplified by differences in thousands of base pairs acquired by HGT

  13. Decomposing Additive Genetic Variance Revealed Novel Insights into Trait Evolution in Synthetic Hexaploid Wheat

    Directory of Open Access Journals (Sweden)

    Abdulqader Jighly

    2018-02-01

    Full Text Available Whole genome duplication (WGD is an evolutionary phenomenon, which causes significant changes to genomic structure and trait architecture. In recent years, a number of studies decomposed the additive genetic variance explained by different sets of variants. However, they investigated diploid populations only and none of the studies examined any polyploid organism. In this research, we extended the application of this approach to polyploids, to differentiate the additive variance explained by the three subgenomes and seven sets of homoeologous chromosomes in synthetic allohexaploid wheat (SHW to gain a better understanding of trait evolution after WGD. Our SHW population was generated by crossing improved durum parents (Triticum turgidum; 2n = 4x = 28, AABB subgenomes with the progenitor species Aegilops tauschii (syn Ae. squarrosa, T. tauschii; 2n = 2x = 14, DD subgenome. The population was phenotyped for 10 fungal/nematode resistance traits as well as two abiotic stresses. We showed that the wild D subgenome dominated the additive effect and this dominance affected the A more than the B subgenome. We provide evidence that this dominance was not inflated by population structure, relatedness among individuals or by longer linkage disequilibrium blocks observed in the D subgenome within the population used for this study. The cumulative size of the three homoeologs of the seven chromosomal groups showed a weak but significant positive correlation with their cumulative explained additive variance. Furthermore, an average of 69% for each chromosomal group's cumulative additive variance came from one homoeolog that had the highest explained variance within the group across all 12 traits. We hypothesize that structural and functional changes during diploidization may explain chromosomal group relations as allopolyploids keep balanced dosage for many genes. Our results contribute to a better understanding of trait evolution mechanisms in polyploidy

  14. SSR marker variations in Brassica species provide insight into the origin and evolution of Brassica amphidiploids.

    Science.gov (United States)

    Thakur, Ajay Kumar; Singh, Kunwar Harendra; Singh, Lal; Nanjundan, Joghee; Khan, Yasin Jeshima; Singh, Dhiraj

    2018-01-01

    Oilseed Brassica represents an important group of oilseed crops with a long history of evolution and cultivation. To understand the origin and evolution of Brassica amphidiploids, simple sequence repeat (SSR) markers were used to unravel genetic variations in three diploids and three amphidiploid Brassica species of U's triangle along with Eruca sativa as an outlier. Of 124 Brassica-derived SSR loci assayed, 100% cross-transferability was obtained for B. juncea and three subspecies of B. rapa , while lowest cross-transferability (91.93%) was obtained for Eruca sativa . The average % age of cross-transferability across all the seven species was 98.15%. The number of alleles detected at each locus ranged from one to six with an average of 3.41 alleles per primer pair. Neighbor-Joining-based dendrogram divided all the 40 accessions into two main groups composed of B. juncea / B. nigra/B. rapa and B. carinata/B. napus/B. oleracea . C-genome of oilseed Brassica species remained relatively more conserved than A- and B-genome. A- genome present in B. juncea and B. napus seems distinct from each other and hence provides great opportunity for generating diversity through synthesizing amphidiploids from different sources of A- genome. B. juncea had least intra-specific distance indicating narrow genetic base. B. rapa appears to be more primitive species from which other two diploid species might have evolved. The SSR marker set developed in this study will assist in DNA fingerprinting of various Brassica species cultivars, evaluating the genetic diversity in Brassica germplasm, genome mapping and construction of linkage maps, gene tagging and various other genomics-related studies in Brassica species. Further, the evolutionary relationship established among various Brassica species would assist in formulating suitable breeding strategies for widening the genetic base of Brassica amphidiploids by exploiting the genetic diversity present in diploid progenitor gene pools.

  15. Hormones and the Evolution of Complex Traits: Insights from Artificial Selection on Behavior.

    Science.gov (United States)

    Garland, Theodore; Zhao, Meng; Saltzman, Wendy

    2016-08-01

    Although behavior may often be a fairly direct target of natural or sexual selection, it cannot evolve without changes in subordinate traits that cause or permit its expression. In principle, changes in endocrine function could be a common mechanism underlying behavioral evolution because they are well positioned to mediate integrated responses to behavioral selection. More specifically, hormones can influence both motivational (e.g., brain) and performance (e.g., muscles) components of behavior simultaneously and in a coordinated fashion. If the endocrine system is often "used" as a general mechanism to effect responses to selection, then correlated responses in other aspects of behavior, life history, and organismal performance (e.g., locomotor abilities) should commonly occur because any cell with appropriate receptors could be affected. Ways in which behavior coadapts with other aspects of the phenotype can be studied directly through artificial selection and experimental evolution. Several studies have targeted rodent behavior for selective breeding and reported changes in other aspects of behavior, life history, and lower-level effectors of these organismal traits, including endocrine function. One example involves selection for high levels of voluntary wheel running, one aspect of physical activity, in four replicate High Runner (HR) lines of mice. Circulating levels of several hormones (including insulin, testosterone, thyroxine, triiodothyronine) have been characterized, three of which-corticosterone, leptin, and adiponectin-differ between HR and control lines, depending on sex, age, and generation. Potential changes in circulating levels of other behaviorally and metabolically relevant hormones, as well as in other components of the endocrine system (e.g., receptors), have yet to be examined. Overall, results to date identify promising avenues for further studies on the endocrine basis of activity levels. © The Author 2016. Published by Oxford University

  16. Late Guadalupian evolution of the Delaware Basin: insights from stable isotope and trace element geochemistry

    Science.gov (United States)

    Smith, B.; Kerans, C.

    2017-12-01

    Accurate characterization of mixed carbonate and evaporite deposits requires an understanding of basin-scale physical, chemical, and biological processes. In these settings, carbonate geochemistry often responds to changes in the prevailing conditions in the water column. It follows that the geochemical record presents a potential aid for interpretation of depositional systems provided that it is relatively free of diagenetic overprint. This is seldom the case in shallow-water settings as processes such as meteoric diagenesis and early dolomitization obscure or erase the original geochemical signal. Fine grained deep-water sediments are more likely to retain their original geochemical characteristics. If reliable shelf-to-basin correlations can be established, then basinal deposits provide critical data not only for the interpretation of deep water environments, but overall basin evolution as well. This study examines variations in trace element and stable isotope geochemistry from the Delaware Basin of West Texas and New Mexico. Interpretation of geochemical data within a pre-existing shelf-to-basin stratigraphic framework suggests a link between basin water chemistry and sea level changes during the entirety of the Guadalupian. This link is supported analogies to modern silled basins where changes in sea level and thus recharge across the sill can control nutrient input, circulation, and bottom water oxygenation. In light of these relationships, the filling of the Delaware Basin with basin-centered evaporites at the end of the Guadalupian likely represents the culmination of a more gradual, cyclic evolution towards basin restriction. Ongoing work will continue to focus on tying regional-scale changes in basin water chemistry to the combined geochemical and physical sedimentological records.

  17. Karyological characterization of the endemic Iberian rock lizard, Iberolacerta monticola (Squamata, Lacertidae): insights into sex chromosome evolution.

    Science.gov (United States)

    Rojo, V; Giovannotti, M; Naveira, H; Nisi Cerioni, P; González-Tizón, A M; Caputo Barucchi, V; Galán, P; Olmo, E; Martínez-Lage, A

    2014-01-01

    Rock lizards of the genus Iberolacerta constitute a promising model to examine the process of sex chromosome evolution, as these closely related taxa exhibit remarkable diversity in the degree of sex chromosome differentiation with no clear phylogenetic segregation, ranging from cryptic to highly heteromorphic ZW chromosomes and even multiple chromosome systems (Z1Z1Z2Z2/Z1Z2W). To gain a deeper insight into the patterns of karyotype and sex chromosome evolution, we performed a cytogenetic analysis based on conventional staining, banding techniques and fluorescence in situ hybridization in the species I. monticola, for which previous cytogenetic investigations did not detect differentiated sex chromosomes. The karyotype is composed of 2n = 36 acrocentric chromosomes. NORs and the major ribosomal genes were located in the subtelomeric region of chromosome pair 6. Hybridization signals of the telomeric sequences (TTAGGG)n were visualized at the telomeres of all chromosomes and interstitially in 5 chromosome pairs. C-banding showed constitutive heterochromatin at the centromeres of all chromosomes, as well as clear pericentromeric and light telomeric C-bands in several chromosome pairs. These results highlight some chromosomal markers which can be useful to identify species-specific diagnostic characters, although they may not accurately reflect the phylogenetic relationships among the taxa. In addition, C-banding revealed the presence of a heteromorphic ZW sex chromosome pair, where W is smaller than Z and almost completely heterochromatic. This finding sheds light on sex chromosome evolution in the genus Iberolacerta and suggests that further comparative cytogenetic analyses are needed to understand the processes underlying the origin, differentiation and plasticity of sex chromosome systems in lacertid lizards. © 2013 S. Karger AG, Basel.

  18. Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence

    Directory of Open Access Journals (Sweden)

    Rands Chris M

    2013-02-01

    Full Text Available Abstract Background A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos finches (Thraupidae, Passeriformes. Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris. Results 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1 have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins. Conclusions These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches.

  19. Evolution and functional insights of different ancestral orthologous clades of chitin synthase genes in the fungal tree of life

    Directory of Open Access Journals (Sweden)

    Mu eLi

    2016-02-01

    Full Text Available Chitin synthases (CHSs are key enzymes in the biosynthesis of chitin, an important structural component of fungal cell walls that can trigger innate immune responses in host plants and animals. Members of CHS gene family perform various functions in fungal cellular processes. Previous studies focused primarily on classifying diverse CHSs into different classes, regardless of their functional diversification, or on characterizing their functions in individual fungal species. A complete and systematic comparative analysis of CHS genes based on their orthologous relationships will be valuable for elucidating the evolution and functions of different CHS genes in fungi. Here, we identified and compared members of the CHS gene family across the fungal tree of life, including 18 divergent fungal lineages. Phylogenetic analysis revealed that the fungal CHS gene family is comprised of at least 10 ancestral orthologous clades, which have undergone multiple independent duplications and losses in different fungal lineages during evolution. Interestingly, one of these CHS clades (class III was expanded in plant or animal pathogenic fungi belonging to different fungal lineages. Two clades (classes VIb and VIc identified for the first time in this study occurred mainly in plant pathogenic fungi from Sordariomycetes and Dothideomycetes. Moreover, members of classes III and VIb were specifically up-regulated during plant infection, suggesting important roles in pathogenesis. In addition, CHS-associated networks conserved among plant pathogenic fungi are involved in various biological processes, including sexual reproduction and plant infection. We also identified specificity-determining sites, many of which are located at or adjacent to important structural and functional sites that are potentially responsible for functional divergence of different CHS classes. Overall, our results provide new insights into the evolution and function of members of CHS gene

  20. Cyclicity, episodicity, and continuity in accretionary wedge evolution: insights from geophysical imaging and physical analogue experiments

    Science.gov (United States)

    Kukowski, N.

    2009-04-01

    Geophysical profiles across active convergent margins reveal different styles and locations of sediment accretion, thrust slices dipping successively steeper towards the hinterland, splay faults, and blind thrusts as well as accumulation spaces e. g. thrust top basins and larger basins formed by regional subsidence, of very variable size and position. Morphologically, the continental slope at most margins can be sub-divided in a lower, middle, and upper slope, with often the middle slope being the most shallowly inclined, suggesting segmented wedges. Beneath the forearc, a subduction channel of a few hundred meters to a few km thickness marks a layer of material transport into greater depth that also hosts the plate interface and décollement zone. The petrographical composition of accretionary wedges and subduction channels as well as related pressures and temperatures are accessible through deep drilling or sampling fossil accretionary complexes now exhumed. The structure, lithology, and tectonic history of forearcs as identified from geophysical and geology field observations hint to parameters possibly controlling material transfer at convergent margins. Among them, sediment supply, which itself is largely controlled by climate, width of the subduction channel, and interplate frictional properties, which also exhibit control on plate coupling and therefore the seismic potential of a forearc, are suggested to be of major importance. These parameters further may undergo temporal fluctuation, e.g. when climate changes or when different material is entering the trench and therefore potentially also the subduction channel. High resolution monitoring of material flux and the evolution of fault zone kinematics of analogue experimental wedges made of granular materials exhibiting frictional behaviour equivalent to that of upper crustal rocks shows that accretionary cycles proceed as a chain of sub-processes, i.e. the development of a thrust slice from initial failure

  1. Seed coat development in Velloziaceae: primary homology assessment and insights on seed coat evolution.

    Science.gov (United States)

    Sousa-Baena, Mariane S; de Menezes, Nanuza L

    2014-09-01

    • Seed coat characteristics have historically been used to infer taxonomic relationships and are a potential source of characters for phylogenetic reconstruction. In particular, seed coat morphoanatomy has never been studied in detail in Velloziaceae. One character based on seed surface microsculpture has been used in phylogenies, but was excluded from recent studies owing to problems in primary homology. This work aimed to clarify the origin and general composition of seed coat cell layers in Velloziaceae and to propose hypotheses of primary homology among seed characters.• Seed coat development of 24 Velloziaceae species, comprising nine genera, and one species of Pandanaceae (outgroup) was studied using standard anatomical methods. Developmental data were interpreted in the light of a recently published phylogeny.• Eight types of seed coat were identified. Whereas the most common type has four distinct cell layers (two-layered tegmen and testa), we encountered much more variation in seed coat composition than previously reported, the analysis of which revealed some potential synapomorphies. For instance, an exotesta with spiral thickenings may be a synapomorphy of Barbacenia.• Our results showed that the character states previously used in phylogenies are not based on homologous layers and that the same state was misattributed to species exhibiting quite different seed coats. This study is a first step toward a better understanding of seed coat structure evolution in Velloziaceae. © 2014 Botanical Society of America, Inc.

  2. New Insights into the Structure, Origin, and Evolution of Pluto and Charon

    Science.gov (United States)

    McKinnon, W. B.; Stern, A.; Weaver, H. A., Jr.; Spencer, J. R.; Nimmo, F.; Lisse, C. M.; Umurhan, O. M.; Moore, J. M.; Buie, M. W.; Porter, S.; Olkin, C.; Young, L. A.; Ennico Smith, K.

    2015-12-01

    The July 2015 New Horizons flyby has removed a long-standing obstacle to understanding the cosmogony of the Pluto-Charon system: the uncertain radius of Pluto. Combined with precise astrometric fits to the barycenter of the Pluto-Charon binary from HST observations of the more distant, small satellites (M. Brozović et al., Icarus 246, 317-329, 2015), the densities of both Pluto and Charon are now known. At the 10% level, the densities of Pluto and Charon are rather similar, as opposed to the more divergent density estimates of years past in which Charon was thought to be substantially icier. In the context of a giant impact origin for binaries, a rock-poor Charon corresponds to an iron-poor Moon in the terrestrial case, with differentiated precursors being implied in both cases. A rock-rich Charon, however, implies that the precursor impacting bodies were at most only partially differentiated — possessing relatively thin ice shells (R.M. Canup, Astron. J. 141, 35, 2011). This suggests some combination of relatively slow and/or late accretion in the ancestral Kuiper belt. A more rock-rich Charon also implies a more vigorous geological history, all other things being equal. For Pluto, the evolution to the surface of a substantial mass of supervolatile ices increases the likelihood that internal volatiles such as ammonia and methanol have been sequestered in an internal, aqueous layer (or ocean).

  3. Insights into the red algae and eukaryotic evolution from the genome of Porphyra umbilicalis (Bangiophyceae, Rhodophyta).

    Science.gov (United States)

    Brawley, Susan H; Blouin, Nicolas A; Ficko-Blean, Elizabeth; Wheeler, Glen L; Lohr, Martin; Goodson, Holly V; Jenkins, Jerry W; Blaby-Haas, Crysten E; Helliwell, Katherine E; Chan, Cheong Xin; Marriage, Tara N; Bhattacharya, Debashish; Klein, Anita S; Badis, Yacine; Brodie, Juliet; Cao, Yuanyu; Collén, Jonas; Dittami, Simon M; Gachon, Claire M M; Green, Beverley R; Karpowicz, Steven J; Kim, Jay W; Kudahl, Ulrich Johan; Lin, Senjie; Michel, Gurvan; Mittag, Maria; Olson, Bradley J S C; Pangilinan, Jasmyn L; Peng, Yi; Qiu, Huan; Shu, Shengqiang; Singer, John T; Smith, Alison G; Sprecher, Brittany N; Wagner, Volker; Wang, Wenfei; Wang, Zhi-Yong; Yan, Juying; Yarish, Charles; Zäuner-Riek, Simone; Zhuang, Yunyun; Zou, Yong; Lindquist, Erika A; Grimwood, Jane; Barry, Kerrie W; Rokhsar, Daniel S; Schmutz, Jeremy; Stiller, John W; Grossman, Arthur R; Prochnik, Simon E

    2017-08-01

    Porphyra umbilicalis (laver) belongs to an ancient group of red algae (Bangiophyceae), is harvested for human food, and thrives in the harsh conditions of the upper intertidal zone. Here we present the 87.7-Mbp haploid Porphyra genome (65.8% G + C content, 13,125 gene loci) and elucidate traits that inform our understanding of the biology of red algae as one of the few multicellular eukaryotic lineages. Novel features of the Porphyra genome shared by other red algae relate to the cytoskeleton, calcium signaling, the cell cycle, and stress-tolerance mechanisms including photoprotection. Cytoskeletal motor proteins in Porphyra are restricted to a small set of kinesins that appear to be the only universal cytoskeletal motors within the red algae. Dynein motors are absent, and most red algae, including Porphyra , lack myosin. This surprisingly minimal cytoskeleton offers a potential explanation for why red algal cells and multicellular structures are more limited in size than in most multicellular lineages. Additional discoveries further relating to the stress tolerance of bangiophytes include ancestral enzymes for sulfation of the hydrophilic galactan-rich cell wall, evidence for mannan synthesis that originated before the divergence of green and red algae, and a high capacity for nutrient uptake. Our analyses provide a comprehensive understanding of the red algae, which are both commercially important and have played a major role in the evolution of other algal groups through secondary endosymbioses.

  4. Analyses of pig genomes provide insight into porcine demography and evolution

    Science.gov (United States)

    Groenen, Martien A. M.; Archibald, Alan L.; Uenishi, Hirohide; Tuggle, Christopher K.; Takeuchi, Yasuhiro; Rothschild, Max F.; Rogel-Gaillard, Claire; Park, Chankyu; Milan, Denis; Megens, Hendrik-Jan; Li, Shengting; Larkin, Denis M.; Kim, Heebal; Frantz, Laurent A. F.; Caccamo, Mario; Ahn, Hyeonju; Aken, Bronwen L.; Anselmo, Anna; Anthon, Christian; Auvil, Loretta; Badaoui, Bouabid; Beattie, Craig W.; Bendixen, Christian; Berman, Daniel; Blecha, Frank; Blomberg, Jonas; Bolund, Lars; Bosse, Mirte; Botti, Sara; Bujie, Zhan; Bystrom, Megan; Capitanu, Boris; Silva, Denise Carvalho; Chardon, Patrick; Chen, Celine; Cheng, Ryan; Choi, Sang-Haeng; Chow, William; Clark, Richard C.; Clee, Christopher; Crooijmans, Richard P. M. A.; Dawson, Harry D.; Dehais, Patrice; De Sapio, Fioravante; Dibbits, Bert; Drou, Nizar; Du, Zhi-Qiang; Eversole, Kellye; Fadista, João; Fairley, Susan; Faraut, Thomas; Faulkner, Geoffrey J.; Fowler, Katie E.; Fredholm, Merete; Fritz, Eric; Gilbert, James G. R.; Giuffra, Elisabetta; Gorodkin, Jan; Griffin, Darren K.; Harrow, Jennifer L.; Hayward, Alexander; Howe, Kerstin; Hu, Zhi-Liang; Humphray, Sean J.; Hunt, Toby; Hornshøj, Henrik; Jeon, Jin-Tae; Jern, Patric; Jones, Matthew; Jurka, Jerzy; Kanamori, Hiroyuki; Kapetanovic, Ronan; Kim, Jaebum; Kim, Jae-Hwan; Kim, Kyu-Won; Kim, Tae-Hun; Larson, Greger; Lee, Kyooyeol; Lee, Kyung-Tai; Leggett, Richard; Lewin, Harris A.; Li, Yingrui; Liu, Wansheng; Loveland, Jane E.; Lu, Yao; Lunney, Joan K.; Ma, Jian; Madsen, Ole; Mann, Katherine; Matthews, Lucy; McLaren, Stuart; Morozumi, Takeya; Murtaugh, Michael P.; Narayan, Jitendra; Nguyen, Dinh Truong; Ni, Peixiang; Oh, Song-Jung; Onteru, Suneel; Panitz, Frank; Park, Eung-Woo; Park, Hong-Seog; Pascal, Geraldine; Paudel, Yogesh; Perez-Enciso, Miguel; Ramirez-Gonzalez, Ricardo; Reecy, James M.; Zas, Sandra Rodriguez; Rohrer, Gary A.; Rund, Lauretta; Sang, Yongming; Schachtschneider, Kyle; Schraiber, Joshua G.; Schwartz, John; Scobie, Linda; Scott, Carol; Searle, Stephen; Servin, Bertrand; Southey, Bruce R.; Sperber, Goran; Stadler, Peter; Sweedler, Jonathan V.; Tafer, Hakim; Thomsen, Bo; Wali, Rashmi; Wang, Jian; Wang, Jun; White, Simon; Xu, Xun; Yerle, Martine; Zhang, Guojie; Zhang, Jianguo; Zhang, Jie; Zhao, Shuhong; Rogers, Jane; Churcher, Carol; Schook, Lawrence B.

    2013-01-01

    For 10,000 years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ~1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model. PMID:23151582

  5. Metagenomic insights into evolution of heavy metal-contaminated groundwater microbial community

    Energy Technology Data Exchange (ETDEWEB)

    Hemme, C.L.; Deng, Y.; Gentry, T.J.; Fields, M.W.; Wu, L.; Barua, S.; Barry, K.; Green-Tringe, S.; Watson, D.B.; He, Z.; Hazen, T.C.; Tiedje, J.M.; Rubin, E.M.; Zhou, J.

    2010-07-01

    Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents ({approx}50 years) has resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying {gamma}- and {beta}-proteobacterial populations. The resulting community is overabundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could have a key function in rapid response and adaptation to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

  6. Metagenomic Insights into Evolution of a Heavy Metal-Contaminated Groundwater Microbial Community

    Energy Technology Data Exchange (ETDEWEB)

    Hemme, Christopher L.; Deng, Ye; Gentry, Terry J.; Fields, Matthew W.; Wu, Liyou; Barua, Soumitra; Barry, Kerrie; Tringe, Susannah G.; Watson, David B.; He, Zhili; Hazen, Terry C.; Tiedje, James M.; Rubin, Edward M.; Zhou, Jizhong

    2010-02-15

    Understanding adaptation of biological communities to environmental change is a central issue in ecology and evolution. Metagenomic analysis of a stressed groundwater microbial community reveals that prolonged exposure to high concentrations of heavy metals, nitric acid and organic solvents (~;;50 years) have resulted in a massive decrease in species and allelic diversity as well as a significant loss of metabolic diversity. Although the surviving microbial community possesses all metabolic pathways necessary for survival and growth in such an extreme environment, its structure is very simple, primarily composed of clonal denitrifying ?- and ?-proteobacterial populations. The resulting community is over-abundant in key genes conferring resistance to specific stresses including nitrate, heavy metals and acetone. Evolutionary analysis indicates that lateral gene transfer could be a key mechanism in rapidly responding and adapting to environmental contamination. The results presented in this study have important implications in understanding, assessing and predicting the impacts of human-induced activities on microbial communities ranging from human health to agriculture to environmental management, and their responses to environmental changes.

  7. Evolution and current status of demand response (DR) in electricity markets: Insights from PJM and NYISO

    International Nuclear Information System (INIS)

    Walawalkar, Rahul; Fernands, Stephen; Thakur, Netra; Chevva, Konda Reddy

    2010-01-01

    In electricity markets, traditional demand side management programs are slowly getting replaced with demand response (DR) programs. These programs have evolved since the early pilot programs launched in late 1990s. With the changes in market rules the opportunities have generally increased for DR for participating in emergency, economic and ancillary service programs. In recent times, various regulators have suggested that DR can also be used as a solution to meet supply - demand fluctuations in scenarios with significant penetration of variable renewable sources in grid. This paper provides an overview of the evolution of the DR programs in PJM and NYISO markets as well as analyzes current opportunities. Although DR participation has grown, most of the current participation is in the reliability programs, which are designed to provide load curtailment during peak days. This suggests that there is a significant gap between perception of ability of DR to mitigate variability of renewables and reality of current participation. DR in future can be scaled to play a more dynamic role in electricity markets, but that would require changes both on technology as well as policy front. Advances in building technologies and energy storage combined with appropriate price signals can lead to enhanced DR participation. (author)

  8. Collagen cross-linking: insights on the evolution of metazoan extracellular matrix.

    Science.gov (United States)

    Rodriguez-Pascual, Fernando; Slatter, David Anthony

    2016-11-23

    Collagens constitute a large family of extracellular matrix (ECM) proteins that play a fundamental role in supporting the structure of various tissues in multicellular animals. The mechanical strength of fibrillar collagens is highly dependent on the formation of covalent cross-links between individual fibrils, a process initiated by the enzymatic action of members of the lysyl oxidase (LOX) family. Fibrillar collagens are present in a wide variety of animals, therefore often being associated with metazoan evolution, where the emergence of an ancestral collagen chain has been proposed to lead to the formation of different clades. While LOX-generated collagen cross-linking metabolites have been detected in different metazoan families, there is limited information about when and how collagen acquired this particular modification. By analyzing telopeptide and helical sequences, we identified highly conserved, potential cross-linking sites throughout the metazoan tree of life. Based on this analysis, we propose that they have importantly contributed to the formation and further expansion of fibrillar collagens.

  9. Has snake fang evolution lost its bite? New insights from a structural mechanics viewpoint.

    Science.gov (United States)

    Broeckhoven, Chris; du Plessis, Anton

    2017-08-01

    Venomous snakes-the pinnacle of snake evolution-are characterized by their possession of venom-conducting fangs ranging from grooved phenotypes characterizing multiple lineages of rear-fanged taxa to tubular phenotypes present in elapids, viperids and atractaspidines. Despite extensive research, controversy still exists on the selective pressures involved in fang phenotype diversification. Here, we test the hypothesis that larger fangs and consequently a shift to an anterior position in the maxilla evolved to compensate for the costs of structural changes, i.e. higher stress upon impact in tubular fangs compared to grooved fangs. Direct voxel-based stress simulations conducted on high-resolution µCT scans, analysed within a phylogenetic framework, showed no differences in stress distribution between the three fang phenotypes, despite differences in (relative) fang length. These findings suggest that additional compensatory mechanisms are responsible for the biomechanical optimization and that fang length might instead be related to differential striking behaviour strategies. © 2017 The Author(s).

  10. The Medicago Genome Provides Insight into the Evolution of Rhizobial Symbioses

    Science.gov (United States)

    Young, Nevin D.; Debellé, Frédéric; Oldroyd, Giles E. D.; Geurts, Rene; Cannon, Steven B.; Udvardi, Michael K.; Benedito, Vagner A.; Mayer, Klaus F. X.; Gouzy, Jérôme; Schoof, Heiko; Van de Peer, Yves; Proost, Sebastian; Cook, Douglas R.; Meyers, Blake C.; Spannagl, Manuel; Cheung, Foo; De Mita, Stéphane; Krishnakumar, Vivek; Gundlach, Heidrun; Zhou, Shiguo; Mudge, Joann; Bharti, Arvind K.; Murray, Jeremy D.; Naoumkina, Marina A.; Rosen, Benjamin; Silverstein, Kevin A. T.; Tang, Haibao; Rombauts, Stephane; Zhao, Patrick X.; Zhou, Peng; Barbe, Valérie; Bardou, Philippe; Bechner, Michael; Bellec, Arnaud; Berger, Anne; Bergès, Hélène; Bidwell, Shelby; Bisseling, Ton; Choisne, Nathalie; Couloux, Arnaud; Denny, Roxanne; Deshpande, Shweta; Dai, Xinbin; Doyle, Jeff; Dudez, Anne-Marie; Farmer, Andrew D.; Fouteau, Stéphanie; Franken, Carolien; Gibelin, Chrystel; Gish, John; Goldstein, Steven; González, Alvaro J.; Green, Pamela J.; Hallab, Asis; Hartog, Marijke; Hua, Axin; Humphray, Sean; Jeong, Dong-Hoon; Jing, Yi; Jöcker, Anika; Kenton, Steve M.; Kim, Dong-Jin; Klee, Kathrin; Lai, Hongshing; Lang, Chunting; Lin, Shaoping; Macmil, Simone L; Magdelenat, Ghislaine; Matthews, Lucy; McCorrison, Jamison; Monaghan, Erin L.; Mun, Jeong-Hwan; Najar, Fares Z.; Nicholson, Christine; Noirot, Céline; O’Bleness, Majesta; Paule, Charles R.; Poulain, Julie; Prion, Florent; Qin, Baifang; Qu, Chunmei; Retzel, Ernest F.; Riddle, Claire; Sallet, Erika; Samain, Sylvie; Samson, Nicolas; Sanders, Iryna; Saurat, Olivier; Scarpelli, Claude; Schiex, Thomas; Segurens, Béatrice; Severin, Andrew J.; Sherrier, D. Janine; Shi, Ruihua; Sims, Sarah; Singer, Susan R.; Sinharoy, Senjuti; Sterck, Lieven; Viollet, Agnès; Wang, Bing-Bing; Wang, Keqin; Wang, Mingyi; Wang, Xiaohong; Warfsmann, Jens; Weissenbach, Jean; White, Doug D.; White, Jim D.; Wiley, Graham B.; Wincker, Patrick; Xing, Yanbo; Yang, Limei; Yao, Ziyun; Ying, Fu; Zhai, Jixian; Zhou, Liping; Zuber, Antoine; Dénarié, Jean; Dixon, Richard A.; May, Gregory D.; Schwartz, David C.; Rogers, Jane; Quétier, Francis; Town, Christopher D.; Roe, Bruce A.

    2011-01-01

    Legumes (Fabaceae or Leguminosae) are unique among cultivated plants for their ability to carry out endosymbiotic nitrogen fixation with rhizobial bacteria, a process that takes place in a specialized structure known as the nodule. Legumes belong to one of the two main groups of eurosids, the Fabidae, which includes most species capable of endosymbiotic nitrogen fixation 1. Legumes comprise several evolutionary lineages derived from a common ancestor 60 million years ago (Mya). Papilionoids are the largest clade, dating nearly to the origin of legumes and containing most cultivated species 2. Medicago truncatula (Mt) is a long-established model for the study of legume biology. Here we describe the draft sequence of the Mt euchromatin based on a recently completed BAC-assembly supplemented with Illumina-shotgun sequence, together capturing ~94% of all Mt genes. A whole-genome duplication (WGD) approximately 58 Mya played a major role in shaping the Mt genome and thereby contributed to the evolution of endosymbiotic nitrogen fixation. Subsequent to the WGD, the Mt genome experienced higher levels of rearrangement than two other sequenced legumes, Glycine max (Gm) and Lotus japonicus (Lj). Mt is a close relative of alfalfa (M. sativa), a widely cultivated crop with limited genomics tools and complex autotetraploid genetics. As such, the Mt genome sequence provides significant opportunities to expand alfalfa’s genomic toolbox. PMID:22089132

  11. Directed evolution of a model primordial enzyme provides insights into the development of the genetic code.

    Directory of Open Access Journals (Sweden)

    Manuel M Müller

    Full Text Available The contemporary proteinogenic repertoire contains 20 amino acids with diverse functional groups and side chain geometries. Primordial proteins, in contrast, were presumably constructed from a subset of these building blocks. Subsequent expansion of the proteinogenic alphabet would have enhanced their capabilities, fostering the metabolic prowess and organismal fitness of early living systems. While the addition of amino acids bearing innovative functional groups directly enhances the chemical repertoire of proteomes, the inclusion of chemically redundant monomers is difficult to rationalize. Here, we studied how a simplified chorismate mutase evolves upon expanding its amino acid alphabet from nine to potentially 20 letters. Continuous evolution provided an enhanced enzyme variant that has only two point mutations, both of which extend the alphabet and jointly improve protein stability by >4 kcal/mol and catalytic activity tenfold. The same, seemingly innocuous substitutions (Ile→Thr, Leu→Val occurred in several independent evolutionary trajectories. The increase in fitness they confer indicates that building blocks with very similar side chain structures are highly beneficial for fine-tuning protein structure and function.

  12. Analysis of horse genomes provides insight into the diversification and adaptive evolution of karyotype.

    Science.gov (United States)

    Huang, Jinlong; Zhao, Yiping; Shiraigol, Wunierfu; Li, Bei; Bai, Dongyi; Ye, Weixing; Daidiikhuu, Dorjsuren; Yang, Lihua; Jin, Burenqiqige; Zhao, Qinan; Gao, Yahan; Wu, Jing; Bao, Wuyundalai; Li, Anaer; Zhang, Yuhong; Han, Haige; Bai, Haitang; Bao, Yanqing; Zhao, Lele; Zhai, Zhengxiao; Zhao, Wenjing; Sun, Zikui; Zhang, Yan; Meng, He; Dugarjaviin, Manglai

    2014-05-14

    Karyotypic diversification is more prominent in Equus species than in other mammals. Here, using next generation sequencing technology, we generated and de novo assembled quality genomes sequences for a male wild horse (Przewalski's horse) and a male domestic horse (Mongolian horse), with about 93-fold and 91-fold coverage, respectively. Portion of Y chromosome from wild horse assemblies (3 M bp) and Mongolian horse (2 M bp) were also sequenced and de novo assembled. We confirmed a Robertsonian translocation event through the wild horse's chromosomes 23 and 24, which contained sequences that were highly homologous with those on the domestic horse's chromosome 5. The four main types of rearrangement, insertion of unknown origin, inserted duplication, inversion, and relocation, are not evenly distributed on all the chromosomes, and some chromosomes, such as the X chromosome, contain more rearrangements than others, and the number of inversions is far less than the number of insertions and relocations in the horse genome. Furthermore, we discovered the percentages of LINE_L1 and LTR_ERV1 are significantly increased in rearrangement regions. The analysis results of the two representative Equus species genomes improved our knowledge of Equus chromosome rearrangement and karyotype evolution.

  13. Switchgrass genomic diversity, ploidy, and evolution: novel insights from a network-based SNP discovery protocol.

    Directory of Open Access Journals (Sweden)

    Fei Lu

    Full Text Available Switchgrass (Panicum virgatum L. is a perennial grass that has been designated as an herbaceous model biofuel crop for the United States of America. To facilitate accelerated breeding programs of switchgrass, we developed both an association panel and linkage populations for genome-wide association study (GWAS and genomic selection (GS. All of the 840 individuals were then genotyped using genotyping by sequencing (GBS, generating 350 GB of sequence in total. As a highly heterozygous polyploid (tetraploid and octoploid species lacking a reference genome, switchgrass is highly intractable with earlier methodologies of single nucleotide polymorphism (SNP discovery. To access the genetic diversity of species like switchgrass, we developed a SNP discovery pipeline based on a network approach called the Universal Network-Enabled Analysis Kit (UNEAK. Complexities that hinder single nucleotide polymorphism discovery, such as repeats, paralogs, and sequencing errors, are easily resolved with UNEAK. Here, 1.2 million putative SNPs were discovered in a diverse collection of primarily upland, northern-adapted switchgrass populations. Further analysis of this data set revealed the fundamentally diploid nature of tetraploid switchgrass. Taking advantage of the high conservation of genome structure between switchgrass and foxtail millet (Setaria italica (L. P. Beauv., two parent-specific, synteny-based, ultra high-density linkage maps containing a total of 88,217 SNPs were constructed. Also, our results showed clear patterns of isolation-by-distance and isolation-by-ploidy in natural populations of switchgrass. Phylogenetic analysis supported a general south-to-north migration path of switchgrass. In addition, this analysis suggested that upland tetraploid arose from upland octoploid. All together, this study provides unparalleled insights into the diversity, genomic complexity, population structure, phylogeny, phylogeography, ploidy, and evolutionary dynamics

  14. X-ray structure reveals a new class and provides insight into evolution of alkaline phosphatases.

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    Subhash C Bihani

    Full Text Available The alkaline phosphatase (AP is a bi-metalloenzyme of potential applications in biotechnology and bioremediation, in which phosphate monoesters are nonspecifically hydrolysed under alkaline conditions to yield inorganic phosphate. The hydrolysis occurs through an enzyme intermediate in which the catalytic residue is phosphorylated. The reaction, which also requires a third metal ion, is proposed to proceed through a mechanism of in-line displacement involving a trigonal bipyramidal transition state. Stabilizing the transition state by bidentate hydrogen bonding has been suggested to be the reason for conservation of an arginine residue in the active site. We report here the first crystal structure of alkaline phosphatase purified from the bacterium Sphingomonas. sp. Strain BSAR-1 (SPAP. The crystal structure reveals many differences from other APs: 1 the catalytic residue is a threonine instead of serine, 2 there is no third metal ion binding pocket, and 3 the arginine residue forming bidentate hydrogen bonding is deleted in SPAP. A lysine and an aspargine residue, recruited together for the first time into the active site, bind the substrate phosphoryl group in a manner not observed before in any other AP. These and other structural features suggest that SPAP represents a new class of APs. Because of its direct contact with the substrate phosphoryl group, the lysine residue is proposed to play a significant role in catalysis. The structure is consistent with a mechanism of in-line displacement via a trigonal bipyramidal transition state. The structure provides important insights into evolutionary relationships between members of AP superfamily.

  15. Insights on fluid-rock interaction evolution during deformation from fracture network geochemistry at reservoir-scale

    Science.gov (United States)

    Beaudoin, Nicolas; Koehn, Daniel; Lacombe, Olivier; Bellahsen, Nicolas; Emmanuel, Laurent

    2015-04-01

    Fluid migration and fluid-rock interactions during deformation is a challenging problematic to picture. Numerous interplays, as between porosity-permeability creation and clogging, or evolution of the mechanical properties of rock, are key features when it comes to monitor reservoir evolution, or to better understand seismic cycle n the shallow crust. These phenomenoms are especially important in foreland basins, where various fluids can invade strata and efficiently react with limestones, altering their physical properties. Stable isotopes (O, C, Sr) measurements and fluid inclusion microthermometry of faults cement and veins cement lead to efficient reconstruction of the origin, temperature and migration pathways for fluids (i.e. fluid system) that precipitated during joints opening or faults activation. Such a toolbox can be used on a diffuse fracture network that testifies the local and/or regional deformation history experienced by the rock at reservoir-scale. This contribution underlines the advantages and limits of geochemical studies of diffuse fracture network at reservoir-scale by presenting results of fluid system reconstruction during deformation in folded structures from various thrust-belts, tectonic context and deformation history. We compare reconstructions of fluid-rock interaction evolution during post-deposition, post-burial growth of basement-involved folds in the Sevier-Laramide American Rocky Mountains foreland, a reconstruction of fluid-rock interaction evolution during syn-depostion shallow detachment folding in the Southern Pyrenean foreland, and a preliminary reconstruction of fluid-rock interactions in a post-deposition, post-burial development of a detachment fold in the Appenines. Beyond regional specification for the nature of fluids, a common behavior appears during deformation as in every fold, curvature-related joints (related either to folding or to foreland flexure) connected vertically the pre-existing stratified fluid system

  16. Functional characterization and evolution of PTH/PTHrP receptors: insights from the chicken

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    Pinheiro Pedro LC

    2012-07-01

    Full Text Available Abstract Background The parathyroid hormone (PTH-family consists of a group of structurally related factors that regulate calcium and bone homeostasis and are also involved in development of organs such as the heart, mammary gland and immune system. They interact with specific members of family 2 B1 G-protein coupled receptors (GPCRs, which have been characterised in teleosts and mammals. Two PTH/PTHrP receptors, PTH1R and PTH2R exist in mammals and in teleost fish a further receptor PTH3R has also been identified. Recently in chicken, PTH-family members involved in calcium transport were characterized and specific PTHRs are suggested to exist although they have not yet been isolated or functionally characterized. The aim of this study is to further explore the evolution and function of the vertebrate PTH/PTHrP system through the isolation, phylogenetic analysis and functional characterization of the chicken receptors. Results Two PTHRs were isolated in chicken and sequence comparison and phylogenetic analysis indicate that the chicken receptors correspond to PTH1R and PTH3R, which emerged prior to the teleost/tetrapod divergence since they are present in cartilaginous fish. The vertebrate PTH2R receptor and its ligand TIP39 have been lost from bird genomes. Chicken PTH1R and PTH3R have a divergent and widespread tissue expression and are also evident in very early embryonic stages of development. Receptor stimulation studies using HEK293 cells stably expressing the chicken PTH1R and PTH3R and monitoring cAMP production revealed they are activated by chicken 1–34 N-terminal PTH-family peptides in a dose dependent manner. PTH-L and PTHrP were the most effective peptides in activating PTH1R (EC50 = 7.7 nM and EC50 = 22.7 nM, respectively. In contrast, PTH-L (100 nM produced a small cAMP accumulation on activation of PTH3R but PTHrP and PTH (EC50 = 2.5 nM and EC50 = 22.1 nM, respectively readily activated the receptor. PTHr

  17. Tectono-metamorphic evolution of the Chinese Altai, central Asia: new insights from microstructures

    Science.gov (United States)

    Jiang, Yingde; Zhang, Jian; Schulmann, Karel; Sun, Min; Zhao, Guochun

    2013-04-01

    The Altai Orogen, extending from Russia, through northeast Kazakhstan and northwest China, to western and southern Mongolia, occupies a pivotal position in understanding the accretionary process of the Central Asian Orogenic Belt and has drawn much attention in recent years. However, its orogenic evolution remains poorly constrained, because previous studies were mainly focused on the geochronological and geochemical signatures and much less work has been done on metamorphic and structural studies. Metamorphic rocks widely occur in the southern Altai Range and have previously been separated into high-T/low-P and medium-P types. Recent studies demonstrated that these two kinds of rocks may have similar protoliths, i.e. early Paleozoic arc-related assemblages, but experienced different metamorphic histories. The development of biotite, garnet, staurolite and kyanite metamorphic zonal sequences in the low- to medium- grade rocks, demonstrate typical medium-pressure metamorphism that has been suggested as a major consequence of the orogenesis. The high-T/low-P metamorphism, represented by the growth of garnet+cordierite+sillimanite+k-feldspar and was accompanied by extensive anatexis, remains its tectonic significance poorly constrained. Field structural investigation in the Chinese Altai reveals that the high-T/low-P metamorphic rocks have major S-L fabrics (defined by the strongly aligned biotite and sillimanite) exactly in the same orientations as those developed in the associated medium-P grade rocks. Geochronological studies constrain the major fabrics in both kinds of rocks developed during mid-Devonian, coeval with the strong magmatism in the region. Micro-structural investigation on both kinds of rocks show similar prograde metamorphic history featured by clockwise P-T path evolution. Phase equilibrium modeling in the MnNCKFMASH system indicates that the development of major fabrics in the medium-P metamorphic rocks mainly recorded the notable increase of

  18. Evolution of the insect terminal patterning system--insights from the milkweed bug, Oncopeltus fasciatus.

    Science.gov (United States)

    Weisbrod, Anat; Cohen, Mira; Chipman, Ariel D

    2013-08-01

    The anterior and posterior ends of the insect embryo are patterned through the terminal patterning system, which is best known from the fruitfly Drosophila melanogaster. In Drosophila, the RTK receptor Torso and its presumed co-activator Torso-like initiate a signaling cascade, which activates two terminal gap genes, tailless and huckebein. These in turn interact with various patterning genes to define terminal structures. Work on other insect species has shown that this system is poorly conserved, and not all of its components have been found in all cases studied. We place the variability of the system within a broader phylogenetic framework. We describe the expression and knock-down phenotypes of the homologues of terminal patterning genes in the hemimetabolous Oncopeltus fasciatus. We have examined the interactions among these genes and between them and other patterning genes. We demonstrate that all of these genes have different roles in Oncopeltus relative to Drosophila; torso-like is expressed in follicle cells during oogenesis and is involved in the invagination of the blastoderm to form the germ band, and possibly also in defining the growth zone; tailless is regulated by orthodenticle and has a role only in anterior determination; huckebein is expressed only in the middle of the blastoderm; finally, torso was not found in Oncopeltus and its role in terminal patterning seems novel within holometabolous insects. We then use our data, together with published data on other insects, to reconstruct the evolution of the terminal patterning gene network in insects. We suggest that the Drosophila terminal patterning network evolved recently in the lineage leading to the Diptera, and represents an example of evolutionary "tinkering", where pre-existing pathways are co-opted for a new function. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Wing shape of four new bee fossils (Hymenoptera: Anthophila provides insights to bee evolution.

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    Manuel Dehon

    Full Text Available Bees (Anthophila are one of the major groups of angiosperm-pollinating insects and accordingly are widely studied in both basic and applied research, for which it is essential to have a clear understanding of their phylogeny, and evolutionary history. Direct evidence of bee evolutionary history has been hindered by a dearth of available fossils needed to determine the timing and tempo of their diversification, as well as episodes of extinction. Here we describe four new compression fossils of bees from three different deposits (Miocene of la Cerdanya, Spain; Oligocene of Céreste, France; and Eocene of the Green River Formation, U.S.A.. We assess the similarity of the forewing shape of the new fossils with extant and fossil taxa using geometric morphometrics analyses. Predictive discriminant analyses show that three fossils share similar forewing shapes with the Apidae [one of uncertain tribal placement and perhaps near Euglossini, one definitive bumble bee (Bombini, and one digger bee (Anthophorini], while one fossil is more similar to the Andrenidae. The corbiculate fossils are described as Euglossopteryx biesmeijeri De Meulemeester, Michez, & Engel, gen. nov. sp. nov. (type species of Euglossopteryx Dehon & Engel, n. gen. and Bombus cerdanyensis Dehon, De Meulemeester, & Engel, sp. nov. They provide new information on the distribution and timing of particular corbiculate groups, most notably the extension into North America of possible Eocene-Oligocene cooling-induced extinctions. Protohabropoda pauli De Meulemeester & Michez, gen. nov. sp. nov. (type species of Protohabropoda Dehon & Engel, n. gen. reinforces previous hypotheses of anthophorine evolution in terms of ecological shifts by the Oligocene from tropical to mesic or xeric habitats. Lastly, a new fossil of the Andreninae, Andrena antoinei Michez & De Meulemeester, sp. nov., further documents the presence of the today widespread genus Andrena Fabricius in the Late Oligocene of France.

  20. Wing shape of four new bee fossils (Hymenoptera: Anthophila) provides insights to bee evolution.

    Science.gov (United States)

    Dehon, Manuel; Michez, Denis; Nel, André; Engel, Michael S; De Meulemeester, Thibaut

    2014-01-01

    Bees (Anthophila) are one of the major groups of angiosperm-pollinating insects and accordingly are widely studied in both basic and applied research, for which it is essential to have a clear understanding of their phylogeny, and evolutionary history. Direct evidence of bee evolutionary history has been hindered by a dearth of available fossils needed to determine the timing and tempo of their diversification, as well as episodes of extinction. Here we describe four new compression fossils of bees from three different deposits (Miocene of la Cerdanya, Spain; Oligocene of Céreste, France; and Eocene of the Green River Formation, U.S.A.). We assess the similarity of the forewing shape of the new fossils with extant and fossil taxa using geometric morphometrics analyses. Predictive discriminant analyses show that three fossils share similar forewing shapes with the Apidae [one of uncertain tribal placement and perhaps near Euglossini, one definitive bumble bee (Bombini), and one digger bee (Anthophorini)], while one fossil is more similar to the Andrenidae. The corbiculate fossils are described as Euglossopteryx biesmeijeri De Meulemeester, Michez, & Engel, gen. nov. sp. nov. (type species of Euglossopteryx Dehon & Engel, n. gen.) and Bombus cerdanyensis Dehon, De Meulemeester, & Engel, sp. nov. They provide new information on the distribution and timing of particular corbiculate groups, most notably the extension into North America of possible Eocene-Oligocene cooling-induced extinctions. Protohabropoda pauli De Meulemeester & Michez, gen. nov. sp. nov. (type species of Protohabropoda Dehon & Engel, n. gen.) reinforces previous hypotheses of anthophorine evolution in terms of ecological shifts by the Oligocene from tropical to mesic or xeric habitats. Lastly, a new fossil of the Andreninae, Andrena antoinei Michez & De Meulemeester, sp. nov., further documents the presence of the today widespread genus Andrena Fabricius in the Late Oligocene of France.

  1. Echidna venom gland transcriptome provides insights into the evolution of monotreme venom.

    Directory of Open Access Journals (Sweden)

    Emily S W Wong

    Full Text Available Monotremes (echidna and platypus are egg-laying mammals. One of their most unique characteristic is that males have venom/crural glands that are seasonally active. Male platypuses produce venom during the breeding season, delivered via spurs, to aid in competition against other males. Echidnas are not able to erect their spurs, but a milky secretion is produced by the gland during the breeding season. The function and molecular composition of echidna venom is as yet unknown. Hence, we compared the deeply sequenced transcriptome of an in-season echidna crural gland to that of a platypus and searched for putative venom genes to provide clues into the function of echidna venom and the evolutionary history of monotreme venom. We found that the echidna venom gland transcriptome was markedly different from the platypus with no correlation between the top 50 most highly expressed genes. Four peptides found in the venom of the platypus were detected in the echidna transcriptome. However, these genes were not highly expressed in echidna, suggesting that they are the remnants of the evolutionary history of the ancestral venom gland. Gene ontology terms associated with the top 100 most highly expressed genes in echidna, showed functional terms associated with steroidal and fatty acid production, suggesting that echidna "venom" may play a role in scent communication during the breeding season. The loss of the ability to erect the spur and other unknown evolutionary forces acting in the echidna lineage resulted in the gradual decay of venom components and the evolution of a new role for the crural gland.

  2. Novel insights into early neuroanatomical evolution in penguins from the oldest described penguin brain endocast.

    Science.gov (United States)

    Proffitt, J V; Clarke, J A; Scofield, R P

    2016-08-01

    Digital methodologies for rendering the gross morphology of the brain from X-ray computed tomography data have expanded our current understanding of the origin and evolution of avian neuroanatomy and provided new perspectives on the cognition and behavior of birds in deep time. However, fossil skulls germane to extracting digital endocasts from early stem members of extant avian lineages remain exceptionally rare. Data from early-diverging species of major avian subclades provide key information on ancestral morphologies in Aves and shifts in gross neuroanatomical structure that have occurred within those groups. Here we describe data on the gross morphology of the brain from a mid-to-late Paleocene penguin fossil from New Zealand. This most basal and geochronologically earliest-described endocast from the penguin clade indicates that described neuroanatomical features of early stem penguins, such as lower telencephalic lateral expansion, a relatively wider cerebellum, and lack of cerebellar folding, were present far earlier in penguin history than previously inferred. Limited dorsal expansion of the wulst in the new fossil is a feature seen in outgroup waterbird taxa such as Gaviidae (Loons) and diving Procellariiformes (Shearwaters, Diving Petrels, and allies), indicating that loss of flight may not drastically affect neuroanatomy in diving taxa. Wulst enlargement in the penguin lineage is first seen in the late Eocene, at least 25 million years after loss of flight and cooption of the flight stroke for aquatic diving. Similar to the origin of avian flight, major shifts in gross brain morphology follow, but do not appear to evolve quickly after, acquisition of a novel locomotor mode. Enlargement of the wulst shows a complex pattern across waterbirds, and may be linked to sensory modifications related to prey choice and foraging strategy. © 2016 Anatomical Society.

  3. Genome-wide analysis of ionotropic receptors provides insight into their evolution in Heliconius butterflies.

    Science.gov (United States)

    van Schooten, Bas; Jiggins, Chris D; Briscoe, Adriana D; Papa, Riccardo

    2016-03-22

    In a world of chemical cues, smell and taste are essential senses for survival. Here we focused on Heliconius, a diverse group of butterflies that exhibit variation in pre- and post-zygotic isolation and chemically-mediated behaviors across their phylogeny. Our study examined the ionotropic receptors, a recently discovered class of receptors that are some of the most ancient chemical receptors. We found more ionotropic receptors in Heliconius (31) than in Bombyx mori (25) or in Danaus plexippus (27). Sixteen genes in Lepidoptera were not present in Diptera. Only IR7d4 was exclusively found in butterflies and two expansions of IR60a were exclusive to Heliconius. A genome-wide comparison between 11 Heliconius species revealed instances of pseudogenization, gene gain, and signatures of positive selection across the phylogeny. IR60a2b and IR60a2d are unique to the H. melpomene, H. cydno, and H. timareta clade, a group where chemosensing is likely involved in pre-zygotic isolation. IR60a2b also displayed copy number variations (CNVs) in distinct populations of H. melpomene and was the only gene significantly higher expressed in legs and mouthparts than in antennae, which suggests a gustatory function. dN/dS analysis suggests more frequent positive selection in some intronless IR genes and in particular in the sara/sapho and melpomene/cydno/timareta clades. IR60a1 was the only gene with an elevated dN/dS along a major phylogenetic branch associated with pupal mating. Only IR93a was differentially expressed between sexes. All together these data make Heliconius butterflies one of the very few insects outside Drosophila where IRs have been characterized in detail. Our work outlines a dynamic pattern of IR gene evolution throughout the Heliconius radiation which could be the result of selective pressure to find potential mates or host-plants.

  4. Protein phylogenetic analysis of Ca2+/cation antiporters and insights into their evolution in plants

    Directory of Open Access Journals (Sweden)

    Laura eEmery

    2012-01-01

    Full Text Available Cation transport is a critical process in all organisms and is essential for mineral nutrition, ion stress tolerance, and signal transduction. Transporters that are members of the Ca2+/Cation Antiporter (CaCA superfamily are involved in the transport of Ca2+ and/or other cations using the counter exchange of another ion such as H+ or Na+. The CaCA superfamily has been previously divided into five transporter families: the YRBG, NCX, NCKX, CAX and CCX families, which include the well-characterized Na+/Ca2+ exchanger (NCX and H+/cation exchanger (CAX transporters. To examine the evolution of CaCA transporters within higher plants and the green plant lineage, CaCA genes were identified from the genomes of sequenced flowering plants, a bryophyte, lycophyte, and freshwater and marine algae, and compared with those from non-plant species. We found evidence of the expansion and increased diversity of flowering plant genes within the CAX and CCX families. Genes related to the NCX family are present in land plant though they encode distinct MHX homologs which probably have an altered transport function. In contrast, the NCX and NCKX genes which are absent in land plants have been retained in many species of algae, especially the marine algae, indicating that these organisms may share ‘animal-like’ characteristics of Ca2+ homeostasis and signaling. A group of genes encoding novel CAX-like proteins containing an EF hand domain were identified from plants and selected algae but appeared to be lacking in any other species. Lack of functional data for most of the CaCA proteins make it impossible to reliably predict substrate specificity and function for many of the groups or individual proteins. The abundance and diversity of CaCA genes throughout all branches of life indicates the importance of this class of cation transporter, and that many transporters with novel functions are waiting to be discovered.

  5. Asymmetrical nature of the Trollius-Chiastocheta interaction: insights into the evolution of nursery pollination systems.

    Science.gov (United States)

    Suchan, Tomasz; Beauverd, Mélanie; Trim, Naïké; Alvarez, Nadir

    2015-11-01

    The mutualistic versus antagonistic nature of an interaction is defined by costs and benefits of each partner, which may vary depending on the environment. Contrasting with this dynamic view, several pollination interactions are considered as strictly obligate and mutualistic. Here, we focus on the interaction between Trollius europaeus and Chiastocheta flies, considered as a specialized and obligate nursery pollination system - the flies are thought to be exclusive pollinators of the plant and their larvae develop only in T. europaeus fruits. In this system, features such as the globelike flower shape are claimed to have evolved in a coevolutionary context. We examine the specificity of this pollination system and measure traits related to offspring fitness in isolated T. europaeus populations, in some of which Chiastocheta flies have gone extinct. We hypothesize that if this interaction is specific and obligate, the plant should experience dramatic drop in its relative fitness in the absence of Chiastocheta. Contrasting with this hypothesis, T. europaeus populations without flies demonstrate a similar relative fitness to those with the flies present, contradicting the putative obligatory nature of this pollination system. It also agrees with our observation that many other insects also visit and carry pollen among T. europaeus flowers. We propose that the interaction could have evolved through maximization of by-product benefits of the Chiastocheta visits, through the male flower function, and selection on floral traits by the most effective pollinator. We argue this mechanism is also central in the evolution of other nursery pollination systems.

  6. Metallogenic epoch of the Jiapigou gold belt, Jilin Province, China

    Indian Academy of Sciences (India)

    Metallogenic epoch of the Jiapigou gold belt, Jilin Province, China: ... The Jiapigou gold belt is located on the northern margin of the North China Craton, and is one of the ... 29, Xueyuan Road, Beijing 100083, People's Republic of China.

  7. Insights into evolution in Andean Polystichum (Dryopteridaceae) from expanded understanding of the cytosolic phosphoglucose isomerase gene.

    Science.gov (United States)

    Lyons, Brendan M; McHenry, Monique A; Barrington, David S

    2017-07-01

    provided new insights into reticulate relationships among Andean taxa. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Magma evolution at Copahue volcano (Chile/Argentina border): insights from melt inclusions

    Science.gov (United States)

    Cannatelli, C.; Aracena, C.; Leisen, M.; Moncada, D.; Roulleau, E.; Vinet, N.; Petrelli, M.; Paolillo, A.; Barra, F.; Morata, D.

    2016-12-01

    Copahue volcano is an active stratovolcano in the Andean Southern Volcanic Zone (SVZ), straddling at the border between Central Chile and Argentina. The volcano's eruptive style during its history has changed from mainly effusive in the Pleistocene to explosive in the Holocene. The prehistoric eruptions can be divided into pre-glacial (PG), syn-glacial (SG) and post-glacial (PM) stages, with products ranging from basaltic andesites to andesites. In order to investigate the evolution of the magma source and volatiles through time, we have focused our study on the eruptive products from the SG to the 2014 eruption (SUM2014). Sampled rocks are glomero-porphyritic, with a paragenetic mineral sequence of feldspars, ortho- and clinopyroxene, and olivine in order of abundance. All samples present a variable number of vesicles, with SUM2014 samples containing the biggest amount. Feldspar composition varies from Na-rich (andesine) in SG to Ca-rich (labradorite) in SUM2014. Two pyroxene types are present in SG and PM samples (augite and enstatite), while SUM2014 presents augite, pigeonite and enstatite. Thermobarometric estimation, based on mineral chemistry, show a bimodal distribution for SG and SUM2014 (P=10-12 kbars and 5-8 kbars) and only one interval for PM (P=7-8 kbars). Melt Inclusions Assemblages (MIAs) are found in all mineral phases, mostly re-crystallized, with one or more bubbles and daughter oxide minerals. Compositions vary from trachy-andesitic to dacitic for SG, andesitic to trachydacitic for PM, and basaltic andesitic to trachydacitic for SUM2014. Major elements systematics show the existence of a bimodal distribution of pyroxene and feldspar hosted-MIA in SUM2014, which together with the co-presence of pigeonite (low-Ca pyroxene) and augite and the bimodal distribution of P, can be interpreted as evidence of mixing of two types of magmas, evolving at different depths. Trace elements systematics for MIA in SG, PM and SUM2014 show a negative anomaly for Nb

  9. Protein Phylogenetic Analysis of Ca2+/cation Antiporters and Insights into their Evolution in Plants

    Science.gov (United States)

    Emery, Laura; Whelan, Simon; Hirschi, Kendal D.; Pittman, Jon K.

    2012-01-01

    Cation transport is a critical process in all organisms and is essential for mineral nutrition, ion stress tolerance, and signal transduction. Transporters that are members of the Ca2+/cation antiporter (CaCA) superfamily are involved in the transport of Ca2+ and/or other cations using the counter exchange of another ion such as H+ or Na+. The CaCA superfamily has been previously divided into five transporter families: the YRBG, Na+/Ca2+ exchanger (NCX), Na+/Ca2+, K+ exchanger (NCKX), H+/cation exchanger (CAX), and cation/Ca2+ exchanger (CCX) families, which include the well-characterized NCX and CAX transporters. To examine the evolution of CaCA transporters within higher plants and the green plant lineage, CaCA genes were identified from the genomes of sequenced flowering plants, a bryophyte, lycophyte, and freshwater and marine algae, and compared with those from non-plant species. We found evidence of the expansion and increased diversity of flowering plant genes within the CAX and CCX families. Genes related to the NCX family are present in land plant though they encode distinct MHX homologs which probably have an altered transport function. In contrast, the NCX and NCKX genes which are absent in land plants have been retained in many species of algae, especially the marine algae, indicating that these organisms may share “animal-like” characteristics of Ca2+ homeostasis and signaling. A group of genes encoding novel CAX-like proteins containing an EF-hand domain were identified from plants and selected algae but appeared to be lacking in any other species. Lack of functional data for most of the CaCA proteins make it impossible to reliably predict substrate specificity and function for many of the groups or individual proteins. The abundance and diversity of CaCA genes throughout all branches of life indicates the importance of this class of cation transporter, and that many transporters with novel functions are waiting to be discovered. PMID:22645563

  10. The Transcriptome of Nacobbus aberrans Reveals Insights into the Evolution of Sedentary Endoparasitism in Plant-Parasitic Nematodes

    Science.gov (United States)

    Eves-van den Akker, Sebastian; Lilley, Catherine J.; Danchin, Etienne G. J.; Rancurel, Corinne; Cock, Peter J. A.; Urwin, Peter E.; Jones, John T.

    2014-01-01

    Within the phylum Nematoda, plant-parasitism is hypothesized to have arisen independently on at least four occasions. The most economically damaging plant-parasitic nematode species, and consequently the most widely studied, are those that feed as they migrate destructively through host roots causing necrotic lesions (migratory endoparasites) and those that modify host root tissue to create a nutrient sink from which they feed (sedentary endoparasites). The false root-knot nematode Nacobbus aberrans is the only known species to have both migratory endoparasitic and sedentary endoparasitic stages within its life cycle. Moreover, its sedentary stage appears to have characteristics of both the root-knot and the cyst nematodes. We present the first large-scale genetic resource of any false-root knot nematode species. We use RNAseq to describe relative abundance changes in all expressed genes across the life cycle to provide interesting insights into the biology of this nematode as it transitions between modes of parasitism. A multigene phylogenetic analysis of N. aberrans with respect to plant-parasitic nematodes of all groups confirms its proximity to both cyst and root-knot nematodes. We present a transcriptome-wide analysis of both lateral gene transfer events and the effector complement. Comparing parasitism genes of typical root-knot and cyst nematodes to those of N. aberrans has revealed interesting similarities. Importantly, genes that were believed to be either cyst nematode, or root-knot nematode, “specific” have both been identified in N. aberrans. Our results provide insights into the characteristics of a common ancestor and the evolution of sedentary endoparasitism of plants by nematodes. PMID:25123114

  11. Centromeric DNA characterization in the model grass Brachypodium distachyon provides insights on the evolution of the genus.

    Science.gov (United States)

    Li, Yinjia; Zuo, Sheng; Zhang, Zhiliang; Li, Zhanjie; Han, Jinlei; Chu, Zhaoqing; Hasterok, Robert; Wang, Kai

    2018-03-01

    Brachypodium distachyon is a well-established model monocot plant, and its small and compact genome has been used as an accurate reference for the much larger and often polyploid genomes of cereals such as Avena sativa (oats), Hordeum vulgare (barley) and Triticum aestivum (wheat). Centromeres are indispensable functional units of chromosomes and they play a core role in genome polyploidization events during evolution. As the Brachypodium genus contains about 20 species that differ significantly in terms of their basic chromosome numbers, genome size, ploidy levels and life strategies, studying their centromeres may provide important insight into the structure and evolution of the genome in this interesting and important genus. In this study, we isolated the centromeric DNA of the B. distachyon reference line Bd21 and characterized its composition via the chromatin immunoprecipitation of the nucleosomes that contain the centromere-specific histone CENH3. We revealed that the centromeres of Bd21 have the features of typical multicellular eukaryotic centromeres. Strikingly, these centromeres contain relatively few centromeric satellite DNAs; in particular, the centromere of chromosome 5 (Bd5) consists of only ~40 kb. Moreover, the centromeric retrotransposons in B. distachyon (CRBds) are evolutionarily young. These transposable elements are located both within and adjacent to the CENH3 binding domains, and have similar compositions. Moreover, based on the presence of CRBds in the centromeres, the species in this study can be grouped into two distinct lineages. This may provide new evidence regarding the phylogenetic relationships within the Brachypodium genus. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

  12. Diversification, phylogeny and evolution of auxin response factor (ARF) family: insights gained from analyzing maize ARF genes.

    Science.gov (United States)

    Wang, Yijun; Deng, Dexiang; Shi, Yating; Miao, Nan; Bian, Yunlong; Yin, Zhitong

    2012-03-01

    Auxin response factors (ARFs), member of the plant-specific B3 DNA binding superfamily, target specifically to auxin response elements (AuxREs) in promoters of primary auxin-responsive genes and heterodimerize with Aux/IAA proteins in auxin signaling transduction cascade. In previous research, we have isolated and characterized maize Aux/IAA genes in whole-genome scale. Here, we report the comprehensive analysis of ARF genes in maize. A total of 36 ARF genes were identified and validated from the B73 maize genome through an iterative strategy. Thirty-six maize ARF genes are distributed in all maize chromosomes except chromosome 7. Maize ARF genes expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaption locate in promoters of maize ARF genes. Expression patterns vary greatly between clades and sister pairs of maize ARF genes. The B3 DNA binding and auxin response factor domains of maize ARF proteins are primarily subjected to negative selection during selective sweep. The mixed selective forces drive the diversification and evolution of genomic regions outside of B3 and ARF domains. Additionally, the dicot-specific proliferation of ARF genes was detected. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing ARF homologs are highly syntenic. This study provides insights into the distribution, phylogeny and evolution of ARF gene family.

  13. Comparative transcriptional profiling provides insights into the evolution and development of the zygomorphic flower of Vicia sativa (Papilionoideae.

    Directory of Open Access Journals (Sweden)

    Zhipeng Liu

    Full Text Available BACKGROUND: Vicia sativa (the common vetch possesses a predominant zygomorphic flower and belongs to the subfamily Papilionoideae, which is related to Arabidopsis thaliana in the eurosid II clade of the core eudicots. Each vetch flower consists of 21 concentrically arranged organs: the outermost five sepals, then five petals and ten stamens, and a single carpel in the center. METHODOLOGY/PRINCIPAL FINDINGS: We explored the floral transcriptome to examine a genome-scale genetic model of the zygomorphic flower of vetch. mRNA was obtained from an equal mixture of six floral organs, leaves and roots. De novo assembly of the vetch transcriptome using Illumina paired-end technology produced 71,553 unigenes with an average length of 511 bp. We then compared the expression changes in the 71,553 unigenes in the eight independent organs through RNA-Seq Quantification analysis. We predominantly analyzed gene expression patterns specific to each floral organ and combinations of floral organs that corresponded to the traditional ABC model domains. Comparative analyses were performed in the floral transcriptomes of vetch and Arabidopsis, and genomes of vetch and Medicago truncatula. CONCLUSIONS/SIGNIFICANCE: Our comparative analysis of vetch and Arabidopsis showed that the vetch flowers conform to a strict ABC model. We analyzed the evolution and expression of the TCP gene family in vetch at a whole-genome level, and several unigenes specific to three different vetch petals, which might offer some clues toward elucidating the molecular mechanisms underlying floral zygomorphy. Our results provide the first insights into the genome-scale molecular regulatory network that controls the evolution and development of the zygomorphic flower in Papilionoideae.

  14. Seeking the epoch of maximum luminosity for dusty quasars

    International Nuclear Information System (INIS)

    Vardanyan, Valeri; Weedman, Daniel; Sargsyan, Lusine

    2014-01-01

    Infrared luminosities νL ν (7.8 μm) arising from dust reradiation are determined for Sloan Digital Sky Survey (SDSS) quasars with 1.4 10 46.6 erg s –1 for all 2 epoch when quasars first reached their maximum luminosity has not yet been identified at any redshift below 5. The most ultraviolet luminous quasars, defined by rest frame νL ν (0.25 μm), have the largest values of the ratio νL ν (0.25 μm)/νL ν (7.8 μm) with a maximum ratio at z = 2.9. From these results, we conclude that the quasars most luminous in the ultraviolet have the smallest dust content and appear luminous primarily because of lessened extinction. Observed ultraviolet/infrared luminosity ratios are used to define 'obscured' quasars as those having >5 mag of ultraviolet extinction. We present a new summary of obscured quasars discovered with the Spitzer Infrared Spectrograph and determine the infrared luminosity function of these obscured quasars at z ∼ 2.1. This is compared with infrared luminosity functions of optically discovered, unobscured quasars in the SDSS and in the AGN and Galaxy Evolution Survey. The comparison indicates comparable numbers of obscured and unobscured quasars at z ∼ 2.1 with a possible excess of obscured quasars at fainter luminosities.

  15. The MESSENGER mission to Mercury: new insights into geological processes and evolution

    Science.gov (United States)

    Head, James W., III; Solomon, Sean C.; McNutt, Ralph L., Jr.; Blewett, David T.; Chapman, Clark R.; Domingue, Deborah L.; Evans, Larry G.; Gillis-Davis, Jeffrey J.; Hawkins, S. Edward, III; Helbert, Jörn; Holsclaw, Gregory M.; Izenberg, Noam R.; McClintock, William E.; McCoy, Timothy J.; Merline, William J.; Murchie, Scott L.; Nittler, Larrz R.; Phillips, Roger J.; Prockter, Louise M.; Robinson, Mark S.; Sprague, Ann L.; Strom, Robert G.; Vilas, Faith; Watters, Thomas R.; Zuber, Maria T.

    2008-09-01

    The MErcury Surface, Space ENvironment, GEochemistry, and Ranging (MESSENGER) mission, a part of NASA's Discovery Program, was designed to answer six questions [1]: (1) What planetary formational processes led to Mercury's high ratio of metal to silicate? (2) What is the geological history of Mercury? (3) What are the nature and origin of Mercury's magnetic field? (4) What are the structure and state of Mercury's core? (5) What are the radar-reflective materials at Mercury's poles? (6) What are the important volatile species and their sources and sinks near Mercury? MESSENGER is currently midway through a complex interplanetary cruise phase that involves three flybys of Mercury. The first of these, on 14 January 2008, provided important new information relating to several of the questions above [2-13]. Here we summarize observations made during the flyby that are most relevant to new insights about geological processes that have operated on Mercury and implications for the planet's history [3, 8-13]. The instruments that provided the most direct information on the geological history of Mercury during this first encounter were the Mercury Dual Imaging System (MDIS) [14], the Mercury Atmospheric and Surface Composition Spectrometer (MASCS) [15], and the Mercury Laser Altimeter (MLA) [16]. Among the many specific questions remaining following the Mariner 10 mission to Mercury (1974- 1975) were (1) the level of mineralogical and compositional diversity of the crust, which appeared relatively bland in Mariner 10 data, (2) the nature of the rest of the huge Caloris impact basin seen only partially in Mariner 10 images, (3) the origin of the extensive plains observed on the surface (ponded impact ejecta or extrusive lava flows?), (4) the diversity and global distribution of tectonic features that have deformed the crust and their implications for strain as a function of time, and (5) the bombardment chronology and geological history of Mercury [1, 17-19]. The viewing

  16. The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees.

    Directory of Open Access Journals (Sweden)

    Jian Huang

    2016-12-01

    Full Text Available Jujube (Ziziphus jujuba Mill. belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa. Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to the recent insertions of transposable elements in the 'Dongzao' genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication.

  17. The Jujube Genome Provides Insights into Genome Evolution and the Domestication of Sweetness/Acidity Taste in Fruit Trees.

    Science.gov (United States)

    Huang, Jian; Zhang, Chunmei; Zhao, Xing; Fei, Zhangjun; Wan, KangKang; Zhang, Zhong; Pang, Xiaoming; Yin, Xiao; Bai, Yang; Sun, Xiaoqing; Gao, Lizhi; Li, Ruiqiang; Zhang, Jinbo; Li, Xingang

    2016-12-01

    Jujube (Ziziphus jujuba Mill.) belongs to the Rhamnaceae family and is a popular fruit tree species with immense economic and nutritional value. Here, we report a draft genome of the dry jujube cultivar 'Junzao' and the genome resequencing of 31 geographically diverse accessions of cultivated and wild jujubes (Ziziphus jujuba var. spinosa). Comparative analysis revealed that the genome of 'Dongzao', a fresh jujube, was ~86.5 Mb larger than that of the 'Junzao', partially due to the recent insertions of transposable elements in the 'Dongzao' genome. We constructed eight proto-chromosomes of the common ancestor of Rhamnaceae and Rosaceae, two sister families in the order Rosales, and elucidated the evolutionary processes that have shaped the genome structures of modern jujubes. Population structure analysis revealed the complex genetic background of jujubes resulting from extensive hybridizations between jujube and its wild relatives. Notably, several key genes that control fruit organic acid metabolism and sugar content were identified in the selective sweep regions. We also identified S-locus genes controlling gametophytic self-incompatibility and investigated haplotype patterns of the S locus in the jujube genomes, which would provide a guideline for parent selection for jujube crossbreeding. This study provides valuable genomic resources for jujube improvement, and offers insights into jujube genome evolution and its population structure and domestication.

  18. Spatiotemporal evolution of premonitory fault slip prior to stick-slip instability: New insight into the earthquake preparation

    Science.gov (United States)

    Zhuo, Y. Q.; Liu, P.; Guo, Y.; Ji, Y.; Ma, J.

    2017-12-01

    Premonitory fault slip, which begins with quasistatic propagation followed by quasidynamic propagation, may be a key clue bridging the "stick" state and "slip" state of a fault. More attentions have been paid for a long time to the temporal resolution of measurement than the spatial resolution, leading to the incomplete interpretation for the spatial evolution of premonitory slip, particularly during the quasistatic phase. In the present study, measurement of the quasistatic propagation of premonitory slip is achieved at an ultrahigh spatial resolution via a digital image correlation method. Multiple premonitory slip zones are observed and found to be controlled spatially by the fault contact heterogeneity, particularly the strong contact patches that prevent the propagation of premonitory slip and accumulate strain. As a result, premonitory slip is accelerated within constrained week contact spaces and consequently triggers the breakout of quasidynamic propagation. The results provide new insights into the quasistatic propagation of premonitory slip and may offer new interpretations for the earthquake nucleation process. This work is fund by the National Natural Science Foundation of China (Grant No. 41572181), the Basic Scientific Funding of Chinese National Nonprofit Institutes (Grant No. IGCEA1415, IGCEA1525), and the Early-Stage Work of Key Breakthrough Plan in Seismology from China Earthquake Administration.

  19. Insights into archaeal evolution and symbiosis from the genomes of a Nanoarchaeon and its crenarchaeal host from Yellowstone National Park

    Energy Technology Data Exchange (ETDEWEB)

    Podar, Mircea [ORNL; Graham, David E [ORNL; Reysenbach, Anna-Louise [Portland State University; Koonin, Eugene [National Center for Biotechnology Information; Wolf, Yuri [National Center for Biotechnology Information; Makarova, Kira S. [National Center for Biotechnology Information

    2013-01-01

    A hyperthemophilic member of the Nanoarchaeota from Obsidian Pool, a thermal feature in Yellowstone National Park was characterized using single cell isolation and sequencing, together with its putative host, a Sulfolobales archaeon. This first representative of a non-marine Nanoarchaeota (Nst1) resembles Nanoarchaeum equitans by lacking most biosynthetic capabilities, the two forming a deep-branching archaeal lineage. However, the Nst1 genome is over 20% larger, encodes a complete gluconeogenesis pathway and a full complement of archaeal flagellum proteins. Comparison of the two genomes suggests that the marine and terrestrial Nanoarchaeota lineages share a common ancestor that was already a symbiont of another archaeon. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. The two distinct Nanoarchaeota-host genomic data sets offer insights into the evolution of archaeal symbiosis and parasitism and will further enable studies of the cellular and molecular mechanisms of these relationships.

  20. Evolution and structure of Tomato spotted wilt virus populations: evidence of extensive reassortment and insights into emergence processes.

    Science.gov (United States)

    Tentchev, Diana; Verdin, Eric; Marchal, Cécile; Jacquet, Monique; Aguilar, Juan M; Moury, Benoît

    2011-04-01

    Tomato spotted wilt virus (TSWV; genus Tospovirus, family Bunyaviridae) genetic diversity was evaluated by sequencing parts of the three RNA genome segments of 224 isolates, mostly from pepper and tomato crops in southern Europe. Eighty-three per cent of the isolates showed consistent clustering into three clades, corresponding to their geographical origin, Spain, France or the USA, for the three RNA segments. In contrast, the remaining 17% of isolates did not belong to the same clade for the three RNA segments and were shown to be reassortants. Among them, eight different reassortment patterns were observed. Further phylogenetic analyses provided insights into the dynamic processes of the worldwide resurgence of TSWV that, since the 1980s, has followed the worldwide dispersal of the western flower thrips (Frankliniella occidentalis) tospovirus vector. For two clades composed essentially of Old World (OW) isolates, tree topology suggested a local re-emergence of indigenous TSWV populations following F. occidentalis introductions, while it could not be excluded that the ancestors of two other OW clades were introduced from North America contemporarily with F. occidentalis. Finally, estimation of the selection intensity that has affected the evolution of the NSs and nucleocapsid proteins encoded by RNA S of TSWV suggests that the former could be involved in the breakdown of resistance conferred by the Tsw gene in pepper.

  1. Nature(andculture in the anthropocene epoch

    Directory of Open Access Journals (Sweden)

    Grażyna Gajewska

    2012-01-01

    Full Text Available The article deals with a New Understanding of nature and culture, which is being crystallized in the intellectual current defined by the name of post-humanities. The starting point for the analysis of work of art from the area of bioart – transgenic plant named Edunia, which is a part of a larger project Natural History of the Enigma. Edunia, which does not occur in nature but was created by the artist Eduardo Kac by means of specialists in the field of genetic engineering. A new form of life defined as plantimal shows a DNA expression of the artist included into decorative flowers of petunia. Rose petals of flowers are “interspersed” by dark red vessels the feature of which is the expression of Kac’s gene; this because the artist took care of that that his DNA was found just in the venation of the flower. In the article I present two interpretation paths of this work of bioart which, however, are not a sharp counterpoint to one another, but somewhat differently place accents between nature and culture in their mutual entanglements. One of these paths may be defined as an attempt at making others realise or reminding them about our evolutional species condition, while the other one as an attempt at treating nature as an important actor of the sociopolitical activities.

  2. Structure and tectonic evolution of the southwestern Trinidad dome, Escambray complex, Central Cuba: Insights into deformation in an accretionary wedge

    Science.gov (United States)

    Despaigne-Díaz, Ana Ibis; García Casco, Antonio; Cáceres Govea, Dámaso; Wilde, Simon A.; Millán Trujillo, Guillermo

    2017-10-01

    insights into the tectonic evolution of accretionary wedges in an intra-arc setting.

  3. z~2: An Epoch of Disk Assembly

    Science.gov (United States)

    Simons, Raymond C.; Kassin, Susan A.; Weiner, Benjamin; Heckman, Timothy M.; Trump, Jonathan; SIGMA, DEEP2

    2018-01-01

    At z = 0, the majority of massive star-forming galaxies contain thin, rotationally supported gas disks. It was once accepted that galaxies form thin disks early: collisional gas with high velocity dispersion should dissipate energy, conserve angular momentum, and develop strong rotational support in only a few galaxy crossing times (~few hundred Myr). However, this picture is complicated at high redshift, where the processes governing galaxy assembly tend to be violent and inhospitable to disk formation. We present results from our SIGMA survey of star-forming galaxy kinematics at z = 2. These results challenge the simple picture described above: galaxies at z = 2 are unlike local well-ordered disks. Their kinematics tend to be much more disordered, as quantified by their low ratios of rotational velocity to gas velocity dispersion (Vrot/σg): less than 35% of galaxies have Vrot/σg > 3. For comparison, nearly 100% of local star-forming galaxies meet this same threshold. We combine our high redshift sample with a similar low redshift sample from the DEEP2 survey. This combined sample covers a continuous redshift baseline over 0.1 < z < 2.5, spanning 10 Gyrs of cosmic time. Over this period, galaxies exhibit remarkably smooth kinematic evolution on average. All galaxies tend towards rotational support with time, and it is reached earlier in higher mass systems. This is due to both a significant decline in gas velocity dispersion and a mild rise in ordered rotational motions. These results indicate that z = 2 is a period of disk assembly, during which the strong rotational support present in today’s massive disk galaxies is only just beginning to emerge.

  4. Discovery of cyclotides in the fabaceae plant family provides new insights into the cyclization, evolution, and distribution of circular proteins.

    Science.gov (United States)

    Poth, Aaron G; Colgrave, Michelle L; Philip, Reynold; Kerenga, Bomai; Daly, Norelle L; Anderson, Marilyn A; Craik, David J

    2011-04-15

    Cyclotides are plant proteins whose defining structural features are a head-to-tail cyclized backbone and three interlocking disulfide bonds, which in combination are known as a cyclic cystine knot. This unique structural motif confers cyclotides with exceptional resistance to proteolysis. Their endogenous function is thought to be as plant defense agents, associated with their insecticidal and larval growth-inhibitory properties. However, in addition, an array of pharmaceutically relevant biological activities has been ascribed to cyclotides, including anti-HIV, anthelmintic, uterotonic, and antimicrobial effects. So far, >150 cyclotides have been elucidated from members of the Rubiaceae, Violaceae, and Cucurbitaceae plant families, but their wider distribution among other plant families remains unclear. Clitoria ternatea (Butterfly pea) is a member of plant family Fabaceae and through its usage in traditional medicine to aid childbirth bears similarity to Oldenlandia affinis, from which many cyclotides have been isolated. Using a combination of nanospray and matrix-assisted laser desorption ionization-time-of-flight (MALDI-TOF) analyses, we examined seed extracts of C. ternatea and discovered cyclotides in the Fabaceae, the third-largest family of flowering plants. We characterized 12 novel cyclotides, thus expanding knowledge of cyclotide distribution and evolution within the plant kingdom. The discovery of cyclotides containing novel sequence motifs near the in planta cyclization site has provided new insights into cyclotide biosynthesis. In particular, MS analyses of the novel cyclotides from C. ternatea suggest that Asn to Asp variants at the cyclization site are more common than previously recognized. Moreover, this study provides impetus for the examination of other economically and agriculturally significant species within Fabaceae, now the largest plant family from which cyclotides have been described.

  5. The 2010 Eyja eruption evolution by using IR satellite sensors measurements: retrieval comparison and insights into explosive volcanic processes

    Science.gov (United States)

    Piscini, A.; Corradini, S.; Merucci, L.; Scollo, S.

    2010-12-01

    The 2010 April-May Eyja eruption caused an unprecedented disruption to economic, political and cultural activities in Europe and across the world. Because of the harming effects of fine ash particles on aircrafts, many European airports were in fact closed causing millions of passengers to be stranded, and with a worldwide airline industry loss estimated of about 2.5 billion Euros. Both security and economical issues require robust and affordable volcanic cloud retrievals that may be really improved through the intercomparison among different remote sensing instruments. In this work the Thermal InfraRed (TIR) measurements of different polar and geostationary satellites instruments as the Moderate Resolution Imaging Spectroradiometer (MODIS), the Advanced Very High Resolution Radiometer (AVHRR) and the Spin Enhanced Visible and Infrared Imager (SEVIRI), have been used to retrieve the volcanic ash and SO2 in the entire eruption period over Iceland. The ash retrievals (mass, AOD and effective radius) have been carried out by means of the split window BTD technique using the channels centered around 11 and 12 micron. The least square fit procedure is used for the SO2 retrieval by using the 7.3 and 8.7 micron channels. The simulated TOA radiance Look-Up Table (LUT) needed for both the ash and SO2 column abundance retrievals have been computed using the MODTRAN 4 Radiative Transfer Model. Further, the volcanic plume column altitude and ash density have been computed and compared, when available, with ground observations. The results coming from the retrieval of different IR sensors show a good agreement over the entire eruption period. The column height, the volcanic ash and the SO2 emission trend confirm the indentified different phases occurred during the Eyja eruption. We remark that the retrieved volcanic plume evolution can give important insights into eruptive dynamics during long-lived explosive activity.

  6. Centromere Destiny in Dicentric Chromosomes: New Insights from the Evolution of Human Chromosome 2 Ancestral Centromeric Region.

    Science.gov (United States)

    Chiatante, Giorgia; Giannuzzi, Giuliana; Calabrese, Francesco Maria; Eichler, Evan E; Ventura, Mario

    2017-07-01

    Dicentric chromosomes are products of genomic rearrangements that place two centromeres on the same chromosome. Due to the presence of two primary constrictions, they are inherently unstable and overcome their instability by epigenetically inactivating and/or deleting one of the two centromeres, thus resulting in functionally monocentric chromosomes that segregate normally during cell division. Our understanding to date of dicentric chromosome formation, behavior and fate has been largely inferred from observational studies in plants and humans as well as artificially produced de novo dicentrics in yeast and in human cells. We investigate the most recent product of a chromosome fusion event fixed in the human lineage, human chromosome 2, whose stability was acquired by the suppression of one centromere, resulting in a unique difference in chromosome number between humans (46 chromosomes) and our most closely related ape relatives (48 chromosomes). Using molecular cytogenetics, sequencing, and comparative sequence data, we deeply characterize the relicts of the chromosome 2q ancestral centromere and its flanking regions, gaining insight into the ancestral organization that can be easily broadened to all acrocentric chromosome centromeres. Moreover, our analyses offered the opportunity to trace the evolutionary history of rDNA and satellite III sequences among great apes, thus suggesting a new hypothesis for the preferential inactivation of some human centromeres, including IIq. Our results suggest two possible centromere inactivation models to explain the evolutionarily stabilization of human chromosome 2 over the last 5-6 million years. Our results strongly favor centromere excision through a one-step process. © The Author 2017. 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.

  7. The Mars water cycle at other epochs: History of the polar caps and layered terrain

    Science.gov (United States)

    Jakosky, Bruce M.; Henderson, Bradley G.; Mellon, Michael T.

    1992-01-01

    The atmospheric water cycle at the present epoch involves summertime sublimation of water from the north polar cap, transport of water through the atmosphere, and condensation on one or both winter CO2 caps. Exchange with the regolith is important seasonally, but the water content of the atmosphere appears to be controlled by the polar caps. The net annual transport through the atmosphere, integrated over long timescales, must be the driving force behind the long-term evolution of the polar caps; clearly, this feeds back into the evolution of the layered terrain. We have investigated the behavior of the seasonal water cycle and the net integrated behavior at the pole for the last 10 exp 7 years. Our model of the water cycle includes the solar input, CO2 condensation and sublimation, and summertime water sublimation through the seasonal cycles, and incorporates the long-term variations in the orbital elements describing the Martian orbit.

  8. The Cosmic Dawn and Epoch of Reionisation with SKA

    NARCIS (Netherlands)

    Koopmans, L.; Pritchard, J.; Mellema, G.; Aguirre, J.; Ahn, K.; Barkana, R.; van Bemmel, I.; Bernardi, G.; Bonaldi, A.; Briggs, F.; de Bruyn, A. G.; Chang, T. C.; Chapman, E.; Chen, X.; Ciardi, B.; Dayal, P.; Ferrara, A.; Fialkov, A.; Fiore, F.; Ichiki, K.; Illiev, I. T.; Inoue, S.; Jelic, V.; Jones, M.; Lazio, J.; Maio, U.; Majumdar, S.; Mack, K. J.; Mesinger, A.; Morales, M. F.; Parsons, A.; Pen, U. L.; Santos, M.; Schneider, R.; Semelin, B.; de Souza, R. S.; Subrahmanyan, R.; Takeuchi, T.; Vedantham, H.; Wagg, J.; Webster, R.; Wyithe, S.; Datta, K. K.; Trott, C.

    2014-01-01

    Concerted effort is currently ongoing to open up the Epoch of Reionization (EoR) ($z\\sim$15-6) for studies with IR and radio telescopes. Whereas IR detections have been made of sources (Lyman-$\\alpha$ emitters, quasars and drop-outs) in this redshift regime in relatively small fields of view, no

  9. The Cosmic Dawn and Epoch of Reionisation with SKA

    NARCIS (Netherlands)

    Koopmans, L.; Pritchard, J.; Mellema, G.; Aguirre, J.; Ahn, K.; Barkana, R.; van Bemmel, I.; Bernardi, G.; Bonaldi, A.; Briggs, F.; de Bruyn, A. G.; Chang, T. C.; Chapman, E.; Chen, X.; Ciardi, B.; Dayal, P.; Ferrara, A.; Fialkov, A.; Fiore, F.; Ichiki, K.; Illiev, I. T.; Inoue, S.; Jelic, V.; Jones, M.; Lazio, J.; Maio, U.; Majumdar, S.; Mack, K. J.; Mesinger, A.; Morales, M. F.; Parsons, A.; Pen, U. L.; Santos, M.; Schneider, R.; Semelin, B.; de Souza, R. S.; Subrahmanyan, R.; Takeuchi, T.; Vedantham, H.; Wagg, J.; Webster, R.; Wyithe, S.; Datta, K. K.; Trott, C.

    2015-01-01

    Concerted effort is currently ongoing to open up the Epoch of Reionization (EoR) ($z\\sim$15-6) for studies with IR and radio telescopes. Whereas IR detections have been made of sources (Lyman-$\\alpha$ emitters, quasars and drop-outs) in this redshift regime in relatively small fields of view, no

  10. Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins.

    Science.gov (United States)

    Van Doorslaer, Koenraad; Ruoppolo, Valeria; Schmidt, Annie; Lescroël, Amelie; Jongsomjit, Dennis; Elrod, Megan; Kraberger, Simona; Stainton, Daisy; Dugger, Katie M; Ballard, Grant; Ainley, David G; Varsani, Arvind

    2017-07-01

    estimated the divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins.

  11. Unique genome organization of non-mammalian papillomaviruses provides insights into the evolution of viral early proteins

    Science.gov (United States)

    Van Doorslaer, Koenraad; Ruoppolo, Valeria; Schmidt, Annie; Lescroël, Amelie; Jongsomjit, Dennis; Elrod, Megan; Kraberger, Simona; Stainton, Daisy; Dugger, Katie M.; Ballard, Grant; Ainley, David G.; Varsani, Arvind

    2017-01-01

    divergence time between Northern fulmar-associated papillomavirus and the other Sauropsid papillomaviruses be to around 250 million years ago, during the Paleozoic-Mesozoic transition and our analysis dates the root of the papillomavirus tree between 400 and 600 million years ago. Our analysis shows evidence for niche adaptation and that these non-mammalian viruses have highly divergent E6 and E7 proteins, providing insights into the evolution of the early viral (onco-)proteins.

  12. Phanerozoic polycyclic evolution of the southwestern Angola margin: New insights for apatite fission track and (U-Th)/He methodologies

    Science.gov (United States)

    Venancio da Silva, Bruno; Hackspacher, Peter; Carina Siqueira Ribeiro, Marli; Glasmacher, Ulrich Anton

    2016-04-01

    The low-temperature thermochronology has been an important tool to quantify geological process in passive continental margins. In this context, the Angolan margin shows evidence of a polycyclic post-rift evolution marked by different events of uplift, basin inversion and changes in sedimentation rates to the marginal basins, which have controlled the salt tectonics and the hydrocarbon deposits (1,2,3,4). To understand the post break-up evolution of the southwestern Angola margin, it were collected outcrop samples for apatite fission track (AFT) and (U-Th)/He analysis ranging in elevation from 79 m to 1675 m from the coast toward the interior plateau in a profile between Namibe and Lubango cities. The area lies on the edge of Central and Southern Atlantic segments a few kilometers northward the Walvis ridge and encompasses the Archean and Proterozoic basement rocks of the Congo craton. The AFT ages ranging from 120.6 ± 8.9 Ma to 328.8 ± 28.5 Ma and they show a trend of increasing age toward the Great Escarpment with some exceptions. The partial mean track lengths (MTLs) vary between 11.77 ± 1.82 μm to 12.34 ± 1.13 μm with unimodal track length distributions (TDLs). The partial (U-Th)/He ages ranging from 104.85 ± 3.15 Ma to 146.95 ± 4.41 Ma and show the same trend of increasing ages landward, little younger than the AFT ages, which could be interpreted as a fast exhumation episode in Late Jurassic - Early Cretaceous times. The thermal histories modelling has been constrained with the kinetic parameters Dpar (5) and c-axis angle (6) by the software Hefty (7). Both AFT and (U-Th)/He thermal histories modelling indicate three episodes of denudation/uplift driven cooling: (a) from Late Jurassic to Early Cretaceous, (b) a smallest one in the Late Cretaceous and (c) from Oligocene-Miocene to recent, which are compatible with geophysical data of the offshore Namibe basin that estimate the greater thickness of sediments formed in the first and third episodes

  13. A search for changing look quasars in second epoch imaging

    Science.gov (United States)

    Findlay, Joseph; Myers, Adam; McGreer, Ian

    2018-01-01

    Over nearly two decades, the Sloan Digital Sky Survey has compiled a catalog of over half a million confirmed quasars. During that period approximately ten percent of these objects have been spectroscopically observed in two or more epochs over baselines of ten or more years. This led recently to the discovery of the largest change in luminosity ever before observed in a quasar. The dimming emission was a reflection of very significant changes in continuum and broad line properties, the source had effectively transitioned from a Type I quasar to a Type II AGN. Since then several more "changing look" quasars have been discovered in multi-epoch SDSS spectroscopy. Among them are objects with rising and falling luminosities, appearing and disappearing broad lines. The origin of this behavior is still very uncertain, currently favored is the scenario in which an accreting black hole is simply starved of fuel. Other plausible scenarios include flaring due to stellar tidal disruption close to the black hole or large changes in accretion flow, which can occur during transitions between radiatively efficient and inefficient accretion regimes. Monitoring of larger numbers of changing look quasars will help to elucidate these ideas.In this poster, we report on the progress of a pilot study in which we hope to learn how to select changing look quasars in multi-epoch imaging. This will allow us to take advantage of the entire SDSS quasar catalog rather than just the ten percent of objects with multi-epoch spectroscopy. Comparing archival SDSS and more recent Legacy Survey imaging over ten-year baselines we select objects whose photometry is consistent with the large changes in luminosity expected in changing look quasars. We aim to build up a catalog of both transitioned and transitioning objects for future monitoring.

  14. Epoch-based Entropy for Early Screening of Alzheimer's Disease.

    Science.gov (United States)

    Houmani, N; Dreyfus, G; Vialatte, F B

    2015-12-01

    In this paper, we introduce a novel entropy measure, termed epoch-based entropy. This measure quantifies disorder of EEG signals both at the time level and spatial level, using local density estimation by a Hidden Markov Model on inter-channel stationary epochs. The investigation is led on a multi-centric EEG database recorded from patients at an early stage of Alzheimer's disease (AD) and age-matched healthy subjects. We investigate the classification performances of this method, its robustness to noise, and its sensitivity to sampling frequency and to variations of hyperparameters. The measure is compared to two alternative complexity measures, Shannon's entropy and correlation dimension. The classification accuracies for the discrimination of AD patients from healthy subjects were estimated using a linear classifier designed on a development dataset, and subsequently tested on an independent test set. Epoch-based entropy reached a classification accuracy of 83% on the test dataset (specificity = 83.3%, sensitivity = 82.3%), outperforming the two other complexity measures. Furthermore, it was shown to be more stable to hyperparameter variations, and less sensitive to noise and sampling frequency disturbances than the other two complexity measures.

  15. Ancient duplications and functional divergence in the interferon regulatory factors of vertebrates provide insights into the evolution of vertebrate immune systems.

    Science.gov (United States)

    Du, Kang; Zhong, Zaixuan; Fang, Chengchi; Dai, Wei; Shen, Yanjun; Gan, Xiaoni; He, Shunping

    2018-04-01

    Interferon regulatory factors (IRFs) were first discovered as transcription factors that regulate the transcription of human interferon (IFN)-β. Increasing evidence shows that they might be important players involved in Adaptive immune system (AIS) evolution. Although numbers of IRFs have been identified in chordates, the evolutionary history and functional diversity of this gene family during the early evolution of vertebrates have remained obscure. Using IRF HMM profile and HMMER searches, we identified 148 IRFs in 11 vertebrates and 4 protochordates. For them, we reconstructed the phylogenetic relationships, determined the synteny conservation, investigated the profile of natural selection, and analyzed the expression patterns in four "living fossil" vertebrates: lamprey, elephant shark, coelacanth and bichir. The results from phylogeny and synteny analysis imply that vertebrate IRFs evolved from three predecessors, instead of four as suggested in a previous study, as results from an ancient duplication followed by special expansions and lost during the vertebrate evolution. The profile of natural selection and expression reveals functional dynamics during the process. Together, they suggest that the 2nd whole-genome duplication (2WGD) provided raw materials for innovation in the IRF family, and that the birth of type-I IFN might be an important factor inducing the establishment of IRF-mediated immune networks. As a member involved in the AIS evolution, IRF provide insights into the process and mechanism involved in the complexity and novelties of vertebrate immune systems. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

  16. A Lyman Break Galaxy in the Epoch of Reionization from Hubble Space Telescope (HST) Grism Spectroscopy

    Science.gov (United States)

    Rhoads, James E.; Malhotra, Sangeeta; Stern, Daniel K.; Gardner, Jonathan P.; Dickinson, Mark; Pirzkal, Norbert; Spinrad, Hyron; Reddy, Naveen; Dey, Arjun; Hathi, Nimish; hide

    2013-01-01

    Slitless grism spectroscopy from space offers dramatic advantages for studying high redshift galaxies: high spatial resolution to match the compact sizes of the targets, a dark and uniform sky background, and simultaneous observation over fields ranging from five square arcminutes (HST) to over 1000 square arcminutes (Euclid). Here we present observations of a galaxy at z = 6.57 the end of the reioinization epoch identified using slitless HST grism spectra from the PEARS survey (Probing Evolution And Reionization Spectroscopically) and reconfirmed with Keck + DEIMOS. This high redshift identification is enabled by the depth of the PEARS survey. Substantially higher redshifts are precluded for PEARS data by the declining sensitivity of the ACS grism at greater than lambda 0.95 micrometers. Spectra of Lyman breaks at yet higher redshifts will be possible using comparably deep observations with IR-sensitive grisms.

  17. Insights into magmatic evolution and recharge history in Capraia Volcano (Italy) from chemical and isotopic zoning in plagioclase phenocrysts

    DEFF Research Database (Denmark)

    Gagnevin, D.; Waight, Tod Earle; Daly, J.S.

    2007-01-01

    Plagioclase phenocrysts in dacites from the high-K calc-alkaline CapraiaVolcano were investigated for major, trace element and Sr isotope variations in order to gain better insight into the proposed open-system behaviour of the volcano. Repeated dissolution zone in plagioclases from the early-eru...

  18. Geochemical evolution of the acid crater lake of Poas volcano (Costa Rica): Insights into volcanic-hydrothermal processes

    NARCIS (Netherlands)

    Martínez Cruz, María

    2008-01-01

    This thesis describes the evolution of Laguna Caliente, an acid crater lake at the summit of Po:is, a persistently active volcano in central Costa Rica. The appearance, volume, temperature and chemical composition of the lake have continuously changed over the entire known period of its

  19. The evolution of amphibian metamorphosis: insights based on the transformation of the aortic arches of Pelobates fuscus (Anura)

    Czech Academy of Sciences Publication Activity Database

    Kolesová, H.; Lametschwandtner, A.; Roček, Zbyněk

    2007-01-01

    Roč. 210, č. 4 (2007), s. 379-393 ISSN 0021-8782 Institutional research plan: CEZ:AV0Z30130516 Keywords : Anura * circulatory system * development * evolution * metamorphosis Subject RIV: EG - Zoology Impact factor: 2.547, year: 2007

  20. The Evolution of Community Self-Organization in Interaction With Government Institutions: Cross-Case Insights From Three Countries

    NARCIS (Netherlands)

    J. Edelenbos (Jurian); I.F. van Meerkerk (Ingmar); Schenk, T. (Todd)

    2018-01-01

    textabstractThis article deals with the evolution of community self-organization in public administration. Within the literature of interactive governance, increasing attention is being paid to how communities take initiative in dealing with societal issues. However, we know little about the factors

  1. 'Anthropocene': An Ethical Crisis, Not a Geological Epoch

    Science.gov (United States)

    Cuomo, Chris

    2017-04-01

    The term 'anthropocene' has gained enormous popularity among scientists who believe we are in a global phase distinguished by the extensive and lasting impacts of social activities on Earth's sedimentary record and vital systems. Beyond its widespread informal use, a working group of the International Union of Geological Sciences seeks to formalize the term to name a new geological epoch, implying that the Holocene epoch has ended. I argue that the move to formalize the 'anthropocene' and to declare the demise of the Holocene is premature and ethically misguided, at best, and that the very name 'anthropocene' obscures rather than illuminates the serious moral and political/economic implications of the dire warnings evident in recent stratigraphic and ecological changes. If human-caused mass extinction and other ecological catastrophes are serious harms, ethical responses are required. Instead, the move to formalize the idea of an 'anthropocene' epoch treats dire ethical warnings as an opportunity to redefine the current dangerous situation as a new status quo. Have we met our responsibilities to protect Holocene Earth? This presentation will focus on the ethical implications of using the power and discourse of geology to demote Holocene ecological states from their role as the foundational benchmarks for guiding and assessing human relationships with nature and other species. Have geoscientists adequately consulted the biological, ecological and social sciences before declaring the end of the Holocene epoch? Upon what do we base environmental ethics if the Holocene is considered past history? I will also examine the ethical dimensions of naming the so-called 'anthropocene', asking: who is the presumed 'anthro' in the 'anthropocene'? Are the phenomena identified with the 'anthropocene' (nuclear fallout, mass species endangerment, ocean acidification, fossil fuel pollution, deforestation, mining) definitive accomplishments of the human species? Should the practices

  2. Cluster evolution

    International Nuclear Information System (INIS)

    Schaeffer, R.

    1987-01-01

    The galaxy and cluster luminosity functions are constructed from a model of the mass distribution based on hierarchical clustering at an epoch where the matter distribution is non-linear. These luminosity functions are seen to reproduce the present distribution of objects as can be inferred from the observations. They can be used to deduce the redshift dependence of the cluster distribution and to extrapolate the observations towards the past. The predicted evolution of the cluster distribution is quite strong, although somewhat less rapid than predicted by the linear theory

  3. Genomics, transcriptomics and proteomics: enabling insights into social evolution and disease challenges for managed and wild bees.

    Science.gov (United States)

    Trapp, Judith; McAfee, Alison; Foster, Leonard J

    2017-02-01

    Globally, there are over 20 000 bee species (Hymenoptera: Apoidea: Anthophila) with a host of biologically fascinating characteristics. Although they have long been studied as models for social evolution, recent challenges to bee health (mainly diseases and pesticides) have gathered the attention of both public and research communities. Genome sequences of twelve bee species are now complete or under progress, facilitating the application of additional 'omic technologies. Here, we review recent developments in honey bee and native bee research in the genomic era. We discuss the progress in genome sequencing and functional annotation, followed by the enabled comparative genomics, proteomics and transcriptomics applications regarding social evolution and health. Finally, we end with comments on future challenges in the postgenomic era. © 2016 John Wiley & Sons Ltd.

  4. The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution.

    Directory of Open Access Journals (Sweden)

    Eva Heinz

    Full Text Available The dynamics of reductive genome evolution for eukaryotes living inside other eukaryotic cells are poorly understood compared to well-studied model systems involving obligate intracellular bacteria. Here we present 8.5 Mb of sequence from the genome of the microsporidian Trachipleistophora hominis, isolated from an HIV/AIDS patient, which is an outgroup to the smaller compacted-genome species that primarily inform ideas of evolutionary mode for these enormously successful obligate intracellular parasites. Our data provide detailed information on the gene content, genome architecture and intergenic regions of a larger microsporidian genome, while comparative analyses allowed us to infer genomic features and metabolism of the common ancestor of the species investigated. Gene length reduction and massive loss of metabolic capacity in the common ancestor was accompanied by the evolution of novel microsporidian-specific protein families, whose conservation among microsporidians, against a background of reductive evolution, suggests they may have important functions in their parasitic lifestyle. The ancestor had already lost many metabolic pathways but retained glycolysis and the pentose phosphate pathway to provide cytosolic ATP and reduced coenzymes, and it had a minimal mitochondrion (mitosome making Fe-S clusters but not ATP. It possessed bacterial-like nucleotide transport proteins as a key innovation for stealing host-generated ATP, the machinery for RNAi, key elements of the early secretory pathway, canonical eukaryotic as well as microsporidian-specific regulatory elements, a diversity of repetitive and transposable elements, and relatively low average gene density. Microsporidian genome evolution thus appears to have proceeded in at least two major steps: an ancestral remodelling of the proteome upon transition to intracellular parasitism that involved reduction but also selective expansion, followed by a secondary compaction of genome

  5. The Complete Chloroplast and Mitochondrial Genome Sequences of Boea hygrometrica: Insights into the Evolution of Plant Organellar Genomes

    Science.gov (United States)

    Wang, Xumin; Deng, Xin; Zhang, Xiaowei; Hu, Songnian; Yu, Jun

    2012-01-01

    The complete nucleotide sequences of the chloroplast (cp) and mitochondrial (mt) genomes of resurrection plant Boea hygrometrica (Bh, Gesneriaceae) have been determined with the lengths of 153,493 bp and 510,519 bp, respectively. The smaller chloroplast genome contains more genes (147) with a 72% coding sequence, and the larger mitochondrial genome have less genes (65) with a coding faction of 12%. Similar to other seed plants, the Bh cp genome has a typical quadripartite organization with a conserved gene in each region. The Bh mt genome has three recombinant sequence repeats of 222 bp, 843 bp, and 1474 bp in length, which divide the genome into a single master circle (MC) and four isomeric molecules. Compared to other angiosperms, one remarkable feature of the Bh mt genome is the frequent transfer of genetic material from the cp genome during recent Bh evolution. We also analyzed organellar genome evolution in general regarding genome features as well as compositional dynamics of sequence and gene structure/organization, providing clues for the understanding of the evolution of organellar genomes in plants. The cp-derived sequences including tRNAs found in angiosperm mt genomes support the conclusion that frequent gene transfer events may have begun early in the land plant lineage. PMID:22291979

  6. Hydrogeochemical Characteristics and Evolution of Hot Springs in Eastern Tibetan Plateau Geothermal Belt, Western China: Insight from Multivariate Statistical Analysis

    Directory of Open Access Journals (Sweden)

    Zheming Shi

    2017-01-01

    Full Text Available The eastern Tibetan Plateau geothermal belt is one of the important medium-high temperature geothermal belts in China. However, less work has been done on the hydrochemical characteristic and its geological origin. Understanding the chemical characteristics and the hydrochemical evolution processes is important in evaluating the geothermal energy potential in this area. In the present study, we discussed the hydrochemical properties and their origins of 39 hot springs located in the eastern Tibetan Plateau geothermal belt (Kangding-Litang-Batang geothermal belt. Cluster analysis and factor analysis are employed to character the hydrochemical properties of hot springs in different fault zones and the possible hydrochemical evolution processes of these hot springs. Our study shows that the hot springs can be divided into three groups based on their locations. The hot springs in the first group mainly originate from the volcanic rock and the springs in the second group originate from the metamorphic rock while the springs in the third group originate from the result of mixture of shallow water. Water-rock interaction, cation exchange, and the water environment are the three dominant factors that control the hydrochemical evolution process in the eastern Tibetan Plateau. These results are also in well agreement with the isotopic and chemical analysis.

  7. Autogenic Versus Allogenic Controls on the Evolution of a Coupled Fluvial Megafan-Mountainous Catchment System: Insight from Numerical Modelling

    Science.gov (United States)

    Mouchene, M.; van der Beek, P.; Carretier, S.; Mouthereau, F.

    2017-12-01

    Alluvial megafans are sensitive recorders of landscape evolution, controlled by both autogenic processes and allogenic forcing, and they are influenced by the coupled dynamics of the fan with its mountainous catchment. The Mio-Pliocene Lannemezan megafan in the northern Pyrenean foreland (SW France) was abandoned by its mountainous feeder stream during the Quaternary and subsequently incised. The flight of alluvial terraces abandoned along the stream network may suggest a climatic control on the incision. We use a landscape evolution numerical model (CIDRE) to explore the relative roles of autogenic processes and external forcing in the building, abandonment and incision of a foreland megafan, and we compare the results with the inferred evolution of the Lannemezan megafan. Autogenic processes are sufficient to explain the building of a megafan and the long-term entrenchment of its feeding river on time and space scales that match the Lannemezan setting. Climate, through temporal variations in precipitation rate, may have played a role in the episodic pattern of incision on a shorter timescale. In contrast, base-level changes, tectonic activity in the mountain range or tilting of the foreland through flexural isostatic rebound do not appear to have played a role in the abandonment of the megafan.

  8. Role of erosion and isostasy in the Cordillera Blanca uplift: Insights from landscape evolution modeling (northern Peru, Andes)

    Science.gov (United States)

    Margirier, Audrey; Braun, Jean; Robert, Xavier; Audin, Laurence

    2018-03-01

    The processes driving uplift and exhumation of the highest Peruvian peaks (the Cordillera Blanca) are not well understood. Uplift and exhumation seem closely linked to the formation and movement on the Cordillera Blanca normal fault (CBNF) that delimits and shapes the western flank of the Cordillera Blanca. Several models have been proposed to explain the presence of this major normal fault in a compressional setting, but the CBNF and the Cordillera Blanca recent rapid uplift remain enigmatic. Whereas the Cordillera Blanca morphology demonstrates important erosion and thus a significant mass of rocks removal, the impact of erosion and isostasy on the evolution of the Cordillera Blanca uplift rates has never been explored. We address the role of erosion and associated flexural rebound in the uplift and exhumation of the Cordillera Blanca with numerical modeling of landscape evolution. We perform inversions of the broad features of the present-day topography, total exhumation and thermochronological data using a landscape evolution model (FastScape) to provide constraints on the erosion efficiency factor, the uplift rate and the temperature gradient. Our results evidence the not negligible contribution of erosion and associated flexural rebound to the uplift of the Cordillera Blanca and allow us to question the models previously proposed for the formation of the CBNF.

  9. Primordial black hole formation during the QCD epoch

    International Nuclear Information System (INIS)

    Jedamzik, K.

    1997-01-01

    We consider the formation of horizon-size primordial black holes (PBH close-quote s) from pre-existing density fluctuations during cosmic phase transitions. It is pointed out that the formation of PBH close-quote s should be particularly efficient during the QCD epoch due to a substantial reduction of pressure forces during adiabatic collapse, or equivalently, a significant decrease in the effective speed of sound during the color-confinement transition. Our considerations imply that for generic initial density perturbation spectra PBH mass functions are expected to exhibit a pronounced peak on the QCD-horizon mass scale ∼1M circle-dot . This mass scale is roughly coincident with the estimated masses for compact objects recently observed in our galactic halo by the MACHO Collaboration. Black holes formed during the QCD epoch may offer an attractive explanation for the origin of halo dark matter evading possibly problematic nucleosynthesis and luminosity bounds on baryonic halo dark matter. copyright 1997 The American Physical Society

  10. Insights from Earth Sciences into Human Evolution studies: The example of prehistoric landscape use in Africa and the Levant

    Science.gov (United States)

    Devès, Maud H.; Reynolds, Sally; King, Geoffrey C. P.; Kuebler, Simon; Sturdy, Derek; Godet, Nan

    2015-07-01

    Fossil remains are embedded in a continually evolving landscape. Earth scientists have the methods and approaches to study the processes that shape the landscape at various temporal and spatial scales. Some of these methods can generate insights that are of potential use for researchers in other fields, such as archaeology and palaeoanthropology. Here we present two case studies to illustrate how a broader landscape perspective can provide new insights into the land use by Pliocene hominins in southern Africa, and more recently, by Palaeolithic hominins in the southern Levant. Key landscape attributes can help explain why humans, hominins and the wider animal community exploit certain types of landscapes in predictable ways. Our first case study examines how active tectonics or volcanism appears to be important in creating fertile regions with reliable water sources and complex topography. While relatively easy for agile primates such as hominins to negotiate, zones of complex topography are harder for certain predators and prey animals to traverse. In the second case study, we consider that differences in soil edaphics can exert a major control on animals by supplying or failing to supply necessary trace elements, such as selenium, copper, phosphate and potassium (Henkin et al., 1995). We show that the pattern of trace element distribution can accurately map animal movements between areas of suitable grazing. This predictability could have enabled Levantine humans to ambush megafauna during these seasonal migrations. By studying the landscape attributes around fossil site locations, Earth scientists can offer new insights and perspectives into the past, particularly on the ways in which the inhabitants would have used their landscapes.

  11. New insights on the geological evolution of the continental margin of Southeastern Brazil derived from zircon and apatite (U-Th-Sm)/He and fission-track data

    Science.gov (United States)

    Krob, Florian; Stippich, Christian; Glasmacher, Ulrich A.; Hackspacher, Peter

    2017-04-01

    New insights on the geological evolution of the continental margin of Southeastern Brazil derived from zircon and apatite (U-Th-Sm)/He and fission-track data Krob, F.C.1, Stippich, C. 1, Glasmacher, U.A.1, Hackspacher, P.C.2 (1) Institute of Earth Sciences, Research Group Thermochronology and Archaeometry, Heidelberg University, INF 234, 69120, Heidelberg, Germany (2) Instituto de Geociências e Ciências Exatas, Universidade Estadual Paulista, Av. 24-A, 1515 Rio Claro, SP, 13506-900, Brazil Passive continental margins are important geoarchives related to mantle dynamics, the breakup of continents, lithospheric dynamics, and other processes. The main concern yields the quantifying long-term lithospheric evolution of the continental margin between São Paulo and Laguna in southeastern Brazil since the Neoproterozoic. We put special emphasis on the reactivation of old fracture zones running into the continent and their constrains on the landscape evolution. In this contribution, we represent already consisting thermochronological data attained by fission-track and (U-Th-Sm)/He analysis on apatites and zircons. The zircon fission-track ages range between 108.4 (15.0) and 539.9 (68.4) Ma, the zircon (U-Th-Sm)/He ages between 72.9 (5.8) and 427.6 (1.8) Ma whereas the apatite fission-track ages range between 40.0 (5.3) and 134.7 (8.0) Ma, and the apatite (U-Th-Sm)/He ages between 32.1 (1.52) and 92.0 (1.86) Ma. These thermochronological ages from metamorphic, sedimentary and intrusive rocks show six distinct blocks (Laguna, Florianópolis, Curitiba, Ilha Comprida, Peruibe and Santos) with different evolution cut by old fracture zones. Furthermore, models of time-temperature evolution illustrate the differences in Pre- to post-rift exhumation histories of these blocks. The presented data will provide an insight into the complex exhumation history of the continental margin based on the existing literature data on the evolution of the Paraná basin in Brazil and the latest

  12. The mitochondrial genome of Frankliniella intonsa: insights into the evolution of mitochondrial genomes at lower taxonomic levels in Thysanoptera.

    Science.gov (United States)

    Yan, Dankan; Tang, Yunxia; Hu, Min; Liu, Fengquan; Zhang, Dongfang; Fan, Jiaqin

    2014-10-01

    Thrips is an ideal group for studying the evolution of mitochondrial (mt) genomes in the genus and family due to independent rearrangements within this order. The complete sequence of the mitochondrial DNA (mtDNA) of the flower thrips Frankliniella intonsa has been completed and annotated in this study. The circular genome is 15,215bp in length with an A+T content of 75.9% and contains the typical 37 genes and it has triplicate putative control regions. Nucleotide composition is A+T biased, and the majority of the protein-coding genes present opposite CG skew which is reflected by the nucleotide composition, codon and amino acid usage. Although the known thrips have massive gene rearrangements, it showed no reversal of strand asymmetry. Gene rearrangements have been found in the lower taxonomic levels of thrips. Three tRNA genes were translocated in the genus Frankliniella and eight tRNA genes in the family Thripidae. Although the gene arrangements of mt genomes of all three thrips species differ massively from the ancestral insect, they are all very similar to each other, indicating that there was a large rearrangement somewhere before the most recent common ancestor of these three species and very little genomic evolution or rearrangements after then. The extremely similar sequences among the CRs suggest that they are ongoing concerted evolution. Analyses of the up and downstream sequence of CRs reveal that the CR2 is actually the ancestral CR. The three CRs are in the same spot in each of the three thrips mt genomes which have the identical inverted genes. These characteristics might be obtained from the most recent common ancestor of this three thrips. Above observations suggest that the mt genomes of the three thrips keep a single massive rearrangement from the common ancestor and have low evolutionary rates among them. Copyright © 2014 Elsevier Inc. All rights reserved.

  13. Discussion on final rifting evolution and breakup : insights from the Mid Norwegian - North East Greenland rifted system

    Science.gov (United States)

    Peron-Pinvidic, Gwenn; Terje Osmundsen, Per

    2016-04-01

    In terms of rifted margin studies, the characteristics of the distal and outer domains are among the today's most debated questions. The architecture and composition of deep margins are rarely well constrained and hence little understood. Except from in a handful number of cases (eg. Iberia-Newfoundland, Southern Australia, Red Sea), basement samples are not available to decipher between the various interpretations allowed by geophysical models. No consensus has been reached on the basement composition, tectonic structures, sedimentary geometries or magmatic content. The result is that non-unique end-member interpretations and models are still proposed in the literature. So, although these domains mark the connection between continents and oceans, and thus correspond to unique stages in the Earth's lithospheric life cycle, their spatial and temporal evolution are still unresolved. The Norwegian-Greenland Sea rift system represents an exceptional laboratory to work on questions related to rifting, rifted margin formation and sedimentary basin evolution. It has been extensively studied for decades by both the academic and the industry communities. The proven and expected oil and gas potentials led to the methodical acquisition of world-class geophysical datasets, which permit the detailed research and thorough testing of concepts at local and regional scales. This contribution is issued from a three years project funded by ExxonMobil aiming at better understanding the crustal-scale nature and evolution of the Norwegian-Greenland Sea. The idea was to take advantage of the data availability on this specific rift system to investigate further the full crustal conjugate scale history of rifting, confronting the various available datasets. In this contribution, we will review the possible structural and sedimentary geometries of the distal margin, and their connection to the oceanic domain. We will discuss the definition of 'breakup' and introduce a first order conceptual

  14. The GC-Rich Mitochondrial and Plastid Genomes of the Green Alga Coccomyxa Give Insight into the Evolution of Organelle DNA Nucleotide Landscape

    Energy Technology Data Exchange (ETDEWEB)

    Smith, David Roy; Burki, Fabien; Yamada, Takashi; Grimwood, Jane; Grigoriev, Igor V.; Van Etten, James L.; Keeling, Patrick J.

    2011-05-13

    Most of the available mitochondrial and plastid genome sequences are biased towards adenine and thymine (AT) over guanine and cytosine (GC). Examples of GC-rich organelle DNAs are limited to a small but eclectic list of species, including certain green algae. Here, to gain insight in the evolution of organelle nucleotide landscape, we present the GC-rich mitochondrial and plastid DNAs from the trebouxiophyte green alga Coccomyxa sp. C-169. We compare these sequences with other GC-rich organelle DNAs and argue that the forces biasing them towards G and C are nonadaptive and linked to the metabolic and/or life history features of this species. The Coccomyxa organelle genomes are also used for phylogenetic analyses, which highlight the complexities in trying to resolve the interrelationships among the core chlorophyte green algae, but ultimately favour a sister relationship between the Ulvophyceae and Chlorophyceae, with the Trebouxiophyceae branching at the base of the chlorophyte crown.

  15. Neuromuscular study of early branching Diuronotus aspetos (Paucitubulatina) yields insights into the evolution of organs systems in Gastrotricha

    DEFF Research Database (Denmark)

    Bekkouche, Nicolas Tarik; Worsaae, Katrine

    2016-01-01

    BACKGROUND: Diuronotus is one of the most recently described genera of Paucitubulatina, one of the three major clades in Gastrotricha. Its morphology suggests that Diuronotus is an early branch of Paucitubulatina, making it a key taxon for understanding the evolution of this morphologically...... constitute new apomorphies of Paucitubulatina, or even Gastrotricha. In order to test these new evolutionary hypotheses, comparable morphological data from other understudied gastrotrich branches and a better resolution of the basal nodes of the gastrotrich phylogeny are warranted. Nonetheless, the present...

  16. Characterization of Small HSPs from Anemonia viridis Reveals Insights into Molecular Evolution of Alpha Crystallin Genes among Cnidarians

    OpenAIRE

    Nicosia, Aldo; Maggio, Teresa; Mazzola, Salvatore; Gianguzza, Fabrizio; Cuttitta, Angela; Costa, Salvatore

    2014-01-01

    Gene family encoding small Heat-Shock Proteins (sHSPs containing α-crystallin domain) are found both in prokaryotic and eukaryotic organisms; however, there is limited knowledge of their evolution. In this study, two small HSP genes termed AvHSP28.6 and AvHSP27, both organized in one intron and two exons, were characterised in the Mediterranean snakelocks anemone Anemonia viridis. The release of the genome sequence of Hydra magnipapillata and Nematostella vectensis enabled a comprehensive stu...

  17. Gravitationally neutral dark matter-dark antimatter universe crystal with epochs of decelerated and accelerated expansion

    Science.gov (United States)

    Gribov, I. A.; Trigger, S. A.

    2016-11-01

    A large-scale self-similar crystallized phase of finite gravitationally neutral universe (GNU)—huge GNU-ball—with spherical 2D-boundary immersed into an endless empty 3D- space is considered. The main principal assumptions of this universe model are: (1) existence of stable elementary particles-antiparticles with the opposite gravitational “charges” (M+gr and M -gr), which have the same positive inertial mass M in = |M ±gr | ≥ 0 and are equally presented in the universe during all universe evolution epochs; (2) the gravitational interaction between the masses of the opposite charges” is repulsive; (3) the unbroken baryon-antibaryon symmetry; (4) M+gr-M-gr “charges” symmetry, valid for two equally presented matter-antimatter GNU-components: (a) ordinary matter (OM)-ordinary antimatter (OAM), (b) dark matter (DM)-dark antimatter (DAM). The GNU-ball is weightless crystallized dust of equally presented, mutually repulsive (OM+DM) clusters and (OAM+DAM) anticlusters. Newtonian GNU-hydrodynamics gives the observable spatial flatness and ideal Hubble flow. The GNU in the obtained large-scale self-similar crystallized phase preserves absence of the cluster-anticluster collisions and simultaneously explains the observable large-scale universe phenomena: (1) the absence of the matter-antimatter clusters annihilation, (2) the self-similar Hubble flow stability and homogeneity, (3) flatness, (4) bubble and cosmic-net structures as 3D-2D-1D decrystallization phases with decelerative (a ≤ 0) and accelerative (a ≥ 0) expansion epochs, (5) the dark energy (DE) phenomena with Λ VACUUM = 0, (6) the DE and DM fine-tuning nature and predicts (7) evaporation into isolated huge M±gr superclusters without Big Rip.

  18. Gravitationally neutral dark matter–dark antimatter universe crystal with epochs of decelerated and accelerated expansion

    International Nuclear Information System (INIS)

    Gribov, I A; Trigger, S A

    2016-01-01

    A large-scale self-similar crystallized phase of finite gravitationally neutral universe (GNU)—huge GNU-ball—with spherical 2D-boundary immersed into an endless empty 3D- space is considered. The main principal assumptions of this universe model are: (1) existence of stable elementary particles-antiparticles with the opposite gravitational “charges” ( M + gr and M -gr ), which have the same positive inertial mass M in = | M ±gr | ≥ 0 and are equally presented in the universe during all universe evolution epochs; (2) the gravitational interaction between the masses of the opposite charges” is repulsive; (3) the unbroken baryon-antibaryon symmetry; (4) M +gr -M -gr “charges” symmetry, valid for two equally presented matter-antimatter GNU-components: (a) ordinary matter (OM)-ordinary antimatter (OAM), (b) dark matter (DM)-dark antimatter (DAM). The GNU-ball is weightless crystallized dust of equally presented, mutually repulsive (OM+DM) clusters and (OAM+DAM) anticlusters. Newtonian GNU-hydrodynamics gives the observable spatial flatness and ideal Hubble flow. The GNU in the obtained large-scale self-similar crystallized phase preserves absence of the cluster-anticluster collisions and simultaneously explains the observable large-scale universe phenomena: (1) the absence of the matter-antimatter clusters annihilation, (2) the self-similar Hubble flow stability and homogeneity, (3) flatness, (4) bubble and cosmic-net structures as 3D-2D-1D decrystallization phases with decelerative (a ≤ 0) and accelerative (a ≥ 0) expansion epochs, (5) the dark energy (DE) phenomena with Λ VACUUM = 0, (6) the DE and DM fine-tuning nature and predicts (7) evaporation into isolated huge M ±gr superclusters without Big Rip. (paper)

  19. Plastome Evolution in the Sole Hemiparasitic Genus Laurel Dodder (Cassytha) and Insights into the Plastid Phylogenomics of Lauraceae.

    Science.gov (United States)

    Wu, Chung-Shien; Wang, Ting-Jen; Wu, Chia-Wen; Wang, Ya-Nan; Chaw, Shu-Miaw

    2017-10-01

    To date, little is known about the evolution of plastid genomes (plastomes) in Lauraceae. As one of the top five largest families in tropical forests, the Lauraceae contain many species that are important ecologically and economically. Lauraceous species also provide wonderful materials to study the evolutionary trajectory in response to parasitism because they contain both nonparasitic and parasitic species. This study compared the plastomes of nine Lauraceous species, including the sole hemiparasitic and herbaceous genus Cassytha (laurel dodder; here represented by Cassytha filiformis). We found differential contractions of the canonical inverted repeat (IR), resulting in two IR types present in Lauraceae. These two IR types reinforce Cryptocaryeae and Neocinnamomum-Perseeae-Laureae as two separate clades. Our data reveal several traits unique to Cas. filiformis, including loss of IRs, loss or pseudogenization of 11 ndh and rpl23 genes, richness of repeats, and accelerated rates of nucleotide substitutions in protein-coding genes. Although Cas. filiformis is low in chlorophyll content, our analysis based on dN/dS ratios suggests that both its plastid house-keeping and photosynthetic genes are under strong selective constraints. Hence, we propose that short generation time and herbaceous lifestyle rather than reduced photosynthetic ability drive the accelerated rates of nucleotide substitutions in Cas. filiformis. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

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

    Science.gov (United States)

    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.

  1. IslandFAST: A Semi-numerical Tool for Simulating the Late Epoch of Reionization

    Energy Technology Data Exchange (ETDEWEB)

    Xu, Yidong; Chen, Xuelei [Key Laboratory for Computational Astrophysics, National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China); Yue, Bin [National Astronomical Observatories, Chinese Academy of Sciences, Beijing 100012 (China)

    2017-08-01

    We present the algorithm and main results of our semi-numerical simulation, islandFAST, which was developed from 21cmFAST and designed for the late stage of reionization. The islandFAST simulation predicts the evolution and size distribution of the large-scale underdense neutral regions (neutral islands), and we find that the late Epoch of Reionization proceeds very fast, showing a characteristic scale of the neutral islands at each redshift. Using islandFAST, we compare the impact of two types of absorption systems, i.e., the large-scale underdense neutral islands versus small-scale overdense absorbers, in regulating the reionization process. The neutral islands dominate the morphology of the ionization field, while the small-scale absorbers dominate the mean-free path of ionizing photons, and also delay and prolong the reionization process. With our semi-numerical simulation, the evolution of the ionizing background can be derived self-consistently given a model for the small absorbers. The hydrogen ionization rate of the ionizing background is reduced by an order of magnitude in the presence of dense absorbers.

  2. The 21-cm Signal from the cosmological epoch of recombination

    Energy Technology Data Exchange (ETDEWEB)

    Fialkov, A. [Departement de Physique, Ecole Normale Superieure, CNRS, 24 rue Lhomond, Paris, 75005 (France); Loeb, A., E-mail: anastasia.fialkov@phys.ens.fr, E-mail: aloeb@cfa.harvard.edu [Department of Astronomy, Harvard University, 60 Garden Street, MS-51, Cambridge, MA, 02138 (United States)

    2013-11-01

    The redshifted 21-cm emission by neutral hydrogen offers a unique tool for mapping structure formation in the early universe in three dimensions. Here we provide the first detailed calculation of the 21-cm emission signal during and after the epoch of hydrogen recombination in the redshift range of z ∼ 500–1,100, corresponding to observed wavelengths of 100–230 meters. The 21-cm line deviates from thermal equilibrium with the cosmic microwave background (CMB) due to the excess Lyα radiation from hydrogen and helium recombinations. The resulting 21-cm signal reaches a brightness temperature of a milli-Kelvin, orders of magnitude larger than previously estimated. Its detection by a future lunar or space-based observatory could improve dramatically the statistical constraints on the cosmological initial conditions compared to existing two-dimensional maps of the CMB anisotropies.

  3. The 21-cm Signal from the cosmological epoch of recombination

    International Nuclear Information System (INIS)

    Fialkov, A.; Loeb, A.

    2013-01-01

    The redshifted 21-cm emission by neutral hydrogen offers a unique tool for mapping structure formation in the early universe in three dimensions. Here we provide the first detailed calculation of the 21-cm emission signal during and after the epoch of hydrogen recombination in the redshift range of z ∼ 500–1,100, corresponding to observed wavelengths of 100–230 meters. The 21-cm line deviates from thermal equilibrium with the cosmic microwave background (CMB) due to the excess Lyα radiation from hydrogen and helium recombinations. The resulting 21-cm signal reaches a brightness temperature of a milli-Kelvin, orders of magnitude larger than previously estimated. Its detection by a future lunar or space-based observatory could improve dramatically the statistical constraints on the cosmological initial conditions compared to existing two-dimensional maps of the CMB anisotropies

  4. Novel endophytic lineages of Tolypocladium provide new insights into the ecology and evolution of Cordyceps-like fungi.

    Science.gov (United States)

    Gazis, Romina; Skaltsas, Demetra; Chaverri, Priscila

    2014-01-01

    The objective of this study was to identify a group of unknown endophytic fungal isolates from the living sapwood of wild and planted Hevea (rubber tree) populations. Three novel lineages of Tolypocladium are described based on molecular and morphological data. Findings from this study open a window for novel hypotheses regarding the ecology and role of endophytes within plant communities as well as trait evolution and potential forces driving diversification of Cordyceps-like fungi. This study stresses the importance of integrating asexual and sexual fungal states for a more complete understanding of the natural history of this diverse group. In addition, it highlights the study of fungi in the sapwood of tropical trees as habitat for the discovery of novel fungal lineages and substrate associations. © 2014 by The Mycological Society of America.

  5. Molecular phylogenetic analysis of Commiphora (Burseraceae) yields insight on the evolution and historical biogeography of an "impossible" genus.

    Science.gov (United States)

    Weeks, Andrea; Simpson, Beryl B

    2007-01-01

    Expansion of the arid zone of sub-Saharan tropical Africa during the Miocene is posited as a significant contributing factor in the evolution of contemporary African flora. Nevertheless, few molecular phylogenetic studies have tested this hypothesis using reconstructed historical biogeographies of plants within this zone. Here, we present a molecular phylogeny of Commiphora, a predominantly tropical African, arid-adapted tree genus, in order to test the monophyly of its taxonomic sections and identify clades that will help direct future study of this species-rich and geographically widespread taxon. We then use multiple fossil calibrations of Commiphora phylogeny to determine the timing of well-supported diversification events within the genus and interpret these age estimates to determine the relative contribution of vicariance and dispersal in the expansion of Commiphora's geographic range. We find that Commiphora is sister to Vietnamese Bursera tonkinensis and that its crown group radiation corresponds with the onset of the Miocene.

  6. Deglaciation and its impact on permafrost and rock glacier evolution: New insight from two adjacent cirques in Austria.

    Science.gov (United States)

    Kellerer-Pirklbauer, Andreas; Kaufmann, Viktor

    2018-04-15

    Glaciers and permafrost are strongly linked to each other in mid-latitude mountain regions particularly with polythermal glaciers. This linkage is not only climatically defined but also in terms of geomorphic and glaciological processes. We studied two adjacent cirques located in the Central Austria. We focussed on the deglaciation since the Little Ice Age (LIA) maximum (c.1850CE) and its relevance for permafrost and rock glacier evolution since then. One cirque is occupied by a glacier remnant whereas the second one is occupied by an active rock glacier which was partly overridden by a glacier during the LIA. We applied a multidisciplinary approach using field-based techniques including geoelectrics, geodetic measurements, and automatic monitoring as well as historic maps and photographs, remote sensing, and digital terrain analysis. Results indicate almost complete deglaciation by the end of the last millennium. Small-scale tongue-shaped landforms of complex origin formed during the last decades at finer-grained slope deposits below the cirque headwalls. Field evidences and geophysics results proved the existence of widespread sedimentary ice beneath a thin veneer of debris at these slopes. The variable thickness of the debris layer has a major impact on differential ablation and landform evolution in both cirques. The comparison of digital elevation models revealed clear mass losses at both cirques with low rates between 1954 and 2002 and significantly higher rates since then. The central and lower part of the rock glacier moves fast transporting sediments and ice downvalley. In contrast, the upper part of the rock glacier is characterised by low debris and ice input rates. Both effects cause a significant decoupling of the main rock glacier body from its nourishment area leading eventually to rock glacier starvation. This study demonstrates the importance of a decadal-scale and multidisciplinary research approach in determining the development of alpine

  7. Venom-related transcripts from Bothrops jararaca tissues provide novel molecular insights into the production and evolution of snake venom.

    Science.gov (United States)

    Junqueira-de-Azevedo, Inácio L M; Bastos, Carolina Mancini Val; Ho, Paulo Lee; Luna, Milene Schmidt; Yamanouye, Norma; Casewell, Nicholas R

    2015-03-01

    Attempts to reconstruct the evolutionary history of snake toxins in the context of their co-option to the venom gland rarely account for nonvenom snake genes that are paralogous to toxins, and which therefore represent important connectors to ancestral genes. In order to reevaluate this process, we conducted a comparative transcriptomic survey on body tissues from a venomous snake. A nonredundant set of 33,000 unigenes (assembled transcripts of reference genes) was independently assembled from six organs of the medically important viperid snake Bothrops jararaca, providing a reference list of 82 full-length toxins from the venom gland and specific products from other tissues, such as pancreatic digestive enzymes. Unigenes were then screened for nontoxin transcripts paralogous to toxins revealing 1) low level coexpression of approximately 20% of toxin genes (e.g., bradykinin-potentiating peptide, C-type lectin, snake venom metalloproteinase, snake venom nerve growth factor) in body tissues, 2) the identity of the closest paralogs to toxin genes in eight classes of toxins, 3) the location and level of paralog expression, indicating that, in general, co-expression occurs in a higher number of tissues and at lower levels than observed for toxin genes, and 4) strong evidence of a toxin gene reverting back to selective expression in a body tissue. In addition, our differential gene expression analyses identify specific cellular processes that make the venom gland a highly specialized secretory tissue. Our results demonstrate that the evolution and production of venom in snakes is a complex process that can only be understood in the context of comparative data from other snake tissues, including the identification of genes paralogous to venom toxins. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. Characterization of small HSPs from Anemonia viridis reveals insights into molecular evolution of alpha crystallin genes among cnidarians.

    Directory of Open Access Journals (Sweden)

    Aldo Nicosia

    Full Text Available Gene family encoding small Heat-Shock Proteins (sHSPs containing α-crystallin domain are found both in prokaryotic and eukaryotic organisms; however, there is limited knowledge of their evolution. In this study, two small HSP genes termed AvHSP28.6 and AvHSP27, both organized in one intron and two exons, were characterised in the Mediterranean snakelocks anemone Anemonia viridis. The release of the genome sequence of Hydra magnipapillata and Nematostella vectensis enabled a comprehensive study of the molecular evolution of α-crystallin gene family among cnidarians. Most of the H. magnipapillata sHSP genes share the same gene organization described for AvHSP28.6 and AvHSP27, differing from the sHSP genes of N. vectensis which mainly show an intronless architecture. The different genomic organization of sHSPs, the phylogenetic analyses based on protein sequences, and the relationships among Cnidarians, suggest that the A.viridis sHSPs represent the common ancestor from which H. magnipapillata genes directly evolved through segmental genome duplication. Additionally retroposition events may be considered responsible for the divergence of sHSP genes of N. vectensis from A. viridis. Analyses of transcriptional expression profile showed that AvHSP28.6 was constitutively expressed among different tissues from both ectodermal and endodermal layers of the adult sea anemones, under normal physiological conditions and also under different stress condition. Specifically, we profiled the transcriptional activation of AvHSP28.6 after challenges with different abiotic/biotic stresses showing induction by extreme temperatures, heavy metals exposure and immune stimulation. Conversely, no AvHSP27 transcript was detected in such dissected tissues, in adult whole body cDNA library or under stress conditions. Hence, the involvement of AvHSP28.6 gene in the sea anemone defensome is strongly suggested.

  9. Characterization of small HSPs from Anemonia viridis reveals insights into molecular evolution of alpha crystallin genes among cnidarians.

    Science.gov (United States)

    Nicosia, Aldo; Maggio, Teresa; Mazzola, Salvatore; Gianguzza, Fabrizio; Cuttitta, Angela; Costa, Salvatore

    2014-01-01

    Gene family encoding small Heat-Shock Proteins (sHSPs containing α-crystallin domain) are found both in prokaryotic and eukaryotic organisms; however, there is limited knowledge of their evolution. In this study, two small HSP genes termed AvHSP28.6 and AvHSP27, both organized in one intron and two exons, were characterised in the Mediterranean snakelocks anemone Anemonia viridis. The release of the genome sequence of Hydra magnipapillata and Nematostella vectensis enabled a comprehensive study of the molecular evolution of α-crystallin gene family among cnidarians. Most of the H. magnipapillata sHSP genes share the same gene organization described for AvHSP28.6 and AvHSP27, differing from the sHSP genes of N. vectensis which mainly show an intronless architecture. The different genomic organization of sHSPs, the phylogenetic analyses based on protein sequences, and the relationships among Cnidarians, suggest that the A.viridis sHSPs represent the common ancestor from which H. magnipapillata genes directly evolved through segmental genome duplication. Additionally retroposition events may be considered responsible for the divergence of sHSP genes of N. vectensis from A. viridis. Analyses of transcriptional expression profile showed that AvHSP28.6 was constitutively expressed among different tissues from both ectodermal and endodermal layers of the adult sea anemones, under normal physiological conditions and also under different stress condition. Specifically, we profiled the transcriptional activation of AvHSP28.6 after challenges with different abiotic/biotic stresses showing induction by extreme temperatures, heavy metals exposure and immune stimulation. Conversely, no AvHSP27 transcript was detected in such dissected tissues, in adult whole body cDNA library or under stress conditions. Hence, the involvement of AvHSP28.6 gene in the sea anemone defensome is strongly suggested.

  10. Insights into the evolution, biogeography and natural history of the acorn ants, genus Temnothorax Mayr (hymenoptera: Formicidae).

    Science.gov (United States)

    Prebus, Matthew

    2017-12-13

    Temnothorax (Formicidae: Myrmicinae) is a diverse genus of ants found in a broad spectrum of ecosystems across the northern hemisphere. These diminutive ants have long served as models for social insect behavior, leading to discoveries about social learning and inspiring hypotheses about the process of speciation and the evolution of social parasitism. This genus is highly morphologically and behaviorally diverse, and this has caused a great deal of taxonomic confusion in recent years. Past efforts to estimate the phylogeny of this genus have been limited in taxonomic scope, leaving the broader evolutionary patterns in Temnothorax unclear. To establish the monophyly of Temnothorax, resolve the evolutionary relationships, reconstruct the historical biogeography and investigate trends in the evolution of key traits, I generated, assembled, and analyzed two molecular datasets: a traditional multi-locus Sanger sequencing dataset, and an ultra-conserved element (UCE) dataset. Using maximum likelihood, Bayesian, and summary-coalescent based approaches, I analyzed 22 data subsets consisting of 103 ingroup taxa and a maximum of 1.8 million base pairs in 2485 loci. The results of this study suggest an origin of Temnothorax at the Eocene-Oligocene transition, concerted transitions to arboreal nesting habits in several clades during the Oligocene, coinciding with ancient global cooling, and several convergent origins of social parasitism in the Miocene and Pliocene. As with other Holarctic taxa, Temnothorax has a history of migration across Beringia during the Miocene. Temnothorax is corroborated as a natural group, and the notion that many of the historical subgeneric and species group concepts are artificial is reinforced. The strict form of Emery's Rule, in which a socially parasitic species is sister to its host species, is not well supported in Temnothorax.

  11. Contrasting Patterns of Nucleotide Substitution Rates Provide Insight into Dynamic Evolution of Plastid and Mitochondrial Genomes of Geranium.

    Science.gov (United States)

    Park, Seongjun; Ruhlman, Tracey A; Weng, Mao-Lun; Hajrah, Nahid H; Sabir, Jamal S M; Jansen, Robert K

    2017-06-01

    Geraniaceae have emerged as a model system for investigating the causes and consequences of variation in plastid and mitochondrial genomes. Incredible structural variation in plastid genomes (plastomes) and highly accelerated evolutionary rates have been reported in selected lineages and functional groups of genes in both plastomes and mitochondrial genomes (mitogenomes), and these phenomena have been implicated in cytonuclear incompatibility. Previous organelle genome studies have included limited sampling of Geranium, the largest genus in the family with over 400 species. This study reports on rates and patterns of nucleotide substitutions in plastomes and mitogenomes of 17 species of Geranium and representatives of other Geraniaceae. As detected across other angiosperms, substitution rates in the plastome are 3.5 times higher than the mitogenome in most Geranium. However, in the branch leading to Geranium brycei/Geranium incanum mitochondrial genes experienced significantly higher dN and dS than plastid genes, a pattern that has only been detected in one other angiosperm. Furthermore, rate accelerations differ in the two organelle genomes with plastomes having increased dN and mitogenomes with increased dS. In the Geranium phaeum/Geranium reflexum clade, duplicate copies of clpP and rpoA genes that experienced asymmetric rate divergence were detected in the single copy region of the plastome. In the case of rpoA, the branch leading to G. phaeum/G. reflexum experienced positive selection or relaxation of purifying selection. Finally, the evolution of acetyl-CoA carboxylase is unusual in Geraniaceae because it is only the second angiosperm family where both prokaryotic and eukaryotic ACCases functionally coexist in the plastid. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  12. Multiphase Structural Evolution of a Continental Margin During Obduction Orogeny: Insights From the Jebel Akhdar Dome, Oman Mountains

    Science.gov (United States)

    Grobe, A.; Virgo, S.; von Hagke, C.; Urai, J. L.; Littke, R.

    2018-03-01

    The structural evolution of the carbonate platform in the footwall of the Semail ophiolite emplaced onto the passive continental margin of Arabia helps to better understand the early stages of obduction-related orogens. These early stages are rarely observable in other orogens as they are mostly overprinted by later mountain building phases. We present an extensive structural analysis of the Jebel Akhdar anticline, the largest tectonic window of the Oman Mountains, and integrate it on different scales. Outcrop observations can be linked to plate motion data, providing an absolute timeframe for structural generations consistent with radiometric dating of veins. Top-to-S overthrusting of the Semail ophiolite and Hawasina nappes onto the carbonate platform during high plate convergence rates between Arabia and Eurasia caused rapid burial and overpressure, generation and migration of hydrocarbons, and bedding-confined veins, but no major deformation in the carbonate platform. At reduced convergence rates, subsequent tectonic thinning of the ophiolite took place above a top-to-NNE, crustal-scale ductile shear zone, deforming existing veins and forming a cleavage in clay-rich layers in early Campanian times. Ongoing extension occurred along normal- to oblique-slip faults, forming horst-graben structures and a precursor of the Jebel Akhdar dome (Campanian to Maastrichtian). This was followed by NE-SW oriented ductile shortening and the formation of the Jebel Akhdar dome, deforming the earlier structures. Thereafter, exhumation was associated with low-angle normal faults on the northern flank of the anticline. We correlate the top-to-NNE crustal-scale shear zone with a similar structure in the Saih Hatat window to develop a unified model of the tectonic evolution of the Oman Mountains.

  13. Insights into the molecular evolution of the PDZ/LIM family and identification of a novel conserved protein motif.

    Directory of Open Access Journals (Sweden)

    Aartjan J W Te Velthuis

    Full Text Available The PDZ and LIM domain-containing protein family is encoded by a diverse group of genes whose phylogeny has currently not been analyzed. In mammals, ten genes are found that encode both a PDZ- and one or several LIM-domains. These genes are: ALP, RIL, Elfin (CLP36, Mystique, Enigma (LMP-1, Enigma homologue (ENH, ZASP (Cypher, Oracle, LMO7 and the two LIM domain kinases (LIMK1 and LIMK2. As conventional alignment and phylogenetic procedures of full-length sequences fell short of elucidating the evolutionary history of these genes, we started to analyze the PDZ and LIM domain sequences themselves. Using information from most sequenced eukaryotic lineages, our phylogenetic analysis is based on full-length cDNA-, EST-derived- and genomic- PDZ and LIM domain sequences of over 25 species, ranging from yeast to humans. Plant and protozoan homologs were not found. Our phylogenetic analysis identifies a number of domain duplication and rearrangement events, and shows a single convergent event during evolution of the PDZ/LIM family. Further, we describe the separation of the ALP and Enigma subfamilies in lower vertebrates and identify a novel consensus motif, which we call 'ALP-like motif' (AM. This motif is highly-conserved between ALP subfamily proteins of diverse organisms. We used here a combinatorial approach to define the relation of the PDZ and LIM domain encoding genes and to reconstruct their phylogeny. This analysis allowed us to classify the PDZ/LIM family and to suggest a meaningful model for the molecular evolution of the diverse gene architectures found in this multi-domain family.

  14. Large-scale evolution of the central-east Greenland margin: New insights to the North Atlantic glaciation history

    Science.gov (United States)

    Pérez, Lara F.; Nielsen, Tove; Knutz, Paul C.; Kuijpers, Antoon; Damm, Volkmar

    2018-04-01

    The continental shelf of central-east Greenland is shaped by several glacially carved transverse troughs that form the oceanward extension of the major fjord systems. The evolution of these troughs through time, and their relation with the large-scale glaciation of the Northern Hemisphere, is poorly understood. In this study seismostratigraphic analyses have been carried out to determine the morphological and structural development of this important sector of the East Greenland glaciated margin. The age of major stratigraphic discontinuities has been constrained by a direct tie to ODP site 987 drilled in the Greenland Sea basin plain off Scoresby Sund fan system. The areal distribution and internal facies of the identified seismic units reveal the large-scale depositional pattern formed by ice-streams draining a major part of the central-east Greenland ice sheet. Initial sedimentation along the margin was, however, mainly controlled by tectonic processes related to the margin construction, continental uplift, and fluvial processes. From late Miocene to present, progradational and erosional patterns point to repeated glacial advances across the shelf. The evolution of depo-centres suggests that ice sheet advances over the continental shelf have occurred since late Miocene, about 2 Myr earlier than previously assumed. This cross-shelf glaciation is more pronounced during late Miocene and early Pliocene along Blosseville Kyst and around the Pliocene/Pleistocene boundary off Scoresby Sund; indicating a northward migration of the glacial advance. The two main periods of glaciation were separated by a major retreat of the ice sheet to an inland position during middle Pliocene. Mounded-wavy deposits interpreted as current-related deposits suggest the presence of changing along-slope current dynamics in concert with the development of the modern North Atlantic oceanographic pattern.

  15. Continued internal and external research efforts of RAG. New insights for the geological evolution of the Molasse Basin of Austria

    Energy Technology Data Exchange (ETDEWEB)

    Hinsch, R. [Rohoel-Aufsuchungs AG, Vienna (Austria)

    2008-10-23

    The understanding of the detailed geological evolution of the Molasse Basin is crucial for the continued success of exploration in this mature basin. Results from several research projects help to find new play types and increase the understanding of stratigraphic traps by characterising the sedimentological processes that control them. Risks associated with play types can be better assessed considering their evolutionary framework. Several studies focussed on that subject have been concluded in recent years or are still ongoing. This presentation will give an overview of the objectives, results and implications of these initiatives for evaluation and analysis of the geological evolution and for exploration of the Molasse Basin. An initial collaboration with Stanford University integrated sedimentological core analyses with 3D seismic, wireline log data interpretation and outcrop studies in analogue settings. The study yielded a modern sedimentological model for the Upper Puchkirchen Formation which was subsequently applied to exploration. A sequence stratigraphic study examined the sequence framework of the Molasse Basin fill and was able to correlate 5 sequences from the shelf into the deep basin. Studies on seismic and core analyses from the south slope of the Puchkirchen trough show how slope morphology and confinement control sediment distribution in the southern slope deposits. The transition from deep to more shallow marine conditions and the progradation of deltaic sequences into the basin in Eggenburgian/Burdigalian times is described by an intense 3-D seismic interpretation in combination with sedimentological core work. Working on a more local scale, other projects are improving the understanding of the detailed architecture of distinct play elements such as the Upper Puchkirchen Channel or the Basal Hall Formation Channel. In general, these studies highlight the complex interaction of processes that control sediment distribution in the basin. Morphology

  16. Spinning Gland Transcriptomics from Two Main Clades of Spiders (Order: Araneae) - Insights on Their Molecular, Anatomical and Behavioral Evolution

    Science.gov (United States)

    Prosdocimi, Francisco; Bittencourt, Daniela; da Silva, Felipe Rodrigues; Kirst, Matias; Motta, Paulo C.; Rech, Elibio L.

    2011-01-01

    Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium) to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae) and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade). Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily) were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i) anatomical differentiation of spinning glands and (ii) behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution. PMID:21738742

  17. Spinning gland transcriptomics from two main clades of spiders (order: Araneae--insights on their molecular, anatomical and behavioral evolution.

    Directory of Open Access Journals (Sweden)

    Francisco Prosdocimi

    Full Text Available Characterized by distinctive evolutionary adaptations, spiders provide a comprehensive system for evolutionary and developmental studies of anatomical organs, including silk and venom production. Here we performed cDNA sequencing using massively parallel sequencers (454 GS-FLX Titanium to generate ∼80,000 reads from the spinning gland of Actinopus spp. (infraorder: Mygalomorphae and Gasteracantha cancriformis (infraorder: Araneomorphae, Orbiculariae clade. Actinopus spp. retains primitive characteristics on web usage and presents a single undifferentiated spinning gland while the orbiculariae spiders have seven differentiated spinning glands and complex patterns of web usage. MIRA, Celera Assembler and CAP3 software were used to cluster NGS reads for each spider. CAP3 unigenes passed through a pipeline for automatic annotation, classification by biological function, and comparative transcriptomics. Genes related to spider silks were manually curated and analyzed. Although a single spidroin gene family was found in Actinopus spp., a vast repertoire of specialized spider silk proteins was encountered in orbiculariae. Astacin-like metalloproteases (meprin subfamily were shown to be some of the most sampled unigenes and duplicated gene families in G. cancriformis since its evolutionary split from mygalomorphs. Our results confirm that the evolution of the molecular repertoire of silk proteins was accompanied by the (i anatomical differentiation of spinning glands and (ii behavioral complexification in the web usage. Finally, a phylogenetic tree was constructed to cluster most of the known spidroins in gene clades. This is the first large-scale, multi-organism transcriptome for spider spinning glands and a first step into a broad understanding of spider web systems biology and evolution.

  18. A new fossil dolphin Dilophodelphis fordycei provides insight into the evolution of supraorbital crests in Platanistoidea (Mammalia, Cetacea)

    Science.gov (United States)

    Boersma, Alexandra T.; McCurry, Matthew R.; Pyenson, Nicholas D.

    2017-05-01

    Many odontocete groups have developed enlarged facial crests, although these crests differ in topography, composition and function. The most elaborate crests occur in the South Asian river dolphin (Platanista gangetica), in which they rise dorsally as delicate, pneumatized wings anterior of the facial bones. Their position wrapping around the melon suggests their involvement in sound propagation for echolocation. To better understand the origin of crests in this lineage, we examined facial crests among fossil and living Platanistoidea, including a new taxon, Dilophodelphis fordycei, nov. gen. and sp., described herein, from the Early Miocene Astoria Formation of Oregon, USA. We measured the physical extent and thickness of platanistoid crests, categorized their relative position and used computed tomography scans to examine their internal morphology and relative bone density. Integrating these traits in a phylogenetic context, we determined that the onset of crest elaboration or enlargement and the evolution of crest pneumatization among the platanistoids were separate events, with crest enlargement beginning in the Oligocene. However, we find no evidence for pneumatization until possibly the Early Miocene, although certainly by the Middle Miocene. Such an evolutionary context, including data from the fossil record, should inform modelling efforts that seek to understand the diversity of sound generation morphology in Odontoceti.

  19. Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae).

    Science.gov (United States)

    Alverson, Andrew J; Wei, XiaoXin; Rice, Danny W; Stern, David B; Barry, Kerrie; Palmer, Jeffrey D

    2010-06-01

    The mitochondrial genomes of seed plants are unusually large and vary in size by at least an order of magnitude. Much of this variation occurs within a single family, the Cucurbitaceae, whose genomes range from an estimated 390 to 2,900 kb in size. We sequenced the mitochondrial genomes of Citrullus lanatus (watermelon: 379,236 nt) and Cucurbita pepo (zucchini: 982,833 nt)--the two smallest characterized cucurbit mitochondrial genomes--and determined their RNA editing content. The relatively compact Citrullus mitochondrial genome actually contains more and longer genes and introns, longer segmental duplications, and more discernibly nuclear-derived DNA. The large size of the Cucurbita mitochondrial genome reflects the accumulation of unprecedented amounts of both chloroplast sequences (>113 kb) and short repeated sequences (>370 kb). A low mutation rate has been hypothesized to underlie increases in both genome size and RNA editing frequency in plant mitochondria. However, despite its much larger genome, Cucurbita has a significantly higher synonymous substitution rate (and presumably mutation rate) than Citrullus but comparable levels of RNA editing. The evolution of mutation rate, genome size, and RNA editing are apparently decoupled in Cucurbitaceae, reflecting either simple stochastic variation or governance by different factors.

  20. Insights into the venom composition and evolution of an endoparasitoid wasp by combining proteomic and transcriptomic analyses.

    Science.gov (United States)

    Yan, Zhichao; Fang, Qi; Wang, Lei; Liu, Jinding; Zhu, Yu; Wang, Fei; Li, Fei; Werren, John H; Ye, Gongyin

    2016-01-25

    Parasitoid wasps are abundant and diverse hymenopteran insects that lay their eggs into the internal body (endoparasitoid) or on the external surface (ectoparasitoid) of their hosts. To make a more conducive environment for the wasps' young, both ecto- and endoparasitoids inject venoms into the host to modulate host immunity, metabolism and development. Endoparasitoids have evolved from ectoparasitoids independently in different hymenopteran lineages. Pteromalus puparum, a pupal endoparasitoid of various butterflies, represents a relatively recent evolution of endoparasitism within pteromalids. Using a combination of transcriptomic and proteomic approaches, we have identified 70 putative venom proteins in P. puparum. Most of them show higher similarity to venom proteins from the related ectoparasitoid Nasonia vitripennis than from other more distantly related endoparasitoids. In addition, 13 venom proteins are similar to venoms of distantly related endoparasitoids but have no detectable venom matches in Nasonia. These venom proteins may have a role in adaptation to endoparasitism. Overall, these results lay the groundwork for more detailed studies of venom function and adaptation to the endoparasitic lifestyle.

  1. New insight into the evolution of the vertebrate respiratory system and the discovery of unidirectional airflow in iguana lungs.

    Science.gov (United States)

    Cieri, Robert L; Craven, Brent A; Schachner, Emma R; Farmer, C G

    2014-12-02

    The generally accepted framework for the evolution of a key feature of the avian respiratory system, unidirectional airflow, is that it is an adaptation for efficiency of gas exchange and expanded aerobic capacities, and therefore it has historically been viewed as important to the ability of birds to fly and to maintain an endothermic metabolism. This pattern of flow has been presumed to arise from specific features of the respiratory system, such as an enclosed intrapulmonary bronchus and parabronchi. Here we show unidirectional airflow in the green iguana, a lizard with a strikingly different natural history from that of birds and lacking these anatomical features. This discovery indicates a paradigm shift is needed. The selective drivers of the trait, its date of origin, and the fundamental aerodynamic mechanisms by which unidirectional flow arises must be reassessed to be congruent with the natural history of this lineage. Unidirectional flow may serve functions other than expanded aerobic capacity; it may have been present in the ancestral diapsid; and it can occur in structurally simple lungs.

  2. Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles.

    Directory of Open Access Journals (Sweden)

    Ian A Warren

    Full Text Available Scarab beetles exhibit an astonishing variety of rigid exo-skeletal outgrowths, known as "horns". These traits are often sexually dimorphic and vary dramatically across species in size, shape, location, and allometry with body size. In many species, the horn exhibits disproportionate growth resulting in an exaggerated allometric relationship with body size, as compared to other traits, such as wings, that grow proportionately with body size. Depending on the species, the smallest males either do not produce a horn at all, or they produce a disproportionately small horn for their body size. While the diversity of horn shapes and their behavioural ecology have been reasonably well studied, we know far less about the proximate mechanisms that regulate horn growth. Thus, using 454 pyrosequencing, we generated transcriptome profiles, during horn growth and development, in two different scarab beetle species: the Asian rhinoceros beetle, Trypoxylus dichotomus, and the dung beetle, Onthophagus nigriventris. We obtained over half a million reads for each species that were assembled into over 6,000 and 16,000 contigs respectively. We combined these data with previously published studies to look for signatures of molecular evolution. We found a small subset of genes with horn-biased expression showing evidence for recent positive selection, as is expected with sexual selection on horn size. We also found evidence of relaxed selection present in genes that demonstrated biased expression between horned and horn-less morphs, consistent with the theory of developmental decoupling of phenotypically plastic traits.

  3. Evolution of oil-producing trichomes in Sisyrinchium (Iridaceae): insights from the first comprehensive phylogenetic analysis of the genus

    Science.gov (United States)

    Chauveau, Olivier; Eggers, Lilian; Raquin, Christian; Silvério, Adriano; Brown, Spencer; Couloux, Arnaud; Cruaud, Corine; Kaltchuk-Santos, Eliane; Yockteng, Roxana; Souza-Chies, Tatiana T.; Nadot, Sophie

    2011-01-01

    Background and Aims Sisyrinchium (Iridaceae: Iridoideae: Sisyrinchieae) is one of the largest, most widespread and most taxonomically complex genera in Iridaceae, with all species except one native to the American continent. Phylogenetic relationships within the genus were investigated and the evolution of oil-producing structures related to specialized oil-bee pollination examined. Methods Phylogenetic analyses based on eight molecular markers obtained from 101 Sisyrinchium accessions representing 85 species were conducted in the first extensive phylogenetic analysis of the genus. Total evidence analyses confirmed the monophyly of the genus and retrieved nine major clades weakly connected to the subdivisions previously recognized. The resulting phylogenetic hypothesis was used to reconstruct biogeographical patterns, and to trace the evolutionary origin of glandular trichomes present in the flowers of several species. Key Results and Conclusions Glandular trichomes evolved three times independently in the genus. In two cases, these glandular trichomes are oil-secreting, suggesting that the corresponding flowers might be pollinated by oil-bees. Biogeographical patterns indicate expansions from Central America and the northern Andes to the subandean ranges between Chile and Argentina and to the extended area of the Paraná river basin. The distribution of oil-flower species across the phylogenetic trees suggests that oil-producing trichomes may have played a key role in the diversification of the genus, a hypothesis that requires future testing. PMID:21527419

  4. Analysis of the WUSCHEL-RELATED HOMEOBOX gene family in Pinus pinaster: New insights into the gene family evolution.

    Science.gov (United States)

    Alvarez, José M; Bueno, Natalia; Cañas, Rafael A; Avila, Concepción; Cánovas, Francisco M; Ordás, Ricardo J

    2018-02-01

    WUSCHEL-RELATED HOMEOBOX (WOX) genes are key players controlling stem cells in plants and can be divided into three clades according to the time of their appearance during plant evolution. Our knowledge of stem cell function in vascular plants other than angiosperms is limited, they separated from gymnosperms ca 300 million years ago and their patterning during embryogenesis differs significantly. For this reason, we have used the model gymnosperm Pinus pinaster to identify WOX genes and perform a thorough analysis of their gene expression patterns. Using transcriptomic data from a comprehensive range of tissues and stages of development we have shown three major outcomes: that the P. pinaster genome encodes at least fourteen members of the WOX family spanning all the major clades, that the genome of gymnosperms contains a WOX gene with no homologues in angiosperms representing a transitional stage between intermediate- and WUS-clade proteins, and that we can detect discrete WUS and WOX5 transcripts for the first time in a gymnosperm. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

  5. The Apollo peak-ring impact basin: Insights into the structure and evolution of the South Pole-Aitken basin

    Science.gov (United States)

    Potter, Ross W. K.; Head, James W.; Guo, Dijun; Liu, Jianzhong; Xiao, Long

    2018-05-01

    The 492 km-diameter Apollo impact basin post-dates, and is located at the inner edge of, the ∼2240 km-diameter South Pole-Aitken (SPA) basin, providing an opportunity to assess the SPA substructure and lateral heterogeneity. Gravity Recovery and Interior Laboratory gravity data suggest an average crustal thickness on the floor of SPA of ∼20 km and within the Apollo basin of ∼5 km, yet remote sensing data reveal no conclusive evidence for the presence of exposed mantle material. We use the iSALE shock physics code to model the formation of the Apollo basin and find that the observational data are best fit by the impact of a 40 km diameter body traveling at 15 km/s into 20-40 km thick crustal material. These results strongly suggest that the Apollo impact occurred on ejecta deposits and collapsed crustal material of the SPA basin and could help place constraints on the location, size and geometry of the SPA transient cavity. The peak ring in the interior of Apollo basin is plausibly interpreted to be composed of inwardly collapsed lower crustal material that experienced peak shock pressures in excess of 35 GPa, consistent with remote sensing observations that suggest shocked plagioclase. Proposed robotic and/or human missions to SPA and Apollo would present an excellent opportunity to test the predictions of this work and address many scientific questions about SPA basin evolution and structure.

  6. The evolution and ascent paths of mantle xenolith-bearing magma: Observations and insights from Cenozoic basalts in Southeast China

    Science.gov (United States)

    Sun, Pu; Niu, Yaoling; Guo, Pengyuan; Cui, Huixia; Ye, Lei; Liu, Jinju

    2018-06-01

    Studies have shown that mantle xenolith-bearing magmas must ascend rapidly to carry mantle xenoliths to the surface. It has thus been inferred inadvertently that such rapid ascending melt must have undergone little crystallization or evolution. However, this inference is apparently inconsistent with the widespread observation that xenolith-bearing alkali basalts are variably evolved with Mg# ≤72. In this paper, we discuss this important, yet overlooked, petrological problem and offer new perspectives with evidence. We analyzed the Cenozoic mantle xenolith-bearing alkali basalts from several locations in Southeast China that have experienced varying degrees of fractional crystallization (Mg# = 48-67). The variably evolved composition of host alkali basalts is not in contradiction with rapid ascent, but rather reflects inevitability of crystallization during ascent. Thermometry calculations for clinopyroxene (Cpx) megacrysts give equilibrium temperatures of 1238-1390 °C, which is consistent with the effect of conductive cooling and melt crystallization during ascent because TMelt > TLithosphere. The equilibrium pressure (18-27 kbar) of these Cpx megacrysts suggests that the crystallization takes place under lithospheric mantle conditions. The host melt must have experienced limited low-pressure residence in the shallower levels of lithospheric mantle and crust. This is in fact consistent with the rapid ascent of the host melt to bring mantle xenoliths to the surface.

  7. Insights into the development and evolution of exaggerated traits using de novo transcriptomes of two species of horned scarab beetles.

    Science.gov (United States)

    Warren, Ian A; Vera, J Cristobal; Johns, Annika; Zinna, Robert; Marden, James H; Emlen, Douglas J; Dworkin, Ian; Lavine, Laura C

    2014-01-01

    Scarab beetles exhibit an astonishing variety of rigid exo-skeletal outgrowths, known as "horns". These traits are often sexually dimorphic and vary dramatically across species in size, shape, location, and allometry with body size. In many species, the horn exhibits disproportionate growth resulting in an exaggerated allometric relationship with body size, as compared to other traits, such as wings, that grow proportionately with body size. Depending on the species, the smallest males either do not produce a horn at all, or they produce a disproportionately small horn for their body size. While the diversity of horn shapes and their behavioural ecology have been reasonably well studied, we know far less about the proximate mechanisms that regulate horn growth. Thus, using 454 pyrosequencing, we generated transcriptome profiles, during horn growth and development, in two different scarab beetle species: the Asian rhinoceros beetle, Trypoxylus dichotomus, and the dung beetle, Onthophagus nigriventris. We obtained over half a million reads for each species that were assembled into over 6,000 and 16,000 contigs respectively. We combined these data with previously published studies to look for signatures of molecular evolution. We found a small subset of genes with horn-biased expression showing evidence for recent positive selection, as is expected with sexual selection on horn size. We also found evidence of relaxed selection present in genes that demonstrated biased expression between horned and horn-less morphs, consistent with the theory of developmental decoupling of phenotypically plastic traits.

  8. Extended mitogenomic phylogenetic analyses yield new insight into crocodylian evolution and their survival of the Cretaceous-Tertiary boundary.

    Science.gov (United States)

    Roos, Jonas; Aggarwal, Ramesh K; Janke, Axel

    2007-11-01

    The mitochondrial genomes of the dwarf crocodile, Osteolaemus tetraspis, and two species of dwarf caimans, the smooth-fronted caiman, Paleosuchus trigonatus, and Cuvier's dwarf caiman, Paleosuchus palpebrosus, were sequenced and included in a mitogenomic phylogenetic study. The phylogenetic analyses, which included a total of ten crocodylian species, yielded strong support to a basal split between Crocodylidae and Alligatoridae. Osteolaemus fell within the Crocodylidae as the sister group to Crocodylus. Gavialis and Tomistoma, which joined on a common branch, constituted a sister group to Crocodylus/Osteolaemus. This suggests that extant crocodylians are organized in two families: Alligatoridae and Crocodylidae. Within the Alligatoridae there was a basal split between Alligator and a branch that contained Paleosuchus and Caiman. The analyses also provided molecular estimates of various divergences applying recently established crocodylian and outgroup fossil calibration points. Molecular estimates based on amino acid data placed the divergence between Crocodylidae and Alligatoridae at 97-103 million years ago and that between Alligator and Caiman/Paleosuchus at 65-72 million years ago. Other crocodilian divergences were placed after the Cretaceous-Tertiary boundary. Thus, according to the molecular estimates, three extant crocodylian lineages have their roots in the Cretaceous. Considering the crocodylian diversification in the Cretaceous the molecular datings suggest that the extinction of the dinosaurs was also to some extent paralleled in the crocodylian evolution. However, for whatever reason, some crocodylian lineages survived into the Tertiary.

  9. Molecular characterization of Babesia peircei and Babesia ugwidiensis provides insight into the evolution and host specificity of avian piroplasmids

    Directory of Open Access Journals (Sweden)

    Michael J. Yabsley

    2017-12-01

    Full Text Available There are 16 recognized species of avian-infecting Babesia spp. (Piroplasmida: Babesiidae. While the classification of piroplasmids has been historically based on morphological differences, geographic isolation and presumed host and/or vector specificities, recent studies employing gene sequence analysis have provided insight into their phylogenetic relationships and host distribution and specificity. In this study, we analyzed the sequences of the 18S rRNA gene and ITS-1 and ITS-2 regions of two Babesia species from South African seabirds: Babesia peircei from African penguins (Spheniscus demersus and Babesia ugwidiensis from Bank and Cape cormorants (Phalacrocorax neglectus and P. capensis, respectively. Our results show that avian Babesia spp. are not monophyletic, with at least three distinct phylogenetic groups. B. peircei and B. ugwidiensis are closely related, and fall within the same phylogenetic group as B. ardeae (from herons Ardea cinerea, B. poelea (from boobies Sula spp. and B. uriae (from murres Uria aalge. The validity of B. peircei and B. ugwidiensis as separate species is corroborated by both morphological and genetic evidence. On the other hand, our results indicate that B. poelea might be a synonym of B. peircei, which in turn would be a host generalist that infects seabirds from multiple orders. Further studies combining morphological and molecular methods are warranted to clarify the taxonomy, phylogeny and host distribution of avian piroplasmids. Keywords: Africa, Babesia, Piroplasmida, Phalacrocoracidae, Spheniscidae, Tick-borne pathogen

  10. Temporal evolution of brain reorganization under cross-modal training: insights into the functional architecture of encoding and retrieval networks

    Science.gov (United States)

    Likova, Lora T.

    2015-03-01

    specialization in terms of either encoding or retrieval as a function of the stage of learning. Moreover, several distinct patterns of learning-evolution within the patches as a function of their anatomical location, implying a complex reorganization of the object processing sub-networks through the learning period. These first findings of complex patterns of training-based encoding/retrieval reorganization thus have broad implications for a newly emerging view of the perception/memory interactions and their reorganization through the learning process. Note that the temporal evolution of these forms of extended functional reorganization could not be uncovered with conventional assessment paradigms used in the traditional approaches to functional mapping, which may therefore have to be revisited. Moreover, as the present results are obtained in learning under life-long blindness, they imply modality-independent operations, transcending the usual tight association with visual processing. The present approach of memory drawing training in blindness, has the dual-advantage of being both non-visual and causal intervention, which makes it a promising 'scalpel' to disentangle interactions among diverse cognitive functions.

  11. Strain rate effect on fault slip and rupture evolution: Insight from meter-scale rock friction experiments

    Science.gov (United States)

    Xu, Shiqing; Fukuyama, Eiichi; Yamashita, Futoshi; Mizoguchi, Kazuo; Takizawa, Shigeru; Kawakata, Hironori

    2018-05-01

    We conduct meter-scale rock friction experiments to study strain rate effect on fault slip and rupture evolution. Two rock samples made of Indian metagabbro, with a nominal contact dimension of 1.5 m long and 0.1 m wide, are juxtaposed and loaded in a direct shear configuration to simulate the fault motion. A series of experimental tests, under constant loading rates ranging from 0.01 mm/s to 1 mm/s and under a fixed normal stress of 6.7 MPa, are performed to simulate conditions with changing strain rates. Load cells and displacement transducers are utilized to examine the macroscopic fault behavior, while high-density arrays of strain gauges close to the fault are used to investigate the local fault behavior. The observations show that the macroscopic peak strength, strength drop, and the rate of strength drop can increase with increasing loading rate. At the local scale, the observations reveal that slow loading rates favor generation of characteristic ruptures that always nucleate in the form of slow slip at about the same location. In contrast, fast loading rates can promote very abrupt rupture nucleation and along-strike scatter of hypocenter locations. At a given propagation distance, rupture speed tends to increase with increasing loading rate. We propose that a strain-rate-dependent fault fragmentation process can enhance the efficiency of fault healing during the stick period, which together with healing time controls the recovery of fault strength. In addition, a strain-rate-dependent weakening mechanism can be activated during the slip period, which together with strain energy selects the modes of fault slip and rupture propagation. The results help to understand the spectrum of fault slip and rock deformation modes in nature, and emphasize the role of heterogeneity in tuning fault behavior under different strain rates.

  12. Insights into the evolution of a cryptic radiation of bats: dispersal and ecological radiation of Malagasy Miniopterus (Chiroptera: Miniopteridae).

    Science.gov (United States)

    Christidis, Les; Goodman, Steven M; Naughton, Kate; Appleton, Belinda

    2014-01-01

    The past decade has seen a proliferation of new species of Miniopterus bats (family Miniopteridae) recognized from Madagascar and the neighboring Comoros archipelago. The interspecific relationships of these taxa, their colonization history, and the evolution of this presumed adaptive radiation have not been sufficiently explored. Using the mitochondrial cytochrome-b gene, we present a phylogeny of the Malagasy members of this widespread Old World genus, based on 218 sequences, of which 82 are new and 136 derived from previous studies. Phylogenetic analyses recovered 18 clades, which divide into five primary lineages: (1) M. griveaudi; (2) M. mahafaliensis, M. sororculus and X3; (3) M. majori, M. gleni and M. griffithsi; (4) M. brachytragos; M. aelleniA, and M. aelleniB; and (5) M. manavi and M. petersoni recovered as sister species, which were in turn linked to a group comprising M. egeri and five genetically distinct populations referred to herein as P3, P4, P5, P6 and P7. Beast analysis indicated that the initial divergence within the Malagasy Miniopterus radiation took place 4.5 Myr; most species diverged between 4 and 2.5 Myr, and a secondary period was between 1.25 and 1 Myr. DNA K2P-distances between recognized taxa ranged from 12.9% to 2.5% and intraspecific variation was less than 1.8%. Of the 18 identified clades, Latin binomials are only associated with 11, which indicates much greater differentiation than currently recognized for Malagasy Miniopterus. These data are placed in a context of the dispersal history of this genus on the island and patterns of ecological diversity.

  13. La Galite Archipelago (Tunisia, North Africa): Stratigraphic and petrographic revision and insights for geodynamic evolution of the Maghrebian Chain

    Science.gov (United States)

    Belayouni, Habib; Brunelli, Daniele; Clocchiatti, Roberto; Di Staso, Angelida; El Hassani, Iz-Eddine El Amrani; Guerrera, Francesco; Kassaa, Samia; Ouazaa, Nejia Laridhi; Martín, Manuel Martín; Serrano, Francisco; Tramontana, Mario

    2010-01-01

    The location of the La Galite Archipelago on the Internal/External Zones of the Maghrebian Chain holds strong interest for the reconstruction of the geodynamic evolution of the Mesomediterranean Microplate-Africa Plate Boundary Zone. New stratigraphic and petrographic data on sedimentary successions intruded upon by plutonic rocks enabled a better definition of the palaeogeographic and palaeotectonic evolutionary model of the area during the early-middle Miocene. The lower Miocene sedimentary units ( La Galite Flysch and Numidian-like Flysch) belong to the Mauritanian (internal) and Massylian (external) sub-Domains of the Maghrebian Chain, respectively. These deposits are related to a typical syn-orogenic deposition in the Maghrebian Flysch Basin Domain, successively backthrusted above the internal units. The backthrusting age is post-Burdigalian (probably Langhian-Serravallian) and the compressional phase represents the last stage in the building of the accretionary wedge of the Maghrebian orogen. These flysch units may be co-relatable to the similar well-known formations along the Maghrebian and Betic Chains. The emplacement of potassic peraluminous magmatism, caused local metamorphism in the Late Serravallian-Early Tortonian (14-10 Ma), after the last compressional phase (backthrusting), during an extensional tectonic event. This extensional phase is probably due to the opening of a slab break-off in the deep subduction system. La Galite Archipelago represents a portion of the Maghrebian Flysch Basin tectonically emplaced above the southern margin of the "Mesomediterranean Microplate" which separated the Piemontese-Ligurian Ocean from a southern oceanic branch of the Tethys (i.e. the Maghrebian Flysch Basin). The possible presence of an imbricate thrust system between La Galite Archipelago and northern Tunisia may be useful to exclude the petroleum exploration from the deformed sectors of the offshore area considered.

  14. Germ warfare in a microbial mat community: CRISPRs provide insights into the co-evolution of host and viral genomes.

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    John F Heidelberg

    Full Text Available CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B' as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B' genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B', but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as "viritopes" to emphasize their critical role in viral immunity were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities.

  15. Sixteen kiwi (Apteryx spp) transcriptomes provide a wealth of genetic markers and insight into sex chromosome evolution in birds.

    Science.gov (United States)

    Ramstad, Kristina M; Miller, Hilary C; Kolle, Gabriel

    2016-05-26

    Kiwi represent the most basal extant avian lineage (paleognaths) and exhibit biological attributes that are unusual or extreme among living birds, such as large egg size, strong olfaction, nocturnality, flightlessness and long lifespan. Despite intense interest in their evolution and their threatened status, genomic resources for kiwi were virtually non-existent until the recent publication of a single genome. Here we present the most comprehensive kiwi transcriptomes to date, obtained via Illumina sequencing of whole blood and de novo assembly of mRNA sequences of eight individuals from each of the two rarest kiwi species, little spotted kiwi (LSK; Apteryx owenii) and rowi (A. rowi). Sequences obtained were orthologous with a wide diversity of functional genes despite the sequencing of a single tissue type. Individual and composite assemblies contain more than 7900 unique protein coding transcripts in each of LSK and rowi that show strong homology with chicken (Gallus gallus), including those associated with growth, development, disease resistance, reproduction and behavior. The assemblies also contain 66,909 SNPs that distinguish between LSK and rowi, 12,384 SNPs among LSK (associated with 3088 genes), and 29,313 SNPs among rowi (associated with 4953 genes). We found 3084 transcripts differentially expressed between LSK and rowi and 150 transcripts differentially expressed between the sexes. Of the latter, 83 could be mapped to chicken chromosomes with 95% syntenic with chromosome Z. Our study has simultaneously sequenced multiple species, sexes, and individual kiwi at thousands of genes, and thus represents a significant leap forward in genomic resources available for kiwi. The expression pattern we observed among chromosome Z related genes in kiwi is similar to that observed in ostriches and emu, suggesting a common and ancestral pattern of sex chromosome homomorphy, recombination, and gene dosage among living paleognaths. The transcriptome assemblies described

  16. Insights on the evolution of prolyl 3-hydroxylation sites from comparative analysis of chicken and Xenopus fibrillar collagens.

    Science.gov (United States)

    Hudson, David M; Weis, Maryann; Eyre, David R

    2011-05-03

    Recessive mutations that prevent 3-hydroxyproline formation in type I collagen have been shown to cause forms of osteogenesis imperfecta. In mammals, all A-clade collagen chains with a GPP sequence at the A1 site (P986), except α1(III), have 3Hyp at residue P986. Available avian, amphibian and reptilian type III collagen sequences from the genomic database (Ensembl) all differ in sequence motif from mammals at the A1 site. This suggests a potential evolutionary distinction in prolyl 3-hydroxylation between mammals and earlier vertebrates. Using peptide mass spectrometry, we confirmed that this 3Hyp site is fully occupied in α1(III) from an amphibian, Xenopus laevis, as it is in chicken. A thorough characterization of all predicted 3Hyp sites in collagen types I, II, III and V from chicken and xenopus revealed further differences in the pattern of occupancy of the A3 site (P707). In mammals only α2(I) and α2(V) chains had any 3Hyp at the A3 site, whereas in chicken all α-chains except α1(III) had A3 at least partially 3-hydroxylated. The A3 site was also partially 3-hydroxylated in xenopus α1(I). Minor differences in covalent cross-linking between chicken, xenopus and mammal type I and III collagens were also found as a potential index of evolving functional differences. The function of 3Hyp is still unknown but observed differences in site occupancy during vertebrate evolution are likely to give important clues.

  17. Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera.

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    Hélène Badouin

    Full Text Available BACKGROUND: Despite the recent sequencing of seven ant genomes, no genomic data are available for the genus Formica, an important group for the study of eusocial traits. We sequenced the transcriptome of the ant Formica exsecta with the 454 FLX Titanium technology from a pooled sample of workers from 70 Finnish colonies. RESULTS: About 1,000,000 reads were obtained from a normalised cDNA library. We compared the assemblers MIRA3.0 and Newbler2.6 and showed that the latter performed better on this dataset due to a new option which is dedicated to improve contig formation in low depth portions of the assemblies. The 29,579 contigs represent 27 Mb. 50% showed similarity with known proteins and 25% could be assigned a category of gene ontology. We found more than 13,000 high-quality single nucleotide polymorphisms. The Δ9 desaturase gene family is an important multigene family involved in chemical communication in insects. We found six Δ9 desaturases in this Formica exsecta transcriptome dataset that were used to reconstruct a maximum-likelihood phylogeny of insect desaturases and to test for signatures of positive selection in this multigene family in ant lineages. We found differences with previous phylogenies of this gene family in ants, and found two clades potentially under positive selection. CONCLUSION: This first transcriptome reference sequence of Formica exsecta provided sequence and polymorphism data that will allow researchers working on Formica ants to develop studies to tackle the genetic basis of eusocial phenotypes. In addition, this study provided some general guidelines for de novo transcriptome assembly that should be useful for future transcriptome sequencing projects. Finally, we found potential signatures of positive selection in some clades of the Δ9 desaturase gene family in ants, which suggest the potential role of sequence divergence and adaptive evolution in shaping the large diversity of chemical cues in social insects.

  18. Freshwater Biogeography and Limnological Evolution of the Tibetan Plateau - Insights from a Plateau-Wide Distributed Gastropod Taxon (Radix spp.)

    Science.gov (United States)

    von Oheimb, Parm Viktor; Albrecht, Christian; Riedel, Frank; Du, Lina; Yang, Junxing; Aldridge, David C.; Bößneck, Ulrich; Zhang, Hucai; Wilke, Thomas

    2011-01-01

    Background The Tibetan Plateau is not only the highest and largest plateau on earth; it is also home to numerous freshwater lakes potentially harbouring endemic faunal elements. As it remains largely unknown whether these lakes have continuously existed during the Last Glacial Maximum (LGM), questions arise as to whether taxa have been able to exist on the plateau since before the latest Pleistocene, from where and how often the plateau was colonized, and by which mechanisms organisms conquered remote high altitude lentic freshwater systems. In this study, species of the plateau-wide distributed freshwater gastropod genus Radix are used to answer these biogeographical questions. Methodology/Principal Findings Based on a broad spatial sampling of Radix spp. on the Tibetan Plateau, and phylogenetic analyses of mtDNA sequence data, three probably endemic and one widespread major Radix clade could be identified on the plateau. Two of the endemic clades show a remarkably high genetic diversity, indicating a relatively great phylogenetic age. Phylogeographical analyses of individuals belonging to the most widely distributed clade indicate that intra-plateau distribution cannot be explained by drainage-related dispersal alone. Conclusions/Significance Our study reveals that Radix spp. persisted throughout the LGM on the Tibetan Plateau. Therefore, we assume the continuous existence of suitable water bodies during that time. The extant Radix diversity on the plateau might have been caused by multiple colonization events combined with a relatively long intra-plateau evolution. At least one colonization event has a Palaearctic origin. In contrast to freshwater fishes, passive dispersal, probably by water birds, might be an important mechanism for conquering remote areas on the plateau. Patterns found in Radix spp. are shared with some terrestrial plateau taxa, indicating that Radix may be a suitable model taxon for inferring general patterns of biotic origin, dispersal and

  19. Structure, Function and Evolution of Clostridium botulinum C2 and C3 Toxins: Insight to Poultry and Veterinary Vaccines.

    Science.gov (United States)

    Chellapandi, Paulchamy; Prisilla, Arokiyasamy

    2017-01-01

    Clostridium botulinum group III strains are able to produce cytotoxins, C2 toxin and C3 exotoxin, along with botulinum neurotoxin types C and D. C2 toxin and C3 exotoxin produced by this organism are the most important members of bacterial ADP-ribosyltransferase superfamily. Both toxins have distinct pathophysiological functions in the avian and mammalian hosts. The members of this superfamily transfer an ADP-ribose moiety of NAD+ to specific eukaryotic target proteins. The present review describes the structure, function and evolution aspects of these toxins with a special emphasis to the development of veterinary vaccines. C2 toxin is a binary toxin that consists of a catalytic subunit (C2I) and a translocation subunit (C2II). C2I component is structurally and functionally similar to the VIP2 and iota A toxin whereas C2II component shows a significant homology with the protective antigen from anthrax toxin and iota B. Unlike C2 toxin, C3 toxin is devoid of translocation/binding subunit. Extensive studies on their sequence-structure-function link spawn additional efforts to understand the catalytic mechanisms and target recognition. Structural and functional relationships with them are often determined by using evolutionary constraints as valuable biological measures. Enzyme-deficient mutants derived from these toxins have been used as drug/protein delivery systems in eukaryotic cells. Thus, current knowledge on their molecular diversity is a well-known perspective to design immunotoxin or subunit vaccine for C. botulinum infection. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  20. Insights on the evolution of prolyl 3-hydroxylation sites from comparative analysis of chicken and Xenopus fibrillar collagens.

    Directory of Open Access Journals (Sweden)

    David M Hudson

    2011-05-01

    Full Text Available Recessive mutations that prevent 3-hydroxyproline formation in type I collagen have been shown to cause forms of osteogenesis imperfecta. In mammals, all A-clade collagen chains with a GPP sequence at the A1 site (P986, except α1(III, have 3Hyp at residue P986. Available avian, amphibian and reptilian type III collagen sequences from the genomic database (Ensembl all differ in sequence motif from mammals at the A1 site. This suggests a potential evolutionary distinction in prolyl 3-hydroxylation between mammals and earlier vertebrates. Using peptide mass spectrometry, we confirmed that this 3Hyp site is fully occupied in α1(III from an amphibian, Xenopus laevis, as it is in chicken. A thorough characterization of all predicted 3Hyp sites in collagen types I, II, III and V from chicken and xenopus revealed further differences in the pattern of occupancy of the A3 site (P707. In mammals only α2(I and α2(V chains had any 3Hyp at the A3 site, whereas in chicken all α-chains except α1(III had A3 at least partially 3-hydroxylated. The A3 site was also partially 3-hydroxylated in xenopus α1(I. Minor differences in covalent cross-linking between chicken, xenopus and mammal type I and III collagens were also found as a potential index of evolving functional differences. The function of 3Hyp is still unknown but observed differences in site occupancy during vertebrate evolution are likely to give important clues.

  1. Does the oxytocin receptor polymorphism (rs2254298 confer 'vulnerability' for psychopathology or 'differential susceptibility'? insights from evolution

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    Brüne Martin

    2012-04-01

    Full Text Available Abstract The diathesis-stress model of psychiatric conditions has recently been challenged by the view that it might be more accurate to speak of 'differential susceptibility' or 'plasticity' genes, rather than one-sidedly focusing on individual vulnerability. That is, the same allelic variation that predisposes to a psychiatric disorder if associated with (developmentally early environmental adversity may lead to a better-than-average functional outcome in the same domain under thriving (or favourable environmental conditions. Studies of polymorphic variations of the serotonin transporter gene, the monoamino-oxidase-inhibitor A coding gene or the dopamine D4 receptor gene indicate that the early environment plays a crucial role in the development of favourable versus unfavourable outcomes. Current evidence is limited, however, to establishing a link between genetic variation and behavioural phenotypes. In contrast, little is known about how plasticity may be expressed at the neuroanatomical level as a 'hard-wired' correlate of observable behaviour. The present review article seeks to further strengthen the argument in favour of the differential susceptibility theory by incorporating findings from behavioural and neuroanatomical studies in relation to genetic variation of the oxytocin receptor gene. It is suggested that polymorphic variation at the oxytocin receptor gene (rs2254298 is associated with sociability, amygdala volume and differential risk for psychiatric conditions including autism, depression and anxiety disorder, depending on the quality of early environmental experiences. Seeing genetic variation at the core of developmental plasticity can explain, in contrast to the diathesis-stress perspective, why evolution by natural selection has maintained such 'risk' alleles in the gene pool of a population. Please see related manuscript: http://www.biomedcentral.com/1741-7015/10/37

  2. Mosasauroid phylogeny under multiple phylogenetic methods provides new insights on the evolution of aquatic adaptations in the group.

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    Tiago R Simões

    Full Text Available Mosasauroids were a successful lineage of squamate reptiles (lizards and snakes that radiated during the Late Cretaceous (95-66 million years ago. They can be considered one of the few lineages in the evolutionary history of tetrapods to have acquired a fully aquatic lifestyle, similarly to whales, ichthyosaurs and plesiosaurs. Despite a long history of research on this group, their phylogenetic relationships have only been tested so far using traditional (unweighted maximum parsimony. However, hypotheses of mosasauroid relationships and the recently proposed multiple origins of aquatically adapted pelvic and pedal features in this group can be more thoroughly tested by methods that take into account variation in branch lengths and evolutionary rates. In this study, we present the first mosasauroid phylogenetic analysis performed under different analytical methods, including maximum likelihood, Bayesian inference, and implied weighting maximum parsimony. The results indicate a lack of congruence in the topological position of halisaurines and Dallasaurus. Additionally, the genus Prognathodon is paraphyletic under all hypotheses. Interestingly, a number of traditional mosasauroid clades become weakly supported, or unresolved, under Bayesian analyses. The reduced resolutions in some consensus trees create ambiguities concerning the evolution of fully aquatic pelvic/pedal conditions under many analyses. However, when enough resolution was obtained, reversals of the pelvic/pedal conditions were favoured by parsimony and likelihood ancestral state reconstructions instead of independent origins of aquatic features in mosasauroids. It is concluded that most of the observed discrepancies among the results can be associated with different analytical procedures, but also due to limited postcranial data on halisaurines, yaguarasaurines and Dallasaurus.

  3. Mechanical evolution of transpression zones affected by fault interactions: Insights from 3D elasto-plastic finite element models

    Science.gov (United States)

    Nabavi, Seyed Tohid; Alavi, Seyed Ahmad; Mohammadi, Soheil; Ghassemi, Mohammad Reza

    2018-01-01

    The mechanical evolution of transpression zones affected by fault interactions is investigated by a 3D elasto-plastic mechanical model solved with the finite-element method. Ductile transpression between non-rigid walls implies an upward and lateral extrusion. The model results demonstrate that a, transpression zone evolves in a 3D strain field along non-coaxial strain paths. Distributed plastic strain, slip transfer, and maximum plastic strain occur within the transpression zone. Outside the transpression zone, fault slip is reduced because deformation is accommodated by distributed plastic shear. With progressive deformation, the σ3 axis (the minimum compressive stress) rotates within the transpression zone to form an oblique angle to the regional transport direction (∼9°-10°). The magnitude of displacement increases faster within the transpression zone than outside it. Rotation of the displacement vectors of oblique convergence with time suggests that transpression zone evolves toward an overall non-plane strain deformation. The slip decreases along fault segments and with increasing depth. This can be attributed to the accommodation of bulk shortening over adjacent fault segments. The model result shows an almost symmetrical domal uplift due to off-fault deformation, generating a doubly plunging fold and a 'positive flower' structure. Outside the overlap zone, expanding asymmetric basins subside to 'negative flower' structures on both sides of the transpression zone and are called 'transpressional basins'. Deflection at fault segments causes the fault dip fall to less than 90° (∼86-89°) near the surface (∼1.5 km). This results in a pure-shear-dominated, triclinic, and discontinuous heterogeneous flow of the transpression zone.

  4. New insights into the evolution of Wolbachia infections in filarial nematodes inferred from a large range of screened species.

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    Emanuele Ferri

    Full Text Available Wolbachia are intriguing symbiotic endobacteria with a peculiar host range that includes arthropods and a single nematode family, the Onchocercidae encompassing agents of filariases. This raises the question of the origin of infection in filariae. Wolbachia infect the female germline and the hypodermis. Some evidences lead to the theory that Wolbachia act as mutualist and coevolved with filariae from one infection event: their removal sterilizes female filariae; all the specimens of a positive species are infected; Wolbachia are vertically inherited; a few species lost the symbiont. However, most data on Wolbachia and filaria relationships derive from studies on few species of Onchocercinae and Dirofilariinae, from mammals.We investigated the Wolbachia distribution testing 35 filarial species, including 28 species and 7 genera and/or subgenera newly screened, using PCR, immunohistochemical staining, whole mount fluorescent analysis, and cocladogenesis analysis. (i Among the newly screened Onchocercinae from mammals eight species harbour Wolbachia but for some of them, bacteria are absent in the hypodermis, or in variable density. (ii Wolbachia are not detected in the pathological model Monanema martini and in 8, upon 9, species of Cercopithifilaria. (iii Supergroup F Wolbachia is identified in two newly screened Mansonella species and in Cercopithifilaria japonica. (iv Type F Wolbachia infect the intestinal cells and somatic female genital tract. (v Among Oswaldofilariinae, Waltonellinae and Splendidofilariinae, from saurian, anuran and bird respectively, Wolbachia are not detected.The absence of Wolbachia in 63% of onchocercids, notably in the ancestral Oswaldofilariinae estimated 140 mya old, the diverse tissues or specimens distribution, and a recent lateral transfer in supergroup F Wolbachia, modify the current view on the role and evolution of the endosymbiont and their hosts. Further genomic analyses on some of the newly sampled species

  5. Insights on the evolution of metabolic networks of unicellular translationally biased organisms from transcriptomic data and sequence analysis.

    Science.gov (United States)

    Carbone, Alessandra; Madden, Richard

    2005-10-01

    Codon bias is related to metabolic functions in translationally biased organisms, and two facts are argued about. First, genes with high codon bias describe in meaningful ways the metabolic characteristics of the organism; important metabolic pathways corresponding to crucial characteristics of the lifestyle of an organism, such as photosynthesis, nitrification, anaerobic versus aerobic respiration, sulfate reduction, methanogenesis, and others, happen to involve especially biased genes. Second, gene transcriptional levels of sets of experiments representing a significant variation of biological conditions strikingly confirm, in the case of Saccharomyces cerevisiae, that metabolic preferences are detectable by purely statistical analysis: the high metabolic activity of yeast during fermentation is encoded in the high bias of enzymes involved in the associated pathways, suggesting that this genome was affected by a strong evolutionary pressure that favored a predominantly fermentative metabolism of yeast in the wild. The ensemble of metabolic pathways involving enzymes with high codon bias is rather well defined and remains consistent across many species, even those that have not been considered as translationally biased, such as Helicobacter pylori, for instance, reveal some weak form of translational bias for this genome. We provide numerical evidence, supported by experimental data, of these facts and conclude that the metabolic networks of translationally biased genomes, observable today as projections of eons of evolutionary pressure, can be analyzed numerically and predictions of the role of specific pathways during evolution can be derived. The new concepts of Comparative Pathway Index, used to compare organisms with respect to their metabolic networks, and Evolutionary Pathway Index, used to detect evolutionarily meaningful bias in the genetic code from transcriptional data, are introduced.

  6. Mosasauroid phylogeny under multiple phylogenetic methods provides new insights on the evolution of aquatic adaptations in the group

    Science.gov (United States)

    Vernygora, Oksana; Paparella, Ilaria; Jimenez-Huidobro, Paulina; Caldwell, Michael W.

    2017-01-01

    Mosasauroids were a successful lineage of squamate reptiles (lizards and snakes) that radiated during the Late Cretaceous (95–66 million years ago). They can be considered one of the few lineages in the evolutionary history of tetrapods to have acquired a fully aquatic lifestyle, similarly to whales, ichthyosaurs and plesiosaurs. Despite a long history of research on this group, their phylogenetic relationships have only been tested so far using traditional (unweighted) maximum parsimony. However, hypotheses of mosasauroid relationships and the recently proposed multiple origins of aquatically adapted pelvic and pedal features in this group can be more thoroughly tested by methods that take into account variation in branch lengths and evolutionary rates. In this study, we present the first mosasauroid phylogenetic analysis performed under different analytical methods, including maximum likelihood, Bayesian inference, and implied weighting maximum parsimony. The results indicate a lack of congruence in the topological position of halisaurines and Dallasaurus. Additionally, the genus Prognathodon is paraphyletic under all hypotheses. Interestingly, a number of traditional mosasauroid clades become weakly supported, or unresolved, under Bayesian analyses. The reduced resolutions in some consensus trees create ambiguities concerning the evolution of fully aquatic pelvic/pedal conditions under many analyses. However, when enough resolution was obtained, reversals of the pelvic/pedal conditions were favoured by parsimony and likelihood ancestral state reconstructions instead of independent origins of aquatic features in mosasauroids. It is concluded that most of the observed discrepancies among the results can be associated with different analytical procedures, but also due to limited postcranial data on halisaurines, yaguarasaurines and Dallasaurus. PMID:28467456

  7. The genome of Aeromonas salmonicida subsp. salmonicida A449: insights into the evolution of a fish pathogen

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    Murphy Colleen

    2008-09-01

    Aeromonas species. Conclusion Relative to the A. hydrophila ATCC 7966T genome, the A. salmonicida subsp. salmonicida genome has acquired multiple mobile genetic elements, undergone substantial rearrangement and developed a significant number of pseudogenes. These changes appear to be a consequence of adaptation to a specific host, salmonid fish, and provide insights into the mechanisms used by the bacterium for infection and avoidance of host defence systems.

  8. Integrated gene mapping and synteny studies give insights into the evolution of a sex proto-chromosome in Solea senegalensis.

    Science.gov (United States)

    Portela-Bens, Silvia; Merlo, Manuel Alejandro; Rodríguez, María Esther; Cross, Ismael; Manchado, Manuel; Kosyakova, Nadezda; Liehr, Thomas; Rebordinos, Laureana

    2017-03-01

    The evolution of genes related to sex and reproduction in fish shows high plasticity and, to date, the sex determination system has only been identified in a few species. Solea senegalensis has 42 chromosomes and an XX/XY chromosome system for sex determination, while related species show the ZZ/ZW system. Next-generation sequencing (NGS), multi-color fluorescence in situ hybridization (mFISH) techniques, and bioinformatics analysis have been carried out, with the objective of revealing new information about sex determination and reproduction in S. senegalensis. To that end, several bacterial artificial chromosome (BAC) clones that contain candidate genes involved in such processes (dmrt1, dmrt2, dmrt3, dmrt4, sox3, sox6, sox8, sox9, lh, cyp19a1a, amh, vasa, aqp3, and nanos3) were analyzed and compared with the same region in other related species. Synteny studies showed that the co-localization of dmrt1-dmrt2-drmt3 in the largest metacentric chromosome of S. senegalensis is coincident with that found in the Z chromosome of Cynoglossus semilaevis, which would potentially make this a sex proto-chromosome. Phylogenetic studies show the close proximity of S. senegalensis to Oryzias latipes, a species with an XX/XY system and a sex master gene. Comparative mapping provides evidence of the preferential association of these candidate genes in particular chromosome pairs. By using the NGS and mFISH techniques, it has been possible to obtain an integrated genetic map, which shows that 15 out of 21 chromosome pairs of S. senegalensis have at least one BAC clone. This result is important for distinguishing those chromosome pairs of S. senegalensis that are similar in shape and size. The mFISH analysis shows the following co-localizations in the same chromosomes: dmrt1-dmrt2-dmrt3, dmrt4-sox9-thrb, aqp3-sox8, cyp19a1a-fshb, igsf9b-sox3, and lysg-sox6.

  9. The evolution of the magmatic arc of Southern Peru (200-60 Ma), Arequipa area: insight from geochemical modeling

    Science.gov (United States)

    Demouy, S.; Benoit, M.; De Saint Blanquat, M.; Brunet, P.

    2012-12-01

    Cordilleran-type batholiths are built by prolonged arc activity along continental margins and may provide detailed magmatic records of the subduction system evolution. The magmas produced in subduction context involve both mantellic and crustal end members and are subject to various petrological processes. The MASH zones (Hildreth and Moorbath, 1988), at the basis of the continental crust, are the best places for the genesis of such hybrid magmas. The various geochemical signatures observed in the plutonic rocks, may also be attributed to source heterogeneities or generated by subsequent petrological processes. This study has focused in the Arequipa section of the Coastal Batholith of Southern Peru (200-60 Ma), in an area extending over 80x40 km. Major and trace elements as well as Sr and Nd isotopic analyses were performed in a set of 100 samples ranging from gabbro to granite. The obtained data highlight the wide heterogeneity of the geochemical signatures that is not related to the classification of the rocks. In first step, Rb/Sr systematic was used to isolate a set of samples plotting along a Paleocene isochron and defining a cogenetic suite. This suite appears to have evolved by simple fractional crystallization. By using reverse modeling, the parameters controlling the fractional crystallization process were defined, as partition coefficients, initial concentrations and amount of fractional crystallization. The other magmatic suites display a wide range of isotopic and geochemical signatures. To explain this heterogeneity, a model involving competition between fractional crystallization and magma mixing into MASH zones was proposed. A large range of hybrid magma types is potentially generated during the maturation of the system, but this range tends to disappear as fractionation and mixing occurs. Finally the model predicts the genesis of a homogeneous reservoir created at depth, from which magmas may evolve only by fractional crystallization. Therefore

  10. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

    Science.gov (United States)

    Battistuzzi, Fabia U.; Feijao, Andreia; Hedges, S. Blair

    2004-01-01

    BACKGROUND: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. RESULTS: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5-3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1-4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8-4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8-3.1 Ga, and an origin of aerobic methanotrophy 2.5-2.8 Ga. CONCLUSIONS: Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8-2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by

  11. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

    Directory of Open Access Journals (Sweden)

    Hedges S Blair

    2004-11-01

    Full Text Available Abstract Background The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (~7600 amino acids common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. Results Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5–3.2 billion years ago (Ga while those for archaebacteria are mostly between 3.1–4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga, an early origin of methanogenesis (3.8–4.1 Ga, an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8–3.1 Ga, and an origin of aerobic methanotrophy 2.5–2.8 Ga. Conclusions Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8–2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically

  12. Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments

    Directory of Open Access Journals (Sweden)

    Wuxia Guo

    2017-05-01

    Full Text Available Mangroves are woody plants that grow at the interface between land and sea in tropical and subtropical latitudes, where they exist in conditions of high salinity, extreme tides, strong winds, high temperatures, and muddy, anaerobic soils. Rhizophoraceae is a key mangrove family, with highly developed morphological and physiological adaptations to extreme conditions. It is an ideal system for the study of the origin and adaptive evolution of mangrove plants. In this study, we characterized and comprehensively compared the transcriptomes of four mangrove species, from all four mangrove genera, as well as their closest terrestrial relative in Rhizophoraceae, using RNA-Seq. We obtained 41,936–48,845 unigenes with N50 values of 982–1,185 bp and 61.42–69.48% annotated for the five species in Rhizophoraceae. Orthology annotations of Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and Clusters of Orthologous Groups revealed overall similarities in the transcriptome profiles among the five species, whereas enrichment analysis identified remarkable genomic characteristics that are conserved across the four mangrove species but differ from their terrestrial relative. Based on 1,816 identified orthologs, phylogeny analysis and divergence time estimation revealed a single origin for mangrove species in Rhizophoraceae, which diverged from the terrestrial lineage ~56.4 million years ago (Mya, suggesting that the transgression during the Paleocene–Eocene Thermal Maximum may have been responsible for the entry of the mangrove lineage of Rhizophoraceae into intertidal environments. Evidence showed that the ancestor of Rhizophoraceae may have experienced a whole genome duplication event ~74.6 Mya, which may have increased the adaptability and survival chances of Rhizophoraceae during and following the Cretaceous–Tertiary extinction. The analysis of positive selection identified 10 positively selected genes from the ancestor branch of

  13. Insights into characteristics, sources, and evolution of submicron aerosols during harvest seasons in the Yangtze River delta region, China

    Science.gov (United States)

    Zhang, Y. J.; Tang, L. L.; Wang, Z.; Yu, H. X.; Sun, Y. L.; Liu, D.; Qin, W.; Canonaco, F.; Prévôt, A. S. H.; Zhang, H. L.; Zhou, H. C.

    2015-02-01

    Atmospheric submicron particulate matter (PM1) is one of the most significant pollution components in China. Despite its current popularity in the studies of aerosol chemistry, the characteristics, sources and evolution of atmospheric PM1 species are still poorly understood in China, particularly for the two harvest seasons, namely, the summer wheat harvest and autumn rice harvest. An Aerodyne Aerosol Chemical Speciation Monitor (ACSM) was deployed for online monitoring of PM1 components during summer and autumn harvest seasons in urban Nanjing, in the Yangtze River delta (YRD) region of China. PM1 components were shown to be dominated by organic aerosol (OA, 39 and 41%) and nitrate (23 and 20%) during the harvest seasons (the summer and autumn harvest). Positive matrix factorization (PMF) analysis of the ACSM OA mass spectra resolved four OA factors: hydrocarbon-like mixed with cooking-related OA (HOA + COA), fresh biomass-burning OA (BBOA), oxidized biomass-burning-influenced OA (OOA-BB), and highly oxidized OA (OOA); in particular the oxidized BBOA contributes ~80% of the total BBOA loadings. Both fresh and oxidized BBOA exhibited apparent diurnal cycles with peak concentration at night, when the high ambient relative humidity and low temperature facilitated the partitioning of semi-volatile organic species into the particle phase. The fresh BBOA concentrations for the harvests are estimated as BBOA = 15.1 × (m/z 60-0.26% × OA), where m/z (mass-to-charge ratio) 60 is a marker for levoglucosan-like species. The (BBOA + OOA-BB)/ΔCO, (ΔCO is the CO minus background CO), decreases as a function of f44 (fraction of m/z 44 in OA signal), which might indicate that BBOA was oxidized to less volatile OOA, e.g., more aged and low volatility OOA (LV-OOA) during the aging process. Analysis of air mass back trajectories indicates that the high BB pollutant concentrations are linked to the air masses from the western (summer harvest) and southern (autumn harvest) areas.

  14. Structural, metamorphic and geochronological insights on the Variscan evolution of the Alpine basement in the Belledonne Massif (France)

    Science.gov (United States)

    Fréville, Kévin; Trap, Pierre; Faure, Michel; Melleton, Jérémie; Li, Xian-Hua; Lin, Wei; Blein, Olivier; Bruguier, Olivier; Poujol, Marc

    2018-02-01

    A structural and petrochronological study was carried out in the southern part of the Belledonne crystalline massif. A first tectonometamorphic event, Dx, corresponds to the eastward thrusting of the Chamrousse ophiolitic complex characterized by a low-temperature-moderate-pressure metamorphism reaching 0.535 ± 0.045 GPa and 427.5 ± 17.5 °C. A subsequent D1 deformation is defined by a penetrative S1 foliation that mostly dips toward the west and displays an E-W- to NE-SW-trending mineral and stretching lineation L1. D1 is associated with a top-to-the east shearing and is responsible for the crustal thickening accommodated by the eastward nappe stacking and the emplacement of the Chamrousse ophiolitic complex upon the Rioupéroux-Livet unit. This event is characterized by an amphibolite facies metamorphism (0.58 GPa ± 0.06; 608 ± 14 °C) that attains partial melting at the base of the nappe pile (0.78 ± 0.07 GPa; 680.5 ± 11.5 °C). LA-ICP-MS U-Pb dating of monazite grains from the mica schists of the Rioupéroux-Livet unit constrain the age of D1 to 337 ± 7 Ma. The D2 tectono-metamorphic event is characterized by NE-SW trending, upright to NE-verging synfolial folding. Folding associated with D2 is pervasively developed in all lithotectonic units with the development of a steeply-dipping S2 foliation. In particular, D2 involves the uppermost weakly metamorphosed Taillefer unit. LA-ICP-MS U-Pb dating performed on detrital zircon grains shows that the Taillefer conglomerates was deposited during the Visean. A zircon SIMS U-Pb age of 352 ± 1 Ma from a plagioglase-rich leucocratic sill of the Rioupéroux-Livet unit is interpreted as the age of magmatic emplacement. Our results suggest that the D2 event took place between 330 Ma and 310 Ma. We propose a new interpretation of the tectonometamorphic evolution of the southern part of the Belledonne massif, focusing on the Middle Carboniferous stages of the Variscan orogeny.

  15. The mating type locus (MAT and sexual reproduction of Cryptococcus heveanensis: insights into the evolution of sex and sex-determining chromosomal regions in fungi.

    Directory of Open Access Journals (Sweden)

    Banu Metin

    2010-05-01

    transitions in sexuality concomitant with emergence of a pathogenic clade. These studies provide insight into convergent processes that independently punctuated evolution of sex-determining loci and sex chromosomes in fungi, plants, and animals.

  16. Transition in organ function during the evolution of air-breathing; insights from Arapaima gigas, an obligate air-breathing teleost from the Amazon.

    Science.gov (United States)

    Brauner, C J; Matey, V; Wilson, J M; Bernier, N J; Val, A L

    2004-04-01

    The transition from aquatic to aerial respiration is associated with dramatic physiological changes in relation to gas exchange, ion regulation, acid-base balance and nitrogenous waste excretion. Arapaima gigas is one of the most obligate extant air-breathing fishes, representing a remarkable model system to investigate (1) how the transition from aquatic to aerial respiration affects gill design and (2) the relocation of physiological processes from the gills to the kidney during the evolution of air-breathing. Arapaima gigas undergoes a transition from water- to air-breathing during development, resulting in striking changes in gill morphology. In small fish (10 g), the gills are qualitatively similar in appearance to another closely related water-breathing fish (Osteoglossum bicirrhosum); however, as fish grow (100-1000 g), the inter-lamellar spaces become filled with cells, including mitochondria-rich (MR) cells, leaving only column-shaped filaments. At this stage, there is a high density of MR cells and strong immunolocalization of Na(+)/K(+)-ATPase along the outer cell layer of the gill filament. Despite the greatly reduced overall gill surface area, which is typical of obligate air-breathing fish, the gills may remain an important site for ionoregulation and acid-base regulation. The kidney is greatly enlarged in A. gigas relative to that in O. bicirrhosum and may comprise a significant pathway for nitrogenous waste excretion. Quantification of the physiological role of the gill and the kidney in A. gigas during development and in adults will yield important insights into developmental physiology and the evolution of air-breathing.

  17. Insights into highly improved solar-driven photocatalytic oxygen evolution over integrated Ag3PO4/MoS2 heterostructures

    Science.gov (United States)

    Cui, Xingkai; Yang, Xiaofei; Xian, Xiaozhai; Tian, Lin; Tang, Hua; Liu, Qinqin

    2018-04-01

    Oxygen evolution has been considered as the rate-determining step in photocatalytic water splitting due to its sluggish four-electron half-reaction rate, the development of oxygen-evolving photocatalysts with well-defined morphologies and superior interfacial contact is highly important for achieving high-performance solar water splitting. Herein, we report the fabrication of Ag3PO4/MoS2 nanocomposites and, for the first time, their use in photocatalytic water splitting into oxygen under LED light illumination. Ag3PO4 nanoparticles were found to be anchored evenly on the surface of MoS2 nanosheets, confirming an efficient hybridization of two semiconductor materials. A maximum oxygen-generating rate of 201.6 mol L-1 g-1 h-1 was determined when 200 mg MoS2 nanosheets were incorporated into Ag3PO4 nanoparticles, which is around 5 times higher than that of bulk Ag3PO4. Obvious enhancements in light-harvesting property, as well as electron-hole separation and charge transportation are revealed by the combination of different characterizations. ESR analysis verified that more active oxygen-containing radicals generate over illuminated Ag3PO4/MoS2 composite photocatalysts rather than irradiated Ag3PO4. The improvement in oxygen evolution performance of Ag3PO4/MoS2 composite photocatalysts is ascribed to wide spectra response in the visible-light region, more efficient charge separation and enhanced oxidation capacity in the valence band (VB). This study provides new insights into the design and development of novel composite photocatalytic materials for solar-to-fuel conversion.

  18. Patterning of the dorsal-ventral axis in echinoderms: insights into the evolution of the BMP-chordin signaling network.

    Directory of Open Access Journals (Sweden)

    François Lapraz

    2009-11-01

    , we show that Chordin may not be required for long-range diffusion of BMP2/4, describe a striking dorsal-ventral asymmetry in the expression of Glypican 5, a heparin sulphated proteoglycan that regulates BMP mobility, and show that this asymmetry depends on BMP2/4 signaling. Our study provides new insights into the mechanisms by which positional information is established along the dorsal-ventral axis of the sea urchin embryo, and more generally on how a BMP morphogen gradient is established in a multicellular embryo. From an evolutionary point of view, it highlights that although the genes used for dorsal-ventral patterning are highly conserved in bilateria, there are considerable variations, even among deuterostomes, in the manner these genes are used to shape a BMP morphogen gradient.

  19. Thinking social sciences from Latin America at the epochal change

    Directory of Open Access Journals (Sweden)

    Jaime Antonio Preciado Coronado

    2016-07-01

    Full Text Available From the legacy of an original disciplinary approach, as the Dependence theory and its Marxian critics, or the neo-structural economic theory founded by The Economic Commission for Latin America (ECLA, the Latin-American social sciences deny the Anglo-European centered approaches, in the way of reaffirming its own critical thinking, including the neo-colonial practices. The challenge for this critical thinking is to be, simultaneously, cosmopolitan and Latin American’s one. In this process, the Latin-American social thinking is regaining its own originality and its vigorous proposals, thanks to a rich south-south dialogue, that implies a global character of its reflections and the questioning of its universal references. Although neither classical nor western Marxism are hegemonic within critical theory, the (neo Marxism enriched with criticism of the coloniality of power, the theory of World-System, critical geopolitics and political ecology recover the field of critical theory in key founder of an epochal thinking time. Epistemological debates with post-structuralism and postmodern approaches configure various recent developments in critical theory

  20. The “Anthropocene” epoch: Scientific decision or political statement?

    Science.gov (United States)

    Finney, Stanley C.; Edwards, Lucy E.

    2016-01-01

    The proposal for the “Anthropocene” epoch as a formal unit of the geologic time scale has received extensive attention in scientific and public media. However, most articles on the Anthropocene misrepresent the nature of the units of the International Chronostratigraphic Chart, which is produced by the International Commission on Stratigraphy (ICS) and serves as the basis for the geologic time scale. The stratigraphic record of the Anthropocene is minimal, especially with its recently proposed beginning in 1945; it is that of a human lifespan, and that definition relegates considerable anthropogenic change to a “pre-Anthropocene.” The utility of the Anthropocene requires careful consideration by its various potential users. Its concept is fundamentally different from the chronostratigraphic units that are established by ICS in that the documentation and study of the human impact on the Earth system are based more on direct human observation than on a stratigraphic record. The drive to officially recognize the Anthropocene may, in fact, be political rather than scientific.

  1. A dusty, normal galaxy in the epoch of reionization

    DEFF Research Database (Denmark)

    Watson, Darach; Christensen, Lise; Knudsen, Kirsten Kraiberg

    2015-01-01

    Candidates for the modest galaxies that formed most of the stars in the early universe, at redshifts $z > 7$, have been found in large numbers with extremely deep restframe-UV imaging. But it has proved difficult for existing spectrographs to characterise them in the UV. The detailed properties...... of these galaxies could be measured from dust and cool gas emission at far-infrared wavelengths if the galaxies have become sufficiently enriched in dust and metals. So far, however, the most distant UV-selected galaxy detected in dust emission is only at $z = 3.25$, and recent results have cast doubt on whether...... dust and molecules can be found in typical galaxies at this early epoch. Here we report thermal dust emission from an archetypal early universe star-forming galaxy, A1689-zD1. We detect its stellar continuum in spectroscopy and determine its redshift to be $z = 7.5\\pm0.2$ from a spectroscopic detection...

  2. Epoch making NIRS studies seen through citation trends

    International Nuclear Information System (INIS)

    Dan, Ippeita

    2009-01-01

    Near-infrared spectroscopy (NIRS) studies through citation trends are investigated of literature concerning only the brain function measurement and its methodology together with NIRS principle, technological development, present state and future view. Investigation is conducted firstly for the survey of important author name of those concerned papers in Web of Science and Google Scholar with search words of NIRS, brain and optical topography as an option. Second, >100 papers of those authors citing any of them are picked up and their papers are ranked in accordance with Web of Science citation number, of which top-nineteen are presented here. Impact and epoch making papers are reviewed with explanations of: the establishment of measuring technology of cerebral blood flow change and subsequent brain function by NIRS; development with multi-channel detection; simultaneous measurement with other imaging modalities; examination of NIRS validity; spatial analysis of NIRS; and measurement of brain function. The highest times of citation are 1,238 of the paper by F. F. Jobsis in 'Science' (1977). It should be noted that 10 of top 19 papers are those by Japanese authors. However, review articles omitted in the present literature survey are mostly described by foreign authors: an effort to systemize the concerned fields might be required in this country. (K.T.)

  3. Systematic Uncertainties in Black Hole Masses Determined from Single Epoch Spectra

    DEFF Research Database (Denmark)

    Denney, Kelly D.; Peterson, Bradley M.; Dietrich, Matthias

    2008-01-01

    We explore the nature of systematic errors that can arise in measurement of black hole masses from single-epoch spectra of active galactic nuclei (AGNs) by utilizing the many epochs available for NGC 5548 and PG1229+204 from reverberation mapping databases. In particular, we examine systematics due...

  4. Linguistic Engineering and Linguistic of Engineering: Adaptation of Linguistic Paradigm for Circumstance of Engineering Epoch

    OpenAIRE

    Natalya Halina

    2014-01-01

    The article is devoted to the problems of linguistic knowledge in the Engineering Epoch. Engineering Epoch is the time of adaptation to the information flows by knowledge management, The system of adaptation mechanisms is connected with linguistic and linguistic technologies, forming in new linguistic patterns Linguistic Engineering and Linguistic of Engineering.

  5. The Cotesia sesamiae story: insight into host-range evolution in a Hymenoptera parasitoid and implication for its use in biological control programs.

    Science.gov (United States)

    Kaiser, L; Dupas, S; Branca, A; Herniou, E A; Clarke, C W; Capdevielle Dulac, C; Obonyo, J; Benoist, R; Gauthier, J; Calatayud, P A; Silvain, J F; Le Ru, B P

    2017-12-01

    This review covers nearly 20 years of studies on the ecology, physiology and genetics of the Hymenoptera Cotesia sesamiae, an African parasitoid of Lepidoptera that reduces populations of common maize borers in East and South Africa. The first part of the review presents studies based on sampling of C. sesamiae from maize crops in Kenya. From this agrosystem including one host plant and three main host borer species, studies revealed two genetically differentiated populations of C. sesamiae species adapted to their local host community, and showed that their differentiation involved the joint evolution of virulence genes and sensory mechanisms of host acceptance, reinforced by reproductive incompatibility due to Wolbachia infection status and natural inbreeding. In the second part, we consider the larger ecosystem of wild Poales plant species hosting many Lepidoptera stem borer species that are potential hosts for C. sesamiae. The hypothesis of other host-adapted C. sesamiae populations was investigated based on a large sampling of stem borer larvae on various Poales across sub-Saharan Africa. The sampling provided information on the respective contribution of local hosts, biogeography and Wolbachia in the genetic structure of C. sesamiae populations. Molecular evolution analyses highlighted that several bracovirus genes were under positive selection, some of them being under different selection pressure in C. sesamiae populations adapted to different hosts. This suggests that C. sesamiae host races result from co-evolution acting at the local scale on different bracovirus genes. The third part considers the mechanisms driving specialization. C. sesamiae host races are more or less host-specialized. This character is crucial for efficient and environmentally-safe use of natural enemies for biological control of pests. One method to get an insight in the evolutionary stability of host-parasite associations is to characterize the phylogenetic relationships between

  6. Latest Pannonian and Quaternary evolution at the transition between Eastern Alps and Pannonian Basin: new insights from geophysical, sedimentological and geochronological data

    Science.gov (United States)

    Zámolyi, A.; Salcher, B.; Draganits, E.; Exner, U.; Wagreich, M.; Gier, S.; Fiebig, M.; Lomax, J.; Surányi, G.; Diel, M.; Zámolyi, F.

    2017-07-01

    The transition zone between Eastern Alps and Pannonian Basin is a key area for the investigation of the interplay between regional uplift, local tectonic subsidence and depositional environment. Our study area, the western margin of the Little Hungarian Plain, is characterized by gentle hills, plateaus and depressions, of which several are filled by lakes—including one of Austria's largest and shallowest lakes, Lake Neusiedl. Geological investigation is hampered by the scarcity of outcrops, and thus direct observation of sedimentological or structural features is difficult. Despite a long research history in the area, a consistent landscape evolution model considering all relevant constraints is lacking so far. In this study, we apply multidisciplinary methods to decipher the complex tectonic and fluvial depositional evolution of the region. Local data from shallow-lake drilling and seismic investigation are combined with regional data from industrial seismics and core data to gain new insights into the latest Pannonian (Late Miocene) and Quaternary evolution. Shallow-lake seismic data show the erosionally truncated Pannonian sediments dipping and thickening toward southeast, toward the modern depocenter of the Little Hungarian Plain. Overlying Quaternary fluvial sediments show a very similar thickening trend except for the area on the plateau north of the lake indicating ongoing subsidence in major parts of the basin. Drill cores from locations along the lake seismic lines were analyzed concerning their age, mineralogy and heavy minerals and compared with outcrop samples from the surrounding plains and the plateau to derive indications on sediment provenance. A key observation is the apparent lack of a significant gravel layer on top of the tilted Pannonian sediments beneath Lake Neusiedl. Small-scale faults can be observed in the lake seismic sections along with key sedimentary features. Significant differences of the current elevation of the top Pannonian

  7. The Shock Dynamics of Heterogeneous YSO Jets: 3D Simulations Meet Multi-epoch Observations

    Energy Technology Data Exchange (ETDEWEB)

    Hansen, E. C.; Frank, A. [Department of Physics and Astronomy, University of Rochester, Rochester, NY 14627-0171 (United States); Hartigan, P. [Department of Physics and Astronomy, Rice University, 6100 S. Main, Houston, TX 77521-1892 (United States); Lebedev, S. V. [Blackett Laboratory, Imperial College London, Prince Consort Road, London SW7 2BW (United Kingdom)

    2017-03-10

    High-resolution observations of young stellar object (YSO) jets show them to be composed of many small-scale knots or clumps. In this paper, we report results of 3D numerical simulations designed to study how such clumps interact and create morphologies and kinematic patterns seen in emission line observations. Our simulations focus on clump scale dynamics by imposing velocity differences between spherical, over-dense regions, which then lead to the formation of bow shocks as faster clumps overtake slower material. We show that much of the spatial structure apparent in emission line images of jets arises from the dynamics and interactions of these bow shocks. Our simulations show a variety of time-dependent features, including bright knots associated with Mach stems where the shocks intersect, a “frothy” emission structure that arises from the presence of the Nonlinear Thin Shell Instability along the surfaces of the bow shocks, and the merging and fragmentation of clumps. Our simulations use a new non-equilibrium cooling method to produce synthetic emission maps in H α and [S ii]. These are directly compared to multi-epoch Hubble Space Telescope observations of Herbig–Haro jets. We find excellent agreement between features seen in the simulations and the observations in terms of both proper motion and morphologies. Thus we conclude that YSO jets may be dominated by heterogeneous structures and that interactions between these structures and the shocks they produce can account for many details of YSO jet evolution.

  8. Atlas Basemaps in Web 2.0 Epoch

    Science.gov (United States)

    Chabaniuk, V.; Dyshlyk, O.

    2016-06-01

    The authors have analyzed their experience of the production of various Electronic Atlases (EA) and Atlas Information Systems (AtIS) of so-called "classical type". These EA/AtIS have been implemented in the past decade in the Web 1.0 architecture (e.g., National Atlas of Ukraine, Atlas of radioactive contamination of Ukraine, and others). One of the main distinguishing features of these atlases was their static nature - the end user could not change the content of EA/AtIS. Base maps are very important element of any EA/AtIS. In classical type EA/AtIS they were static datasets, which consisted of two parts: the topographic data of a fixed scale and data of the administrative-territorial division of Ukraine. It is important to note that the technique of topographic data production was based on the use of direct channels of topographic entity observation (such as aerial photography) for the selected scale. Changes in the information technology of the past half-decade are characterized by the advent of the "Web 2.0 epoch". Due to this, in cartography appeared such phenomena as, for example, "neo-cartography" and various mapping platforms like OpenStreetMap. These changes have forced developers of EA/AtIS to use new atlas basemaps. Our approach is described in the article. The phenomenon of neo-cartography and/or Web 2.0 cartography are analysed by authors using previously developed Conceptual framework of EA/AtIS. This framework logically explains the cartographic phenomena relations of three formations: Web 1.0, Web 1.0x1.0 and Web 2.0. Atlas basemaps of the Web 2.0 epoch are integrated information systems. We use several ways to integrate separate atlas basemaps into the information system - by building: weak integrated information system, structured system and meta-system. This integrated information system consists of several basemaps and falls under the definition of "big data". In real projects it is already used the basemaps of three strata: Conceptual

  9. Hydrogen Epoch of Reinozation Array (HERA) Calibrated FFT Correlator Simulation

    Science.gov (United States)

    Salazar, Jeffrey David; Parsons, Aaron

    2018-01-01

    The Hydrogen Epoch of Reionization Array (HERA) project is an astronomical radio interferometer array with a redundant baseline configuration. Interferometer arrays are being used widely in radio astronomy because they have a variety of advantages over single antenna systems. For example, they produce images (visibilities) closely matching that of a large antenna (such as the Arecibo observatory), while both the hardware and maintenance costs are significantly lower. However, this method has some complications; one being the computational cost of correlating data from all of the antennas. A correlator is an electronic device that cross-correlates the data between the individual antennas; these are what radio astronomers call visibilities. HERA, being in its early stages, utilizes a traditional correlator system. The correlator cost scales as N2, where N is the number of antennas in the array. The purpose of a redundant baseline configuration array setup is for the use of a more efficient Fast Fourier Transform (FFT) correlator. FFT correlators scale as Nlog2N. The data acquired from this sort of setup, however, inherits geometric delay and uncalibrated antenna gains. This particular project simulates the process of calibrating signals from astronomical sources. Each signal “received” by an antenna in the simulation is given random antenna gain and geometric delay. The “linsolve” Python module was used to solve for the unknown variables in the simulation (complex gains and delays), which then gave a value for the true visibilities. This first version of the simulation only mimics a one dimensional redundant telescope array detecting a small amount of sources located in the volume above the antenna plane. Future versions, using GPUs, will handle a two dimensional redundant array of telescopes detecting a large amount of sources in the volume above the array.

  10. The redshift number density evolution of Mg II absorption systems

    International Nuclear Information System (INIS)

    Chen Zhi-Fu

    2013-01-01

    We make use of the recent large sample of 17 042 Mg II absorption systems from Quider et al. to analyze the evolution of the redshift number density. Regardless of the strength of the absorption line, we find that the evolution of the redshift number density can be clearly distinguished into three different phases. In the intermediate redshift epoch (0.6 ≲ z ≲ 1.6), the evolution of the redshift number density is consistent with the non-evolution curve, however, the non-evolution curve over-predicts the values of the redshift number density in the early (z ≲ 0.6) and late (z ≳ 1.6) epochs. Based on the invariant cross-section of the absorber, the lack of evolution in the redshift number density compared to the non-evolution curve implies the galaxy number density does not evolve during the middle epoch. The flat evolution of the redshift number density tends to correspond to a shallow evolution in the galaxy merger rate during the late epoch, and the steep decrease of the redshift number density might be ascribed to the small mass of halos during the early epoch.

  11. Sun in the Epoch ``LOWERED'' Solar Activity: the Comparative Analysis of the Current 24 Solar Cycle and Past Authentic Low Cycles

    Science.gov (United States)

    Vitaly, Ishkov

    A reliable series of the relative numbers of sunspots (14 solar cycles ‒ 165 years) it leads to the only scenario of solar activity cycles - to the alternation of epochs of “increased” (18 ‒ 22 cycles of solar activity) and “lowered” (12 ‒ 16 and 24 ‒ ...) solar activity with the periods of solar magnetic field reconstruction in solar zone of the sunspots formation (11, 12, 23) from one epoch to another. The regime of the produce of magnetic field significantly changes in these periods, providing to the subsequent 5 cycles the stable conditions of solar activity. Space solar research made it possible to sufficiently fully investigate characteristics and parameters of the solar cycles for the epoch of “increased” (20 ‒ 22 cycles) solar activity and period of the reconstruction (22 ‒ 23 cycles) to the epoch of “lowered” solar activity (24 ‒ ... cycles). In this scenario 24 solar cycle is the first solar cycle of the second epoch of “lowered” solar activity. Therefore his development and characteristics roughly must be described in the context of the low solar cycles development (12, 14, and 16). In the current solar cycle the sunspot-forming activity is lowered, the average areas of the sunspot groups correspond to values for epoch of “lowered “solar activity, average magnetic field in the umbra of sunspots was reduced approximately to 700 gauss, and for this time was observed only 4 very large sunspot groups (≥1500 mvh). Flare activity substantially was lowered: for the time of the current solar cycle development it was occurrence of M-class flares M - 368, class X - 32, from which only 2 solar flares of class X> 5. Solar proton events are observed predominantly small intensity; but only 5 from them were the intensity of ≥100 pfu (S2) and 4 - ≥1000 pfu (S3). The first five years of the 24 cycle evolution confirm this assumption and the possibility to give the qualitative forecast of his evolution and development of the

  12. Identifying individual sleep apnea/hypoapnea epochs using smartphone-based pulse oximetry.

    Science.gov (United States)

    Garde, Ainara; Dekhordi, Parastoo; Ansermino, J Mark; Dumont, Guy A

    2016-08-01

    Sleep apnea, characterized by frequent pauses in breathing during sleep, poses a serious threat to the healthy growth and development of children. Polysomnography (PSG), the gold standard for sleep apnea diagnosis, is resource intensive and confined to sleep laboratories, thus reducing its accessibility. Pulse oximetry alone, providing blood oxygen saturation (SpO2) and blood volume changes in tissue (PPG), has the potential to identify children with sleep apnea. Thus, we aim to develop a tool for at-home sleep apnea screening that provides a detailed and automated 30 sec epoch-by-epoch sleep apnea analysis. We propose to extract features characterizing pulse oximetry (SpO2 and pulse rate variability [PRV], a surrogate measure of heart rate variability) to create a multivariate logistic regression model that identifies epochs containing apnea/hypoapnea events. Overnight pulse oximetry was collected using a smartphone-based pulse oximeter, simultaneously with standard PSG from 160 children at the British Columbia Children's hospital. The sleep technician manually scored all apnea/hypoapnea events during the PSG study. Based on these scores we labeled each epoch as containing or not containing apnea/hypoapnea. We randomly divided the subjects into training data (40%), used to develop the model applying the LASSO method, and testing data (60%), used to validate the model. The developed model was assessed epoch-by-epoch for each subject. The test dataset had a median area under the receiver operating characteristic (ROC) curve of 81%; the model provided a median accuracy of 74% sensitivity of 75%, and specificity of 73% when using a risk threshold similar to the percentage of apnea/hypopnea epochs. Thus, providing a detailed epoch-by-epoch analysis with at-home pulse oximetry alone is feasible with accuracy, sensitivity and specificity values above 73% However, the performance might decrease when analyzing subjects with a low number of apnea/hypoapnea events.

  13. Analysis of chitin-binding proteins from Manduca sexta provides new insights into evolution of peritrophin A-type chitin-binding domains in insects.

    Science.gov (United States)

    Tetreau, Guillaume; Dittmer, Neal T; Cao, Xiaolong; Agrawal, Sinu; Chen, Yun-Ru; Muthukrishnan, Subbaratnam; Haobo, Jiang; Blissard, Gary W; Kanost, Michael R; Wang, Ping

    2015-07-01

    together in the phylogenetic tree. For chitinases and chitin deacetylases, most of phylogenetic analysis performed with the CBD sequences resulted in similar clustering to the one obtained by using catalytic domain sequences alone, suggesting that CBDs were incorporated into these enzymes and evolved in tandem with the catalytic domains before the diversification of different insect orders. Based on these results, the evolution of CBDs in insect CBPs is discussed to provide a new insight into the CBD sequence structure and diversity, and their evolution and expression in insects. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Hydrologic and Agent-based Modelling of Hydro-refugia in East Africa, Insights into the Importance of Water Resources in Hominin Evolution and Dispersal

    Science.gov (United States)

    Ashley, G. M.; Cuthbert, M. O.; Gleeson, T. P.; Reynolds, S. R.; Bennett, M. R.; Newton, A. C.; McCormack, C. J.

    2017-12-01

    Hominin evolution and climate variability have often been linked because of the apparent coincidence of climate fluctuations and speciation or extinctions, although the cause and effect of climate on natural selection is not clear. Climate in the EARS (East African Rift System) where most hominin first occurrences are located experienced an overall drying over the last 7 myr. Superimposed on this trend, Milankovitch cycles generated wet-dry precession cycles ( 23 kyr) that changed both water and food resource availability. During dry periods, lakes became more alkaline and rivers ephemeral but, groundwater, buffered from surface climate effects, remained a potential resource during the driest of times. The possibility of widespread groundwater sources hydro-refugia, such as springs, wetlands and groundwater-fed perennial streams has received little attention with respect to the paleoenvironmental context of hominin evolution or dispersal. We demonstrate that hydrogeological modelling of the modern landscape in East Africa coupled with ABM (agent-based modelling) of hominin movement yields new insight into potential correlates of hominin survival and dispersal. Digitized hydrological mapping of present day rivers, lakes and springs along the EARS (2000 km) from northern Tanzania to Ethiopia provided the modelling framework. Present day conditions are considered analogous to past dry periods; wet period conditions are an expanded hydrologic network including all surface water bodies. Our focus was on perennial springs discharging at 1,000 m3/y (volume to sustain a small wetland). 450 such springs occur and were found to be significantly controlled by geology, not just climate. The ABM was designed to determine if it was possible for humans to walk between hydro-refugia in 3 days. Four climate scenarios were run on ABM: wet, wet-to-dry, dry and dry-to-wet. During dry periods our results suggest that groundwater availability would have been critical to supporting

  15. Organic Chemostratigraphic Markers Characteristic of the (Informally Designated) Anthropocene Epoch

    Science.gov (United States)

    Kruge, M. A.

    2008-12-01

    Recognizing the tremendous collective impact of humans on the environment in the industrial age, the proposed designation of the current time period as the Anthropocene Epoch has considerable merit. One of the signature activities during this time continues to be the intensive extraction, processing, and combustion of fossil fuels. While fossil fuels themselves are naturally-occurring, they are most often millions of years old and associated with deeply buried strata. They may be found at the surface, for example, as natural oil seeps or coal seam outcrops, but these are relatively rare occurrences. Fossil fuels and their myriad by- products become the source of distinctive organic chemostratigraphic marker compounds for the Anthropocene when they occur out of their original geological context, i.e., as widespread contaminants in sediments and soils. These persistent compounds have high long-term preservation potential, particularly when deposited under low oxygen conditions. Fossil fuels can occur as environmental contaminants in raw form (e.g., crude petroleum spilled during transport) or as manufactured products (e.g., diesel oil from a leaking storage facility, coal tar from a manufactured gas plant, plastic waste in a landfill, pesticides from petroleum feedstock in agricultural soils). Distinctive assemblages of hydrocarbon marker compounds including acyclic isoprenoids, hopanes, and steranes can be readily detected by gas chromatography/mass spectrometric analysis of surface sediments and soils. Polycyclic aromatic hydrocarbons (PAHs), along with sulfur-, oxygen-, and nitrogen-containing aromatic compounds, are also characteristic of fossil fuels and are readily detectable as well. More widespread is the airfall deposition of fossil fuel combustion products from vehicular, domestic and industrial sources. These occur in higher concentrations in large urban centers, but are also detected in remote areas. Parent (nonmethylated) PAHs such as phenanthrene

  16. Insights into archaeal evolution and symbiosis from the genomes of a nanoarchaeon and its inferred crenarchaeal host from Obsidian Pool, Yellowstone National Park.

    Science.gov (United States)

    Podar, Mircea; Makarova, Kira S; Graham, David E; Wolf, Yuri I; Koonin, Eugene V; Reysenbach, Anna-Louise

    2013-04-22

    A single cultured marine organism, Nanoarchaeum equitans, represents the Nanoarchaeota branch of symbiotic Archaea, with a highly reduced genome and unusual features such as multiple split genes. The first terrestrial hyperthermophilic member of the Nanoarchaeota was collected from Obsidian Pool, a thermal feature in Yellowstone National Park, separated by single cell isolation, and sequenced together with its putative host, a Sulfolobales archaeon. Both the new Nanoarchaeota (Nst1) and N. equitans lack most biosynthetic capabilities, and phylogenetic analysis of ribosomal RNA and protein sequences indicates that the two form a deep-branching archaeal lineage. However, the Nst1 genome is more than 20% larger, and encodes a complete gluconeogenesis pathway as well as the full complement of archaeal flagellum proteins. With a larger genome, a smaller repertoire of split protein encoding genes and no split non-contiguous tRNAs, Nst1 appears to have experienced less severe genome reduction than N. equitans. These findings imply that, rather than representing ancestral characters, the extremely compact genomes and multiple split genes of Nanoarchaeota are derived characters associated with their symbiotic or parasitic lifestyle. The inferred host of Nst1 is potentially autotrophic, with a streamlined genome and simplified central and energetic metabolism as compared to other Sulfolobales. Comparison of the N. equitans and Nst1 genomes suggests that the marine and terrestrial lineages of Nanoarchaeota share a common ancestor that was already a symbiont of another archaeon. The two distinct Nanoarchaeota-host genomic data sets offer novel insights into the evolution of archaeal symbiosis and parasitism, enabling further studies of the cellular and molecular mechanisms of these relationships. This article was reviewed by Patrick Forterre, Bettina Siebers (nominated by Michael Galperin) and Purification Lopez-Garcia.

  17. New insights into the distribution and evolution of the Cenozoic Tan-Lu Fault Zone in the Liaohe sub-basin of the Bohai Bay Basin, eastern China

    Science.gov (United States)

    Huang, Lei; Liu, Chi-yang; Xu, Chang-gui; Wu, Kui; Wang, Guang-yuan; Jia, Nan

    2018-01-01

    As the largest strike-slip fault system in eastern China, the northeast-trending Tan-Lu Fault Zone (TLFZ) is a significant tectonic element contributing to the Mesozoic-Cenozoic regional geologic evolution of eastern Asia, as well as to the formation of ore deposits and oilfields. Because of the paucity of data, its distribution and evolutionary history in the offshore Liaohe sub-basin of the northern Bohai Bay Basin (BBB) are still poorly understood. Investigations of the strike-slip fault system in the western portion of the offshore Liaohe sub-basin via new seismic data provide us with new insights into the characteristics of the Cenozoic TLFZ. Results of this study show that Cenozoic dextral strike-slip faults occurred near the center of the Liaoxi graben in the offshore Liaohe sub-basin; these strike-slip faults connect with their counterparts to the north, the western part of the onshore Liaohe sub-basin, and have similar characteristics to those in other areas of the BBB in terms of kinematics, evolutionary history, and distribution; consequently, these faults are considered as the western branch of the TLFZ. All strike-slip faults within the Liaoxi graben merge at depth with a central subvertical basement fault induced by the reactivation of a pre-existing strike-slip basement fault, the pre-Cenozoic TLFZ. Data suggest that the TLFZ across the whole Liaohe sub-basin comprises two branches and that the Cenozoic distribution of this system was inherited from the pre-Cenozoic TLFZ. This characteristic distribution might be possessed by the whole TLFZ, thus the new understandings about the distribution and evolutionary model of the TLFZ in this study can be inferred in many research fields along the whole fault zone, such as regional geology, ore deposits, petroleum exploration and earthquake hazard.

  18. Expression and phylogenetic analyses of the Gel/Gas proteins of Tuber melanosporum provide insights into the function and evolution of glucan remodeling enzymes in fungi.

    Science.gov (United States)

    Sillo, Fabiano; Gissi, Carmela; Chignoli, Daniele; Ragni, Enrico; Popolo, Laura; Balestrini, Raffaella

    2013-04-01

    The β(1,3)-glucanosyltransferases of the GH72 family are redundant enzymes that are essential for the formation and dynamic remodeling of the fungal wall during different stages of the life cycle. Four putative genes encoding glycosylphosphatidylinositol (GPI)-anchored β(1,3)-glucanosyltransferases, designated TmelGEL1, TmelGEL2, TmelGEL4 and TmelGAS4, have been annotated in the genome of Tuber melanosporum, an ectomycorrhizal fungus that also produces a hypogeous fruiting body (FB) of great commercial value (black truffle). This work focuses on the characterization and expression of this multigene family by taking advantage of a laser microdissection (LMD) technology that has been used to separate two distinct compartments in the FB, the hyphae and the asci containing the ascospores. Of the four genes, TmelGEL1 was the most up-regulated in the FB compared to the free-living mycelium. Inside the FB, the expression of TmelGEL1 was restricted to the hyphal compartment. A phylogenetic analysis of the Gel/Gas protein family of T. melanosporum was also carried out. A total of 237 GH72 proteins from 51 Ascomycotina and 3 Basidiomycota (outgroup) species were analyzed. The resulting tree provides insight into the evolution of the T. melanosporum proteins and identifies new GH72 paralogs/subfamilies. Moreover, it represents a starting point to formulate new hypotheses on the significance of the striking GH72 gene redundancy in fungal biology. Copyright © 2013 Elsevier Inc. All rights reserved.

  19. Insights into the evolution of mammalian telomerase: Platypus TERT shares similarities with genes of birds and other reptiles and localizes on sex chromosomes

    Directory of Open Access Journals (Sweden)

    Hrdličková Radmila

    2012-06-01

    Full Text Available Abstract Background The TERT gene encodes the catalytic subunit of the telomerase complex and is responsible for maintaining telomere length. Vertebrate telomerase has been studied in eutherian mammals, fish, and the chicken, but less attention has been paid to other vertebrates. The platypus occupies an important evolutionary position, providing unique insight into the evolution of mammalian genes. We report the cloning of a platypus TERT (OanTERT ortholog, and provide a comparison with genes of other vertebrates. Results The OanTERT encodes a protein with a high sequence similarity to marsupial TERT and avian TERT. Like the TERT of sauropsids and marsupials, as well as that of sharks and echinoderms, OanTERT contains extended variable linkers in the N-terminal region suggesting that they were present already in basal vertebrates and lost independently in ray-finned fish and eutherian mammals. Several alternatively spliced OanTERT variants structurally similar to avian TERT variants were identified. Telomerase activity is expressed in all platypus tissues like that of cold-blooded animals and murine rodents. OanTERT was localized on pseudoautosomal regions of sex chromosomes X3/Y2, expanding the homology between human chromosome 5 and platypus sex chromosomes. Synteny analysis suggests that TERT co-localized with sex-linked genes in the last common mammalian ancestor. Interestingly, female platypuses express higher levels of telomerase in heart and liver tissues than do males. Conclusions OanTERT shares many features with TERT of the reptilian outgroup, suggesting that OanTERT represents the ancestral mammalian TERT. Features specific to TERT of eutherian mammals have, therefore, evolved more recently after the divergence of monotremes.

  20. Biochemical and genetic analyses of the oomycete Pythium insidiosum provide new insights into clinical identification and urease-based evolution of metabolism-related traits

    Directory of Open Access Journals (Sweden)

    Theerapong Krajaejun

    2018-06-01

    biochemical characteristics and drew new insights into clinical identification and urease-related evolution of P. insidiosum.

  1. Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06

    Directory of Open Access Journals (Sweden)

    White Brian

    2010-11-01

    Full Text Available Abstract Background The genus Neisseria contains two important yet very different pathogens, N. meningitidis and N. gonorrhoeae, in addition to non-pathogenic species, of which N. lactamica is the best characterized. Genomic comparisons of these three bacteria will provide insights into the mechanisms and evolution of pathogenesis in this group of organisms, which are applicable to understanding these processes more generally. Results Non-pathogenic N. lactamica exhibits very similar population structure and levels of diversity to the meningococcus, whilst gonococci are essentially recent descendents of a single clone. All three species share a common core gene set estimated to comprise around 1190 CDSs, corresponding to about 60% of the genome. However, some of the nucleotide sequence diversity within this core genome is particular to each group, indicating that cross-species recombination is rare in this shared core gene set. Other than the meningococcal cps region, which encodes the polysaccharide capsule, relatively few members of the large accessory gene pool are exclusive to one species group, and cross-species recombination within this accessory genome is frequent. Conclusion The three Neisseria species groups represent coherent biological and genetic groupings which appear to be maintained by low rates of inter-species horizontal genetic exchange within the core genome. There is extensive evidence for exchange among positively selected genes and the accessory genome and some evidence of hitch-hiking of housekeeping genes with other loci. It is not possible to define a 'pathogenome' for this group of organisms and the disease causing phenotypes are therefore likely to be complex, polygenic, and different among the various disease-associated phenotypes observed.

  2. Persistent near-tropical warmth on the Antarctic continent during the early Eocene epoch.

    Science.gov (United States)

    Pross, Jörg; Contreras, Lineth; Bijl, Peter K; Greenwood, David R; Bohaty, Steven M; Schouten, Stefan; Bendle, James A; Röhl, Ursula; Tauxe, Lisa; Raine, J Ian; Huck, Claire E; van de Flierdt, Tina; Jamieson, Stewart S R; Stickley, Catherine E; van de Schootbrugge, Bas; Escutia, Carlota; Brinkhuis, Henk

    2012-08-02

    The warmest global climates of the past 65 million years occurred during the early Eocene epoch (about 55 to 48 million years ago), when the Equator-to-pole temperature gradients were much smaller than today and atmospheric carbon dioxide levels were in excess of one thousand parts per million by volume. Recently the early Eocene has received considerable interest because it may provide insight into the response of Earth's climate and biosphere to the high atmospheric carbon dioxide levels that are expected in the near future as a consequence of unabated anthropogenic carbon emissions. Climatic conditions of the early Eocene 'greenhouse world', however, are poorly constrained in critical regions, particularly Antarctica. Here we present a well-dated record of early Eocene climate on Antarctica from an ocean sediment core recovered off the Wilkes Land coast of East Antarctica. The information from biotic climate proxies (pollen and spores) and independent organic geochemical climate proxies (indices based on branched tetraether lipids) yields quantitative, seasonal temperature reconstructions for the early Eocene greenhouse world on Antarctica. We show that the climate in lowland settings along the Wilkes Land coast (at a palaeolatitude of about 70° south) supported the growth of highly diverse, near-tropical forests characterized by mesothermal to megathermal floral elements including palms and Bombacoideae. Notably, winters were extremely mild (warmer than 10 °C) and essentially frost-free despite polar darkness, which provides a critical new constraint for the validation of climate models and for understanding the response of high-latitude terrestrial ecosystems to increased carbon dioxide forcing.

  3. ATLAS BASEMAPS IN WEB 2.0 EPOCH

    Directory of Open Access Journals (Sweden)

    V. Chabaniuk

    2016-06-01

    Full Text Available The authors have analyzed their experience of the production of various Electronic Atlases (EA and Atlas Information Systems (AtIS of so-called "classical type". These EA/AtIS have been implemented in the past decade in the Web 1.0 architecture (e.g., National Atlas of Ukraine, Atlas of radioactive contamination of Ukraine, and others. One of the main distinguishing features of these atlases was their static nature - the end user could not change the content of EA/AtIS. Base maps are very important element of any EA/AtIS. In classical type EA/AtIS they were static datasets, which consisted of two parts: the topographic data of a fixed scale and data of the administrative-territorial division of Ukraine. It is important to note that the technique of topographic data production was based on the use of direct channels of topographic entity observation (such as aerial photography for the selected scale. Changes in the information technology of the past half-decade are characterized by the advent of the “Web 2.0 epoch”. Due to this, in cartography appeared such phenomena as, for example, "neo-cartography" and various mapping platforms like OpenStreetMap. These changes have forced developers of EA/AtIS to use new atlas basemaps. Our approach is described in the article. The phenomenon of neo-cartography and/or Web 2.0 cartography are analysed by authors using previously developed Conceptual framework of EA/AtIS. This framework logically explains the cartographic phenomena relations of three formations: Web 1.0, Web 1.0x1.0 and Web 2.0. Atlas basemaps of the Web 2.0 epoch are integrated information systems. We use several ways to integrate separate atlas basemaps into the information system – by building: weak integrated information system, structured system and meta-system. This integrated information system consists of several basemaps and falls under the definition of "big data". In real projects it is already used the basemaps of three strata

  4. Assessing worst case scenarios in movement demands derived from global positioning systems during international rugby union matches: Rolling averages versus fixed length epochs

    Science.gov (United States)

    Cunningham, Daniel J.; Shearer, David A.; Carter, Neil; Drawer, Scott; Pollard, Ben; Bennett, Mark; Eager, Robin; Cook, Christian J.; Farrell, John; Russell, Mark

    2018-01-01

    The assessment of competitive movement demands in team sports has traditionally relied upon global positioning system (GPS) analyses presented as fixed-time epochs (e.g., 5–40 min). More recently, presenting game data as a rolling average has become prevalent due to concerns over a loss of sampling resolution associated with the windowing of data over fixed periods. Accordingly, this study compared rolling average (ROLL) and fixed-time (FIXED) epochs for quantifying the peak movement demands of international rugby union match-play as a function of playing position. Elite players from three different squads (n = 119) were monitored using 10 Hz GPS during 36 matches played in the 2014–2017 seasons. Players categorised broadly as forwards and backs, and then by positional sub-group (FR: front row, SR: second row, BR: back row, HB: half back, MF: midfield, B3: back three) were monitored during match-play for peak values of high-speed running (>5 m·s-1; HSR) and relative distance covered (m·min-1) over 60–300 s using two types of sample-epoch (ROLL, FIXED). Irrespective of the method used, as the epoch length increased, values for the intensity of running actions decreased (e.g., For the backs using the ROLL method, distance covered decreased from 177.4 ± 20.6 m·min-1 in the 60 s epoch to 107.5 ± 13.3 m·min-1 for the 300 s epoch). For the team as a whole, and irrespective of position, estimates of fixed effects indicated significant between-method differences across all time-points for both relative distance covered and HSR. Movement demands were underestimated consistently by FIXED versus ROLL with differences being most pronounced using 60 s epochs (95% CI HSR: -6.05 to -4.70 m·min-1, 95% CI distance: -18.45 to -16.43 m·min-1). For all HSR time epochs except one, all backs groups increased more (p < 0.01) from FIXED to ROLL than the forward groups. Linear mixed modelling of ROLL data highlighted that for HSR (except 60 s epoch), SR was the only group not

  5. The morphology and distribution of submerged reefs in the Maui-Nui Complex, Hawaii: New insights into their evolution since the Early Pleistocene

    Science.gov (United States)

    Faichney, Iain D.E.; Webster, James M.; Clague, David A.; Kelley, Chris; Applegate, Bruce; Moore, James G.

    2009-01-01

    Reef drowning and backstepping have long been recognised as reef responses to sea-level rise on subsiding margins. During the Late Pleistocene (~500–14 ka) Hawaiian reefs grew in response to rapid subsidence and 120 m 100 kyr sea-level cycles, with recent work on the submerged drowned reefs around the big island of Hawaii, and in other locations from the last deglacial, providing insight into reef development under these conditions. In contrast, reefs of the Early Pleistocene (~1.8–0.8 Ma) remain largely unexplored despite developing in response to significantly different 60–70 m 41 kyr sea-level cycles. The Maui-Nui Complex (MNC — forming the islands of Maui, Molokai, Lanai and Kahoolawe), provides a natural laboratory to study reef evolution throughout this time period as recent data indicate the reefs grew from 1.1 to 0.5 Ma. We use new high resolution bathymetric and backscatter data as well as sub-bottom profiling seismic data and field observations from ROV and submersible dives to make a detailed analysis of reef morphology and structure around the MNC. We focus specifically on the south-central region of the complex that provides the best reef exposure and find that the morphology of the reefs varies both regionally and temporally within this region. Barrier and pinnacle features dominate the steeper margins in the north of the study area whilst broad backstepping of the reefs is observed in the south. Within the Au'au channel in the central region between the islands, closely spaced reef and karst morphology indicates repeated subaerial exposure. We propose that this variation in the morphology and structure of the reefs within the MNC has been controlled by three main factors; the subsidence rate of the complex, the amplitude and period of eustatic sea-level cycles, and the slope and continuity of the basement substrate. We provide a model of reef development within the MNC over the last 1.2 Ma highlighting the effect that the interaction

  6. Insights into the evolution of enzyme substrate promiscuity after the discovery of (βα)₈ isomerase evolutionary intermediates from a diverse metagenome.

    Science.gov (United States)

    Noda-García, Lianet; Juárez-Vázquez, Ana L; Ávila-Arcos, María C; Verduzco-Castro, Ernesto A; Montero-Morán, Gabriela; Gaytán, Paul; Carrillo-Tripp, Mauricio; Barona-Gómez, Francisco

    2015-06-10

    ) predicted to adopt a (βα)6-fold, and thus entirely lacking a C-terminus phosphate-binding site, was identified and shown to have HisA activity. As expected, reconstruction of the evolution of PriA from HisA with HMM profiles suggest that functional shifts involve mutations in evolutionarily intermediate enzymes of otherwise functionally essential residues or motifs. These results are in agreement with a link between promiscuous enzymes and intragenic epistasis. HMM provides a convenient approach for gaining insights into these evolutionary processes.

  7. Relative Contribution of the Hydrogen 2 s Two-Photon Decay and Lyman- α Escape Channels during the Epoch of Cosmological Recombination

    Science.gov (United States)

    Rubiño-Martin, J. A.; Sunyaev, R. A.

    2018-01-01

    We discuss the evolution of the ratio in number of recombinations due to 2 s two photon escape and due to the escape of Lyman- α photons from the resonance during the epoch of cosmological recombination, within the width of the last scattering surface and near its boundaries. We discuss how this ratio evolves in time, and how it defines the profile of the Lyman- α line in the spectrum of CMB. One of the key reasons for explaining its time dependence is the strong overpopulation of the 2 p level relative to the 2 s level at redshifts z ≲ 750.

  8. Brain network segregation and integration during an epoch-related working memory fMRI experiment.

    Science.gov (United States)

    Fransson, Peter; Schiffler, Björn C; Thompson, William Hedley

    2018-05-17

    The characterization of brain subnetwork segregation and integration has previously focused on changes that are detectable at the level of entire sessions or epochs of imaging data. In this study, we applied time-varying functional connectivity analysis together with temporal network theory to calculate point-by-point estimates in subnetwork segregation and integration during an epoch-based (2-back, 0-back, baseline) working memory fMRI experiment as well as during resting-state. This approach allowed us to follow task-related changes in subnetwork segregation and integration at a high temporal resolution. At a global level, the cognitively more taxing 2-back epochs elicited an overall stronger response of integration between subnetworks compared to the 0-back epochs. Moreover, the visual, sensorimotor and fronto-parietal subnetworks displayed characteristic and distinct temporal profiles of segregation and integration during the 0- and 2-back epochs. During the interspersed epochs of baseline, several subnetworks, including the visual, fronto-parietal, cingulo-opercular and dorsal attention subnetworks showed pronounced increases in segregation. Using a drift diffusion model we show that the response time for the 2-back trials are correlated with integration for the fronto-parietal subnetwork and correlated with segregation for the visual subnetwork. Our results elucidate the fast-evolving events with regard to subnetwork integration and segregation that occur in an epoch-related task fMRI experiment. Our findings suggest that minute changes in subnetwork integration are of importance for task performance. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  9. Faint Object Detection in Multi-Epoch Observations via Catalog Data Fusion

    Energy Technology Data Exchange (ETDEWEB)

    Budavári, Tamás; Szalay, Alexander S. [Department of Physics and Astronomy, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 (United States); Loredo, Thomas J. [Cornell Center for Astrophysics and Planetary Science, Cornell University, Ithaca, NY 14853 (United States)

    2017-03-20

    Astronomy in the time-domain era faces several new challenges. One of them is the efficient use of observations obtained at multiple epochs. The work presented here addresses faint object detection and describes an incremental strategy for separating real objects from artifacts in ongoing surveys. The idea is to produce low-threshold single-epoch catalogs and to accumulate information across epochs. This is in contrast to more conventional strategies based on co-added or stacked images. We adopt a Bayesian approach, addressing object detection by calculating the marginal likelihoods for hypotheses asserting that there is no object or one object in a small image patch containing at most one cataloged source at each epoch. The object-present hypothesis interprets the sources in a patch at different epochs as arising from a genuine object; the no-object hypothesis interprets candidate sources as spurious, arising from noise peaks. We study the detection probability for constant-flux objects in a Gaussian noise setting, comparing results based on single and stacked exposures to results based on a series of single-epoch catalog summaries. Our procedure amounts to generalized cross-matching: it is the product of a factor accounting for the matching of the estimated fluxes of the candidate sources and a factor accounting for the matching of their estimated directions. We find that probabilistic fusion of multi-epoch catalogs can detect sources with similar sensitivity and selectivity compared to stacking. The probabilistic cross-matching framework underlying our approach plays an important role in maintaining detection sensitivity and points toward generalizations that could accommodate variability and complex object structure.

  10. Faint Object Detection in Multi-Epoch Observations via Catalog Data Fusion

    International Nuclear Information System (INIS)

    Budavári, Tamás; Szalay, Alexander S.; Loredo, Thomas J.

    2017-01-01

    Astronomy in the time-domain era faces several new challenges. One of them is the efficient use of observations obtained at multiple epochs. The work presented here addresses faint object detection and describes an incremental strategy for separating real objects from artifacts in ongoing surveys. The idea is to produce low-threshold single-epoch catalogs and to accumulate information across epochs. This is in contrast to more conventional strategies based on co-added or stacked images. We adopt a Bayesian approach, addressing object detection by calculating the marginal likelihoods for hypotheses asserting that there is no object or one object in a small image patch containing at most one cataloged source at each epoch. The object-present hypothesis interprets the sources in a patch at different epochs as arising from a genuine object; the no-object hypothesis interprets candidate sources as spurious, arising from noise peaks. We study the detection probability for constant-flux objects in a Gaussian noise setting, comparing results based on single and stacked exposures to results based on a series of single-epoch catalog summaries. Our procedure amounts to generalized cross-matching: it is the product of a factor accounting for the matching of the estimated fluxes of the candidate sources and a factor accounting for the matching of their estimated directions. We find that probabilistic fusion of multi-epoch catalogs can detect sources with similar sensitivity and selectivity compared to stacking. The probabilistic cross-matching framework underlying our approach plays an important role in maintaining detection sensitivity and points toward generalizations that could accommodate variability and complex object structure.

  11. Understanding the epoch of cosmic reionization challenges and progress

    CERN Document Server

    2016-01-01

    The aim of this volume is to summarize the current status and future outlook of the reionization field on both the theoretical and observational fronts. It brings together leading experts in many sub-disciplines, highlighting the measurements that are likely to drive the growing understanding of reionization and the cosmic dawn, and lays out a roadmap to interpreting the wealth of upcoming observations. The birth of the first stars and galaxies, and their impact on the diffuse matter perme­ating the early Universe, is one of the final frontiers in cosmology. Recently, measure­ments of the fluctuations in the cosmic microwave background (CMB), sourced only a few hundred thousand years after the Big Bang, provided robust insight into the overall physical content of our Universe. On the other end of the timeline, groundbreaking telescopes provide us a picture of the complexities of the galaxy-rich universe in which we now live. However, we know almost nothing about the astrophysics of the first billion years. ...

  12. What next-generation 21 cm power spectrum measurements can teach us about the epoch of reionization

    International Nuclear Information System (INIS)

    Pober, Jonathan C.; Morales, Miguel F.; Liu, Adrian; McQuinn, Matthew; Parsons, Aaron R.; Dillon, Joshua S.; Hewitt, Jacqueline N.; Tegmark, Max; Aguirre, James E.; Bowman, Judd D.; Jacobs, Daniel C.; Bradley, Richard F.; Carilli, Chris L.; DeBoer, David R.; Werthimer, Dan J.

    2014-01-01

    A number of experiments are currently working toward a measurement of the 21 cm signal from the epoch of reionization (EoR). Whether or not these experiments deliver a detection of cosmological emission, their limited sensitivity will prevent them from providing detailed information about the astrophysics of reionization. In this work, we consider what types of measurements will be enabled by the next generation of larger 21 cm EoR telescopes. To calculate the type of constraints that will be possible with such arrays, we use simple models for the instrument, foreground emission, and the reionization history. We focus primarily on an instrument modeled after the ∼0.1 km 2 collecting area Hydrogen Epoch of Reionization Array concept design and parameterize the uncertainties with regard to foreground emission by considering different limits to the recently described 'wedge' footprint in k space. Uncertainties in the reionization history are accounted for using a series of simulations that vary the ionizing efficiency and minimum virial temperature of the galaxies responsible for reionization, as well as the mean free path of ionizing photons through the intergalactic medium. Given various combinations of models, we consider the significance of the possible power spectrum detections, the ability to trace the power spectrum evolution versus redshift, the detectability of salient power spectrum features, and the achievable level of quantitative constraints on astrophysical parameters. Ultimately, we find that 0.1 km 2 of collecting area is enough to ensure a very high significance (≳ 30σ) detection of the reionization power spectrum in even the most pessimistic scenarios. This sensitivity should allow for meaningful constraints on the reionization history and astrophysical parameters, especially if foreground subtraction techniques can be improved and successfully implemented.

  13. THE EPOCH OF DISK SETTLING: z ∼ 1 TO NOW

    International Nuclear Information System (INIS)

    Kassin, Susan A.; Gardner, Jonathan P.; Weiner, Benjamin J.; Willmer, C. N. A.; Faber, S. M.; Guhathakurta, Puragra; Koo, David C.; Coil, Alison L.; Cooper, Michael C.; Devriendt, Julien; Dutton, Aaron A.; Metevier, A. J.; Noeske, Kai G.; Primack, Joel R.

    2012-01-01

    We present evidence from a sample of 544 galaxies from the DEEP2 Survey for evolution of the internal kinematics of blue galaxies with stellar masses ranging 8.0 * (M ☉ ) g ). It is unlike the typical pressure-supported velocity dispersion measured for early type galaxies and galaxy bulges. Because both seeing and the width of our spectral slits comprise a significant fraction of the galaxy sizes, σ g integrates over velocity gradients on large scales which can correspond to non-ordered gas kinematics. We compile measurements of galaxy kinematics from the literature over 1.2 < z < 3.8 and do not find any trends with redshift, likely for the most part, because these data sets are biased toward the most highly star-forming systems. In summary, over the last ∼8 billion years since z = 1.2, blue galaxies evolve from disordered to ordered systems as they settle to become the rotation-dominated disk galaxies observed in the universe today, with the most massive galaxies being the most evolved at any time.

  14. Heavy metals in human bones in different historical epochs.

    Science.gov (United States)

    Martínez-García, M J; Moreno, J M; Moreno-Clavel, J; Vergara, N; García-Sánchez, A; Guillamón, A; Portí, M; Moreno-Grau, S

    2005-09-15

    The concentration of the metals lead, copper, zinc, cadmium and iron was determined in bone remains belonging to 30 individuals buried in the Region of Cartagena dating from different historical periods and in eight persons who had died in recent times. The metals content with respect to lead, cadmium and copper was determined either by anodic stripping voltammetry or by atomic absorption spectroscopy on the basis of the concentrations present in the bone remains. In all cases, zinc and iron were quantified by means of atomic absorption spectroscopy. The lead concentrations found in the bone remains in our city are greater than those reported in the literature for other locations. This led to the consideration of the sources of these metals in our area, both the contribution from atmospheric aerosols as well as that from the soil in the area. Correlation analysis leads us to consider the presence of the studied metals in the analysed bone samples to be the consequence of analogous inputs, namely the inhalation of atmospheric aerosols and diverse contributions in the diet. The lowest values found in the studied bone remains correspond to the Neolithic period, with similar contents to present-day samples with respect to lead, copper, cadmium and iron. As regards the evolution over time of the concentrations of the metals under study, a clear increase in these is observed between the Neolithic period and the grouping made up of the Bronze Age, Roman domination and the Byzantine period. The trend lines used to classify the samples into 7 periods show that the maximum values of lead correspond to the Roman and Byzantine periods. For copper, this peak is found in the Byzantine Period and for iron, in the Islamic Period. Zinc shows an increasing tendency over the periods under study and cadmium is the only metal whose trend lines shows a decreasing slope.

  15. Stochastic evolution of cosmological parameters in the early universe

    Indian Academy of Sciences (India)

    We develop a stochastic formulation of cosmology in the early universe, after considering the scatter in the redshift-apparent magnitude diagram in the early epochs as an observational evidence for the non-deterministic evolution of early universe. We consider the stochastic evolution of density parameter in the early ...

  16. The Square Kilometre Array Epoch of Reionisation and Cosmic Dawn Experiment

    Science.gov (United States)

    Trott, Cathryn M.

    2018-05-01

    The Square Kilometre Array (SKA) Epoch of Reionisation and Cosmic Dawn (EoR/CD) experiments aim to explore the growth of structure and production of ionising radiation in the first billion years of the Universe. Here I describe the experiments planned for the future low-frequency components of the Observatory, and work underway to define, design and execute these programs.

  17. Different habitats within a region contain evolutionary heritage from different epochs depending on the abiotic environment

    NARCIS (Netherlands)

    Bartish, I.V.; Ozinga, W.A.; Bartish, M.I.; Wamelink, G.W.W.; Hennekens, S.M.; Prinzing, Andreas

    2016-01-01

    Aim: Biodiversity hot-spots are regions containing evolutionary heritage from ancient or recent geological epochs, i.e. evolutionary 'museums' or 'cradles', respectively. We hypothesize that: (1) there are also 'museums' and 'cradles' within regions - some species pools of particular habitat

  18. Detectability of the 21-cm CMB cross-correlation from the epoch of reionization

    NARCIS (Netherlands)

    Tashiro, Hiroyuki; Aghanim, Nabila; Langer, Mathieu; Douspis, Marian; Zaroubi, Saleem; Jelic, Vibor

    The 21-cm line fluctuations and the cosmic microwave background (CMB) are powerful probes of the epoch of reionization of the Universe. We study the potential of the cross-correlation between 21-cm line fluctuations and CMB anisotropy to obtain further constraints on the reionization history. We

  19. Importance of epoch length and registration time on accelerometer measurements in younger children

    DEFF Research Database (Denmark)

    Dencker, M; Svensson, J; El-Naaman, B

    2012-01-01

    The aim of this study was to investigate the effect of epoch length on accumulation of minutes of physical activity per day over a spectrum of intensities, and the effect that selection of number of hours of acceptable registration required per day had on number of days that were considered accep...

  20. Polarization leakage in epoch of reionization windows : The Low Frequency Array Case

    NARCIS (Netherlands)

    Asad, Khan

    2017-01-01

    The farther we look in space, the earlier we see in time. By observing a radio signal of 21cm wavelength coming from the epoch of reionization, when the universe was less than a billion years old, we can understand how the first stars, galaxies and black holes formed. This signal has not been

  1. The Corporate University's Role in Managing an Epoch in Learning Organisation Innovation

    Science.gov (United States)

    Dealtry, Richard

    2006-01-01

    Purpose: The purpose of this paper is to set the scene for some radical epochal thinking about the approach and future strategic directions in the management of organisational learning, following the author's earlier editorial theme concerning the need for exploration and innovation in organisational learning management.…

  2. The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts

    DEFF Research Database (Denmark)

    Bian, Chao; Hu, Yinchang; Ravi, Vydianathan

    2016-01-01

    five Hox clusters. Differential gene expression among three varieties provides insights into the genetic basis of colour variation. A potential heterogametic sex chromosome is identified in the female arowana karyotype, suggesting that the sex is determined by a ZW/ZZ sex chromosomal system. The high...

  3. The effect of epoch length on estimated EEG functional connectivity and brain network organisation

    Science.gov (United States)

    Fraschini, Matteo; Demuru, Matteo; Crobe, Alessandra; Marrosu, Francesco; Stam, Cornelis J.; Hillebrand, Arjan

    2016-06-01

    Objective. Graph theory and network science tools have revealed fundamental mechanisms of functional brain organization in resting-state M/EEG analysis. Nevertheless, it is still not clearly understood how several methodological aspects may bias the topology of the reconstructed functional networks. In this context, the literature shows inconsistency in the chosen length of the selected epochs, impeding a meaningful comparison between results from different studies. Approach. The aim of this study was to provide a network approach insensitive to the effects that epoch length has on functional connectivity and network reconstruction. Two different measures, the phase lag index (PLI) and the amplitude envelope correlation (AEC) were applied to EEG resting-state recordings for a group of 18 healthy volunteers using non-overlapping epochs with variable length (1, 2, 4, 6, 8, 10, 12, 14 and 16 s). Weighted clustering coefficient (CCw), weighted characteristic path length (L w) and minimum spanning tree (MST) parameters were computed to evaluate the network topology. The analysis was performed on both scalp and source-space data. Main results. Results from scalp analysis show a decrease in both mean PLI and AEC values with an increase in epoch length, with a tendency to stabilize at a length of 12 s for PLI and 6 s for AEC. Moreover, CCw and L w show very similar behaviour, with metrics based on AEC more reliable in terms of stability. In general, MST parameters stabilize at short epoch lengths, particularly for MSTs based on PLI (1-6 s versus 4-8 s for AEC). At the source-level the results were even more reliable, with stability already at 1 s duration for PLI-based MSTs. Significance. The present work suggests that both PLI and AEC depend on epoch length and that this has an impact on the reconstructed network topology, particularly at the scalp-level. Source-level MST topology is less sensitive to differences in epoch length, therefore enabling the comparison of brain

  4. The evolution of Tibetan representation and preferentiality in public employment during the Post-fenpei period in China: Insights from new data sources

    NARCIS (Netherlands)

    A.M. Fischer (Andrew Martín); A. Zenz (Adrian)

    2016-01-01

    textabstractThis paper exploits a new and exciting source of data on public employment recruitment in order to analyse the evolution of Tibetan representation and preferential hiring practices in public employment in all Tibetan areas from 2007 to 2015. Despite the limitations of these data, they

  5. The Sustainability of Habitability on Terrestrial Planets: Insights, Questions, and Needed Measurements from Mars for Understanding the Evolution of Earth-Like Worlds

    Science.gov (United States)

    Ehlmann, B. L.; Anderson, F. S.; Andrews-Hanna, J.; Catling, D. C.; Christensen, P. R.; Cohen, B. A.; Dressing, C. D.; Edwards, C. S.; Elkins-Tanton, L. T.; Farley, K. A.; hide

    2016-01-01

    What allows a planet to be both within a potentially habitable zone and sustain habitability over long geologic time? With the advent of exoplanetary astronomy and the ongoing discovery of terrestrial-type planets around other stars, our own solar system becomes a key testing ground for ideas about what factors control planetary evolution. Mars provides the solar systems longest record of the interplay of the physical and chemical processes relevant to habitability on an accessible rocky planet with an atmosphere and hydrosphere. Here we review current understanding and update the timeline of key processes in early Mars history. We then draw on knowledge of exoplanets and the other solar system terrestrial planets to identify six broad questions of high importance to the development and sustaining of habitability (unprioritized): (1) Is small planetary size fatal? (2) How do magnetic fields influence atmospheric evolution? (3) To what extent does starting composition dictate subsequent evolution, including redox processes and the availability of water and organics? (4) Does early impact bombardment have a net deleterious or beneficial influence? (5) How do planetary climates respond to stellar evolution, e.g., sustaining early liquid water in spite of a faint young Sun? (6) How important are the timescales of climate forcing and their dynamical drivers? Finally, we suggest crucial types of Mars measurements (unprioritized) to address these questions: (1) in situ petrology at multiple units/sites; (2) continued quantification of volatile reservoirs and new isotopic measurements of H, C, N, O, S, Cl, and noble gases in rocks that sample multiple stratigraphic sections; (3) radiometric age dating of units in stratigraphic sections and from key volcanic and impact units; (4) higher-resolution measurements of heat flux, subsurface structure, and magnetic field anomalies coupled with absolute age dating. Understanding the evolution of early Mars will feed forward to

  6. Modeling the Radio Foreground for Detection of CMB Spectral Distortions from the Cosmic Dawn and the Epoch of Reionization

    Energy Technology Data Exchange (ETDEWEB)

    Sathyanarayana Rao, Mayuri; Subrahmanyan, Ravi; Shankar, N Udaya [Raman Research Institute, C V Raman Avenue, Sadashivanagar, Bangalore 560080 (India); Chluba, Jens, E-mail: mayuris@rri.res.in [Jodrell Bank Centre for Astrophysics, University of Manchester, Oxford Road, M13 9PL (United Kingdom)

    2017-05-01

    Cosmic baryon evolution during the Cosmic Dawn and Reionization results in redshifted 21-cm spectral distortions in the cosmic microwave background (CMB). These encode information about the nature and timing of first sources over redshifts 30–6 and appear at meter wavelengths as a tiny CMB distortion along with the Galactic and extragalactic radio sky, which is orders of magnitude brighter. Therefore, detection requires precise methods to model foregrounds. We present a method of foreground fitting using maximally smooth (MS) functions. We demonstrate the usefulness of MS functions over traditionally used polynomials to separate foregrounds from the Epoch of Reionization (EoR) signal. We also examine the level of spectral complexity in plausible foregrounds using GMOSS, a physically motivated model of the radio sky, and find that they are indeed smooth and can be modeled by MS functions to levels sufficient to discern the vanilla model of the EoR signal. We show that MS functions are loss resistant and robustly preserve EoR signal strength and turning points in the residuals. Finally, we demonstrate that in using a well-calibrated spectral radiometer and modeling foregrounds with MS functions, the global EoR signal can be detected with a Bayesian approach with 90% confidence in 10 minutes’ integration.

  7. Multi-epoch analysis of the X-ray spectrum of the active galactic nucleus in NGC 5506

    Science.gov (United States)

    Sun, Shangyu; Guainazzi, Matteo; Ni, Qingling; Wang, Jingchun; Qian, Chenyang; Shi, Fangzheng; Wang, Yu; Bambi, Cosimo

    2018-05-01

    We present a multi-epoch X-ray spectroscopy analysis of the nearby narrow-line Seyfert I galaxy NGC 5506. For the first time, spectra taken by Chandra, XMM-Newton, Suzaku, and NuSTAR - covering the 2000-2014 time span - are analyzed simultaneously, using state-of-the-art models to describe reprocessing of the primary continuum by optical thick matter in the AGN environment. The main goal of our study is determining the spin of the supermassive black hole (SMBH). The nuclear X-ray spectrum is photoelectrically absorbed by matter with column density ≃ 3 × 1022 cm-2. A soft excess is present at energies lower than the photoelectric cut-off. Both photo-ionized and collisionally ionized components are required to fit it. This component is constant over the time-scales probed by our data. The spectrum at energies higher than 2 keV is variable. We propose that its evolution could be driven by flux-dependent changes in the geometry of the innermost regions of the accretion disk. The black hole spin in NGC ,5506 is constrained to be 0.93± _{ 0.04 }^{0.04} at 90% confidence level for one interesting parameter.

  8. X-Ray, UV and Optical Observations of Classical Cepheids: New Insights into Cepheid Evolution, and the Heating and Dynamics of Their Atmospheres

    OpenAIRE

    Engle, Scott G.; Guinan, Edward F.

    2012-01-01

    To broaden the understanding of classical Cepheid structure, evolution and atmospheres, we have extended our continuing secret lives of Cepheids program by obtaining XMM/Chandra X-ray observations, and Hubble space telescope (HST) / cosmic origins spectrograph (COS) FUV-UV spectra of the bright, nearby Cepheids Polaris, {\\delta} Cep and {\\beta} Dor. Previous studies made with the international ultraviolet explorer (IUE) showed a limited number of UV emission lines in Cepheids. The well-known ...

  9. Herbicide resistance-endowing ACCase gene mutations in hexaploid wild oat (Avena fatua): insights into resistance evolution in a hexaploid species

    Science.gov (United States)

    Yu, Q; Ahmad-Hamdani, M S; Han, H; Christoffers, M J; Powles, S B

    2013-01-01

    Many herbicide-resistant weed species are polyploids, but far too little about the evolution of resistance mutations in polyploids is understood. Hexaploid wild oat (Avena fatua) is a global crop weed and many populations have evolved herbicide resistance. We studied plastidic acetyl-coenzyme A carboxylase (ACCase)-inhibiting herbicide resistance in hexaploid wild oat and revealed that resistant individuals can express one, two or three different plastidic ACCase gene resistance mutations (Ile-1781-Leu, Asp-2078-Gly and Cys-2088-Arg). Using ACCase resistance mutations as molecular markers, combined with genetic, molecular and biochemical approaches, we found in individual resistant wild-oat plants that (1) up to three unlinked ACCase gene loci assort independently following Mendelian laws for disomic inheritance, (2) all three of these homoeologous ACCase genes were transcribed, with each able to carry its own mutation and (3) in a hexaploid background, each individual ACCase resistance mutation confers relatively low-level herbicide resistance, in contrast to high-level resistance conferred by the same mutations in unrelated diploid weed species of the Poaceae (grass) family. Low resistance conferred by individual ACCase resistance mutations is likely due to a dilution effect by susceptible ACCase expressed by homoeologs in hexaploid wild oat and/or differential expression of homoeologous ACCase gene copies. Thus, polyploidy in hexaploid wild oat may slow resistance evolution. Evidence of coexisting non-target-site resistance mechanisms among wild-oat populations was also revealed. In all, these results demonstrate that herbicide resistance and its evolution can be more complex in hexaploid wild oat than in unrelated diploid grass weeds. Our data provide a starting point for the daunting task of understanding resistance evolution in polyploids. PMID:23047200

  10. The role of fusion in ant chromosome evolution: insights from cytogenetic analysis using a molecular phylogenetic approach in the genus mycetophylax.

    Science.gov (United States)

    Cardoso, Danon Clemes; das Graças Pompolo, Silvia; Cristiano, Maykon Passos; Tavares, Mara Garcia

    2014-01-01

    Among insect taxa, ants exhibit one of the most variable chromosome numbers ranging from n = 1 to n = 60. This high karyotype diversity is suggested to be correlated to ants diversification. The karyotype evolution of ants is usually understood in terms of Robertsonian rearrangements towards an increase in chromosome numbers. The ant genus Mycetophylax is a small monogynous basal Attini ant (Formicidae: Myrmicinae), endemic to sand dunes along the Brazilian coastlines. A recent taxonomic revision validates three species, Mycetophylax morschi, M. conformis and M. simplex. In this paper, we cytogenetically characterized all species that belongs to the genus and analyzed the karyotypic evolution of Mycetophylax in the context of a molecular phylogeny and ancestral character state reconstruction. M. morschi showed a polymorphic number of chromosomes, with colonies showing 2n = 26 and 2n = 30 chromosomes. M. conformis presented a diploid chromosome number of 30 chromosomes, while M. simplex showed 36 chromosomes. The probabilistic models suggest that the ancestral haploid chromosome number of Mycetophylax was 17 (Likelihood framework) or 18 (Bayesian framework). The analysis also suggested that fusions were responsible for the evolutionary reduction in chromosome numbers of M. conformis and M. morschi karyotypes whereas fission may determines the M. simplex karyotype. These results obtained show the importance of fusions in chromosome changes towards a chromosome number reduction in Formicidae and how a phylogenetic background can be used to reconstruct hypotheses about chromosomes evolution.

  11. Comparative genomics of phylogenetically diverse unicellular eukaryotes provide new insights into the genetic basis for the evolution of the programmed cell death machinery.

    Science.gov (United States)

    Nedelcu, Aurora M

    2009-03-01

    Programmed cell death (PCD) represents a significant component of normal growth and development in multicellular organisms. Recently, PCD-like processes have been reported in single-celled eukaryotes, implying that some components of the PCD machinery existed early in eukaryotic evolution. This study provides a comparative analysis of PCD-related sequences across more than 50 unicellular genera from four eukaryotic supergroups: Unikonts, Excavata, Chromalveolata, and Plantae. A complex set of PCD-related sequences that correspond to domains or proteins associated with all main functional classes--from ligands and receptors to executors of PCD--was found in many unicellular lineages. Several PCD domains and proteins previously thought to be restricted to animals or land plants are also present in unicellular species. Noteworthy, the yeast, Saccharomyces cerevisiae--used as an experimental model system for PCD research, has a rather reduced set of PCD-related sequences relative to other unicellular species. The phylogenetic distribution of the PCD-related sequences identified in unicellular lineages suggests that the genetic basis for the evolution of the complex PCD machinery present in extant multicellular lineages has been established early in the evolution of eukaryotes. The shaping of the PCD machinery in multicellular lineages involved the duplication, co-option, recruitment, and shuffling of domains already present in their unicellular ancestors.

  12. trash epoch

    Directory of Open Access Journals (Sweden)

    Elena Grigoryeva

    2012-02-01

    Full Text Available Unconventionally, the editorial of this issue begins with two epigraphs:trash1. foolish ideas or talk; nonsense;2. Chiefly US and Canadian useless or unwanted matter or objects;3. a literary or artistic production of poor quality;4. Chiefly US and Canadian a poor or worthless person or a group of such people.[Collins English Dictionary]You got to make good out of bad. That's all there is to make it with. Robert Penn Warren, “All the King’s Men”.But before talking about the topic of the issue, we should pay off the debt. The previous (double issue was completely devoted to Irkutsk’s jubilee. We will fill in the gaps and look back on the events of the past year missed by PB. There are a lot of them: the UIA Congress in Tokyo (5-7, the Zodchestvo Festival and the UAR Plenary Meeting in Moscow (16-29, the review competition of graduation works in Erevan (30–39 and Les Ateliers of Urban Planning and Development in Cergy-Pontoise (48–54.The New Year’s news blends into the topic of the issue. This year in Irkutsk discarded Christmas trees began to be recycled into fertilizer. In the Kemerovo region the old Christmas trees are used as food for cows. So the supercilious attitude toward trash is no longer relevant. In the future we shall eat it; actually, we are already eating it. Artists help us adjust to the idea that we will live in the global dump. Trash Muses inspired Zhenya Kraineva and Konstantin Lidin to a diptych about trash art (66–75.The first essential step in waste recycling is to change our view on waste. In people’s minds the dump is turned into a deposit of valuable resources. The detailed text by Andrei Ivanov (90–99 tells us about a slum district obtaining a new status and turning into a historical heritage.It is very urgent to convert trash into resources. On the Earth, mountains of garbage grow twice as fast as the population. 17% of homes in Sweden are heated with garbage. Japan processes 96% of waste, Germany 95%, Poland 16%, Russia only 5%. At this moment the territory of Russia has accumulated 100 billion tons of garbage – there is scarcely any deposit of such a large scale. Waste recycling plants are a vital task for today’s and tomorrow’s architecture (102–105.The architecture itself is no longer designed for centuries. The green standards contain such an essential item as engineering redesign for dismantled or demolished structures. Instead of the philosophical principle “my house is my fortress”, the impermanence is on the agenda today. A house, like a short-life packing or tomorrow’s garbage, is now under the statement of the problem.This issue returns to its regular sections. In the HERITAGE section there is an article by our American contributor Brian Spencer (124–129; and a debut of Fabio Todeschini, Professor from South Africa (130–136. In the LANDSCAPE section we start publishing a series of articles by Olga Smirnova (142–147, a Krasnoyarsk architect, poet and traveler…

  13. The Galaxy mass function up to z =4 in the GOODS-MUSIC sample: into the epoch of formation of massive galaxies

    Science.gov (United States)

    Fontana, A.; Salimbeni, S.; Grazian, A.; Giallongo, E.; Pentericci, L.; Nonino, M.; Fontanot, F.; Menci, N.; Monaco, P.; Cristiani, S.; Vanzella, E.; de Santis, C.; Gallozzi, S.

    2006-12-01

    Aims.The goal of this work is to measure the evolution of the Galaxy Stellar Mass Function and of the resulting Stellar Mass Density up to redshift ≃4, in order to study the assembly of massive galaxies in the high redshift Universe. Methods: .We have used the GOODS-MUSIC catalog, containing 3000 Ks-selected galaxies with multi-wavelength coverage extending from the U band to the Spitzer 8 μm band, of which 27% have spectroscopic redshifts and the remaining fraction have accurate photometric redshifts. On this sample we have applied a standard fitting procedure to measure stellar masses. We compute the Galaxy Stellar Mass Function and the resulting Stellar Mass Density up to redshift ≃4, taking into proper account the biases and incompleteness effects. Results: .Within the well known trend of global decline of the Stellar Mass Density with redshift, we show that the decline of the more massive galaxies may be described by an exponential timescale of ≃6 Gyr up to z≃ 1.5, and proceeds much faster thereafter, with an exponential timescale of ≃0.6 Gyr. We also show that there is some evidence for a differential evolution of the Galaxy Stellar Mass Function, with low mass galaxies evolving faster than more massive ones up to z≃ 1{-}1.5 and that the Galaxy Stellar Mass Function remains remarkably flat (i.e. with a slope close to the local one) up to z≃ 1{-}1.3. Conclusions: .The observed behaviour of the Galaxy Stellar Mass Function is consistent with a scenario where about 50% of present-day massive galaxies formed at a vigorous rate in the epoch between redshift 4 and 1.5, followed by a milder evolution until the present-day epoch.

  14. Hydro-mechanical evolution of the EDZ as transport path for radionuclides and gas: insights from the Mont Terri rock laboratory (Switzerland)

    International Nuclear Information System (INIS)

    Paul Marschall, P.; Giger, S.; La Vassière De, R.

    2017-01-01

    The excavation damaged zone (EDZ) around the backfilled underground structures of a geological repository represents a release path for radionuclides, which needs to be addressed in the assessment of long-term safety. Additionally, the EDZ may form a highly efficient escape route for corrosion and degradation gases, thus limiting the gas overpressures in the backfilled repository structures. The efficiency of this release path depends not only on the shape and extent of the EDZ, but also on the self-sealing capacity of the host rock formation and the prevailing state conditions, such as in situ stresses and pore pressure. The hydro-mechanical and chemico-osmotic phenomena associated with the formation and temporal evolution of the EDZ are complex, thus precluding a detailed representation of the EDZ in conventional modelling tools for safety assessment. Therefore, simplified EDZ models, able to mimic the safety-relevant functional features of the EDZ in a traceable manner are required. In the framework of the Mont Terri Project, a versatile modelling approach has been developed for the simulation of flow and transport processes along the EDZ with the goal of capturing the evolution of hydraulic significance of the EDZ after closure of the backfilled underground structures. The approach draws on both empirical evidence and experimental data, collected in the niches and tunnels of the Mont Terri rock laboratory. The model was benchmarked with a data set from an in situ self-sealing experiment at the Mont Terri rock laboratory. This paper summarises the outcomes of the benchmark exercise that comprises relevant empirical evidence, experimental data bases and the conceptual framework for modelling the evolution of the hydraulic significance of the EDZ around a backfilled tunnel section during the entire re-saturation phase. (authors)

  15. A novel C-type lysozyme from Mytilus galloprovincialis: insight into innate immunity and molecular evolution of invertebrate C-type lysozymes.

    Directory of Open Access Journals (Sweden)

    Qing Wang

    Full Text Available A c-type lysozyme (named as MgCLYZ gene was cloned from the mussel Mytilus galloprovincialis. Blast analysis indicated that MgCLYZ was a salivary c-type lysozyme which was mainly found in insects. The nucleotide sequence of MgCLYZ was predicted to encode a polypeptide of 154 amino acid residues with the signal peptide comprising the first 24 residues. The deduced mature peptide of MgCLYZ was of a calculated molecular weight of 14.4 kD and a theoretical isoelectric point (pI of 8.08. Evolution analysis suggested that bivalve branch of the invertebrate c-type lysozymes phylogeny tree underwent positive selection during evolution. By quantitative real-time RT-PCR (qRT-PCR analysis, MgCLYZ transcript was widely detected in all examined tissues and responded sensitively to bacterial challenge in hemocytes and hepatopancreas. The optimal temperature and pH of recombinant MgCLYZ (rMgCLYZ were 20°C and 4, respectively. The rMgCLYZ displayed lytic activities against Gram-positive bacteria including Micrococcus luteus and Staphyloccocus aureus, and Gram-negative bacteria including Vibrio anguillarum, Enterobacter cloacae, Pseudomonas putida, Proteus mirabilis and Bacillus aquimaris. These results suggest that MgCLYZ perhaps play an important role in innate immunity of M. galloprovincialis, and invertebrate c-type lysozymes might be under positive selection in a species-specific manner during evolution for undergoing adaptation to different environment and diverse pathogens.

  16. Hydro-mechanical evolution of the EDZ as transport path for radionuclides and gas: insights from the Mont Terri rock laboratory (Switzerland)

    Energy Technology Data Exchange (ETDEWEB)

    Paul Marschall, P.; Giger, S. [National Cooperative for the Disposal of Radioactive Waste (NAGRA), Wettingen (Switzerland); La Vassière De, R. [Agence Nationale pour la Gestion des Déchets Radioactifs ANDRA, Meuse Haute-Marne, Center RD 960, Bure (France); and others

    2017-04-15

    The excavation damaged zone (EDZ) around the backfilled underground structures of a geological repository represents a release path for radionuclides, which needs to be addressed in the assessment of long-term safety. Additionally, the EDZ may form a highly efficient escape route for corrosion and degradation gases, thus limiting the gas overpressures in the backfilled repository structures. The efficiency of this release path depends not only on the shape and extent of the EDZ, but also on the self-sealing capacity of the host rock formation and the prevailing state conditions, such as in situ stresses and pore pressure. The hydro-mechanical and chemico-osmotic phenomena associated with the formation and temporal evolution of the EDZ are complex, thus precluding a detailed representation of the EDZ in conventional modelling tools for safety assessment. Therefore, simplified EDZ models, able to mimic the safety-relevant functional features of the EDZ in a traceable manner are required. In the framework of the Mont Terri Project, a versatile modelling approach has been developed for the simulation of flow and transport processes along the EDZ with the goal of capturing the evolution of hydraulic significance of the EDZ after closure of the backfilled underground structures. The approach draws on both empirical evidence and experimental data, collected in the niches and tunnels of the Mont Terri rock laboratory. The model was benchmarked with a data set from an in situ self-sealing experiment at the Mont Terri rock laboratory. This paper summarises the outcomes of the benchmark exercise that comprises relevant empirical evidence, experimental data bases and the conceptual framework for modelling the evolution of the hydraulic significance of the EDZ around a backfilled tunnel section during the entire re-saturation phase. (authors)

  17. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Science.gov (United States)

    Wilburn, Damien B; Bowen, Kathleen E; Doty, Kari A; Arumugam, Sengodagounder; Lane, Andrew N; Feldhoff, Pamela W; Feldhoff, Richard C

    2014-01-01

    In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP) superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF) is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s) without the immediate need for complementary mutations. Consequently, this unique

  18. Structural insights into the evolution of a sexy protein: novel topology and restricted backbone flexibility in a hypervariable pheromone from the red-legged salamander, Plethodon shermani.

    Directory of Open Access Journals (Sweden)

    Damien B Wilburn

    Full Text Available In response to pervasive sexual selection, protein sex pheromones often display rapid mutation and accelerated evolution of corresponding gene sequences. For proteins, the general dogma is that structure is maintained even as sequence or function may rapidly change. This phenomenon is well exemplified by the three-finger protein (TFP superfamily: a diverse class of vertebrate proteins co-opted for many biological functions - such as components of snake venoms, regulators of the complement system, and coordinators of amphibian limb regeneration. All of the >200 structurally characterized TFPs adopt the namesake "three-finger" topology. In male red-legged salamanders, the TFP pheromone Plethodontid Modulating Factor (PMF is a hypervariable protein such that, through extensive gene duplication and pervasive sexual selection, individual male salamanders express more than 30 unique isoforms. However, it remained unclear how this accelerated evolution affected the protein structure of PMF. Using LC/MS-MS and multidimensional NMR, we report the 3D structure of the most abundant PMF isoform, PMF-G. The high resolution structural ensemble revealed a highly modified TFP structure, including a unique disulfide bonding pattern and loss of secondary structure, that define a novel protein topology with greater backbone flexibility in the third peptide finger. Sequence comparison, models of molecular evolution, and homology modeling together support that this flexible third finger is the most rapidly evolving segment of PMF. Combined with PMF sequence hypervariability, this structural flexibility may enhance the plasticity of PMF as a chemical signal by permitting potentially thousands of structural conformers. We propose that the flexible third finger plays a critical role in PMF:receptor interactions. As female receptors co-evolve, this flexibility may allow PMF to still bind its receptor(s without the immediate need for complementary mutations. Consequently

  19. Field-based insights to the evolution of specialization: plasticity and fitness across habitats in a specialist/generalist species pair.

    Science.gov (United States)

    Griffith, Timothy; Sultan, Sonia E

    2012-04-01

    Factors promoting the evolution of specialists versus generalists have been little studied in ecological context. In a large-scale comparative field experiment, we studied genotypes from naturally evolved populations of a closely related generalist/specialist species pair (Polygonum persicaria and P. hydropiper), reciprocally transplanting replicates of multiple lines into open and partially shaded sites where the species naturally co-occur. We measured relative fitness, individual plasticity, herbivory, and genetic variance expressed in the contrasting light habitats at both low and high densities. Fitness data confirmed that the putative specialist out-performed the generalist in only one environment, the favorable full sun/low-density environment to which it is largely restricted in nature, while the generalist had higher lifetime reproduction in both canopy and dense neighbor shade. The generalist, P. persicaria, also expressed greater adaptive plasticity for biomass allocation and leaf size in shaded conditions than the specialist. We found no evidence that the ecological specialization of P. hydropiper reflects either genetically based fitness trade-offs or maintenance costs of plasticity, two types of genetic constraint often invoked to prevent the evolution of broadly adaptive genotypes. However, the patterns of fitness variance and herbivore damage revealed how release from herbivory in a new range can cause an introduced species to evolve as a specialist in that range, a surprising finding with important implications for invasion biology. Patterns of fitness variance between and within sites are also consistent with a possible role for the process of mutation accumulation (in this case, mutations affecting shade-expressed phenotypes) in the evolution and/or maintenance of specialization in P. hydropiper.

  20. Period, epoch, and prediction errors of ephemerides from continuous sets of timing measurements

    Science.gov (United States)

    Deeg, H. J.

    2015-06-01

    Space missions such as Kepler and CoRoT have led to large numbers of eclipse or transit measurements in nearly continuous time series. This paper shows how to obtain the period error in such measurements from a basic linear least-squares fit, and how to correctly derive the timing error in the prediction of future transit or eclipse events. Assuming strict periodicity, a formula for the period error of these time series is derived, σP = σT (12 / (N3-N))1 / 2, where σP is the period error, σT the timing error of a single measurement, and N the number of measurements. Compared to the iterative method for period error estimation by Mighell & Plavchan (2013), this much simpler formula leads to smaller period errors, whose correctness has been verified through simulations. For the prediction of times of future periodic events, usual linear ephemeris were epoch errors are quoted for the first time measurement, are prone to an overestimation of the error of that prediction. This may be avoided by a correction for the duration of the time series. An alternative is the derivation of ephemerides whose reference epoch and epoch error are given for the centre of the time series. For long continuous or near-continuous time series whose acquisition is completed, such central epochs should be the preferred way for the quotation of linear ephemerides. While this work was motivated from the analysis of eclipse timing measures in space-based light curves, it should be applicable to any other problem with an uninterrupted sequence of discrete timings for which the determination of a zero point, of a constant period and of the associated errors is needed.

  1. EPOCH 0013 - the impact of elevated CO{sub 2} upon the response of European forests

    Energy Technology Data Exchange (ETDEWEB)

    Lee, H.S.J.; Jarvis, P.G. [University of Edinburgh, Edinburgh (United Kingdom). Inst. of Ecology and Resource Management

    1994-12-31

    Apart from details on the EPOCH project, this paper includes information on the currently funded project under the Environment R & D programme (the likely impact of rising CO{sub 2} and temperature on European forests, 1993 & 1994) and the proposed extension of this is Environment R & D, phase II (predicting the response of European forests to global change, 1995 & 1996). Some suggestions for future work under Framework IV are also proposed. 30 refs., 14 refs., 8 tabs.

  2. The Reel Deal: Interpreting HST Multi-Epoch Movies of YSO Jets.

    Science.gov (United States)

    Frank, Adam

    2010-09-01

    The goal of this proposal is to bring the theoretical interpretation of Young Stellar Object jets and their environments to a new level of realism. We propose to build on the results of a successful Cycle 16 observing proposal that has obtained 3rd epoch images of HH jets. We will use Adaptive Mesh Refinement MHD simulations {developed by our team} to carry forward a detailed program of modeling and interpretation of the time-dependent behavior revealed in the new, extended multi-epoch data set. Only with the third epoch observations can we explore forces: i.e. accelerations, decelerations and structural changes to develop an accurate understanding of physical processes occurring in hypersonic, magnetized jet flows. Our studies will allow us to characterize the jets and, therefore, make the crucial link with jet central engines. We note an innovative feature of our project is its link with laboratory astrophysical experiments of jets. Our analysis of the observations will be used to determine future laboratory experiments which will explore A?clumpyA? jet propagation issues.

  3. Clinical and Cost Comparison Evaluation of Inpatient Versus Outpatient Administration of EPOCH-Containing Regimens in Non-Hodgkin Lymphoma.

    Science.gov (United States)

    Evans, Sarah S; Gandhi, Arpita S; Clemmons, Amber B; DeRemer, David L

    2017-08-01

    Etoposide, prednisone, vincristine, cyclophosphamide, doxorubicin (EPOCH)-containing regimens are frequently utilized in non-Hodgkin's lymphoma, however, the incidence of febrile neutropenia (FN) in patients receiving inpatient versus outpatient EPOCH has not been described. Additionally, no comparisons have been made regarding financial implications of EPOCH administration in either setting. This study's primary objective was to compare hospital admissions for FN in patients receiving inpatient or outpatient EPOCH. A single-center, institutional review board-approved review was conducted for adults receiving EPOCH beginning January 2010. Clinical and financial data were collected through chart review and the institution's financial department. Descriptive statistics were utilized for analysis. A total of 25 patients received 86 cycles of an EPOCH-containing regimen (61 [70.9%] inpatient). Five (8.2%) inpatient cycles resulted in an admission for FN compared to 4 (16%) outpatient cycles. Prophylactic antifungal and antiviral agents were prescribed more often after inpatient cycles (>80%) compared to outpatient cycles (cost savings of approximately US$141 116 for both chemotherapy costs and hospital day avoidance. EPOCH-containing regimens can be safely administered in the outpatient setting, which may result in cost savings for healthcare institutions.

  4. Insights into the evolution of the new variant rabbit haemorrhagic disease virus (GI.2) and the identification of novel recombinant strains.

    Science.gov (United States)

    Silvério, D; Lopes, A M; Melo-Ferreira, J; Magalhães, M J; Monterroso, P; Serronha, A; Maio, E; Alves, P C; Esteves, P J; Abrantes, J

    2018-02-11

    Rabbit haemorrhagic disease (RHD) is a viral disease that affects the European rabbit. RHD was detected in 1984 in China and rapidly disseminated worldwide causing a severe decline in wild rabbit populations. The aetiological agent, rabbit haemorrhagic disease virus (RHDV), is an RNA virus of the family Caliciviridae, genus Lagovirus. Pathogenic (G1-G6 or variants GI.1a-GI.1d) and non-pathogenic strains (GI.4) have been characterized. In 2010, a new variant of RHDV, RHDV2/RHDVb/GI.2, was detected in France. GI.2 arrived to the Iberian Peninsula in 2011, and several recombination events were reported. Here, we sequenced full genomes of 19 samples collected in Portugal between 2014 and 2016. New GI.2 recombinant strains were detected, including triple recombinants. These recombinants possess a non-structural protein p16 related to a non-pathogenic strain. Evolutionary analyses were conducted on GI.2 VP60 sequences. Estimated time to the most recent common ancestor (tMRCA) suggests an emergence of GI.2 in July 2008, not distant from its first detection in 2010. This is the first study on GI.2 evolution and highlights the need of continued monitoring and characterization of complete genome sequences when studying lagoviruses' evolution. © 2018 Blackwell Verlag GmbH.

  5. Morphological analysis of Nevado de Toluca volcano (Mexico): new insights into the structure and evolution of an andesitic to dacitic stratovolcano

    Science.gov (United States)

    Norini, Gianluca; Groppelli, Gianluca; Capra, Lucia; De Beni, Emanuela

    2004-09-01

    We present a morphological analysis of Nevado de Toluca volcano located 80 km WSW of Mexico City based on digital elevation model study, where slope and aspect maps have been generated and analysed. Aerial photograph and satellite image observations improve the morphological analysis. The synoptic view which is offered by this analysis allowed for recognition and localization of the main volcanic and tectonic features of the area. On the basis of digital elevation model value distribution and surface textures, five morphological domains were defined. The most interesting domain, south of the crater, reflects the occurrence of an ancient complex volcano distinct from the adjacent areas. Interaction between the volcanic and volcano-tectonic evolution and the basement produced the other domains. Single volcanic edifices, like lava domes and scoria cones, and eruptive fractures were recognized. Finally, flank collapse scarps opened to the east and to the north were identified and four relevant morphostructural lineaments and their possible role in the Nevado de Toluca geological and structural evolution are discussed.

  6. Insight into the Role of Surface Wettability in Electrocatalytic Hydrogen Evolution Reactions Using Light-Sensitive Nanotubular TiO2 Supported Pt Electrodes

    Science.gov (United States)

    Meng, Chenhui; Wang, Bing; Gao, Ziyue; Liu, Zhaoyue; Zhang, Qianqian; Zhai, Jin

    2017-02-01

    Surface wettability is of importance for electrochemical reactions. Herein, its role in electrochemical hydrogen evolution reactions is investigated using light-sensitive nanotubular TiO2 supported Pt as hydrogen evolution electrodes (HEEs). The HEEs are fabricated by photocatalytic deposition of Pt particles on TiO2 nanotubes followed by hydrophobization with vaporized octadecyltrimethoxysilane (OTS) molecules. The surface wettability of HEEs is subsequently regulated in situ from hydrophobicity to hydrophilicity by photocatalytic decomposition of OTS molecules using ultraviolet light. It is found that hydrophilic HEEs demonstrate a larger electrochemical active area of Pt and a lower adhesion force to a gas bubble when compared with hydrophobic ones. The former allows more protons to react on the electrode surface at small overpotential so that a larger current is produced. The latter leads to a quick release of hydrogen gas bubbles from the electrode surface at large overpotential, which ensures the contact between catalysts and electrolyte. These two characteristics make hydrophilic HEEs generate a much high current density for HERs. Our results imply that the optimization of surface wettability is of significance for improving the electrocatalytic activity of HEEs.

  7. Improving the repeatability of Motor Unit Number Index (MUNIX) by introducing additional epochs at low contraction levels.

    Science.gov (United States)

    Peng, Yun; Zhang, Yingchun

    2017-07-01

    To evaluate the repeatability of (Motor Unit Number Index) MUNIX under repeatability conditions, specify the origin of variations and provide strategies for quality control. MUNIX calculations were performed on the bicep brachii muscles of eight healthy subjects. Negative effect of suboptimal electrode positions on MUNIX accuracy was eliminated by employing the high-density surface electromyography technique. MUNIX procedures that utilized a variety of surface interferential pattern (SIP) epoch recruitment strategies (including the original MUNIX procedure, two proposed improvement strategies and their combinations) were described. For each MUNIX procedure, ten thousands of different SIP pools were constructed by randomly recruiting necessary SIP epochs from a large SIP epoch pool (3 datasets, 9 independent electromyography recordings at different contraction levels per dataset and 10 SIP epochs per recording) and implemented for MUNIX calculation. The repeatability of each MUNIX procedure was assessed by summarizing the resulting MUNIX distribution and compared to investigate the effect of SIP epoch selection strategy on repeatability performance. SIP epochs selected at lower contraction levels have a stronger influence on the repeatability of MUNIX than those selected at higher contraction levels. MUNIX under repeatability conditions follows a normal distribution and the standard deviation can be significantly reduced by introducing more epochs near the MUNIX definition line. The MUNIX technique shows an inherent variation attributable to SIP epochs at low contraction levels. It is recommended that more epochs should be sampled at these low contraction levels to improve the repeatability. The present study thoroughly documented the inherent variation of MUNIX and the causes, and offered practical solutions to improve the repeatability of MUNIX. Copyright © 2017 International Federation of Clinical Neurophysiology. Published by Elsevier B.V. All rights reserved.

  8. Crustal structure and evolution of the NW Zagros Mountains (Iran): Insights from numerical modeling of the interplay between surface and tectonic processes

    Science.gov (United States)

    Saura, Eduard; Garcia-Castellanos, Daniel; Casciello, Emilio; Vergés, Jaume

    2014-05-01

    Protracted Arabia-Eurasia convergence resulted in the closure of the >2000 km wide Neo-Tethys Ocean from early Late Cretaceous to Recent. This process was controlled by the structure of the NE margin of the Arabian plate, the NE-dipping oceanic subduction beneath Eurasia, the obduction of oceanic lithosphere and the collision of small continental and volcanic arc domains of the SW margin of Eurasia. The evolution of the Zagros Amiran and Mesopotamian foreland basins is studied in this work along a ~700 km long transect in NW Zagros constrained by field, seismic and published data. We use the well-defined geometries and ages of the Amiran and Mesopotamian foreland basins to estimate the elastic thickness of the lithosphere and model the evolution of the deformation to quantitatively link the topographic, tectonic and sedimentary evolution of the system. Modelling results show two major stages of emplacement. The obduction (pre-collision) stage involves the thin thrust sheets of the Kermanshah complex together with the Bisotun basement. The collision stage corresponds to the emplacement of the basement duplex and associated crustal thickening, coeval to the out of sequence emplacement of Gaveh Rud and Imbricated Zone in the hinterland. The geodynamic model is consistent with the history of the foreland basins, with the regional isostasy model, and with a simple scenario for the surface process efficiency. The emplacement of Bisotun basement during obduction tectonically loaded and flexed the Arabian plate triggering deposition in the Amiran foreland basin. The basement units emplaced during the last 10 My, flexed the Arabian plate below the Mesopotamian basin. During this stage, material eroded from the Simply Folded belt and the Imbricated zone was not enough to fill the Mesopotamian basin, which, according to our numerical model results, required a maximum additional sediment supply of 80 m/Myr. This additional supply had to be provided by an axial drainage system

  9. Physical, chemical and mineralogical evolution of the Tolhuaca geothermal system, southern Andes, Chile: Insights into the interplay between hydrothermal alteration and brittle deformation

    Science.gov (United States)

    Sanchez-Alfaro, Pablo; Reich, Martin; Arancibia, Gloria; Pérez-Flores, Pamela; Cembrano, José; Driesner, Thomas; Lizama, Martin; Rowland, Julie; Morata, Diego; Heinrich, Christoph A.; Tardani, Daniele; Campos, Eduardo

    2016-09-01

    In this study, we unravel the physical, chemical and mineralogical evolution of the active Tolhuaca geothermal system in the Andes of southern Chile. We used temperature measurements in the deep wells and geochemical analyses of borehole fluid samples to constrain present-day fluid conditions. In addition, we reconstructed the paleo-fluid temperatures and chemistry from microthermometry and LA-ICP-MS analysis of fluid inclusions taken from well-constrained parageneses in vein samples retrieved from a 1000 m borehole core. Based on core logging, mineralogical observations and fluid inclusions data we identify four stages (S1-S4) of progressive hydrothermal alteration. An early heating event (S1) was followed by the formation of a clay-rich cap in the upper zone (propylitic alteration assemblage at greater depth (S2). Boiling, flashing and brecciation occurred later (S3), followed by a final phase of fluid mixing and boiling (S4). The evolution of hydrothermal alteration at Tolhuaca has produced a mineralogical, hydrological and structural vertical segmentation of the system through the development of a low-permeability, low-cohesion clay-rich cap at shallow depth. The quantitative chemical analyses of fluid inclusions and borehole fluids reveal a significant change in chemical conditions during the evolution of Tolhuaca. Whereas borehole (present-day) fluids are rich in Au, B and As, but Cu-poor (B/Na 100.5, As/Na 10- 1.1, Cu/Na 10- 4.2), the paleofluids trapped in fluid inclusions are Cu-rich but poor in B and As (B/Na 10- 1, As/Na 10- 2.5, Cu/Na 10- 2.5 in average). We interpret the fluctuations in fluid chemistry at Tolhuaca as the result of transient supply of metal-rich, magmatically derived fluids where As, Au and Cu are geochemically decoupled. Since these fluctuating physical and chemical conditions at the reservoir produced a mineralogical vertical segmentation of the system that affects the mechanical and hydrological properties of host rock, we explored

  10. The Rhyacian El Cortijo suture zone: Aeromagnetic signature and insights for the geodynamic evolution of the southwestern Rio de la Plata craton, Argentina

    Directory of Open Access Journals (Sweden)

    Carlos J. Chernicoff

    2014-01-01

    We envisage the pre-Neoproterozoic evolution of the Tandilia belt to have been initiated by the extension of Neoarchean (∼2650 Ma crust occurred during Siderian times (2500–2300 Ma, causing the separation between the Balcarce, Tandilia and Buenos Aires terranes, and the development of narrow oceans at both north and south sides of the Tandilia terrane, accompanied by ∼2300–2200 Ma sedimentation over transitional –continental to oceanic– crust, and arc magmatism developed in the Tandilia terrane. The island arc represented by the El Cortijo Formation was also developed at this time. At late Rhyacian times, it occurred in both the closure of the narrow oceans developed previously, the entrapment of the El Cortijo island arc, as well as anatectic magmatism in the Balcarce terrane.

  11. Early Cretaceous high-Ti and low-Ti mafic magmatism in Southeastern Tibet: Insights into magmatic evolution of the Comei Large Igneous Province

    Science.gov (United States)

    Wang, Yaying; Zeng, Lingsen; Asimow, Paul D.; Gao, Li-E.; Ma, Chi; Antoshechkina, Paula M.; Guo, Chunli; Hou, Kejun; Tang, Suohan

    2018-01-01

    The Dala diabase intrusion, at the southeastern margin of the Yardoi gneiss dome, is located within the outcrop area of the 132 Ma Comei Large Igneous Province (LIP), the result of initial activity of the Kerguelen plume. We present new zircon U-Pb geochronology results to show that the Dala diabase was emplaced at 132 Ma and geochemical data (whole-rock element and Sr-Nd isotope ratios, zircon Hf isotopes and Fe-Ti oxide mineral chemistry) to confirm that the Dala diabase intrusion is part of the Comei LIP. The Dala diabase can be divided into a high-Mg/low-Ti series and a low-Mg/high-Ti series. The high-Mg/low-Ti series represents more primitive mafic magma compositions that we demonstrate are parental to the low-Mg/high-Ti series. Fractionation of olivine and clinopyroxene, followed by plagioclase within the low-Mg series, lead to systematic changes in concentrations of mantle compatible elements (Cr, Co, Ni, and V), REEs, HFSEs, and major elements such as Ti and P. Some Dala samples from the low-Mg/high-Ti series contain large ilmenite clusters and show extreme enrichment of Ti with elevated Ti/Y ratios, likely due to settling and accumulation of ilmenite during the magma chamber evolution. However, most samples from throughout the Comei LIP follow the Ti-evolution trend of the typical liquid line of descent (LLD) of primary OIB compositions, showing strong evidence of control of Ti contents by differentiation processes. In many other localities, however, primitive magmas are absent and observed Ti contents of evolved magmas cannot be quantitatively related to source processes. Careful examination of the petrogenetic relationship between co-existing low-Ti and high-Ti mafic rocks is essential to using observed rock chemistry to infer source composition, location, and degree of melting.

  12. Role of pre-existing structures in controlling the Cenozoic tectonic evolution of the eastern Tibetan plateau: New insights from analogue experiments

    Science.gov (United States)

    Sun, Ming; Yin, An; Yan, Danping; Ren, Hongyu; Mu, Hongxu; Zhu, Lutao; Qiu, Liang

    2018-06-01

    Pre-existing weakness due to repeated tectonic, metamorphic, and magmatic events is a fundamental feature of the continental lithosphere on Earth. Because of this, continental deformation results from a combined effect of boundary conditions imposed by plate tectonic processes and heterogeneous and anisotropic mechanical strength inherited from protracted continental evolution. In this study, we assess how this interaction may have controlled the Cenozoic evolution of the eastern Tibetan plateau during the India-Asia collision. Specifically, we use analogue models to evaluate how the pre-Cenozoic structures may have controlled the location, orientation, and kinematics of the northwest-striking Xianshuihe and northeast-striking Longmen Shan fault zones, the two most dominant Cenozoic structures in eastern Tibet. Our best model indicates that the correct location, trend, and kinematics of the two fault systems can only be generated and maintained if the following conditions are met: (1) the northern part of the Songpan-Ganzi terrane in eastern Tibet has a strong basement whereas its southern part has a weak basement, (2) the northern strong basement consists of two pieces bounded by a crustal-scale weak zone that is expressed by the Triassic development of a northwest-trending antiform exposing middle and lower crustal rocks, and (3) the region was under persistent northeast-southwest compression since ∼35 Ma. Our model makes correct prediction on the sequence of deformation in eastern Tibet; the Longmen Shan right-slip transpressional zone was initiated first as an instantaneous response to the northeast-southwest compression, which is followed by the formation of the Xianshuihe fault about a half way after the exertion of northeast-southwest shortening in the model. The success of our model highlights the importance of pre-existing weakness, a key factor that has been largely neglected in the current geodynamic models of continental deformation.

  13. Comparative Genomics of the Dual-Obligate Symbionts from the Treehopper, Entylia carinata (Hemiptera: Membracidae), Provide Insight into the Origins and Evolution of an Ancient Symbiosis.

    Science.gov (United States)

    Mao, Meng; Yang, Xiushuai; Poff, Kirsten; Bennett, Gordon

    2017-06-01

    Insect species in the Auchenorrhyncha suborder (Hemiptera) maintain ancient obligate symbioses with bacteria that provide essential amino acids (EAAs) deficient in their plant-sap diets. Molecular studies have revealed that two complementary symbiont lineages, "Candidatus Sulcia muelleri" and a betaproteobacterium ("Ca. Zinderia insecticola" in spittlebugs [Cercopoidea] and "Ca. Nasuia deltocephalinicola" in leafhoppers [Cicadellidae]) may have persisted in the suborder since its origin ∼300 Ma. However, investigation of how this pair has co-evolved on a genomic level is limited to only a few host lineages. We sequenced the complete genomes of Sulcia and a betaproteobacterium from the treehopper, Entylia carinata (Membracidae: ENCA), as the first representative from this species-rich group. It also offers the opportunity to compare symbiont evolution across a major insect group, the Membracoidea (leafhoppers + treehoppers). Genomic analyses show that the betaproteobacteria in ENCA is a member of the Nasuia lineage. Both symbionts have larger genomes (Sulcia = 218 kb and Nasuia = 144 kb) than related lineages in Deltocephalinae leafhoppers, retaining genes involved in basic cellular functions and information processing. Nasuia-ENCA further exhibits few unique gene losses, suggesting that its parent lineage in the common ancestor to the Membracoidea was already highly reduced. Sulcia-ENCA has lost the abilities to synthesize menaquinone cofactor and to complete the synthesis of the branched-chain EAAs. Both capabilities are conserved in other Sulcia lineages sequenced from across the Auchenorrhyncha. Finally, metagenomic sequencing recovered the partial genome of an Arsenophonus symbiont, although it infects only 20% of individuals indicating a facultative role. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  14. Evaluation of a landscape evolution model to simulate stream piracies: Insights from multivariable numerical tests using the example of the Meuse basin, France

    Science.gov (United States)

    Benaïchouche, Abed; Stab, Olivier; Tessier, Bruno; Cojan, Isabelle

    2016-01-01

    In landscapes dominated by fluvial erosion, the landscape morphology is closely related to the hydrographic network system. In this paper, we investigate the hydrographic network reorganization caused by a headward piracy mechanism between two drainage basins in France, the Meuse and the Moselle. Several piracies occurred in the Meuse basin during the past one million years, and the basin's current characteristics are favorable to new piracies by the Moselle river network. This study evaluates the consequences over the next several million years of a relative lowering of the Moselle River (and thus of its basin) with respect to the Meuse River. The problem is addressed with a numerical modeling approach (landscape evolution model, hereafter LEM) that requires empirical determinations of parameters and threshold values. Classically, fitting of the parameters is based on analysis of the relationship between the slope and the drainage area and is conducted under the hypothesis of equilibrium. Application of this conventional approach to the capture issue yields incomplete results that have been consolidated by a parametric sensitivity analysis. The LEM equations give a six-dimensional parameter space that was explored with over 15,000 simulations using the landscape evolution model GOLEM. The results demonstrate that stream piracies occur in only four locations in the studied reach near the city of Toul. The locations are mainly controlled by the local topography and are model-independent. Nevertheless, the chronology of the captures depends on two parameters: the river concavity (given by the fluvial advection equation) and the hillslope erosion factor. Thus, the simulations lead to three different scenarios that are explained by a phenomenon of exclusion or a string of events.

  15. Gene Expression Data from the Moon Jelly, Aurelia, Provide Insights into the Evolution of the Combinatorial Code Controlling Animal Sense Organ Development.

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    Nagayasu Nakanishi

    Full Text Available In Bilateria, Pax6, Six, Eya and Dach families of transcription factors underlie the development and evolution of morphologically and phyletically distinct eyes, including the compound eyes in Drosophila and the camera-type eyes in vertebrates, indicating that bilaterian eyes evolved under the strong influence of ancestral developmental gene regulation. However the conservation in eye developmental genetics deeper in the Eumetazoa, and the origin of the conserved gene regulatory apparatus controlling eye development remain unclear due to limited comparative developmental data from Cnidaria. Here we show in the eye-bearing scyphozoan cnidarian Aurelia that the ectodermal photosensory domain of the developing medusa sensory structure known as the rhopalium expresses sine oculis (so/six1/2 and eyes absent/eya, but not optix/six3/6 or pax (A&B. In addition, the so and eya co-expression domain encompasses the region of active cell proliferation, neurogenesis, and mechanoreceptor development in rhopalia. Consistent with the role of so and eya in rhopalial development, developmental transcriptome data across Aurelia life cycle stages show upregulation of so and eya, but not optix or pax (A&B, during medusa formation. Moreover, pax6 and dach are absent in the Aurelia genome, and thus are not required for eye development in Aurelia. Our data are consistent with so and eya, but not optix, pax or dach, having conserved functions in sensory structure specification across Eumetazoa. The lability of developmental components including Pax genes relative to so-eya is consistent with a model of sense organ development and evolution that involved the lineage specific modification of a combinatorial code that specifies animal sense organs.

  16. Role of erosion and isostasy in the Cordillera Blanca uplift: insights from Low-T thermochronology and landscape evolution modeling (northern Peru, Andes)

    Science.gov (United States)

    Margirier, A.; Robert, X.; Braun, J.; Laurence, A.

    2017-12-01

    The uplift and exhumation of the highest Peruvian peaks seems closely linked to the Cordillera Blanca normal fault that delimits and shape the western flank of the Cordillera Blanca. Two models have been previously proposed to explain the occurrence of extension and the presence of this active normal fault in a compression setting but the Cordillera Blanca normal fault and the uplift and exhumation of the Cordillera Blanca remain enigmatic. Recent studies suggested an increase of exhumation rates during the Quaternary in the Cordillera Blanca and related this increase to a change in climate and erosion process (glacial erosion vs. fluvial erosion). The Cordillera Blanca granite has been significantly eroded since its emplacement (12-5 Ma) indicating a significant mass of rocks removal. Whereas it has been demonstrated recently that the effect of eroding denser rocks can contribute to an increase of uplift rate, the impact of erosion and isostasy on the increase of the Cordillera Blanca uplift rates has never been explored. Based on numerical modeling of landscape evolution we address the role of erosion and isostasy in the uplift and exhumation of the Cordillera Blanca. We performed inversions of the present-day topography, total exhumation and thermochronological data using a landscape evolution model (FastScape). Our results evidence the contribution of erosion and associated flexural rebound to the uplift of the Cordillera Blanca. Our models suggest that the erosion of the Cordillera Blanca dense intrusion since 3 Ma could also explain the Quaternary exhumation rate increase in this area. Finally, our results allow to question the previous models proposed for the formation of the Cordillera Blanca normal fault.

  17. Characterization of fluid inclusions from mineralized pegmatites of the Damara Belt, Namibia: insight into late-stage fluid evolution and implications for mineralization

    Science.gov (United States)

    Ashworth, Luisa; Kinnaird, Judith Ann; Nex, Paul Andrew Martin; Erasmus, Rudolph Marthinus; Przybyłowicz, Wojciech Józef

    2018-05-01

    Mineralized NYF and LCT pegmatites occur throughout the northeast-trending Neoproterozoic Damara Belt, Namibia. Mineralization in the pegmatites varies geographically, from the northeast, where they are enriched in Li-Be, to the southwest, where they also contain notable Sn and U. Similar fluid inclusion populations occur throughout the pegmatites, regardless of their respective metal enrichments, and primary fluid inclusion textures were destroyed by continued fluid activity. Pseudosecondary to secondary inclusions are aqueo-carbonic, carbonic, and aqueous in composition, and have been divided into five types. The earliest populations are saline (>26.3 eq. wt.% NaCl), homogenizing at temperatures in excess of 300 °C. Their carbonic phase is composed of CO2, with minor CH4, and micro-elemental mapping indicates they contain trace metals, including Ca, Fe, Zn, Cu, and K. Type 3 inclusions formed later, homogenize at 325 °C, and are less saline, with a carbonic phase composed of CO2. Type 4 carbonic inclusions are composed of pure CO2, and represent the latest stages of fluid evolution, while Type 5 aqueous inclusions are believed to be unrelated to the crystallization of the pegmatites, and rather the result of regional Cretaceous magmatism, or the ingress of meteoric water. The similarities in fluid inclusion populations observed in the pegmatites suggest that differences in mineralization were driven by magma composition rather than fluid activity alone, however saline fluids facilitated the enrichment and deposition of metals during the late stages of crystallization. Furthermore, the similarities between fluid inclusion populations in different pegmatites suggests they share a similar fluid evolution.

  18. Genome-wide identification of Jatropha curcas aquaporin genes and the comparative analysis provides insights into the gene family expansion and evolution in Hevea brasiliensis

    Directory of Open Access Journals (Sweden)

    Zhi eZou

    2016-03-01

    Full Text Available Aquaporins (AQPs are channel-forming integral membrane proteins that transport water and other small solutes across biological membranes. Despite the vital role of AQPs, to date, little is known in physic nut (Jatropha curcas L., Euphorbiaceae, an important non-edible oilseed crop with great potential for the production of biodiesel. In this study, 32 AQP genes were identified from the physic nut genome and the family number is relatively small in comparison to 51 in another Euphorbiaceae plant, rubber tree (Hevea brasiliensis Muell. Arg.. Based on the phylogenetic analysis, the JcAQPs were assigned to five subfamilies, i.e., 9 plasma membrane intrinsic proteins (PIPs, 9 tonoplast intrinsic proteins (TIPs, 8 NOD26-like intrinsic proteins (NIPs, 2 X intrinsic proteins (XIPs and 4 small basic intrinsic proteins (SIPs. Like rubber tree and other plant species, functional prediction based on the aromatic/arginine selectivity filter, Froger’s positions and specificity-determining positions showed a remarkable difference in substrate specificity among subfamilies of JcAQPs. Genome-wide comparative analysis revealed the specific expansion of PIP and TIP subfamilies in rubber tree and the specific gene loss of the XIP subfamily in physic nut. Furthermore, by analyzing deep transcriptome sequencing data, the expression evolution especially the expression divergence of duplicated HbAQP genes was also investigated and discussed. Results obtained from this study not only provide valuable information for future functional analysis and utilization of Jc/HbAQP genes, but also provide a useful reference to survey the gene family expansion and evolution in Euphorbiaceae plants and other plant species.

  19. Influence of heme environment structure on dioxygen affinity for the dual function Amphitrite ornata hemoglobin/dehaloperoxidase. Insights into the evolutional structure-function adaptations

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Shengfang; Sono, Masanori; Wang, Chunxue; Du, Jing; Lebioda, Lukasz; Dawson, John H. [SC

    2014-05-15

    Sea worm, Amphitrite ornata, has evolved its globin (an O2 carrier) also to serves as a dehaloperoxidase (DHP) to detoxify haloaromatic pollutants generated by competing species. A previous mutagenesis study by our groups on both DHP and sperm whale myoglobin (SW Mb) revealed some structural factors that influence the dehaloperoxidase activities (significantly lower for Mb) of both proteins. Using an isocyanide/O2 partition constant measurement method in this study, we have examined the effects of these structural factors on the O2 equilibrium constants (KO2) of DHP, SW Mb, and their mutants. A clear trend of decreasing O2 affinity and increasing catalytic activity along with the increase in the distal His Nε–heme iron distance is observed. An H93K/T95H Mb double mutant mimicking the DHP proximal His positioning exhibited markedly enhanced O2 affinity, confirming the essential effect of proximal His rotation on the globin function of DHP. For DHP, the L100F, T56G and M86E variants showed the effects of distal volume, distal His flexibility and proximal electronic push, respectively, on the O2 affinity. This study provides insights into how DHP has evolved its heme environment to gain significantly enhanced peroxidase capability without compromising its primary function as an O2 carrier.

  20. Cenozoic exhumation and tectonic evolution of the Qimen Tagh Range, northern Tibetan Plateau: Insights from the heavy mineral compositions, detrital zircon U-Pb ages and seismic interpretations

    Science.gov (United States)

    Zhu, W.; Wu, C.; Wang, J.; Zhou, T.; Zhang, C.; Li, J.

    2017-12-01

    The Qaidam Basin is the largest intermountain basin within the Tibetan Plateau. The Cenozoic sedimentary flling characteristics of the basin was significantly influenced by the surrounding tectonic belt, such as the Altyn Tagh Range to the north-west and Qimen Tagh Range to the south. The tectonic evolution of the Qimen Tagh Range and the structural relationship between the Qaidam Basin and Qimen Tagh Range remain controversial. To address these issues, we analyzed thousands of heavy mineral data, 720 detrital zircon ages and seismic data of the Qaidam Basin. Based on the regional geological framework and our kinematic analyses, the Cenozoic tectonic evolution of the Qimen Tagh Range can be divided into two stages. From the Early Eocene to the Middle Miocene, the Devonian (400-360 Ma) and Permian to Triassic (300-200 Ma) zircons which were sourced from the Qimen Tagh Range and the heavy mineral assemblage of zircon-leucoxene-garnet-sphene on the north flank of the Qimen Tagh Range indicated that the Qimen Tagh Range has been exhumed before the Eocene and acted as the primary provenance of the Qaidam Basin. The Kunbei fault system (i.e. the Kunbei, Arlar and Hongliuquan faults) in the southwest of the Qaidam Basin, which can be seen as a natural study window of the Qimen Tagh Range, was characterized by left-lateral strike-slip faults and weak south-dipping thrust faults based on the seismic sections. This strike-slip motion was generated by the uplift of the Tibetan Plateau caused by the onset of the Indian-Eurasian collision. Since the Middle Miocene, the primary mineral assemblages along the northern flank of the Qimen Tagh Range changed from the zircon-leucoxene-garnet-sphene assemblage to the epidote-hornblende-garnet-leucoxene assemblage. Simultaneously, the Kunbei fault system underwent intense south-dipping thrusting, and a nearly 2.2-km uplift can be observed in the hanging wall of the Arlar fault. We attributed these variations to the rapid uplift event of

  1. Can we halt health workforce deterioration in failed states? Insights from Guinea-Bissau on the nature, persistence and evolution of its HRH crisis.

    Science.gov (United States)

    Russo, Giuliano; Pavignani, Enrico; Guerreiro, Catia Sá; Neves, Clotilde

    2017-02-07

    Guinea-Bissau is one of the world's poorest and least developed countries. Amid poverty, political turmoil and state withdrawal, its health workforce (HW) has been swamped for the last four decades in a deepening crisis of under-resourcing, poor performance and laissez-faire. The present study aimed at analysing the human resources for health (HRH) situation in Guinea-Bissau in light of the recent literature on distressed health systems, with the objective of contributing to understanding the ways health workers react to protracted turmoil, the resulting distortions and the counter-measures that might be considered. Through document analysis, focus group discussions, 14 semi-structured and 5 in-depth interviews, we explored patterns as they became visible on the ground. Since independence, Guinea-Bissau experienced political events that have reflected on the healthcare arena and on the evolution of its health workforce, such as different coup attempts, waves of diaspora and shifting external assistance. The chronic scarcity of funds and a 'stable political instability' have lead to the commercialisation of public health services and to flawed mechanisms for training and deploying health personnel. In absence of any form of governance, health workers have come to own and run the health system. We show that the HRH crisis in Guinea-Bissau can only be understood by looking at its historical evolution and at the wider socio-economic context. There are no quick fixes for the deterioration of HRH in undergoverned states; however, the recognition of the ingrained distortions and an understanding of the forces determining the behaviour of key actors are essential premises for the identification of solutions. Guinea-Bissau's case study suggests that any policy that does not factor in the limited clout of health authorities over a effectively privatised healthcare arena is doomed from the start. Improving health system governance and quality of training should take

  2. Genotyping-by-sequencing provides the first well-resolved phylogeny for coffee (Coffea) and insights into the evolution of caffeine content in its species: GBS coffee phylogeny and the evolution of caffeine content.

    Science.gov (United States)

    Hamon, Perla; Grover, Corrinne E; Davis, Aaron P; Rakotomalala, Jean-Jacques; Raharimalala, Nathalie E; Albert, Victor A; Sreenath, Hosahalli L; Stoffelen, Piet; Mitchell, Sharon E; Couturon, Emmanuel; Hamon, Serge; de Kochko, Alexandre; Crouzillat, Dominique; Rigoreau, Michel; Sumirat, Ucu; Akaffou, Sélastique; Guyot, Romain

    2017-04-01

    A comprehensive and meaningful phylogenetic hypothesis for the commercially important coffee genus (Coffea) has long been a key objective for coffee researchers. For molecular studies, progress has been limited by low levels of sequence divergence, leading to insufficient topological resolution and statistical support in phylogenetic trees, particularly for the major lineages and for the numerous species occurring in Madagascar. We report here the first almost fully resolved, broadly sampled phylogenetic hypothesis for coffee, the result of combining genotyping-by-sequencing (GBS) technology with a newly developed, lab-based workflow to integrate short read next-generation sequencing for low numbers of additional samples. Biogeographic patterns indicate either Africa or Asia (or possibly the Arabian Peninsula) as the most likely ancestral locality for the origin of the coffee genus, with independent radiations across Africa, Asia, and the Western Indian Ocean Islands (including Madagascar and Mauritius). The evolution of caffeine, an important trait for commerce and society, was evaluated in light of our phylogeny. High and consistent caffeine content is found only in species from the equatorial, fully humid environments of West and Central Africa, possibly as an adaptive response to increased levels of pest predation. Moderate caffeine production, however, evolved at least one additional time recently (between 2 and 4Mya) in a Madagascan lineage, which suggests that either the biosynthetic pathway was already in place during the early evolutionary history of coffee, or that caffeine synthesis within the genus is subject to convergent evolution, as is also the case for caffeine synthesis in coffee versus tea and chocolate. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Evolution of Microbial Quorum Sensing to Human Global Quorum Sensing: An Insight into How Gap Junctional Intercellular Communication Might Be Linked to the Global Metabolic Disease Crisis.

    Science.gov (United States)

    Trosko, James E

    2016-06-15

    The first anaerobic organism extracted energy for survival and reproduction from its source of nutrients, with the genetic means to ensure protection of its individual genome but also its species survival. While it had a means to communicate with its community via simple secreted molecules ("quorum sensing"), the eventual shift to an aerobic environment led to multi-cellular metazoan organisms, with evolutionary-selected genes to form extracellular matrices, stem cells, stem cell niches, and a family of gap junction or "connexin" genes. These germinal and somatic stem cells responded to extracellular signals that triggered intra-cellular signaling to regulate specific genes out of the total genome. These extra-cellular induced intra-cellular signals also modulated gap junctional intercellular communication (GJIC) in order to regulate the new cellular functions of symmetrical and asymmetrical cell division, cell differentiation, modes of cell death, and senescence. Within the hierarchical and cybernetic concepts, differentiated by neurons organized in the brain of the Homo sapiens, the conscious mind led to language, abstract ideas, technology, myth-making, scientific reasoning, and moral decision-making, i.e., the creation of culture. Over thousands of years, this has created the current collision between biological and cultural evolution, leading to the global "metabolic disease" crisis.

  4. Adaptation and evolution of deep-sea scale worms (Annelida: Polynoidae): insights from transcriptome comparison with a shallow-water species

    Science.gov (United States)

    Zhang, Yanjie; Sun, Jin; Chen, Chong; Watanabe, Hiromi K.; Feng, Dong; Zhang, Yu; Chiu, Jill M.Y.; Qian, Pei-Yuan; Qiu, Jian-Wen

    2017-01-01

    Polynoid scale worms (Polynoidae, Annelida) invaded deep-sea chemosynthesis-based ecosystems approximately 60 million years ago, but little is known about their genetic adaptation to the extreme deep-sea environment. In this study, we reported the first two transcriptomes of deep-sea polynoids (Branchipolynoe pettiboneae, Lepidonotopodium sp.) and compared them with the transcriptome of a shallow-water polynoid (Harmothoe imbricata). We determined codon and amino acid usage, positive selected genes, highly expressed genes and putative duplicated genes. Transcriptome assembly produced 98,806 to 225,709 contigs in the three species. There were more positively charged amino acids (i.e., histidine and arginine) and less negatively charged amino acids (i.e., aspartic acid and glutamic acid) in the deep-sea species. There were 120 genes showing clear evidence of positive selection. Among the 10% most highly expressed genes, there were more hemoglobin genes with high expression levels in both deep-sea species. The duplicated genes related to DNA recombination and metabolism, and gene expression were only enriched in deep-sea species. Deep-sea scale worms adopted two strategies of adaptation to hypoxia in the chemosynthesis-based habitats (i.e., rapid evolution of tetra-domain hemoglobin in Branchipolynoe or high expression of single-domain hemoglobin in Lepidonotopodium sp.). PMID:28397791

  5. Insights into the Evolution of a Snake Venom Multi-Gene Family from the Genomic Organization of Echis ocellatus SVMP Genes

    Directory of Open Access Journals (Sweden)

    Libia Sanz

    2016-07-01

    Full Text Available The molecular events underlying the evolution of the Snake Venom Metalloproteinase (SVMP family from an A Disintegrin And Metalloproteinase (ADAM ancestor remain poorly understood. Comparative genomics may provide decisive information to reconstruct the evolutionary history of this multi-locus toxin family. Here, we report the genomic organization of Echis ocellatus genes encoding SVMPs from the PII and PI classes. Comparisons between them and between these genes and the genomic structures of Anolis carolinensis ADAM28 and E. ocellatus PIII-SVMP EOC00089 suggest that insertions and deletions of intronic regions played key roles along the evolutionary pathway that shaped the current diversity within the multi-locus SVMP gene family. In particular, our data suggest that emergence of EOC00028-like PI-SVMP from an ancestral PII(e/d-type SVMP involved splicing site mutations that abolished both the 3′ splice AG acceptor site of intron 12* and the 5′ splice GT donor site of intron 13*, and resulted in the intronization of exon 13* and the consequent destruction of the structural integrity of the PII-SVMP characteristic disintegrin domain.

  6. Label-Free (XIC) Quantification of Venom Procoagulant and Neurotoxin Expression in Related Australian Elapid Snakes Gives Insight into Venom Toxicity Evolution.

    Science.gov (United States)

    Skejic, Jure; Steer, David L; Dunstan, Nathan; Hodgson, Wayne C

    2015-11-06

    This study demonstrates a direct role of venom protein expression alteration in the evolution of snake venom toxicity. Avian skeletal muscle contractile response to exogenously administered acetylcholine is completely inhibited upon exposure to South Australian and largely preserved following exposure to Queensland eastern brown snake Pseudonaja textilis venom, indicating potent postsynaptic neurotoxicity of the former and lack thereof of the latter venom. Label-free quantitative proteomics reveals extremely large differences in the expression of postsynaptic three-finger α-neurotoxins in these venoms, explaining the difference in the muscle contractile response and suggesting that the type of toxicity induced by venom can be modified by altered expression of venom proteins. Furthermore, the onset of neuromuscular paralysis in the rat phrenic nerve-diaphragm preparation occurs sooner upon exposure to the venom (10 μg/mL) with high expression of α-neurotoxins than the venoms containing predominately presynaptic β-neurotoxins. The study also finds that the onset of rat plasma coagulation is faster following exposure to the venoms with higher expression of venom prothrombin activator subunits. This is the first quantitative proteomic study that uses extracted ion chromatogram peak areas (MS1 XIC) of distinct homologous tryptic peptides to directly show the differences in the expression of venom proteins.

  7. Evolution of Microbial Quorum Sensing to Human Global Quorum Sensing: An Insight into How Gap Junctional Intercellular Communication Might Be Linked to the Global Metabolic Disease Crisis

    Directory of Open Access Journals (Sweden)

    James E. Trosko

    2016-06-01

    Full Text Available The first anaerobic organism extracted energy for survival and reproduction from its source of nutrients, with the genetic means to ensure protection of its individual genome but also its species survival. While it had a means to communicate with its community via simple secreted molecules (“quorum sensing”, the eventual shift to an aerobic environment led to multi-cellular metazoan organisms, with evolutionary-selected genes to form extracellular matrices, stem cells, stem cell niches, and a family of gap junction or “connexin” genes. These germinal and somatic stem cells responded to extracellular signals that triggered intra-cellular signaling to regulate specific genes out of the total genome. These extra-cellular induced intra-cellular signals also modulated gap junctional intercellular communication (GJIC in order to regulate the new cellular functions of symmetrical and asymmetrical cell division, cell differentiation, modes of cell death, and senescence. Within the hierarchical and cybernetic concepts, differentiated by neurons organized in the brain of the Homo sapiens, the conscious mind led to language, abstract ideas, technology, myth-making, scientific reasoning, and moral decision–making, i.e., the creation of culture. Over thousands of years, this has created the current collision between biological and cultural evolution, leading to the global “metabolic disease” crisis.

  8. Insight into effects of antibiotics on reactor performance and evolutions of antibiotic resistance genes and microbial community in a membrane reactor.

    Science.gov (United States)

    Wen, Qinxue; Yang, Lian; Zhao, Yaqi; Huang, Long; Chen, Zhiqiang

    2018-04-01

    A lab-scale anoxic/oxic-membrane bioreactor was designed to treat antibiotics containing wastewater at different antibiotics concentrations (0.5 mg/L, 1 mg/L and 3 mg/L of each antibiotic). Overall COD and NH 4 + N removal (more than 90%) were not affected during the exposure to antibiotics and good TN removal was also achieved, while TP removal was significantly affected. The maximum removal efficiency of penicillin and chlorotetracycline reached 97.15% and 96.10% respectively due to strong hydrolysis, and sulfamethoxazole reached 90.07% by biodegradation. However, 63.87% of norfloxacin maximum removal efficiency was achieved mainly by sorption. The system had good ability to reduce ARGs, peaking to more than 4 orders of magnitude, which mainly depended on the biomass retaining of the membrane module. Antibiotics concentration influenced the evolution of ARGs and bacterial communities in the reactor. This research provides great implication to reduce ARGs and antibiotics in antibiotics containing wastewater using A/O-MBR. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Cranial Morphology of the Brachystelechid 'Microsaur' Quasicaecilia texana Carroll Provides New Insights into the Diversity and Evolution of Braincase Morphology in Recumbirostran 'Microsaurs'.

    Directory of Open Access Journals (Sweden)

    Jason D Pardo

    Full Text Available Recumbirostran 'microsaurs,' a group of early tetrapods from the Late Carboniferous and Early Permian, are the earliest known example of adaptation to head-first burrowing in the tetrapod fossil record. However, understanding of the diversity of fossorial adaptation within the Recumbirostra has been hindered by poor anatomical knowledge of the more divergent forms within the group. Here we report the results of μCT study of Quasicaecilia texana, a poorly-known recumbirostran with a unique, broad, shovel-like snout. The organization of the skull roof and braincase of Quasicaecilia is found to be more in line with that of other recumbirostrans than previously described, despite differences in overall shape. The braincase is found to be broadly comparable to Carrolla craddocki, with a large presphenoid that encompasses much of the interorbital septum and the columella ethmoidalis, and a single compound ossification encompassing the sphenoid, otic, and occipital regions. The recumbirostran braincase conserves general structure and topology of braincase regions and cranial nerve foramina, but it is highly variable in the number of ossifications and their extent, likely associated with the reliance on braincase ossifications to resist compression during sediment compaction and mechanical manipulation by epaxial and hypaxial musculature. Expansion of the deep ventral neck musculature in Quasicaecilia, autapomorphic among recumbirostrans, may reflect unique biomechanical function, and underscores the importance of future attention to the role of the cervical musculature in contextualizing the origin and evolution of fossoriality in recumbirostrans.

  10. Mesozoic and Cenozoic structural evolution of North Oman: New insights from high-quality 3D seismic from the Lekhwair area

    Science.gov (United States)

    Bazalgette, Loïc; Salem, Hisham

    2018-06-01

    This paper highlights the role of Triassic-Jurassic extension and late Cretaceous compression in the Mesozoic-Cenozoic (Alpine) structuring of North Oman. The syn/post-Mesozoic regional structural evolution is usually documented as a succession of two stages of deformation. The Alpine 1 phase, late Cretaceous in age, occurred in association with two ophiolite obduction stages (Semail and Masirah ophiolites). It was characterised by strike slip to extensional deformation in the North Oman foreland basin sub-surface. The Alpine 2 phase, Miocene in age, was related to the continental collision responsible for both the Zagros orogen and the uplift of the Oman Mountains. The Alpine 2 deformation was transpressional to compressional. Observation and interpretation of good quality 3D seismic in the Lekhwair High area enabled the distinction of two earlier phases. Early Mesozoic extension occurred concomitantly with the regional Triassic to Jurassic rifting, developing Jurassic-age normal faults. Late Cretaceous compression occurred prior to the main Alpine 1 phase and triggered the inversion of Jurassic-seated normal faults as well as the initiation of compressional folds in the Cretaceous overburden. These early phases have been ignored or overlooked as part of the North Oman history although they are at the origin of structures hosting major local and regional hydrocarbon accumulations.

  11. Gene arrangement and sequence of mitochondrial genomes yield insights into the phylogeny and evolution of bees and sphecid wasps (Hymenoptera: Apoidea).

    Science.gov (United States)

    Zheng, Bo-Ying; Cao, Li-Jun; Tang, Pu; van Achterberg, Kees; Hoffmann, Ary A; Chen, Hua-Yan; Chen, Xue-Xin; Wei, Shu-Jun

    2018-07-01

    The Apoidea represent a large and common superfamily of the Hymenoptera including the bees and sphecid wasps. A robust phylogenetic tree is essential to understanding the diversity, taxonomy and evolution of the Apoidea. In this study, features of apoid mitochondrial genomes were used to reconstruct phylogenetic relationships. Twelve apoid mitochondrial genomes were newly sequenced, representing six families and nine subfamilies. Gene rearrangement events have occurred in all apoid mitochondrial genomes sequenced to date. Sphecid wasps have both tRNA and protein-coding gene rearrangements in 5 of 8 species. In bees, the only rearranged genes are tRNAs; long-tongued bees (Apidae + Megachilidae) are characterized by movement of trnA to the trnI-trnQ-trnM tRNA cluster. Phylogenetic analyses of mitochondrial gene sequences support the known paraphyly of sphecid wasps, with bees nested within this clade. The Ampulicidae is sister to the remaining Apoidea. Crabronidae is paraphyletic, split into Crabronidae s.s. and Philanthidae, with the latter group a sister clade to bees. The monophyletic bees are either classified into two clades, long-tongued bees (Apidae + Megachilidae) and short-tongued bees (Andrenidae + Halictidae + Colletidae + Melitidae), or three groups with the Melitidae sister to the other bees. Our study showed that both gene sequences and arrangements provide information on the phylogeny of apoid families. Copyright © 2018 Elsevier Inc. All rights reserved.

  12. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.

    Science.gov (United States)

    Wang, Zhuo; Pascual-Anaya, Juan; Zadissa, Amonida; Li, Wenqi; Niimura, Yoshihito; Huang, Zhiyong; Li, Chunyi; White, Simon; Xiong, Zhiqiang; Fang, Dongming; Wang, Bo; Ming, Yao; Chen, Yan; Zheng, Yuan; Kuraku, Shigehiro; Pignatelli, Miguel; Herrero, Javier; Beal, Kathryn; Nozawa, Masafumi; Li, Qiye; Wang, Juan; Zhang, Hongyan; Yu, Lili; Shigenobu, Shuji; Wang, Junyi; Liu, Jiannan; Flicek, Paul; Searle, Steve; Wang, Jun; Kuratani, Shigeru; Yin, Ye; Aken, Bronwen; Zhang, Guojie; Irie, Naoki

    2013-06-01

    The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ∼267.9-248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these turtles. Embryonic gene expression analysis identified an hourglass-like divergence of turtle and chicken embryogenesis, with maximal conservation around the vertebrate phylotypic period, rather than at later stages that show the amniote-common pattern. Wnt5a expression was found in the growth zone of the dorsal shell, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty. Our results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell.

  13. The draft genomes of soft–shell turtle and green sea turtle yield insights into the development and evolution of the turtle–specific body plan

    Science.gov (United States)

    Niimura, Yoshihito; Huang, Zhiyong; Li, Chunyi; White, Simon; Xiong, Zhiqiang; Fang, Dongming; Wang, Bo; Ming, Yao; Chen, Yan; Zheng, Yuan; Kuraku, Shigehiro; Pignatelli, Miguel; Herrero, Javier; Beal, Kathryn; Nozawa, Masafumi; Li, Qiye; Wang, Juan; Zhang, Hongyan; Yu, Lili; Shigenobu, Shuji; Wang, Junyi; Liu, Jiannan; Flicek, Paul; Searle, Steve; Wang, Jun; Kuratani, Shigeru; Yin, Ye; Aken, Bronwen; Zhang, Guojie; Irie, Naoki

    2014-01-01

    The unique anatomical features of turtles have raised unanswered questions about the origin of their unique body plan. We generated and analyzed draft genomes of the soft-shell turtle (Pelodiscus sinensis) and the green sea turtle (Chelonia mydas); our results indicated the close relationship of the turtles to the bird-crocodilian lineage, from which they split ~267.9–248.3 million years ago (Upper Permian to Triassic). We also found extensive expansion of olfactory receptor genes in these turtles. Embryonic gene expression analysis identified an hourglass-like divergence of turtle and chicken embryogenesis, with maximal conservation around the vertebrate phylotypic period, rather than at later stages that show the amniote-common pattern. Wnt5a expression was found in the growth zone of the dorsal shell, supporting the possible co-option of limb-associated Wnt signaling in the acquisition of this turtle-specific novelty. Our results suggest that turtle evolution was accompanied by an unexpectedly conservative vertebrate phylotypic period, followed by turtle-specific repatterning of development to yield the novel structure of the shell. PMID:23624526

  14. Early insights into the characteristics and evolution of clinical parameters in a cohort of patients prescribed sacubitril/valsartan in Germany.

    Science.gov (United States)

    Wachter, Rolf; Viriato, Daniel; Klebs, Sven; Grunow, Stefanie S; Schindler, Matthias; Engelhard, Johanna; Proenca, Catia C; Calado, Frederico; Schlienger, Raymond; Dworak, Markus; Balas, Bogdan; Bruce Wirta, Sara

    2018-04-01

    This study aimed to provide early insights into sacubitril/valsartan (sac/val) prescription patterns and the demographic and clinical characteristics of patients prescribed sac/val in primary care and cardiology settings in Germany. The study used electronic medical records from the German IMS® Disease Analyzer database. Patients with ≥1 prescription for sac/val during 1 January-31 December 2016 (n = 1643) were identified and followed up for ≤12 months from first prescription. Patients with ≥1 heart failure (HF) diagnosis during the study period, ≥1 additional HF diagnosis in the full history of the database, and ≥1 prescription for an angiotensin-converting enzyme inhibitor or angiotensin receptor blocker and a β-blocker during the study period, without a prescription for sac/val (n = 25,264), were included as a reference cohort. Changes in clinical parameters in the 12 months before and after sac/val initiation were investigated and compared with those from the PARADIGM-HF study. The characteristics of patients prescribed sac/val more closely resembled those of patients enrolled in PARADIGM-HF (e.g. younger age, higher proportion of men than women, lower systolic blood pressure) than patients in the reference cohort. Most patients were initiated on the lowest dose of sac/val irrespective of clinical setting. Significant decreases (p < 0.001) in NT-proBNP and glycated haemoglobin levels were observed following sac/val initiation. Patients prescribed sac/val had similar baseline demographics and clinical characteristics to those from PARADIGM-HF, and most patients were initiated on the lowest dose. Changes in clinical parameters before and after initiation mirrored findings from the PARADIGM-HF study.

  15. Biochemical, transcriptomic and proteomic analyses of digestion in the scorpion Tityus serrulatus: insights into function and evolution of digestion in an ancient arthropod.

    Science.gov (United States)

    Fuzita, Felipe J; Pinkse, Martijn W H; Patane, José S L; Juliano, Maria A; Verhaert, Peter D E M; Lopes, Adriana R

    2015-01-01

    Scorpions are among the oldest terrestrial arthropods and they have passed through small morphological changes during their evolutionary history on land. They are efficient predators capable of capturing and consuming large preys and due to envenomation these animals can become a human health challenge. Understanding the physiology of scorpions can not only lead to evolutionary insights but also is a crucial step in the development of control strategies. However, the digestive process in scorpions has been scarcely studied. In this work, we describe the combinatory use of next generation sequencing, proteomic analysis and biochemical assays in order to investigate the digestive process in the yellow scorpion Tityus serrulatus, mainly focusing in the initial protein digestion. The transcriptome generated database allowed the quantitative identification by mass spectrometry of different enzymes and proteins involved in digestion. All the results suggested that cysteine cathepsins play an important role in protein digestion. Two digestive cysteine cathepsins were isolated and characterized presenting acidic characteristics (pH optima and stability), zymogen conversion to the mature form after acidic activation and a cross-class inhibition by pepstatin. A more elucidative picture of the molecular mechanism of digestion in a scorpion was proposed based on our results from Tityus serrulatus. The midgut and midgut glands (MMG) are composed by secretory and digestive cells. In fasting animals, the secretory granules are ready for the next predation event, containing enzymes needed for alkaline extra-oral digestion which will compose the digestive fluid, such as trypsins, astacins and chitinase. The digestive vacuoles are filled with an acidic proteolytic cocktail to the intracellular digestion composed by cathepsins L, B, F, D and legumain. Other proteins as lipases, carbohydrases, ctenitoxins and a chitolectin with a perithrophin domain were also detected. Evolutionarily

  16. Pre-eruptive conditions of the Hideaway Park topaz rhyolite: Insights into metal source and evolution of magma parental to the Henderson porphyry molybdenum deposit, Colorado

    Science.gov (United States)

    Mercer, Celestine N.; Hofstra, Albert H.; Todorov, Todor I.; Roberge, Julie; Burgisser, Alain; Adams, David T.; Cosca, Michael A.

    2015-01-01

    The Hideaway Park tuff is the only preserved extrusive volcanic unit related to the Red Mountain intrusive complex, which produced the world-class Henderson porphyry Mo deposit. Located within the Colorado Mineral Belt, USA, Henderson is the second largest Climax-type Mo deposit in the world, and is therefore an excellent location to investigate magmatic processes leading to Climax-type Mo mineralization. We combine an extensive dataset of major element, volatile, and trace element abundances in quartz-hosted melt inclusions and pumice matrix glass with major element geochemistry from phenocrysts to reconstruct the pre-eruptive conditions and the source and evolution of metals within the magma. Melt inclusions are slightly peraluminous topaz rhyolitic in composition and are volatile-charged (≤6 wt % H2O, ≤600 ppm CO2, ∼0·3–1·0 wt % F, ∼2300–3500 ppm Cl) and metal-rich (∼7–24 ppm Mo, ∼4–14 ppm W, ∼21–52 ppm Pb, ∼28–2700 ppm Zn, shallow ascent and eruption. Filter pressing, crystal settling, magma recharge and mixing of less evolved rhyolite melt, and volatile exsolution were important processes during magma evolution; the low estimated viscosities (∼105–1010 Pa s) of these H2O- and F-rich melts probably enhanced these processes. A noteworthy discrepancy between the metal contents in the pumice matrix glass and in the melt inclusions suggests that after quartz crystallization ceased upon shallow magma ascent and eruption, the Hideaway Park magma exsolved an aqueous fluid into which Mo, Bi, Ag, Zn, Mn, Cs, and Y strongly partitioned. Given that the Henderson deposit contains anomalous abundances of not only Mo, but also W, Pb, Zn, Cu, Bi, Ag, and Mn, we suggest that these metals were sourced from similar fluids exsolved from unerupted portions of the same magmatic system. Trace element ratios imply that Mo was sourced deep, from either the lower crust or metasomatized mantle. The origin of sulfur remains unresolved

  17. Late Cenozoic Magmatic and Tectonic Evolution of the Ancestral Cascade Arc in the Bodie Hills, California and Nevada: Insights from Integrated Geologic, Geophysical, Geochemical and Geochronologic Studies

    Science.gov (United States)

    John, D. A.; du Bray, E. A.; Box, S. E.; Blakely, R. J.; Fleck, R. J.; Vikre, P. G.; Cousens, B.; Moring, B. C.

    2012-12-01

    Geologic mapping integrated with new geophysical, geochemical, and geochronologic data characterize the evolution of Bodie Hills volcanic field (BHVF), a long-lived eruptive center in the southern part of the ancestral Cascade arc. The ~700 km2 field was a locus of magmatic activity from ~15 to 8 Ma. It includes >25 basaltic andesite to trachyandesite stratovolcanoes and silicic trachyandesite to rhyolite dome complexes. The southeastern part of the BHVF is overlain by the ~3.9 to 0.1 Ma, post-arc Aurora Volcanic Field. Long-lived BHVF magmatism was localized by crustal-scale tectonic features, including the Precambrian continental margin, the Walker Lane, the Basin and Range Province, and the Mina deflection. BHVF eruptive activity occurred primarily during 3 stages: 1) dominantly trachyandesite stratovolcanoes (~15.0 to 12.9 Ma), 2) coalesced trachydacite and rhyolite lava domes and trachyandesite stratovolcanoes (~11.6 to 9.7 Ma), and 3) dominantly silicic trachyandesite to dacite lava dome complexes (~9.2 to 8.0 Ma). Small rhyolite domes were emplaced at ~6 Ma. Relatively mafic stratovolcanoes surrounded by debris flow aprons lie on the margins of the BHVF, whereas more silicic dome fields occupy its center. Detailed gravity and aeromagnetic data suggest the presence of unexposed cogenetic granitic plutons beneath the center of the BHVF. Isotopic compositions of BHVF rocks are generally more radiogenic with decreasing age (e.g., initial Sr isotope values increase from ~0.7049 to 0.7061), which suggests progressively greater magma contamination by crustal components during evolution of the BHVF. Approximately circular, polygenetic volcanoes and scarcity of dikes suggest a low differential horizontal stress field during BHVF formation. Extensive alluvial gravel deposits that grade laterally into fluvial gravels and finer grained lacustrine sediments and the westerly sourced Eureka Valley Tuff (EVT; ~9.4 Ma) blanket large parts of the BHVF. The earliest sediments

  18. High-spatial resolution SIMS U-Pb zircon dating on Malay tin granites: New insights to crustal evolution of the Malaysian Peninsula

    Science.gov (United States)

    Ng, S.; Searle, M. P.; Whitehouse, M. J.; Chung, S.; Robb, L. J.; Ghani, A. A.; Sone, M.

    2012-12-01

    characteristics, such as in sodium, potassium, ferric and ferrous ion concentration. Exceptionally high rubidium concentration in some samples also hinders the classification. The ɛNd(T) values of most of the samples lie between -2.5 and -9.7, suggesting that crustal remelting played an important role in the granite petrogenesis. Likewise tin mineralization is not restricted to S-type granites throughout all provinces. Further field studies and continuation of the U-Pb dating programme through southern Malaysia to Singapore Island should result in tighter constraints on the magmatic and tectonic evolution of the region. References Cobbing, E. J., Mallick, D. I. J., Pitfield, P. E. J., and Teoh, L. H., 1986, The granites of the Southeast Asian Tin Belt: Journal of Geological Society, v. 143, p. 537-550. Searle, M. P., Whitehouse, M. J., Robb, L. J., Ghani, A. A., Hutchison, C. S., Sone, M., Ng, S. W.-p., Roselee, M. H., Chung, S.-l., and Oliver, G. J. H., 2012, Tectonic evolution of the Sibumasu-Indochina terrane collision zone in Thailand and Malaysia; constraints from new U-Pb zircon chronology of SE Asian tin granitoids: Journal of Geological Society, v. 169, p. 489-500.

  19. First Results from the Lyman Alpha Galaxies in the Epoch of Reionization (LAGER) Survey: Cosmological Reionization at z ∼ 7

    Energy Technology Data Exchange (ETDEWEB)

    Zheng, Zhen-Ya; Jiang, Chunyan [CAS Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Shanghai 200030 (China); Wang, Junxian; Hu, Weida; Kong, Xu [CAS Key Laboratory for Research in Galaxies and Cosmology, Department of Astronomy, University of Science and Technology of China, Hefei, Anhui 230026 (China); Rhoads, James; Malhotra, Sangeeta; Gonzalez, Alicia [School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287 (United States); Infante, Leopoldo; Galaz, Gaspar; Barrientos, L. Felipe [Institute of Astrophysics and Center for Astroengineering, Pontificia Universidad Catolica de Chile, Santiago 7820436 (Chile); Walker, Alistair R. [Cerro Tololo Inter-American Observatory, Casilla 603, La Serena (Chile); Jiang, Linhua [The Kavli Institute for Astronomy and Astrophysics, Peking University, Beijing 100871 (China); Hibon, Pascale [European Southern Observatory, Alonso de Cordova 3107, Casilla 19001, Santiago (Chile); Zheng, XianZhong, E-mail: zhengzy@shao.ac.cn, E-mail: linfante@astro.puc.cl, E-mail: jxw@ustc.edu.cn, E-mail: Sangeeta.Malhotra@asu.edu, E-mail: James.Rhoads@asu.edu [Purple Mountain Observatory, Chinese Academy of Sciences, Nanjing 210008 (China)

    2017-06-20

    We present the first results from the ongoing Lyman Alpha Galaxies in the Epoch of Reionization (LAGER) project, which is the largest narrowband survey for z ∼ 7 galaxies to date. Using a specially built narrowband filter NB964 for the superb large-area Dark Energy Camera (DECam) on the NOAO/CTIO 4 m Blanco telescope, LAGER has collected 34 hr NB964 narrowband imaging data in the 3 deg{sup 2} COSMOS field. We have identified 23 Ly α Emitter candidates at z = 6.9 in the central 2-deg{sup 2} region, where DECam and public COSMOS multi-band images exist. The resulting luminosity function (LF) can be described as a Schechter function modified by a significant excess at the bright end (four galaxies with L {sub Lyα∼} 10{sup 43.4±0.2} erg s{sup −1}). The number density at L {sub Ly} {sub α} ∼ 10{sup 43.4±0.2} erg s{sup −1} is little changed from z = 6.6, while at fainter L {sub Lyα} it is substantially reduced. Overall, we see a fourfold reduction in Ly α luminosity density from z = 5.7 to z = 6.9. Combined with a more modest evolution of the continuum UV luminosity density, this suggests a factor of ∼3 suppression of Ly α by radiative transfer through the z ∼ 7 intergalactic medium (IGM). It indicates an IGM neutral fraction of x {sub Hi} ∼ 0.4–0.6 (assuming Ly α velocity offsets of 100–200 km s{sup −1}). The changing shape of the Ly α LF between z ≲ 6.6 and z = 6.9 supports the hypothesis of ionized bubbles in a patchy reionization at z ∼ 7.

  20. Magma source evolution beneath the Caribbean oceanic plateau: New insights from elemental and Sr-Nd-Pb-Hf isotopic studies of ODP Leg 165, Site 1001 basalts

    Science.gov (United States)

    Kerr, A. C.; Pearson, G.; Nowell, G.

    2008-12-01

    Ocean Drilling Project Leg 165 sampled 38m of the basaltic basement of the Caribbean plate at Site 1001 on the Hess Escarpment. The recovered section consists of 12 basaltic flow units which yield a weighted mean Ar-Ar age of 80.9±0.9 Ma (Sinton et al., 2000). The basalts (6.4-8.5 wt.% MgO) are remarkably homogeneous in composition and are more depleted in incompatible trace elements than N-MORB. Markedly, depleted initial radiogenic isotope ratios reveal a long-term history of depletion. Although the Site 1001 basalts are superficially similar to N-MORB, radiogenic isotopes in conjunction with incompatible trace element ratios show that the basalts have more similarity to the depleted basalts and komatiites of Gorgona Island. This chemical composition strongly implies that the Site 1001 basalts are derived from a depleted mantle plume component and not from depleted ambient upper mantle. Therefore the Site 1001 basalts are, both compositionally and tectonically, a constituent part of the Caribbean oceanic plateau. Mantle melt modelling suggests that the Site 1001 lavas have a composition which is consistent with second-stage melting of compositionally heterogeneous mantle plume source material which had already been melted, most likely to form the 90Ma basalts of the plateau. The prolonged residence (>10m.y.) of residual mantle plume source material below the region, confirms computational model predictions and places significant constraints on tectonic models of Caribbean evolution in the late Cretaceous, and the consequent environmental impact of oceanic plateau volcanism. Reference Sinton, C.W., et al., 2000. Geochronology and petrology of the igneous basement at the lower Nicaraguan Rise, Site 1001. Proceedings of the Ocean Drilling Program, Scientific Results. Leg 165. pp. 233-236.

  1. Quaternary landscape evolution of the Helmand Basin, Afghanistan: Insights from staircase terraces, deltas, and paleoshorelines using high-resolution remote sensing analysis

    Science.gov (United States)

    Evenstar, L. A.; Sparks, R. S. J.; Cooper, F. J.; Lawton, M. N.

    2018-06-01

    The Helmand Basin in southern Afghanistan is a large (310,000 km2), structurally controlled, endorheically drained basin with a hyperarid climate. The basin hosts a high elevation ( 200 m) plateau (the Dasht-i Margo), 11 fluvial staircase terraces (T11 to T1), 7 delta systems (D1 to D7), and 6 paleolake shorelines (SL1 to SL6) within the Sistan Depression on the western side of the basin. Mapping and surveying of these features by remote sensing is integrated with geological observations to reconstruct Quaternary landscape evolution of the basin. The fluvial systems, deltas, and paleolake shorelines are correlated with one another and with the younger terraces (T7 to T1). The shape of fluvial longitudinal profiles changes depending on whether they formed pre-, syn-, or post-growth of the Koh-i Khannesin volcano on the southern margin of the Helmand River. The age of the volcano ( 0.6 Ma) and correlation of the terraces with the global history of glacial-interglacial cycles constrain the age of the younger terraces to the late Pleistocene and indicates that the older terraces are middle Pleistocene (dating back to 800 ka). The Helmand Basin once hosted a large lake, called here the Sistan paleolake, which at SL6 times and before had a surface area >50,000 km2. Since that time the lake elevation and area have decreased, evolving to the present-day dried out Sistan Depression with small ephemeral playa lakes. Episodic formation of terraces, deltas, and paleolake shorelines is attributed to changes in base level modulated by climate change related to Milankovitch cycles.

  2. Evolution of the Chos Malal and Agrio fold and thrust belts, Andes of Neuquén: Insights from structural analysis and apatite fission track dating

    Science.gov (United States)

    Rojas Vera, E. A.; Mescua, J.; Folguera, A.; Becker, T. P.; Sagripanti, L.; Fennell, L.; Orts, D.; Ramos, V. A.

    2015-12-01

    The Chos Malal and Agrio fold and thrust belts are located in the western part of the Neuquén basin, an Andean retroarc basin of central-western Argentina. Both belts show evidence of tectonic inversion at the western part during Late Cretaceous times. The eastern part is dominated by late Miocene deformation which also partially reactivated the western structures. This work focuses on the study of the regional structure and the deformational event that shaped the relief of this part of the Andes. Based on new field work and structural data and previously published works a detailed map of the central part of the Neuquén basin is presented. Three regional structural cross sections were surveyed and balanced using the 2d Move™ software. In order to define a more accurate uplift history, new apatite fission track analyses were carried on selected structures. These data was used for new thermal history modeling of the inner part of the Agrio and Chos Malal fold and thrust belts. The results of the fission track analyses improve the knowledge of how these fold and thrust belts have grown trough time. Two main deformational events are defined in Late Cretaceous to Paleocene and Late Miocene times. Based on this regional structural analysis and the fission track data the precise location of the orogenic front for the Late Cretaceous-Paleocene times is reconstructed and it is proposed a structural evolution of this segment of the Andes. This new exhumation data show how the Late Cretaceous to Paleocene event was a continuous and uninterrupted deformational event.

  3. Complete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes

    Directory of Open Access Journals (Sweden)

    Charu Tripathi

    2017-07-01

    Full Text Available Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C using PacBio RSII SMRT technique. The small genome (2.01 Mbp comprises a chromosome (1.87 Mbp and a plasmid (143 Kbp, designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%. We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI, conserved marker genes (31 and 400, pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5 by recruiting raw metagenomic data (from the same niche against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes. Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.

  4. Legacy ExtraGalactic UV Survey with The Hubble Space Telescope: Stellar Cluster Catalogs and First Insights Into Cluster Formation and Evolution in NGC 628

    Science.gov (United States)

    Adamo, A.; Ryon, J. E.; Messa, M.; Kim, H.; Grasha, K.; Cook, D. O.; Calzetti, D.; Lee, J. C.; Whitmore, B. C.; Elmegreen, B. G.; Ubeda, L.; Smith, L. J.; Bright, S. N.; Runnholm, A.; Andrews, J. E.; Fumagalli, M.; Gouliermis, D. A.; Kahre, L.; Nair, P.; Thilker, D.; Walterbos, R.; Wofford, A.; Aloisi, A.; Ashworth, G.; Brown, T. M.; Chandar, R.; Christian, C.; Cignoni, M.; Clayton, G. C.; Dale, D. A.; de Mink, S. E.; Dobbs, C.; Elmegreen, D. M.; Evans, A. S.; Gallagher, J. S., III; Grebel, E. K.; Herrero, A.; Hunter, D. A.; Johnson, K. E.; Kennicutt, R. C.; Krumholz, M. R.; Lennon, D.; Levay, K.; Martin, C.; Nota, A.; Östlin, G.; Pellerin, A.; Prieto, J.; Regan, M. W.; Sabbi, E.; Sacchi, E.; Schaerer, D.; Schiminovich, D.; Shabani, F.; Tosi, M.; Van Dyk, S. D.; Zackrisson, E.

    2017-06-01

    We report the large effort that is producing comprehensive high-level young star cluster (YSC) catalogs for a significant fraction of galaxies observed with the Legacy ExtraGalactic UV Survey (LEGUS) Hubble treasury program. We present the methodology developed to extract cluster positions, verify their genuine nature, produce multiband photometry (from NUV to NIR), and derive their physical properties via spectral energy distribution fitting analyses. We use the nearby spiral galaxy NGC 628 as a test case for demonstrating the impact that LEGUS will have on our understanding of the formation and evolution of YSCs and compact stellar associations within their host galaxy. Our analysis of the cluster luminosity function from the UV to the NIR finds a steepening at the bright end and at all wavelengths suggesting a dearth of luminous clusters. The cluster mass function of NGC 628 is consistent with a power-law distribution of slopes ˜ -2 and a truncation of a few times 105 {M}⊙ . After their formation, YSCs and compact associations follow different evolutionary paths. YSCs survive for a longer time frame, confirming their being potentially bound systems. Associations disappear on timescales comparable to hierarchically organized star-forming regions, suggesting that they are expanding systems. We find mass-independent cluster disruption in the inner region of NGC 628, while in the outer part of the galaxy there is little or no disruption. We observe faster disruption rates for low mass (≤104 {M}⊙ ) clusters, suggesting that a mass-dependent component is necessary to fully describe the YSC disruption process in NGC 628. Based on observations obtained with the NASA/ESA Hubble Space Telescope, at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555.

  5. X-Ray, UV and Optical Observations of Classical Cepheids: New Insights into Cepheid Evolution, and the Heating and Dynamics of Their Atmospheres

    Directory of Open Access Journals (Sweden)

    Scott G. Engle

    2012-06-01

    Full Text Available To broaden the understanding of classical Cepheid structure, evolution and atmospheres, we have extended our continuing secret lives of Cepheids program by obtaining XMM/Chandra X-ray observations, and Hubble space telescope (HST / cosmic origins spectrograph (COS FUV-UV spectra of the bright, nearby Cepheids Polaris, δ Cep and β Dor. Previous studies made with the international ultraviolet explorer (IUE showed a limited number of UV emission lines in Cepheids. The wellknown problem presented by scattered light contamination in IUE spectra for bright stars, along with the excellent sensitivity & resolution combination offered by HST/COS, motivated this study, and the spectra obtained were much more rich and complex than we had ever anticipated. Numerous emission lines, indicating 104 K up to ~3 × 105 K plasmas, have been observed, showing Cepheids to have complex, dynamic outer atmospheres that also vary with the photospheric pulsation period. The FUV line emissions peak in the phase range φ ≈ 0.8-1.0 and vary by factors as large as 10×. A more complete picture of Cepheid outer atmospheres is accomplished when the HST/COS results are combined with X-ray observations that we have obtained of the same stars with XMM-Newton & Chandra. The Cepheids detected to date have X-ray luminosities of log LX ≈ 28.5-29.1 ergs/sec, and plasma temperatures in the 2–8 × 106 K range. Given the phase-timing of the enhanced emissions, the most plausible explanation is the formation of a pulsation-induced shocks that excite (and heat the atmospheric plasmas surrounding the photosphere. A pulsation-driven α2 equivalent dynamo mechanism is also a viable and interesting alternative. However, the tight phase-space of enhanced emission (peaking near 0.8-1.0 φ favor the shock heating mechanism hypothesis.

  6. X-Ray, UV and Optical Observations of Classical Cepheids: New Insights into Cepheid Evolution, and the Heating and Dynamics of Their Atmospheres

    Science.gov (United States)

    Engle, Scott G.; Guinan, Edward F.

    2012-06-01

    To broaden the understanding of classical Cepheid structure, evolution and atmospheres, we have extended our continuing secret lives of Cepheids program by obtaining XMM/Chandra X-ray observations, and Hubble space telescope (HST) / cosmic origins spectrograph (COS) FUV-UV spectra of the bright, nearby Cepheids Polaris, δ Cep and β Dor. Previous studies made with the international ultraviolet explorer (IUE) showed a limited number of UV emission lines in Cepheids. The well-known problem presented by scattered light contamination in IUE spectra for bright stars, along with the excellent sensitivity & resolution combination offered by HST/COS, motivated this study, and the spectra obtained were much more rich and complex than we had ever anticipated. Numerous emission lines, indicating 10^4 K up to ~3 x 10^5 K plasmas, have been observed, showing Cepheids to have complex, dynamic outer atmospheres that also vary with the photospheric pulsation period. The FUV line emissions peak in the phase range φ ∼ 0.8-1.0 and vary by factors as large as 10x. A more complete picture of Cepheid outer atmospheres is accomplished when the HST/COS results are combined with X-ray observations that we have obtained of the same stars with XMM-Newton & Chandra. The Cepheids detected to date have X-ray luminosities of log Lx ~ 28.5-29.1 ergs/sec, and plasma temperatures in the 2-8 x 10^6 K range. Given the phase-timing of the enhanced emissions, the most plausible explanation is the formation of a pulsation-induced shocks that excite (and heat) the atmospheric plasmas surrounding the photosphere. A pulsation-driven α^2 equivalent dynamo mechanism is also a viable and interesting alternative. However, the tight phase-space of enhanced emission (peaking near 0.8-1.0 φ) favor the shock heating mechanism hypothesis.

  7. Thorium abundances of basalt ponds in South Pole-Aitken basin: Insights into the composition and evolution of the far side lunar mantle

    Science.gov (United States)

    Hagerty, Justin J.; Lawrence, D.J.; Hawke, B.R.

    2011-01-01

    Imbrian-aged basalt ponds, located on the floor of South Pole-Aitken (SPA) basin, are used to provide constraints on the composition and evolution of the far side lunar mantle. We use forward modeling of the Lunar Prospector Gamma Ray Spectrometer thorium data, to suggest that at least five different and distinct portions of the far side lunar mantle contain little or no thorium as of the Imbrian Period. We also use spatial correlations between local thorium enhancements and nonmare material on top of the basalt ponds to support previous assertions that lower crustal materials exposed in SPA basin have elevated thorium abundances, consistent with noritic to gabbronoritic lithologies. We suggest that the lower crust on the far side of the Moon experienced multiple intrusions of thorium-rich basaltic magmas, prior to the formation of SPA basin. The fact that many of the ponds on the lunar far side have elevated titanium abundances indicates that the far side of the Moon experienced extensive fractional crystallization that likely led to the formation of a KREEP-like component. However, because the Imbrian-aged basalts contain no signs of elevated thorium, we propose that the SPA impact event triggered the transport of a KREEP-like component from the lunar far side and concentrated it on the nearside of the Moon. Because of the correlation between basaltic ponds and basins within SPA, we suggest that Imbrian-aged basaltic volcanism on the far side of the Moon was driven by basin-induced decompressional melting.

  8. "On the Fence" versus "All in": Insights from Turtles for the Evolution of Aquatic Locomotor Specializations and Habitat Transitions in Tetrapod Vertebrates.

    Science.gov (United States)

    Blob, Richard W; Mayerl, Christopher J; Rivera, Angela R V; Rivera, Gabriel; Young, Vanessa K H

    2016-12-01

    Though ultimately descended from terrestrial amniotes, turtles have deep roots as an aquatic lineage and are quite diverse in the extent of their aquatic specializations. Many taxa can be viewed as "on the fence" between aquatic and terrestrial realms, whereas others have independently hyperspecialized and moved "all in" to aquatic habitats. Such differences in specialization are reflected strongly in the locomotor system. We have conducted several studies to evaluate the performance consequences of such variation in design, as well as the mechanisms through which specialization for aquatic locomotion is facilitated in turtles. One path to aquatic hyperspecialization has involved the evolutionary transformation of the forelimbs from rowing, tubular limbs with distal paddles into flapping, flattened flippers, as in sea turtles. Prior to the advent of any hydrodynamic advantages, the evolution of such flippers may have been enabled by a reduction in twisting loads on proximal limb bones that accompanied swimming in rowing ancestors, facilitating a shift from tubular to flattened limbs. Moreover, the control of flapping movements appears related primarily to shifts in the activity of a single forelimb muscle, the deltoid. Despite some performance advantages, flapping may entail a locomotor cost in terms of decreased locomotor stability. However, other morphological specializations among rowing species may enhance swimming stability. For example, among highly aquatic pleurodiran turtles, fusion of the pelvis to the shell appears to dramatically reduce motions of the pelvis compared to freshwater cryptodiran species. This could contribute to advantageous increases in aquatic stability among predominantly aquatic pleurodires. Thus, even within the potential constraints of a body plan in which the body is encased by a shell, turtles exhibit diverse locomotor capacities that have enabled diversification into a wide range of aquatic habitats. © The Author 2016. Published

  9. “On the Fence” versus “All in”: Insights from Turtles for the Evolution of Aquatic Locomotor Specializations and Habitat Transitions in Tetrapod Vertebrates

    Science.gov (United States)

    Blob, Richard W.; Mayerl, Christopher J.; Rivera, Angela R. V.; Rivera, Gabriel; Young, Vanessa K. H.

    2016-01-01

    Though ultimately descended from terrestrial amniotes, turtles have deep roots as an aquatic lineage and are quite diverse in the extent of their aquatic specializations. Many taxa can be viewed as “on the fence” between aquatic and terrestrial realms, whereas others have independently hyperspecialized and moved “all in” to aquatic habitats. Such differences in specialization are reflected strongly in the locomotor system. We have conducted several studies to evaluate the performance consequences of such variation in design, as well as the mechanisms through which specialization for aquatic locomotion is facilitated in turtles. One path to aquatic hyperspecialization has involved the evolutionary transformation of the forelimbs from rowing, tubular limbs with distal paddles into flapping, flattened flippers, as in sea turtles. Prior to the advent of any hydrodynamic advantages, the evolution of such flippers may have been enabled by a reduction in twisting loads on proximal limb bones that accompanied swimming in rowing ancestors, facilitating a shift from tubular to flattened limbs. Moreover, the control of flapping movements appears related primarily to shifts in the activity of a single forelimb muscle, the deltoid. Despite some performance advantages, flapping may entail a locomotor cost in terms of decreased locomotor stability. However, other morphological specializations among rowing species may enhance swimming stability. For example, among highly aquatic pleurodiran turtles, fusion of the pelvis to the shell appears to dramatically reduce motions of the pelvis compared to freshwater cryptodiran species. This could contribute to advantageous increases in aquatic stability among predominantly aquatic pleurodires. Thus, even within the potential constraints of a body plan in which the body is encased by a shell, turtles exhibit diverse locomotor capacities that have enabled diversification into a wide range of aquatic habitats. PMID:27940619

  10. Post-collapse evolution of a coastal caldera system: Insights from a 3D multichannel seismic survey from the Campi Flegrei caldera (Italy)

    Science.gov (United States)

    Steinmann, Lena; Spiess, Volkhard; Sacchi, Marco

    2018-01-01

    In this study we present the first 3D high-resolution multichannel seismic dataset from a (partly) submerged caldera setting, the Campi Flegrei caldera (CFc). Our work aims at examining the spatial and temporal evolution of the CFc since the last caldera-forming event, the Neapolitan Yellow Tuff (NYT, 15 ka) eruption. The main objectives are to investigate the caldera's shallow ( 200 m) outer caldera ring-fault zone. The seismic data revealed that the NYT collapse occurred exclusively along the inner caldera ring-fault and that the related NYT caldera depression is filled with on average 61 m of sediment deposited between 15 and 8.6 ka. The geometry of the inner ring-fault, consisting of four fault segments, seems to be strongly influenced by regional NW-SE and NE SW-trending faults. Furthermore, we found that the ring-faults have acted as pathway for the recent (Bank (10.3-9.5 ka), Nisida Island ( 3.98 ka), and Capo Miseno (3.7 ka) eruptions, yielding DRE values of 0.15 km3, 0.1 km3, and 0.08 km3, respectively, and an explosive magnitude of at least moderate-large scale (VEI 3). Our findings highlight that eruption volumes may be underestimated by 3 to 4 times if the submerged portion of a (partly) submerged caldera is not considered, implying severe consequences for the hazard and risk evaluation. The spatial response of the post-collapse (< 15 ka) depositional environment to volcanic activity, deformational processes and sea-level variations is presented in a comprehensive 3D evolutionary model.

  11. Insights into the evolution of an alkaline magmatic system: An in situ trace element study of clinopyroxenes from the Ditrău Alkaline Massif, Romania

    Science.gov (United States)

    Batki, Anikó; Pál-Molnár, Elemér; Jankovics, M. Éva; Kerr, Andrew C.; Kiss, Balázs; Markl, Gregor; Heincz, Adrián; Harangi, Szabolcs

    2018-02-01

    Clinopyroxene is a major constituent in most igneous rock types (hornblendite, diorite, syenite, nepheline syenite, camptonite, tinguaite and ijolite) of the Ditrău Alkaline Massif, Eastern Carpathians, Romania. Phenocryst and antecryst populations have been distinguished based on mineral zoning patterns and geochemical characteristics. Major and trace element compositions of clinopyroxenes reflect three dominant pyroxene types including primitive high-Cr Fe-diopside, intermediate Na-diopside-hedenbergite and evolved high-Zr aegirine-augite. Clinopyroxenes record two major magma sources as well as distinct magma evolution trends. The primitive diopside population is derived from an early camptonitic magma related to basanitic parental melts, whilst the intermediate diopside-hedenbergite crystals represent a Na-, Nb- and Zr-rich magma source recognised for the first time in the Ditrău magmatic system. This magma fractionated towards ijolitic and later phonolitic compositions. Field observations, petrography and clinopyroxene-melt equilibrium calculations reveal magma recharge and mingling, pyroxene recycling, fractional crystallisation and accumulation. Repeated recharge events of the two principal magmas resulted in multiple interactions between more primitive and more fractionated co-existing magma batches. Magma mingling occurred between mafic and felsic magmas by injection of ijolitic magma into fissures (dykes) containing phonolitic (tinguaite) magma. This study shows that antecryst recycling, also described for the first time in Ditrău, is a significant process during magma recharge and demonstrates that incorporated crystals can crucially affect the host magma composition and so whole-rock chemical data should be interpreted with great care.

  12. The α1,6-fucosyltransferase gene (fut8 from the Sf9 lepidopteran insect cell line: insights into fut8 evolution.

    Directory of Open Access Journals (Sweden)

    Sylvie Juliant

    Full Text Available The core alpha1,6-fucosyltransferase (FUT8 catalyzes the transfer of a fucosyl moiety from GDP-fucose to the innermost asparagine-linked N-acetylglucosamine residue of glycoproteins. In mammals, this glycosylation has an important function in many fundamental biological processes and although no essential role has been demonstrated yet in all animals, FUT8 amino acid (aa sequence and FUT8 activity are very well conserved throughout the animal kingdom. We have cloned the cDNA and the complete gene encoding the FUT8 in the Sf9 (Spodoptera frugiperda lepidopteran cell line. As in most animal genomes, fut8 is a single-copy gene organized in different exons. The open reading frame contains 12 exons, a characteristic that seems to be shared by all lepidopteran fut8 genes. We chose to study the gene structure as a way to characterize the evolutionary relationships of the fut8 genes in metazoans. Analysis of the intron-exon organization in 56 fut8 orthologs allowed us to propose a model for fut8 evolution in metazoans. The presence of a highly variable number of exons in metazoan fut8 genes suggests a complex evolutionary history with many intron gain and loss events, particularly in arthropods, but not in chordata. Moreover, despite the high conservation of lepidoptera FUT8 sequences also in vertebrates and hymenoptera, the exon-intron organization of hymenoptera fut8 genes is order-specific with no shared exons. This feature suggests that the observed intron losses and gains may be linked to evolutionary innovations, such as the appearance of new orders.

  13. New insights on lithofacies architecture, sedimentological characteristics and volcanological evolution of pre-caldera (> 22 ka), multi-phase, scoria- and spatter-cones at Somma-Vesuvius

    Science.gov (United States)

    Sparice, Domenico; Scarpati, Claudio; Perrotta, Annamaria; Mazzeo, Fabio Carmine; Calvert, Andrew T.; Lanphere, Marvin A.

    2017-11-01

    Pre-caldera (> 22 ka) lateral activity at Somma-Vesuvius is related to scoria- and spatter-cone forming events of monogenetic or polygenetic nature. A new stratigraphic, sedimentological, textural and lithofacies investigation was performed on five parasitic cones (Pollena cones, Traianello cone, S. Maria a Castello cone and the recently found Terzigno cone) occurring below the Pomici di Base (22 ka) Plinian products emplaced during the first caldera collapse at Somma-Vesuvius. A new Ar/Ar age of 23.6 ± 0.3 ka obtained for the Traianello cone as well as the absence of a paleosol or reworked material between the S. Maria a Castello cone and the Pomici di Base deposits suggest that such cone-forming eruptions occurred near the upper limit of the pre-caldera period (22-39 ky). The stratigraphy of three of these eccentric cones (Pollena cones and Traianello cone) exhibits erosion surfaces, exotic tephras, volcaniclastic layers, paleosols, unconformity and paraconformity between superimposed eruptive units revealing their multi-phase, polygenetic evolution related to activation of separate vents and periods of quiescence. Such eccentric cones have been described as composed of scoria deposits and pure effusive lavas by previous authors. Lavas are here re-interpreted as welded horizons (lava-like) composed of coalesced spatter fragments whose pyroclastic nature is locally revealed by relicts of original fragments and remnants of clast outlines. These welded horizons show, locally, rheomorphic structures allowing to define them as emplaced as clastogenic lava flows. The lava-like facies is transitional, upward and downward, to less welded facies composed of agglutinated to unwelded spatter horizons in which clasts outlines are increasingly discernible. Such textural characteristics and facies variation are consistent with a continuous fall deposition of Hawaiian fire-fountains episodes alternated with Strombolian phases emplacing loose scoria deposits. High enrichment

  14. High-resolution gene maps of horse chromosomes 14 and 21: additional insights into evolution and rearrangements of HSA5 homologs in mammals.

    Science.gov (United States)

    Goh, Glenda; Raudsepp, Terje; Durkin, Keith; Wagner, Michelle L; Schäffer, Alejandro A; Agarwala, Richa; Tozaki, Teruaki; Mickelson, James R; Chowdhary, Bhanu P

    2007-01-01

    High-resolution physically ordered gene maps for equine homologs of human chromosome 5 (HSA5), viz., horse chromosomes 14 and 21 (ECA14 and ECA21), were generated by adding 179 new loci (131 gene-specific and 48 microsatellites) to the existing maps of the two chromosomes. The loci were mapped primarily by genotyping on a 5000-rad horse x hamster radiation hybrid panel, of which 28 were mapped by fluorescence in situ hybridization. The approximately fivefold increase in the number of mapped markers on the two chromosomes improves the average resolution of the map to 1 marker/0.9 Mb. The improved resolution is vital for rapid chromosomal localization of traits of interest on these chromosomes and for facilitating candidate gene searches. The comparative gene mapping data on ECA14 and ECA21 finely align the chromosomes to sequence/gene maps of a range of evolutionarily distantly related species. It also demonstrates that compared to ECA14, the ECA21 segment corresponding to HSA5 is a more conserved region because of preserved gene order in a larger number of and more diverse species. Further, comparison of ECA14 and the distal three-quarters region of ECA21 with corresponding chromosomal segments in 50 species belonging to 11 mammalian orders provides a broad overview of the evolution of these segments in individual orders from the putative ancestral chromosomal configuration. Of particular interest is the identification and precise demarcation of equid/Perissodactyl-specific features that for the first time clearly distinguish the origins of ECA14 and ECA21 from similar-looking status in the Cetartiodactyls.

  15. New Insight into the Hydrogen Evolution Reaction under Buffered Near-Neutral pH Conditions: Enthalpy and Entropy of Activation

    KAUST Repository

    Shinagawa, Tatsuya

    2016-10-06

    Electrochemical conversion of thermodynamically stable chemicals of water and carbon dioxide is regarded as a core technology for achieving sustainability in our society. In both cases, the electrochemical hydrogen evolution reaction (HER) is a key reaction, particularly at near-neutral pH. This study addresses the kinetic aspects of the HER in buffered near-neutral pH conditions using a variety of electrode materials (W, Ni, Pt, Au, and Cu) over a wide temperature range (299–346 K). When the overall performance was summarized with respect to the binding energy of the reaction intermediate species, a classic volcano-shaped relationship was obtained. Interestingly, the temperature sensitivity analysis disclosed that smaller activation energies did not always lead to higher performance in 1.5 mol L–1 K-phosphate solution (pH 5.8). Detailed analysis of the temperature- and potential-dependent parameters revealed that smaller activation energies coincided with smaller values of the pre-exponential factor in the Arrhenius’ equation (associated with the entropy of activation). Due to the trade-off relationship of enthalpy–entropy compensation in the current system, the conventional approach of mixing elements of lower and higher binding energies to the intermediate species failed: even though Ni–Cu showed lower apparent activation energy, its activity toward the HER was between that of Ni and Cu due to the lowered entropy of activation. This study demonstrates the unrevealed fundamental aspects of the HER in buffered near-neutral condition, which contributes to the rational development of efficient energy and material conversion systems.

  16. Newton law corrections and instabilities in f(R) gravity with the effective cosmological constant epoch

    International Nuclear Information System (INIS)

    Nojiri, Shin'ichi; Odintsov, Sergei D.

    2007-01-01

    We consider class of modified f(R) gravities with the effective cosmological constant epoch at the early and late universe. Such models pass most of solar system tests as well they satisfy to cosmological bounds. Despite their very attractive properties, it is shown that one realistic class of such models may lead to significant Newton law corrections at large cosmological scales. Nevertheless, these corrections are small at solar system as well as at the future universe. Another realistic model with acceptable Newton law regime shows the matter instability

  17. Will nonlinear peculiar velocity and inhomogeneous reionization spoil 21 cm cosmology from the epoch of reionization?

    Science.gov (United States)

    Shapiro, Paul R; Mao, Yi; Iliev, Ilian T; Mellema, Garrelt; Datta, Kanan K; Ahn, Kyungjin; Koda, Jun

    2013-04-12

    The 21 cm background from the epoch of reionization is a promising cosmological probe: line-of-sight velocity fluctuations distort redshift, so brightness fluctuations in Fourier space depend upon angle, which linear theory shows can separate cosmological from astrophysical information. Nonlinear fluctuations in ionization, density, and velocity change this, however. The validity and accuracy of the separation scheme are tested here for the first time, by detailed reionization simulations. The scheme works reasonably well early in reionization (≲40% ionized), but not late (≳80% ionized).

  18. Superposed epoch analysis of pressure and magnetic field configuration changes in the plasma sheet

    International Nuclear Information System (INIS)

    Kistler, L.M.; Moebius, E.; Baumjohann, W.; Nagai, T.

    1993-01-01

    The authors report on an analysis of pressure and magnetic configuration within the plasma sheet following the initiation of substorm events. They have constructed this time dependent picture by using an epoch analysis of data from the AMPTE/IRM spacecraft. This analysis procedure can be used to construct a unified picture of events, provided they are reproducible, from a statistical analysis of a series of point measurements. The authors first determine the time dependent pressure changes in the plasma sheet. With some simplifying assumptions they then determine the z dependence of the pressure profiles, and from this distribution determine how field lines in the plasma sheet map to the neutral sheet

  19. Elucidating dark energy with future 21 cm observations at the epoch of reionization

    Energy Technology Data Exchange (ETDEWEB)

    Kohri, Kazunori [The Graduate University for Advanced Studies (SOKENDAI), 1-1 Oho, Tsukuba 305-0801 (Japan); Oyama, Yoshihiko [Institute for Cosmic Ray Research, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8582 (Japan); Sekiguchi, Toyokazu [Center for Theoretical Physics of the Universe, Institute for Basic Science (IBS), 193, Munjiro, Yuseoung-gu, Daejeon 34051 (Korea, Republic of); Takahashi, Tomo, E-mail: kohri@post.kek.jp, E-mail: oyamayo@icrr.u-tokyo.ac.jp, E-mail: sekiguti@ibs.re.kr, E-mail: tomot@cc.saga-u.ac.jp [Department of Physics, Saga University, 1 Honjo, Saga 840-8502 (Japan)

    2017-02-01

    We investigate how precisely we can determine the nature of dark energy such as the equation of state (EoS) and its time dependence by using future observations of 21 cm fluctuations at the epoch of reionization (06.8∼< z ∼<1) such as Square Kilometre Array (SKA) and Omniscope in combination with those from cosmic microwave background, baryon acoustic oscillation, type Ia supernovae and direct measurement of the Hubble constant. We consider several parametrizations for the EoS and find that future 21 cm observations will be powerful in constraining models of dark energy, especially when its EoS varies at high redshifts.

  20. Cosmological constraints on variations of the fine structure constant at the epoch of recombination

    International Nuclear Information System (INIS)

    Menegoni, E; Galli, S; Archidiacono, M; Calabrese, E; Melchiorri, A

    2013-01-01

    In this brief work we investigate any possible variation of the fine structure constant at the epoch of recombination. The recent measurements of the Cosmic Microwave Background anisotropies at arcminute angular scales performed by the ACT and SPT experiments are probing the damping regime of Cosmic Microwave Background fluctuations. We study the role of a mechanism that could affect the shape of the Cosmic Microwave Background angular fluctuations at those scales, namely a change in the recombination process through variations in the fine structure constant α

  1. Multi-epoch VLBA Imaging of 20 New TeV Blazars: Apparent Jet Speeds

    Science.gov (United States)

    Piner, B. Glenn; Edwards, Philip G.

    2018-01-01

    We present 88 multi-epoch Very Long Baseline Array (VLBA) images (most at an observing frequency of 8 GHz) of 20 TeV blazars, all of the high-frequency-peaked BL Lac (HBL) class, that have not been previously studied at multiple epochs on the parsec scale. From these 20 sources, we analyze the apparent speeds of 43 jet components that are all detected at four or more epochs. As has been found for other TeV HBLs, the apparent speeds of these components are relatively slow. About two-thirds of the components have an apparent speed that is consistent (within 2σ) with no motion, and some of these components may be stationary patterns whose apparent speed does not relate to the underlying bulk flow speed. In addition, a superluminal tail to the apparent speed distribution of the TeV HBLs is detected for the first time, with eight components in seven sources having a 2σ lower limit on the apparent speed exceeding 1c. We combine the data from these 20 sources with an additional 18 sources from the literature to analyze the complete apparent speed distribution of all 38 TeV HBLs that have been studied with very long baseline interferometry at multiple epochs. The highest 2σ apparent speed lower limit considering all sources is 3.6c. This suggests that bulk Lorentz factors of up to about 4, but probably not much higher, exist in the parsec-scale radio-emitting regions of these sources, consistent with estimates obtained in the radio by other means such as brightness temperatures. This can be reconciled with the high Lorentz factors estimated from the high-energy data if the jet has velocity structures consisting of different emission regions with different Lorentz factors. In particular, we analyze the current apparent speed data for the TeV HBLs in the context of a model with a fast central spine and a slower outer layer.

  2. The evolution of farnesoid X, vitamin D, and pregnane X receptors: insights from the green-spotted pufferfish (Tetraodon nigriviridis and other non-mammalian species

    Directory of Open Access Journals (Sweden)

    Kullman Seth W

    2011-02-01

    (planar bile alcohols for zebrafish and sterically bent bile acids for the pufferfish and receptor selectivity that matches these differences in endogenous ligands. Our observations to date present an integrated picture of the co-evolution of bile salt structure and changes in the binding pockets of three nuclear hormone receptors across the species studied.

  3. A petrological study of Paleoarchean rocks of the Onverwacht Group: New insights into the geologic evolution of the Barberton Greenstone Belt, South Africa

    Science.gov (United States)

    Grosch, E. G.; Mcloughlin, N.; Abu-Alam, T. S.; Vidal, O.

    2012-12-01

    This study presents a multi-disciplinary petrological approach applied to surface samples and a total of 800 m of scientific drill core that furthers our understanding of the geologic evolution of the ca. 3.5 to 3.2 Ga Onverwacht Group of the Barberton greenstone belt (BGB), South Africa. Detrital zircon grains in coarse (diamictite) to fine-grained clastic sedimentary rocks of the Noisy formation (drill core KD2a) that unconformably overlies the volcanic ca. 3472 Ma Hooggenoeg Formation, are investigated by laser ablation LA-ICP-MS to constrain their 207Pb/206Pb ages for depositional age and provenance. A wide range in 207Pb/206Pb ages between ca. 3600 and 3430 Ma is reported, corresponding to surrounding TTG plutons and the ca.3667-3223 Ma Ancient Gneiss Complex. The youngest detrital zircon grain identified has an age of 3432 ± 10 Ma. Given the short time interval for a major change in geologic environment between ca. 3472 Ma and ca. 3432 Ma, it is argued here, that the Noisy formation is the earliest tectonic basin in the BGB, which developed during major tectonic uplift at ca. 3432 Ma. In the overlying ca. 3334 Ma Kromberg type-section, application of a chlorite thermodynamic multi-equilibrium calculation, dioctahedral mica hydration-temperature curve and pseudosection modelling, indicates a wide range in metamorphic conditions from sub-greenschist to the uppermost greenschist facies across the Kromberg type-section. A central mylonitic fuchsite-bearing zone, referred to as the Kromberg Section Mylonites, records at least two metamorphic events: a high-T, low-P (420 ± 30oC, sedimentary sequence contains detrital and diagenetic pyrites with a significant variation in Δ33S of -0.62 to +1.4‰ and δ34SCDT between -7.00 and +12.6‰ in the upper turbidite unit, to more narrow isotopic ranges with magmatic-atmospheric values in the underlying polymictitic diamictite. A sedimentary quartz-pyrite vein in the diamictite records the largest range and most negative

  4. The optical variability of SDSS quasars from multi-epoch spectroscopy. I. Results from 60 quasars with ≥ six-epoch spectra

    Energy Technology Data Exchange (ETDEWEB)

    Guo, Hengxiao; Gu, Minfeng, E-mail: hxguo@shao.ac.cn, E-mail: gumf@shao.ac.cn [Key Laboratory for Research in Galaxies and Cosmology, Shanghai Astronomical Observatory, Chinese Academy of Sciences, 80 Nandan Road, Shanghai 200030 (China)

    2014-09-01

    In a sample of 60 quasars selected from the Sloan Digital Sky Survey with at least six-epoch spectroscopy, we investigate the variability of emission lines and continuum luminosity at various aspects. A strong anti-correlation between the variability and continuum luminosity at 2500 Å is found for the sample, which is consistent with previous works. In individual sources, we find that half of the sample objects follow the trend of being bluer when brighter, while the remaining half follow the redder-when-brighter (RWB) trend. Although the mechanism for RWB is unclear, the effects of host galaxy contribution due to seeing variations cannot be completely ruled out. As expected from the photoionization model, the positive correlations between the broad emission line and continuum luminosity are found in most individual sources, as well as for the whole sample. We confirm the Baldwin effect in most individual objects and the whole sample, while a negative Baldwin effect is also found in several quasars, which can be at least partly (if not all) due to the host galaxy contamination. We find positive correlations between the broad emission line luminosity and line width in most individual quasars, as well as the whole sample, implying a line base that is more variable than the line core.

  5. Schubert and Beethoven - Adorno’s early antipods of the music in bougeois epoch

    Directory of Open Access Journals (Sweden)

    Jeremić-Molnar Dragana

    2012-01-01

    Full Text Available In this article the authors are reconstructing the dichotomies which the young Theodor Adorno was trying to detect in the music of the bourgeois epoch and personify in two antipodes - Franz Schubert and Ludwig van Beethoven. Although already a devotee of Arnold Schönberg and the 20th century music avantgardism, Adorno was, in his works prior to his exile from Germany (1934, intensively dealing with Schubert and his opposition towards Beethoven. While Beethoven was a bold and progressive revolutionary, fascinated by the “practical reason” and the mission to rise up and reach the stars, Schubert wanted none of it (almost anticipating the failure of the whole revolutionary project. Instead, he was looking backwards, to primordial nature and the possibility of man to participate in its mythic cycles of death and regeneration. The lack of synthesis between this two opposing tendencies in the music of early bourgeois epoch lead to the “negative dialectics” of Schönberg and 20th century music avantgardism and to the final separation of Beethovenian musical progress and Schubertian musical mimesis. [Projekat Ministarstva nauke Republike Srbije, br. 177019: Identiteti srpske muzike u svetskom kulturnom kontekstu, i br. 179035: Izazovi nove društvene integracije u Srbiji - koncepti i akteri

  6. Superposed epoch analysis of O+ auroral outflow during sawtooth events and substorms

    Science.gov (United States)

    Nowrouzi, N.; Kistler, L. M.; Lund, E. J.; Cai, X.

    2017-12-01

    Sawtooth events are repeated injection of energetic particles at geosynchronous orbit. Studies have shown that 94% of sawtooth events occurred during magnetic storm times. The main factor that causes a sawtooth event is still an open question. Simulations have suggested that heavy ions like O+ may play a role in triggering the injections. One of the sources of the O+ in the Earth's magnetosphere is the nightside aurora. O+ ions coming from the nightside auroral region have direct access to the near-earth magnetotail. A model (Brambles et al. 2013) for interplanetary coronal mass ejection driven sawtooth events found that nightside O+ outflow caused the subsequent teeth of the sawtooth event through a feedback mechanism. This work is a superposed epoch analysis to test whether the observed auroral outflow supports this model. Using FAST spacecraft data from 1997-2007, we examine the auroral O+ outflow as a function of time relative to an injection onset. Then we determine whether the profile of outflow flux of O+ during sawtooth events is different from the outflow observed during isolated substorms. The auroral region boundaries are estimated using the method of (Andersson et al. 2004). Subsequently the O+ outflow flux inside these boundaries are calculated and binned as a function of superposed epoch time for substorms and sawtooth "teeth". In this way, we will determine if sawtooth events do in fact have greater O+ outflow, and if that outflow is predominantly from the nightside, as suggested by the model results.

  7. THE HYDROGEN EPOCH OF REIONIZATION ARRAY DISH. I. BEAM PATTERN MEASUREMENTS AND SCIENCE IMPLICATIONS

    Energy Technology Data Exchange (ETDEWEB)

    Neben, Abraham R.; Hewitt, Jacqueline N.; Ewall-Wice, Aaron [MIT Kavli Institute, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States); Bradley, Richard F. [Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA 22904 (United States); DeBoer, David R.; Parsons, Aaron R.; Ali, Zaki S.; Cheng, Carina; Patra, Nipanjana; Dillon, Joshua S. [Department of Astronomy, University of California, Berkeley, CA (United States); Aguirre, James E.; Kohn, Saul A. [Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA (United States); Thyagarajan, Nithyanandan; Bowman, Judd; Jacobs, Daniel C. [Arizona State University, School of Earth and Space Exploration, Tempe, AZ 85287 (United States); Dickenson, Roger; Doolittle, Phillip; Egan, Dennis; Hedrick, Mike; Klima, Patricia J. [National Radio Astronomy Observatory, Charlottesville, VA (United States); and others

    2016-08-01

    The Hydrogen Epoch of Reionization Array (HERA) is a radio interferometer aiming to detect the power spectrum of 21 cm fluctuations from neutral hydrogen from the epoch of reionization (EOR). Drawing on lessons from the Murchison Widefield Array and the Precision Array for Probing the EOR, HERA is a hexagonal array of large (14 m diameter) dishes with suspended dipole feeds. The dish not only determines overall sensitivity, but also affects the observed frequency structure of foregrounds in the interferometer. This is the first of a series of four papers characterizing the frequency and angular response of the dish with simulations and measurements. In this paper, we focus on the angular response (i.e., power pattern), which sets the relative weighting between sky regions of high and low delay and thus apparent source frequency structure. We measure the angular response at 137 MHz using the ORBCOMM beam mapping system of Neben et al. We measure a collecting area of 93 m{sup 2} in the optimal dish/feed configuration, implying that HERA-320 should detect the EOR power spectrum at z ∼ 9 with a signal-to-noise ratio of 12.7 using a foreground avoidance approach with a single season of observations and 74.3 using a foreground subtraction approach. Finally, we study the impact of these beam measurements on the distribution of foregrounds in Fourier space.

  8. The epoch of cosmic heating by early sources of X-rays

    Science.gov (United States)

    Eide, Marius B.; Graziani, Luca; Ciardi, Benedetta; Feng, Yu; Kakiichi, Koki; Di Matteo, Tiziana

    2018-05-01

    Observations of the 21 cm line from neutral hydrogen indicate that an epoch of heating (EoH) might have preceded the later epoch of reionization. Here we study the effects on the ionization state and the thermal history of the intergalactic medium (IGM) during the EoH induced by different assumptions on ionizing sources in the high-redshift Universe: (i) stars; (ii) X-ray binaries (XRBs); (iii) thermal bremsstrahlung of the hot interstellar medium (ISM); and (iv) accreting nuclear black holes (BHs). To this aim, we post-process outputs from the (100 h-1 comoving Mpc)3 hydrodynamical simulation MassiveBlack-II with the cosmological 3D radiative transfer code CRASH, which follows the propagation of ultraviolet and X-ray photons, computing the thermal and ionization state of hydrogen and helium through the EoH. We find that stars determine the fully ionized morphology of the IGM, while the spectrally hard XRBs pave way for efficient subsequent heating and ionization by the spectrally softer ISM. With the seeding prescription in MassiveBlack-II, BHs do not contribute significantly to either ionization or heating. With only stars, most of the IGM remains in a cold state (with a median T = 11 K at z = 10), however, the presence of more energetic sources raises the temperature of regions around the brightest and more clustered sources above that of the cosmic microwave background, opening the possibility to observing the 21 cm signal in emission.

  9. Coordinating supplier-retailer using multiple common replenishment epochs with retailers’ choices

    Directory of Open Access Journals (Sweden)

    Juhwen Hwang

    2013-06-01

    Full Text Available Purpose: Provide a coordination strategy using multiple common replenishment epochs (MCRE for a single-supplier multi-retailer supply chain. Design/methodology/approach: The demand of a product occurs only with a group of heterogeneous and independent retailers with constant rates, whereas all their order requests are fulfilled by the supplier. The supplier decides a set of MCREs with general price and extra bonus to entice the retailers to join any one of the MCREs, or to let them remain with their original order time epochs. A retailer is willing to participate in a CRE as long as the retailer’s cost increase is within its tolerance. This paper provide a mixed integer programming to determine the MCRE strategies in order to minimize the total costs of the supplier. Findings: The results illustrate that MCRE model provided in the paper can generate a better replenishment coordination scheme than single CRE models. Practical implications: Replenishment coordination is one of the most important mechanisms to improve the efficiency in supply chains, e.g., chain convenience stores in the modern retail industry. Originality/value: This is a follow-up research on Joint Economic Lot Size (JELS models with a focus on multiple retailers with their replenishment coordination.

  10. Identification enhancement of auditory evoked potentials in EEG by epoch concatenation and temporal decorrelation.

    Science.gov (United States)

    Zavala-Fernandez, H; Orglmeister, R; Trahms, L; Sander, T H

    2012-12-01

    Event-related potentials (ERP) recorded by electroencephalography (EEG) are brain responses following an external stimulus, e.g., a sound or an image. They are used in fundamental cognitive research and neurological and psychiatric clinical research. ERPs are weaker than spontaneous brain activity and therefore it is difficult or even impossible to identify an ERP in the brain activity following an individual stimulus. For this reason, a blind source separation method relying on statistical information is proposed for the isolation of ERP after auditory stimulation. In this paper it is suggested to integrate epoch concatenation into the popular temporal decorrelation algorithm SOBI/TDSEP relying on time shifted correlations. With the proposed epoch concatenation temporal decorrelation (ecTD) algorithm a component representing the auditory evoked potential (AEP) is found in electroencephalographic data from an auditory stimulation experiment lasting 3min. The ecTD result is compared with the averaged AEP and it is superior to the result from the SOBI/TDSEP algorithm. Furthermore the ecTD processing leads to significant increases in the signal-to-noise ratio (shape SNR) of the AEP and reduces the computation time by 50% if compared to the SOBI/TDSEP calculation. It can be concluded that data concatenation in combination with temporal decorrelation is useful for isolating and improving the properties of an AEP especially in a short duration stimulation experiment. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  11. THE HYDROGEN EPOCH OF REIONIZATION ARRAY DISH. I. BEAM PATTERN MEASUREMENTS AND SCIENCE IMPLICATIONS

    International Nuclear Information System (INIS)

    Neben, Abraham R.; Hewitt, Jacqueline N.; Ewall-Wice, Aaron; Bradley, Richard F.; DeBoer, David R.; Parsons, Aaron R.; Ali, Zaki S.; Cheng, Carina; Patra, Nipanjana; Dillon, Joshua S.; Aguirre, James E.; Kohn, Saul A.; Thyagarajan, Nithyanandan; Bowman, Judd; Jacobs, Daniel C.; Dickenson, Roger; Doolittle, Phillip; Egan, Dennis; Hedrick, Mike; Klima, Patricia J.

    2016-01-01

    The Hydrogen Epoch of Reionization Array (HERA) is a radio interferometer aiming to detect the power spectrum of 21 cm fluctuations from neutral hydrogen from the epoch of reionization (EOR). Drawing on lessons from the Murchison Widefield Array and the Precision Array for Probing the EOR, HERA is a hexagonal array of large (14 m diameter) dishes with suspended dipole feeds. The dish not only determines overall sensitivity, but also affects the observed frequency structure of foregrounds in the interferometer. This is the first of a series of four papers characterizing the frequency and angular response of the dish with simulations and measurements. In this paper, we focus on the angular response (i.e., power pattern), which sets the relative weighting between sky regions of high and low delay and thus apparent source frequency structure. We measure the angular response at 137 MHz using the ORBCOMM beam mapping system of Neben et al. We measure a collecting area of 93 m 2 in the optimal dish/feed configuration, implying that HERA-320 should detect the EOR power spectrum at z ∼ 9 with a signal-to-noise ratio of 12.7 using a foreground avoidance approach with a single season of observations and 74.3 using a foreground subtraction approach. Finally, we study the impact of these beam measurements on the distribution of foregrounds in Fourier space.

  12. A fast pulse phase estimation method for X-ray pulsar signals based on epoch folding

    Directory of Open Access Journals (Sweden)

    Xue Mengfan

    2016-06-01

    Full Text Available X-ray pulsar-based navigation (XPNAV is an attractive method for autonomous deep-space navigation in the future. The pulse phase estimation is a key task in XPNAV and its accuracy directly determines the navigation accuracy. State-of-the-art pulse phase estimation techniques either suffer from poor estimation accuracy, or involve the maximization of generally non-convex object function, thus resulting in a large computational cost. In this paper, a fast pulse phase estimation method based on epoch folding is presented. The statistical properties of the observed profile obtained through epoch folding are developed. Based on this, we recognize the joint probability distribution of the observed profile as the likelihood function and utilize a fast Fourier transform-based procedure to estimate the pulse phase. Computational complexity of the proposed estimator is analyzed as well. Experimental results show that the proposed estimator significantly outperforms the currently used cross-correlation (CC and nonlinear least squares (NLS estimators, while significantly reduces the computational complexity compared with NLS and maximum likelihood (ML estimators.

  13. OPENING THE 21 cm EPOCH OF REIONIZATION WINDOW: MEASUREMENTS OF FOREGROUND ISOLATION WITH PAPER

    Energy Technology Data Exchange (ETDEWEB)

    Pober, Jonathan C.; Parsons, Aaron R.; Ali, Zaki [Astronomy Department, U. California, Berkeley, CA (United States); Aguirre, James E.; Moore, David F. [Department of Physics and Astronomy, U. Pennsylvania, Philadelphia, PA (United States); Bradley, Richard F. [Department of Electrical and Computer Engineering, U. Virginia, Charlottesville, VA (United States); Carilli, Chris L. [National Radio Astronomy Observatory, Socorro, NM (United States); DeBoer, Dave; Dexter, Matthew; MacMahon, Dave [Radio Astronomy Laboratory, U. California, Berkeley, CA (United States); Gugliucci, Nicole E. [Department of Astronomy, U. Virginia, Charlottesville, VA (United States); Jacobs, Daniel C. [School of Earth and Space Exploration, Arizona State U., Tempe, AZ (United States); Klima, Patricia J. [National Radio Astronomy Observatory, Charlottesville, VA (United States); Manley, Jason; Walbrugh, William P. [Square Kilometer Array, South Africa Project, Cape Town (South Africa); Stefan, Irina I. [Cavendish Laboratory, Cambridge (United Kingdom)

    2013-05-10

    We present new observations with the Precision Array for Probing the Epoch of Reionization with the aim of measuring the properties of foreground emission for 21 cm epoch of reionization (EoR) experiments at 150 MHz. We focus on the footprint of the foregrounds in cosmological Fourier space to understand which modes of the 21 cm power spectrum will most likely be compromised by foreground emission. These observations confirm predictions that foregrounds can be isolated to a {sup w}edge{sup -}like region of two-dimensional (k , k{sub Parallel-To })-space, creating a window for cosmological studies at higher k{sub Parallel-To} values. We also find that the emission extends past the nominal edge of this wedge due to spectral structure in the foregrounds, with this feature most prominent on the shortest baselines. Finally, we filter the data to retain only this ''unsmooth'' emission and image its specific k{sub Parallel-To} modes. The resultant images show an excess of power at the lowest modes, but no emission can be clearly localized to any one region of the sky. This image is highly suggestive that the most problematic foregrounds for 21 cm EoR studies will not be easily identifiable bright sources, but rather an aggregate of fainter emission.

  14. A shifting rift—Geophysical insights into the evolution of Rio Grande rift margins and the Embudo transfer zone near Taos, New Mexico

    Science.gov (United States)

    Grauch, V.J.S.; Bauer, Paul W.; Drenth, Benjamin J.; Kelson, Keith I.

    2017-01-01

    We present a detailed example of how a subbasin develops adjacent to a transfer zone in the Rio Grande rift. The Embudo transfer zone in the Rio Grande rift is considered one of the classic examples and has been used as the inspiration for several theoretical models. Despite this attention, the history of its development into a major rift structure is poorly known along its northern extent near Taos, New Mexico. Geologic evidence for all but its young rift history is concealed under Quaternary cover. We focus on understanding the pre-Quaternary evidence that is in the subsurface by integrating diverse pieces of geologic and geophysical information. As a result, we present a substantively new understanding of the tectonic configuration and evolution of the northern extent of the Embudo fault and its adjacent subbasin.We integrate geophysical, borehole, and geologic information to interpret the subsurface configuration of the rift margins formed by the Embudo and Sangre de Cristo faults and the geometry of the subbasin within the Taos embayment. Key features interpreted include (1) an imperfect D-shaped subbasin that slopes to the east and southeast, with the deepest point ∼2 km below the valley floor located northwest of Taos at ∼36° 26′N latitude and 105° 37′W longitude; (2) a concealed Embudo fault system that extends as much as 7 km wider than is mapped at the surface, wherein fault strands disrupt or truncate flows of Pliocene Servilleta Basalt and step down into the subbasin with a minimum of 1.8 km of vertical displacement; and (3) a similar, wider than expected (5–7 km) zone of stepped, west-down normal faults associated with the Sangre de Cristo range front fault.From the geophysical interpretations and subsurface models, we infer relations between faulting and flows of Pliocene Servilleta Basalt and older, buried basaltic rocks that, combined with geologic mapping, suggest a revised rift history involving shifts in the locus of fault activity as

  15. Signals from the epoch of cosmological recombination (Karl Schwarzschild Award Lecture 2008)

    Science.gov (United States)

    Sunyaev, R. A.; Chluba, J.

    2009-07-01

    The physical ingredients to describe the epoch of cosmological recombination are amazingly simple and well-understood. This fact allows us to take into account a very large variety of physical processes, still finding potentially measurable consequences for the energy spectrum and temperature anisotropies of the Cosmic Microwave Background (CMB). In this contribution we provide a short historical overview in connection with the cosmological recombination epoch and its connection to the CMB. Also we highlight some of the detailed physics that were studied over the past few years in the context of the cosmological recombination of hydrogen and helium. The impact of these considerations is two-fold: The associated release of photons during this epoch leads to interesting and unique deviations of the Cosmic Microwave Background (CMB) energy spectrum from a perfect blackbody, which, in particular at decimeter wavelength and the Wien part of the CMB spectrum, may become observable in the near future. Despite the fact that the abundance of helium is rather small, it still contributes a sizeable amount of photons to the full recombination spectrum, leading to additional distinct spectral features. Observing the spectral distortions from the epochs of hydrogen and helium recombination, in principle would provide an additional way to determine some of the key parameters of the Universe (e.g. the specific entropy, the CMB monopole temperature and the pre-stellar abundance of helium). Also it permits us to confront our detailed understanding of the recombination process with direct observational evidence. In this contribution we illustrate how the theoretical spectral template of the cosmological recombination spectrum may be utilized for this purpose. We also show that because hydrogen and helium recombine at very different epochs it is possible to address questions related to the thermal history of our Universe. In particular the cosmological recombination radiation may

  16. Evolution of the Cosmic Web

    Science.gov (United States)

    Einasto, J.

    2017-07-01

    In the evolution of the cosmic web dark energy plays an important role. To understand the role of dark energy we investigate the evolution of superclusters in four cosmological models: standard model SCDM, conventional model LCDM, open model OCDM, and a hyper-dark-energy model HCDM. Numerical simulations of the evolution are performed in a box of size 1024 Mpc/h. Model superclusters are compared with superclusters found for Sloan Digital Sky Survey (SDSS). Superclusters are searched using density fields. LCDM superclusters have properties, very close to properties of observed SDSS superclusters. Standard model SCDM has about 2 times more superclusters than other models, but SCDM superclusters are smaller and have lower luminosities. Superclusters as principal structural elements of the cosmic web are present at all cosmological epochs.

  17. SPECTROPOLARIMETRY OF SUPERLUMINOUS SUPERNOVAE: INSIGHT INTO THEIR GEOMETRY

    Energy Technology Data Exchange (ETDEWEB)

    Inserra, C.; Bulla, M.; Sim, S. A.; Smartt, S. J., E-mail: c.inserra@qub.ac.uk [Astrophysics Research Centre, School of Mathematics and Physics, Queens University Belfast, Belfast BT7 1NN (United Kingdom)

    2016-11-01

    We present the first spectropolarimetric observations of a hydrogen-free superluminous supernova (SLSN) at z = 0.1136, namely SN 2015bn. The transient shows significant polarization at both of the observed epochs: one 24 days before maximum light in the rest-frame, and the other at 27 days after peak luminosity. Analysis of the Q – U plane suggests the presence of a dominant axis and no physical departure from the main axis at either epoch. The polarization spectrum along the dominant axis is characterized by a strong wavelength dependence and an increase in the signal from the first to the second epoch. We use a Monte Carlo code to demonstrate that these properties are consistent with a simple toy model that adopts an axisymmetric ellipsoidal configuration for the ejecta. We find that the wavelength dependence of the polarization is possibly due to a strong wavelength dependence in the line opacity, while the higher level of polarization at the second epoch is a consequence of the increase in the asphericity of the inner layers of the ejecta or the fact that the photosphere recedes into less spherical layers. The geometry of the SLSN is similar to that of stripped-envelope core-collapse SNe connected to GRB, while the overall evolution of the ejecta shape could be consistent with a central engine.

  18. Satellite- and Epoch Differenced Precise Point Positioning Based on a Regional Augmentation Network

    Directory of Open Access Journals (Sweden)

    Bin Wu

    2012-06-01

    Full Text Available Precise Point Positioning (PPP has been demonstrated as a simple and effective approach for user positioning. The key issue in PPP is how to shorten convergence time and improve positioning efficiency. Recent researches mainly focus on the ambiguity resolution by correcting residual phase errors at a single station. The success of this approach (referred to hereafter as NORM-PPP is subject to how rapidly one can fix wide-lane and narrow-lane ambiguities to achieve the first ambiguity-fixed solution. The convergence time of NORM-PPP is receiver type dependent, and normally takes 15–20 min. Different from the general algorithm and theory by which the float ambiguities are estimated and the integer ambiguities are fixed, we concentrate on a differential PPP approach: the satellite- and epoch differenced (SDED approach. In general, the SDED approach eliminates receiver clocks and ambiguity parameters and thus avoids the complicated residual phase modeling procedure. As a further development of the SDED approach, we use a regional augmentation network to derive tropospheric delay and remaining un-modeled errors at user sites. By adding these corrections and applying the Robust estimation, the weak mathematic properties due to the ED operation is much improved. Implementing this new approach, we need only two epochs of data to achieve PPP positioning converging to centimeter-positioning accuracy. Using seven days of GPS data at six CORS stations in Shanghai, we demonstrate the success rate, defined as the case when three directions converging to desired positioning accuracy of 10 cm, reaches 100% when the interval between the two epochs is longer than 15 min. Comparing the results of 15 min’ interval to that of 10 min’, it is observed that the position RMS improves from 2.47, 3.95, 5.78 cm to 2.21, 3.93, 4.90 cm in the North, East and Up directions, respectively. Combining the SDED coordinates at the starting point and the ED relative

  19. Spectral evolution of galaxies

    International Nuclear Information System (INIS)

    Rocca-Volmerange, B.

    1989-01-01

    A recent striking event in Observational Cosmology is the discovery of a large population of galaxies at extreme cosmological distances (extended from spectral redshifts ≅ 1 to ≥ 3) corresponding to a lookback time of 80% of the Universe's age. However when galaxies are observed at such remote epochs, their appearances are affected by at least two simultaneous effects which are respectively a cosmological effect and the intrinsic evolution of their stellar populations which appear younger than in our nearby galaxies. The fundamental problem is first to disentangle the respective contributions of these two effects to apparent magnitudes and colors of distant galaxies. Other effects which are likely to modify the appearance of galaxies are amplification by gravitational lensing and interaction with environment will also be considered. (author)

  20. Evolution of Flat Roofs

    Directory of Open Access Journals (Sweden)

    Şt. Vasiliu

    2009-01-01

    Full Text Available Roofs are constructive subassembles that are located at the top of buildings, which toghether with perimetral walls and some elements of the infrastructure belongs to the subsystem elements that close the building. Roofs must meet resistance requirements to mechanical action, thermal insulating, waterproofing and acoustic, fire resistance, durability, economy and aesthetics. The man saw the need to build roofs from the oldest ancient times. Even if the design of buildings has an empirical character, are known and are preserved until today constructions that are made in antiquity, by the Egyptians, Greeks and Romans with architectural achievements, worthy of admiration and in present time. General composition of civil construction has been influenced throughout the evolution of construction history by the level of production forces and properties of building materials available in every historical epoch. For over five millennia, building materials were stone, wood and ceramic products (concrete was used by theRomans only as filling material.

  1. Direct detection of projectile relics from the end of the lunar basin-forming epoch.

    Science.gov (United States)

    Joy, Katherine H; Zolensky, Michael E; Nagashima, Kazuhide; Huss, Gary R; Ross, D Kent; McKay, David S; Kring, David A

    2012-06-15

    The lunar surface, a key proxy for the early Earth, contains relics of asteroids and comets that have pummeled terrestrial planetary surfaces. Surviving fragments of projectiles in the lunar regolith provide a direct measure of the types and thus the sources of exogenous material delivered to the Earth-Moon system. In ancient [>3.4 billion years ago (Ga)] regolith breccias from the Apollo 16 landing site, we located mineral and lithologic relics of magnesian chondrules from chondritic impactors. These ancient impactor fragments are not nearly as diverse as those found in younger (3.4 Ga to today) regolith breccias and soils from the Moon or that presently fall as meteorites to Earth. This suggests that primitive chondritic asteroids, originating from a similar source region, were common Earth-Moon-crossing impactors during the latter stages of the basin-forming epoch.

  2. Analysis of Accuracy and Epoch on Back-propagation BFGS Quasi-Newton

    Science.gov (United States)

    Silaban, Herlan; Zarlis, Muhammad; Sawaluddin

    2017-12-01

    Back-propagation is one of the learning algorithms on artificial neural networks that have been widely used to solve various problems, such as pattern recognition, prediction and classification. The Back-propagation architecture will affect the outcome of learning processed. BFGS Quasi-Newton is one of the functions that can be used to change the weight of back-propagation. This research tested some back-propagation architectures using classical back-propagation and back-propagation with BFGS. There are 7 architectures that have been tested on glass dataset with various numbers of neurons, 6 architectures with 1 hidden layer and 1 architecture with 2 hidden layers. BP with BFGS improves the convergence of the learning process. The average improvement convergence is 98.34%. BP with BFGS is more optimal on architectures with smaller number of neurons with decreased epoch number is 94.37% with the increase of accuracy about 0.5%.

  3. Modeling high-order synchronization epochs and transitions in the cardiovascular system

    Science.gov (United States)

    García-Álvarez, David; Bahraminasab, Alireza; Stefanovska, Aneta; McClintock, Peter V. E.

    2007-12-01

    We study a system consisting of two coupled phase oscillators in the presence of noise. This system is used as a model for the cardiorespiratory interaction in wakefulness and anaesthesia. We show that longrange correlated noise produces transitions between epochs with different n:m synchronisation ratios, as observed in the cardiovascular system. Also, we see that, the smaller the noise (specially the one acting on the slower oscillator), the bigger the synchronisation time, exactly as happens in anaesthesia compared with wakefulness. The dependence of the synchronisation time on the couplings, in the presence of noise, is studied; such dependence is softened by low-frequency noise. We show that the coupling from the slow oscillator to the fast one (respiration to heart) plays a more important role in synchronisation. Finally, we see that the isolines with same synchronisation time seem to be a linear combination of the two couplings.

  4. The faint-end of galaxy luminosity functions at the Epoch of Reionization

    Science.gov (United States)

    Yue, B.; Castellano, M.; Ferrara, A.; Fontana, A.; Merlin, E.; Amorín, R.; Grazian, A.; Mármol-Queralto, E.; Michałowski, M. J.; Mortlock, A.; Paris, D.; Parsa, S.; Pilo, S.; Santini, P.; Di Criscienzo, M.

    2018-05-01

    During the Epoch of Reionization (EoR), feedback effects reduce the efficiency of star formation process in small halos or even fully quench it. The galaxy luminosity function (LF) may then turn over at the faint-end. We analyze the number counts of z > 5 galaxies observed in the fields of four Frontier Fields (FFs) clusters and obtain constraints on the LF faint-end: for the turn-over magnitude at z ~ 6, MUVT >~-13.3 for the circular velocity threshold of quenching star formation process, vc* <~ 47 km s-1. We have not yet found significant evidence of the presence of feedback effects suppressing the star formation in small galaxies.

  5. The hydrogen epoch of reionization array dish III: measuring chromaticity of prototype element with reflectometry

    Science.gov (United States)

    Patra, Nipanjana; Parsons, Aaron R.; DeBoer, David R.; Thyagarajan, Nithyanandan; Ewall-Wice, Aaron; Hsyu, Gilbert; Leung, Tsz Kuk; Day, Cherie K.; de Lera Acedo, Eloy; Aguirre, James E.; Alexander, Paul; Ali, Zaki S.; Beardsley, Adam P.; Bowman, Judd D.; Bradley, Richard F.; Carilli, Chris L.; Cheng, Carina; Dillon, Joshua S.; Fadana, Gcobisa; Fagnoni, Nicolas; Fritz, Randall; Furlanetto, Steve R.; Glendenning, Brian; Greig, Bradley; Grobbelaar, Jasper; Hazelton, Bryna J.; Jacobs, Daniel C.; Julius, Austin; Kariseb, MacCalvin; Kohn, Saul A.; Lebedeva, Anna; Lekalake, Telalo; Liu, Adrian; Loots, Anita; MacMahon, David; Malan, Lourence; Malgas, Cresshim; Maree, Matthys; Martinot, Zachary; Mathison, Nathan; Matsetela, Eunice; Mesinger, Andrei; Morales, Miguel F.; Neben, Abraham R.; Pieterse, Samantha; Pober, Jonathan C.; Razavi-Ghods, Nima; Ringuette, Jon; Robnett, James; Rosie, Kathryn; Sell, Raddwine; Smith, Craig; Syce, Angelo; Tegmark, Max; Williams, Peter K. G.; Zheng, Haoxuan

    2018-04-01

    Spectral structures due to the instrument response is the current limiting factor for the experiments attempting to detect the redshifted 21 cm signal from the Epoch of Reionization (EoR). Recent advances in the delay spectrum methodology for measuring the redshifted 21 cm EoR power spectrum brought new attention to the impact of an antenna's frequency response on the viability of making this challenging measurement. The delay spectrum methodology provides a somewhat straightforward relationship between the time-domain response of an instrument that can be directly measured and the power spectrum modes accessible to a 21 cm EoR experiment. In this paper, we derive the explicit relationship between antenna reflection coefficient ( S 11) measurements made by a Vector Network Analyzer (VNA) and the extent of additional foreground contaminations in delay space. In the light of this mathematical framework, we examine the chromaticity of a prototype antenna element that will constitute the Hydrogen Epoch of Reionization Array (HERA) between 100 and 200 MHz. These reflectometry measurements exhibit additional structures relative to electromagnetic simulations, but we find that even without any further design improvement, such an antenna element will support measuring spatial k modes with line-of-sight components of k ∥ > 0.2 h Mpc- 1. We also find that when combined with the powerful inverse covariance weighting method used in optimal quadratic estimation of redshifted 21 cm power spectra the HERA prototype elements can successfully measure the power spectrum at spatial modes as low as k ∥ > 0.1 h Mpc- 1. This work represents a major step toward understanding the HERA antenna element and highlights a straightforward method for characterizing instrument response for future experiments designed to detect the 21 cm EoR power spectrum.

  6. SYSTEMATIC UNCERTAINTIES IN BLACK HOLE MASSES DETERMINED FROM SINGLE-EPOCH SPECTRA

    International Nuclear Information System (INIS)

    Denney, Kelly D.; Peterson, Bradley M.; Dietrich, Matthias; Bentz, Misty C.; Vestergaard, Marianne

    2009-01-01

    We explore the nature of systematic errors that can arise in measurement of black hole masses from single-epoch (SE) spectra of active galactic nuclei (AGNs) by utilizing the many epochs available for NGC 5548 and PG1229+204 from reverberation mapping (RM) databases. In particular, we examine systematics due to AGN variability, contamination due to constant spectral components (i.e., narrow lines and host galaxy flux), data quality (i.e., signal-to-noise ratio (S/N)), and blending of spectral features. We investigate the effect that each of these systematics has on the precision and accuracy of SE masses calculated from two commonly used line width measures by comparing these results to recent RM studies. We calculate masses by characterizing the broad Hβ emission line by both the full width at half maximum and the line dispersion, and demonstrate the importance of removing narrow emission-line components and host starlight. We find that the reliability of line width measurements rapidly decreases for S/N lower than ∼ 10-20 (per pixel), and that fitting the line profiles instead of direct measurement of the data does not mitigate this problem but can, in fact, introduce systematic errors. We also conclude that a full spectral decomposition to deblend the AGN and galaxy spectral features is unnecessary, except to judge the contribution of the host galaxy to the luminosity and to deblend any emission lines that may inhibit accurate line width measurements. Finally, we present an error budget which summarizes the minimum observable uncertainties as well as the amount of additional scatter and/or systematic offset that can be expected from the individual sources of error investigated. In particular, we find that the minimum observable uncertainty in SE mass estimates due to variability is ∼ 20 pixel -1 ) spectra.

  7. On the link between extreme floods and excess monsoon epochs in South Asia

    Energy Technology Data Exchange (ETDEWEB)

    Kale, Vishwas [University of Pune, Department of Geography, Pune (India)

    2012-09-15

    This paper provides a synoptic view of extreme monsoon floods on all the nine large rivers of South Asia and their association with the excess (above-normal) monsoon rainfall periods. Annual maximum flood series for 18 gauging stations spread over four countries (India, Pakistan, Bangladesh and Nepal) and long-term monsoon rainfall data were analyzed to ascertain whether the extreme floods were clustered in time and whether they coincided with multi-decade excess monsoon rainfall epochs at the basin level. Simple techniques, such as the Cramer's t-test, regression and Mann-Kendall (MK) tests and Hurst method were used to evaluate the trends and patterns of the flood and rainfall series. MK test reveals absence of any long-term tendency in all the series. However, the Cramer's t test and Hurst-Mandelbrot rescaled range statistic provide evidence that both rainfall and flood time series are persistent. Using the Cramer's t-test the excess monsoon epochs for each basin were identified. The excess monsoon periods for different basins were found to be highly asynchronous with respect to duration as well as the beginning and end. Three main conclusions readily emerge from the analyses. Extreme floods (>90th percentile) in South Asia show a tendency to cluster in time. About three-fourth of the extreme floods have occurred during the excess monsoon periods between {proportional_to}1840 and 2000 AD, implying a noteworthy link between the two. The frequency of large floods was higher during the post-1940 period in general and during three decades (1940s, 1950s and 1980s) in particular. (orig.)

  8. Africa Insight

    African Journals Online (AJOL)

    Africa Insight is a quarterly, peer-reviewed journal of the Africa Institute of South Africa. It is accredited by the South African National Department of Higher Education and Training (DHET) and is indexed in the International Bibliography of Social Science (IBSS). It is a multi-disciplinary journal primarily focusing on African ...

  9. Mobile evolution insights on connectivity and service

    CERN Document Server

    Thalanany, Sebastian

    2015-01-01

    The purpose of this book is to provide information and guidelines pertaining to the strategies and technologies associated with the next-generation mobile ecosystem. The intersection of human communications, next-generation mobile technologies and IP multimedia services demand an identification and distillation of the characteristics of both the human dimension and the technology dimension to examine the unique enabling considerations in the formulation of a vision and a strategy that are relevant for communities, businesses and leadership.

  10. QSO evolution in the interaction model

    International Nuclear Information System (INIS)

    De Robertis, M.

    1985-01-01

    QSO evolution is investigated according to the interaction hypothesis described most recently by Stockton (1982), in which activity results from an interaction between two galaxies resulting in the transfer of gas onto a supermassive black hole (SBH) at the center of at least one participant. Explicit models presented here for interactions in cluster environments show that a peak QSO population can be formed in this way at zroughly-equal2--3, with little activity prior to this epoch. Calculated space densities match those inferred from observations for this epoch. Substantial density evolution is expected in such models, since, after virialization, conditions in the cores of rich clusters lead to the depletion of gas-rich systems through ram-pressure stripping. Density evolution parameters of 6--12 are easily accounted for. At smaller redshifts, however, QSOs should be found primarily in poor clusters or groups. Probability estimates provided by this model are consistent with local estimates for the observed number of QSOs per interaction. Significant luminosity-dependent evolution might also be expected in these models. It is suggested that the mean SBH mass increases with lookback time, leading to a statistical brightening with redshift. Undoubtedly, both forms of evolution contribute to the overall QSO luminosity function

  11. Combinations of Epoch Durations and Cut-Points to Estimate Sedentary Time and Physical Activity among Adolescents

    Science.gov (United States)

    Fröberg, Andreas; Berg, Christina; Larsson, Christel; Boldemann, Cecilia; Raustorp, Anders

    2017-01-01

    The purpose of the current study was to investigate how combinations of different epoch durations and cut-points affect the estimations of sedentary time and physical activity in adolescents. Accelerometer data from 101 adolescents were derived and 30 combinations were used to estimate sedentary time, light, moderate, vigorous, and combined…

  12. THE LICK AGN MONITORING PROJECT: RECALIBRATING SINGLE-EPOCH VIRIAL BLACK HOLE MASS ESTIMATES

    Energy Technology Data Exchange (ETDEWEB)

    Park, Daeseong; Woo, Jong-Hak [Astronomy Program, Department of Physics and Astronomy, Seoul National University, Seoul 151-742 (Korea, Republic of); Treu, Tommaso; Bennert, Vardha N. [Department of Physics, University of California, Santa Barbara, CA 93106 (United States); Barth, Aaron J.; Walsh, Jonelle [Department of Physics and Astronomy, 4129 Frederick Reines Hall, University of California, Irvine, CA 92697-4575 (United States); Bentz, Misty C. [Department of Physics and Astronomy, Georgia State University Atlanta, GA 30303 (United States); Canalizo, Gabriela [Department of Physics and Astronomy, University of California, Riverside, 900 University Ave., Riverside, CA 92521 (United States); Filippenko, Alexei V. [Department of Astronomy, University of California, Berkeley, CA 94720-3411 (United States); Gates, Elinor [Lick Observatory, P.O. Box 85, Mount Hamilton, CA 95140 (United States); Greene, Jenny E. [Department of Astrophysical Sciences, Princeton University, Princeton, NJ 08544 (United States); Malkan, Matthew A., E-mail: woo@astro.snu.ac.kr [Department of Physics and Astronomy, University of California, Los Angeles, CA 90024 (United States)

    2012-03-01

    We investigate the calibration and uncertainties of black hole (BH) mass estimates based on the single-epoch (SE) method, using homogeneous and high-quality multi-epoch spectra obtained by the Lick Active Galactic Nucleus (AGN) Monitoring Project for nine local Seyfert 1 galaxies with BH masses <10{sup 8} M{sub Sun }. By decomposing the spectra into their AGNs and stellar components, we study the variability of the SE H{beta} line width (full width at half-maximum intensity, FWHM{sub H{beta}} or dispersion, {sigma}{sub H{beta}}) and of the AGN continuum luminosity at 5100 A (L{sub 5100}). From the distribution of the 'virial products' ({proportional_to} FWHM{sub H{beta}}{sup 2} L{sup 0.5}{sub 5100} or {sigma}{sub H{beta}}{sup 2} L{sup 0.5}{sub 5100}) measured from SE spectra, we estimate the uncertainty due to the combined variability as {approx}0.05 dex (12%). This is subdominant with respect to the total uncertainty in SE mass estimates, which is dominated by uncertainties in the size-luminosity relation and virial coefficient, and is estimated to be {approx}0.46 dex (factor of {approx}3). By comparing the H{beta} line profile of the SE, mean, and root-mean-square (rms) spectra, we find that the H{beta} line is broader in the mean (and SE) spectra than in the rms spectra by {approx}0.1 dex (25%) for our sample with FWHM{sub H{beta}} <3000 km s{sup -1}. This result is at variance with larger mass BHs where the difference is typically found to be much less than 0.1 dex. To correct for this systematic difference of the H{beta} line profile, we introduce a line-width dependent virial factor, resulting in a recalibration of SE BH mass estimators for low-mass AGNs.

  13. A FLUX SCALE FOR SOUTHERN HEMISPHERE 21 cm EPOCH OF REIONIZATION EXPERIMENTS

    Energy Technology Data Exchange (ETDEWEB)

    Jacobs, Daniel C.; Bowman, Judd [School of Earth and Space Exploration, Arizona State University, Tempe, AZ (United States); Parsons, Aaron R.; Ali, Zaki; Pober, Jonathan C. [Astronomy Department, University of California, Berkeley, CA (United States); Aguirre, James E.; Moore, David F. [Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA (United States); Bradley, Richard F. [Department of Electrical and Computer Engineering, University of Virginia, Charlottesville, VA (United States); Carilli, Chris L. [National Radio Astronomy Observatory, Socorro, NM (United States); DeBoer, David R.; Dexter, Matthew R.; MacMahon, Dave H. E. [Radio Astronomy Lab., University of California, Berkeley, CA (United States); Gugliucci, Nicole E.; Klima, Pat [National Radio Astronomy Observatory, Charlottesville, VA (United States); Manley, Jason R.; Walbrugh, William P. [Square Kilometer Array, South Africa Project, Cape Town (South Africa); Stefan, Irina I. [Cavendish Laboratory, Cambridge (United Kingdom)

    2013-10-20

    We present a catalog of spectral measurements covering a 100-200 MHz band for 32 sources, derived from observations with a 64 antenna deployment of the Donald C. Backer Precision Array for Probing the Epoch of Reionization (PAPER) in South Africa. For transit telescopes such as PAPER, calibration of the primary beam is a difficult endeavor and errors in this calibration are a major source of error in the determination of source spectra. In order to decrease our reliance on an accurate beam calibration, we focus on calibrating sources in a narrow declination range from –46° to –40°. Since sources at similar declinations follow nearly identical paths through the primary beam, this restriction greatly reduces errors associated with beam calibration, yielding a dramatic improvement in the accuracy of derived source spectra. Extrapolating from higher frequency catalogs, we derive the flux scale using a Monte Carlo fit across multiple sources that includes uncertainty from both catalog and measurement errors. Fitting spectral models to catalog data and these new PAPER measurements, we derive new flux models for Pictor A and 31 other sources at nearby declinations; 90% are found to confirm and refine a power-law model for flux density. Of particular importance is the new Pictor A flux model, which is accurate to 1.4% and shows that between 100 MHz and 2 GHz, in contrast with previous models, the spectrum of Pictor A is consistent with a single power law given by a flux at 150 MHz of 382 ± 5.4 Jy and a spectral index of –0.76 ± 0.01. This accuracy represents an order of magnitude improvement over previous measurements in this band and is limited by the uncertainty in the catalog measurements used to estimate the absolute flux scale. The simplicity and improved accuracy of Pictor A's spectrum make it an excellent calibrator in a band important for experiments seeking to measure 21 cm emission from the epoch of reionization.

  14. Evolution of subsidiary competences

    DEFF Research Database (Denmark)

    Geisler Asmussen, Christian; Pedersen, Torben; Dhanaraj, Charles

    of competitive advantage of nations, we hypothesize the contingencies under which heterogeneity in host environments influences subsidiary competence configuration. We test our model with data from more than 2,000 subsidiaries in seven Western European countries. Our results provide new insights on the evolution...

  15. Kinship and Human Evolution

    DEFF Research Database (Denmark)

    Bergendorff, Steen

    This book offers a exiting new explanation of human evolution. Based on insight from Anthropology is shows that human became 'cultured' beings capable of symbolic thought by developing rasting kinship based between groups that could not other wise survive in the harah climate condition during...

  16. Evolution and Education

    Science.gov (United States)

    Washburn, S. L.

    1974-01-01

    Education should give an understanding of the world and of man, as well as offer the vocational training, at which the university excells. The use of case studies to provide immediate insight into advancing knowledge and the study of evolution have important instructional and educational implication for the goal of understanding man. (JH)

  17. Evolution of the TOR Pathway.

    NARCIS (Netherlands)

    Dam, T.J.P. van; Zwartkruis, F.J.; Bos, J.L.; Snel, B.

    2011-01-01

    The TOR kinase is a major regulator of growth in eukaryotes. Many components of the TOR pathway are implicated in cancer and metabolic diseases in humans. Analysis of the evolution of TOR and its pathway may provide fundamental insight into the evolution of growth regulation in eukaryotes and

  18. Polarization leakage in epoch of reionization windows - II. Primary beam model and direction-dependent calibration

    Science.gov (United States)

    Asad, K. M. B.; Koopmans, L. V. E.; Jelić, V.; Ghosh, A.; Abdalla, F. B.; Brentjens, M. A.; de Bruyn, A. G.; Ciardi, B.; Gehlot, B. K.; Iliev, I. T.; Mevius, M.; Pandey, V. N.; Yatawatta, S.; Zaroubi, S.

    2016-11-01

    Leakage of diffuse polarized emission into Stokes I caused by the polarized primary beam of the instrument might mimic the spectral structure of the 21-cm signal coming from the epoch of reionization (EoR) making their separation difficult. Therefore, understanding polarimetric performance of the antenna is crucial for a successful detection of the EoR signal. Here, we have calculated the accuracy of the nominal model beam of Low Frequency ARray (LOFAR) in predicting the leakage from Stokes I to Q, U by comparing them with the corresponding leakage of compact sources actually observed in the 3C 295 field. We have found that the model beam has errors of ≤10 per cent on the predicted levels of leakage of ˜1 per cent within the field of view, I.e. if the leakage is taken out perfectly using this model the leakage will reduce to 10-3 of the Stokes I flux. If similar levels of accuracy can be obtained in removing leakage from Stokes Q, U to I, we can say, based on the results of our previous paper, that the removal of this leakage using this beam model would ensure that the leakage is well below the expected EoR signal in almost the whole instrumental k-space of the cylindrical power spectrum. We have also shown here that direction-dependent calibration can remove instrumentally polarized compact sources, given an unpolarized sky model, very close to the local noise level.

  19. Upper Limits on the 21 cm Epoch of Reionization Power Spectrum from One Night with LOFAR

    Science.gov (United States)

    Patil, A. H.; Yatawatta, S.; Koopmans, L. V. E.; de Bruyn, A. G.; Brentjens, M. A.; Zaroubi, S.; Asad, K. M. B.; Hatef, M.; Jelić, V.; Mevius, M.; Offringa, A. R.; Pandey, V. N.; Vedantham, H.; Abdalla, F. B.; Brouw, W. N.; Chapman, E.; Ciardi, B.; Gehlot, B. K.; Ghosh, A.; Harker, G.; Iliev, I. T.; Kakiichi, K.; Majumdar, S.; Mellema, G.; Silva, M. B.; Schaye, J.; Vrbanec, D.; Wijnholds, S. J.

    2017-03-01

    We present the first limits on the Epoch of Reionization 21 cm H I power spectra, in the redshift range z = 7.9-10.6, using the Low-Frequency Array (LOFAR) High-Band Antenna (HBA). In total, 13.0 hr of data were used from observations centered on the North Celestial Pole. After subtraction of the sky model and the noise bias, we detect a non-zero {{{Δ }}}{{I}}2={(56+/- 13{mK})}2 (1-σ) excess variance and a best 2-σ upper limit of {{{Δ }}}212< {(79.6{mK})}2 at k = 0.053 h cMpc-1 in the range z = 9.6-10.6. The excess variance decreases when optimizing the smoothness of the direction- and frequency-dependent gain calibration, and with increasing the completeness of the sky model. It is likely caused by (I) residual side-lobe noise on calibration baselines, (II) leverage due to nonlinear effects, (III) noise and ionosphere-induced gain errors, or a combination thereof. Further analyses of the excess variance will be discussed in forthcoming publications.

  20. Dynamics of large-scale solar wind streams obtained by the double superposed epoch analysis

    Science.gov (United States)

    Yermolaev, Yu. I.; Lodkina, I. G.; Nikolaeva, N. S.; Yermolaev, M. Yu.

    2015-09-01

    Using the OMNI data for period 1976-2000, we investigate the temporal profiles of 20 plasma and field parameters in the disturbed large-scale types of solar wind (SW): corotating interaction regions (CIR), interplanetary coronal mass ejections (ICME) (both magnetic cloud (MC) and Ejecta), and Sheath as well as the interplanetary shock (IS). To take into account the different durations of SW types, we use the double superposed epoch analysis (DSEA) method: rescaling the duration of the interval for all types in such a manner that, respectively, beginning and end for all intervals of selected type coincide. As the analyzed SW types can interact with each other and change parameters as a result of such interaction, we investigate separately eights sequences of SW types: (1) CIR, (2) IS/CIR, (3) Ejecta, (4) Sheath/Ejecta, (5) IS/Sheath/Ejecta, (6) MC, (7) Sheath/MC, and (8) IS/Sheath/MC. The main conclusion is that the behavior of parameters in Sheath and in CIR are very similar both qualitatively and quantitatively. Both the high-speed stream (HSS) and the fast ICME play a role of pistons which push the plasma located ahead them. The increase of speed in HSS and ICME leads at first to formation of compression regions (CIR and Sheath, respectively) and then to IS. The occurrence of compression regions and IS increases the probability of growth of magnetospheric activity.

  1. An Improved Statistical Point-source Foreground Model for the Epoch of Reionization

    Energy Technology Data Exchange (ETDEWEB)

    Murray, S. G.; Trott, C. M.; Jordan, C. H. [ARC Centre of Excellence for All-sky Astrophysics (CAASTRO) (Australia)

    2017-08-10

    We present a sophisticated statistical point-source foreground model for low-frequency radio Epoch of Reionization (EoR) experiments using the 21 cm neutral hydrogen emission line. Motivated by our understanding of the low-frequency radio sky, we enhance the realism of two model components compared with existing models: the source count distributions as a function of flux density and spatial position (source clustering), extending current formalisms for the foreground covariance of 2D power-spectral modes in 21 cm EoR experiments. The former we generalize to an arbitrarily broken power law, and the latter to an arbitrary isotropically correlated field. This paper presents expressions for the modified covariance under these extensions, and shows that for a more realistic source spatial distribution, extra covariance arises in the EoR window that was previously unaccounted for. Failure to include this contribution can yield bias in the final power-spectrum and under-estimate uncertainties, potentially leading to a false detection of signal. The extent of this effect is uncertain, owing to ignorance of physical model parameters, but we show that it is dependent on the relative abundance of faint sources, to the effect that our extension will become more important for future deep surveys. Finally, we show that under some parameter choices, ignoring source clustering can lead to false detections on large scales, due to both the induced bias and an artificial reduction in the estimated measurement uncertainty.

  2. Diverse properties of interstellar medium embedding gamma-ray bursts at the epoch of reionization

    International Nuclear Information System (INIS)

    Cen, Renyue; Kimm, Taysun

    2014-01-01

    Analysis is performed on ultra-high-resolution large-scale cosmological radiation-hydrodynamic simulations to quantify, for the first time, the physical environment of long-duration gamma-ray bursts (GRBs) at the epoch of reionization. We find that, on parsec scales, 13% of GRBs remain in high-density (≥10 4 cm –3 ) low-temperature star-forming regions, whereas 87% of GRBs occur in low-density (∼10 –2.5 cm –3 ) high-temperature regions heated by supernovae. More importantly, the spectral properties of GRB afterglows, such as the neutral hydrogen column density, total hydrogen column density, dust column density, gas temperature, and metallicity of intervening absorbers, vary strongly from sight line to sight line. Although our model explains extant limited observationally inferred values with respect to circumburst density, metallicity, column density, and dust properties, a substantially larger sample of high-z GRB afterglows would be required to facilitate a statistically solid test of the model. Our findings indicate that any attempt to infer the physical properties (such as metallicity) of the interstellar medium (ISM) of the host galaxy based on a very small number (usually one) of sight lines would be precarious. Utilizing high-z GRBs to probe the ISM and intergalactic medium should be undertaken properly, taking into consideration the physical diversities of the ISM.

  3. An Improved Statistical Point-source Foreground Model for the Epoch of Reionization

    Science.gov (United States)

    Murray, S. G.; Trott, C. M.; Jordan, C. H.

    2017-08-01

    We present a sophisticated statistical point-source foreground model for low-frequency radio Epoch of Reionization (EoR) experiments using the 21 cm neutral hydrogen emission line. Motivated by our understanding of the low-frequency radio sky, we enhance the realism of two model components compared with existing models: the source count distributions as a function of flux density and spatial position (source clustering), extending current formalisms for the foreground covariance of 2D power-spectral modes in 21 cm EoR experiments. The former we generalize to an arbitrarily broken power law, and the latter to an arbitrary isotropically correlated field. This paper presents expressions for the modified covariance under these extensions, and shows that for a more realistic source spatial distribution, extra covariance arises in the EoR window that was previously unaccounted for. Failure to include this contribution can yield bias in the final power-spectrum and under-estimate uncertainties, potentially leading to a false detection of signal. The extent of this effect is uncertain, owing to ignorance of physical model parameters, but we show that it is dependent on the relative abundance of faint sources, to the effect that our extension will become more important for future deep surveys. Finally, we show that under some parameter choices, ignoring source clustering can lead to false detections on large scales, due to both the induced bias and an artificial reduction in the estimated measurement uncertainty.

  4. Study of redshifted H I from the epoch of reionization with drift scan

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Sourabh; Sethi, Shiv K.; Subrahmanyan, Ravi; Shankar, N. Udaya; Dwarakanath, K. S.; Deshpande, Avinash A. [Raman Research Institute, Bangalore (India); Bernardi, Gianni [Square Kilometre Array South Africa (SKA SA), 3rd Floor, The Park, Park Road, Pinelands 7405 (South Africa); Bowman, Judd D. [Arizona State University, Tempe, AZ85281 (United States); Briggs, Frank; Gaensler, Bryan M. [ARC Centre of Excellence for All-sky Astrophysics (CAASTRO), 44 Rosehill Street, Redfern, NSW 2016 (Australia); Cappallo, Roger J.; Corey, Brian E.; Goeke, Robert F. [MIT Haystack Observatory, Westford, MA 01886 (United States); Emrich, David [Curtin University, Perth (Australia); Greenhill, Lincoln J.; Kasper, Justin C. [Harvard-Smithsonian Center for Astrophysics, 60 Garden Street, Cambridge, MA 02138 (United States); Hazelton, Bryna J. [University of Washington, Seattle, WA 98195 (United States); Hewitt, Jacqueline N. [MIT Kavli Institute for Astrophysics and Space Research, 77 Massachusetts Avenue, 37-241, Cambridge, MA 02139 (United States); Johnston-Hollitt, Melanie [Victoria University of Wellington, P.O. Box 600, Wellington 6140 (New Zealand); Kaplan, David L., E-mail: sourabh@rri.res.in, E-mail: sethi@rri.res.in [University of Wisconsin-Milwaukee, Milwaukee, WI 53201 (United States); and others

    2014-09-20

    Detection of the epoch of reionization (EoR) in the redshifted 21 cm line is a challenging task. Here, we formulate the detection of the EoR signal using the drift scan strategy. This method potentially has better instrumental stability compared to the case where a single patch of sky is tracked. We demonstrate that the correlation time between measured visibilities could extend up to 1-2 hr for an interferometer array such as the Murchison Widefield Array, which has a wide primary beam. We estimate the EoR power based on a cross-correlation of visibilities over time and show that the drift scan strategy is capable of detecting the EoR signal with a signal to noise that is comparable/better compared to the tracking case. We also estimate the visibility correlation for a set of bright point sources and argue that the statistical inhomogeneity of bright point sources might allow their separation from the EoR signal.

  5. A New Method for Single-Epoch Ambiguity Resolution with Indoor Pseudolite Positioning.

    Science.gov (United States)

    Li, Xin; Zhang, Peng; Guo, Jiming; Wang, Jinling; Qiu, Weining

    2017-04-21

    Ambiguity resolution (AR) is crucial for high-precision indoor pseudolite positioning. Due to the existing characteristics of the pseudolite positioning system, such as the geometry structure of the stationary pseudolite which is consistently invariant, the indoor signal is easy to interrupt and the first order linear truncation error cannot be ignored, and a new AR method based on the idea of the ambiguity function method (AFM) is proposed in this paper. The proposed method is a single-epoch and nonlinear method that is especially well-suited for indoor pseudolite positioning. Considering the very low computational efficiency of conventional AFM, we adopt an improved particle swarm optimization (IPSO) algorithm to search for the best solution in the coordinate domain, and variances of a least squares adjustment is conducted to ensure the reliability of the solving ambiguity. Several experiments, including static and kinematic tests, are conducted to verify the validity of the proposed AR method. Numerical results show that the IPSO significantly improved the computational efficiency of AFM and has a more elaborate search ability compared to the conventional grid searching method. For the indoor pseudolite system, which had an initial approximate coordinate precision better than 0.2 m, the AFM exhibited good performances in both static and kinematic tests. With the corrected ambiguity gained from our proposed method, indoor pseudolite positioning can achieve centimeter-level precision using a low-cost single-frequency software receiver.

  6. Methodological proposal for the jotted issue of the first epoch of the Hero magazine.

    Directory of Open Access Journals (Sweden)

    Maité Garc