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Sample records for molecular evolution improves

  1. Mistakes and Molecular Evolution.

    ERIC Educational Resources Information Center

    Trevors, J. T.

    1998-01-01

    Examines the role mistakes play in the molecular evolution of bacteria. Discusses the interacting physical, chemical, and biological factors that cause changes in DNA and play a role in prokaryotic evolution. (DDR)

  2. Workshop on Molecular Evolution

    NASA Technical Reports Server (NTRS)

    Cummings, Michael P.

    2004-01-01

    Molecular evolution has become the nexus of many areas of biological research. It both brings together and enriches such areas as biochemistry, molecular biology, microbiology, population genetics, systematics, developmental biology, genomics, bioinformatics, in vitro evolution, and molecular ecology. The Workshop provides an important contribution to these fields in that it promotes interdisciplinary research and interaction, and thus provides a glue that sticks together disparate fields. Due to the wide range of fields addressed by the study of molecular evolution, it is difficult to offer a comprehensive course in a university setting. It is rare for a single institution to maintain expertise in all necessary areas. In contrast, the Workshop is uniquely able to provide necessary breadth and depth by utilizing a large number of faculty with appropriate expertise. Furthermore, the flexible nature of the Workshop allows for rapid adaptation to changes in the dynamic field of molecular evolution. For example, the 2003 Workshop included recently emergent research areas of molecular evolution of development and genomics.

  3. Evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Sevenster, M.

    1993-01-01

    The evolution of interstellar molecular hydrogen was studied, with a special interest for the formation and evolution of molecular clouds and star formation within them, by a two-dimensional hydrodynamical simulation performed on a rectangular grid of physical sizes on the order of 100 pc. It is filled with an initial density of approx. 1 cm(exp -3), except for one cell (approx. 1 pc(exp 2)) at the center of the grid where an accretion core of 1-10(exp 3) solar masses is placed. The grid is co-moving with the gridcenter that is on a circular orbit around the Galactic center and that also is the guiding center of epicyclic approximation of orbits of the matter surrounding it. The initial radial velocity is zero; to account for differential rotation the initial tangential velocity (i.e. the movement around the galactic center) is proportional to the radial distance to the grid center. The rate is comparable to the rotation rate at the Local Standard of Rest. The influence of galactic rotation is noticed by spiral or elliptical forms, but on much longer time scales than self gravitation and cooling processes. Density and temperature are kept constant at the boundaries and no inflow is allowed along the tangential boundaries.

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

    PubMed Central

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

    2011-01-01

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

  5. The Molecular Basis of Evolution.

    ERIC Educational Resources Information Center

    Wilson, Allan C.

    1985-01-01

    Discovery that mutations accumulate at steady rates over time in the genes of all lineages of plants and animals has led to new insights into evolution at the molecular and organismal levels. Discusses molecular evolution, examining deoxyribonuclei acid (DNA) sequences, morphological distances, and codon rate of change. (DH)

  6. Chemical evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Prasad, Sheo S.; Tarafdar, Sankar P.; Villere, Karen R.; Huntress, Wesley T., Jr.

    1987-01-01

    The principles behind the coupled chemical-dynamical evolution of molecular clouds are described. Particular attention is given to current problems involving the simplest species (i.e., C. CO, O2, and H2) in quiescent clouds. The results of a comparison made between the molecular abundances in the Orion ridge and the hot core (Blake, 1986) are presented.

  7. Molecular imprint of dust evolution

    NASA Astrophysics Data System (ADS)

    Akimkin, Vitaly; Zhukovska, Svitlana; Wiebe, Dmitri; Semenov, Dmitry; Pavlyuchenkov, Yaroslav; Vasyunin, Anton; Birnstiel, Til; Henning, Thomas

    2013-07-01

    Evolution of sub-micron grains is an essential process during early stages of planet formation. The dust growth and sedimentation to the midplane affect a spectral energy distribution. At the same time dust evolution can alter significantly the distribution of gas that is a factor of 100 more massive than dust and can be traced with molecular line observations. We present simulations of protoplanetary disk structure with grain evolution using the ANDES code ("AccretioN disk with Dust Evolution and Sedimentation"). ANDES comprises (1) a 1+1D frequency-dependent continuum radiative transfer module, (2) a module to calculate the chemical evolution using an extended gas-grain chemical network with UV/X-ray-driven processes and surface reactions, (3) a module to calculate the gas thermal energy balance, and (4) a 1+1D module that simulates dust grain evolution. Such a set of physical processes allows us to assess the impact of dust evolution on the gas component, which is primarily related to radiation field and total available surface for chemical reactions. Considering cases of (i) evolved dust (2 Myr of grain coagulation, fragmentation and sedimentation) and (ii) pristine dust (well- mixed 0.1 micron grains), we found a sufficient changes in disk physical and chemical structure caused by the dust evolution. Due to higher transparency of the evolved disk model UV-shielded molecular layer is shifted closer to the midplane. The presence of big grains in the disk midplane delays the freeze-out of volatile gas-phase species such as CO, while the depletion is still effective in adjacent upper layers. Molecular concentrations of many species are enhanced in the disk model with dust evolution (CO2, NH2CN, HNO, H2O, HCOOH, HCN, CO) which provides an opportunity to use these molecules as tracers of dust evolution.

  8. Thermal Solutions for Molecular Evolution

    NASA Astrophysics Data System (ADS)

    Mast, Christof B.; Osterman, Natan; Braun, Dieter

    2012-12-01

    The key requirement to solve the origin of life puzzle are disequilibrium conditions. Early molecular evolution cannot be explained by initial high concentrations of energetic chemicals since they would just react towards their chemical equilibrium allowing no further development. We argue here that persistent disequilibria are needed to increase complexity during molecular evolution. We propose thermal gradients as the disequilibrium setting which drove Darwinian molecular evolution. On the one hand the thermal gradient gives rise to laminar thermal convection flow with highly regular temperature oscillations that allow melting and replication of DNA. On the other hand molecules move along the thermal gradient, a mechanism termed Soret effect or thermophoresis. Inside a long chamber a combination of the convection flow and thermophoresis leads to a very efficient accumulation of molecules. Short DNA is concentrated thousand-fold, whereas longer DNA is exponentially better accumulated. We demonstrated both scenarios in the same micrometer-sized setting. Forthcoming experiments will reveal how replication and accumulation of DNA in a system, driven only by a thermal gradient, could create a Darwinian process of replication and selection.

  9. Adaptive evolution of molecular phenotypes

    NASA Astrophysics Data System (ADS)

    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-09-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak.

  10. Bringing Molecules Back into Molecular Evolution

    PubMed Central

    Wilke, Claus O.

    2012-01-01

    Much molecular-evolution research is concerned with sequence analysis. Yet these sequences represent real, three-dimensional molecules with complex structure and function. Here I highlight a growing trend in the field to incorporate molecular structure and function into computational molecular-evolution work. I consider three focus areas: reconstruction and analysis of past evolutionary events, such as phylogenetic inference or methods to infer selection pressures; development of toy models and simulations to identify fundamental principles of molecular evolution; and atom-level, highly realistic computational modeling of molecular structure and function aimed at making predictions about possible future evolutionary events. PMID:22761562

  11. Trends in substitution models of molecular evolution.

    PubMed

    Arenas, Miguel

    2015-01-01

    Substitution models of evolution describe the process of genetic variation through fixed mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost 40 years after the development of first substitution models, highly sophisticated, and data-specific substitution models continue emerging with the aim of better mimicking real evolutionary processes. Here I describe current trends in substitution models of DNA, codon and amino acid sequence evolution, including advantages and pitfalls of the most popular models. The perspective concludes that despite the large number of currently available substitution models, further research is required for more realistic modeling, especially for DNA coding and amino acid data. Additionally, the development of more accurate complex models should be coupled with new implementations and improvements of methods and frameworks for substitution model selection and downstream evolutionary analysis. PMID:26579193

  12. Trends in substitution models of molecular evolution

    PubMed Central

    Arenas, Miguel

    2015-01-01

    Substitution models of evolution describe the process of genetic variation through fixed mutations and constitute the basis of the evolutionary analysis at the molecular level. Almost 40 years after the development of first substitution models, highly sophisticated, and data-specific substitution models continue emerging with the aim of better mimicking real evolutionary processes. Here I describe current trends in substitution models of DNA, codon and amino acid sequence evolution, including advantages and pitfalls of the most popular models. The perspective concludes that despite the large number of currently available substitution models, further research is required for more realistic modeling, especially for DNA coding and amino acid data. Additionally, the development of more accurate complex models should be coupled with new implementations and improvements of methods and frameworks for substitution model selection and downstream evolutionary analysis. PMID:26579193

  13. Molecular evolution and thermal adaptation

    NASA Astrophysics Data System (ADS)

    Chen, Peiqiu

    2011-12-01

    In this thesis, we address problems in molecular evolution, thermal adaptation, and the kinetics of adaptation of bacteria and viruses to elevated environmental temperatures. We use a nearly neutral fitness model where the replication speed of an organism is proportional to the copy number of folded proteins. Our model reproduces the distribution of stabilities of natural proteins in excellent agreement with experiment. We find that species with high mutation rates tend to have less stable proteins compared to species with low mutation rate. We found that a broad distribution of protein stabilities observed in the model and in experiment is the key determinant of thermal response for viruses and bacteria. Our results explain most of the earlier experimental observations: striking asymmetry of thermal response curves, the absence of evolutionary trade-off which was expected but not found in experiments, correlation between denaturation temperature for several protein families and the Optimal Growth Temperature (OGT) of their carrier organisms, and proximity of bacterial or viral OGTs to their evolutionary temperatures. Our theory quantitatively and with high accuracy described thermal response curves for 35 bacterial species. The model also addresses the key to adaptation is in weak-link genes (WLG), which encode least thermodynamically stable essential proteins in the proteome. We observe, as in experiment, a two-stage adaptation process. The first stage is a Luria-Delbruck type of selection, whereby rare WLG alleles, whose proteins are more stable than WLG proteins of the majority of the population (either due to standing genetic variation or due to an early acquired mutation), rapidly rise to fixation. The second stage constitutes subsequent slow accumulation of mutations in an adapted population. As adaptation progresses, selection regime changes from positive to neutral: Selection coefficient of beneficial mutations scales as a negative power of number of

  14. The Molecular Evolution of Actin

    PubMed Central

    Hightower, Robin C.; Meagher, Richard B.

    1986-01-01

    We have investigated the molecular evolution of plant and nonplant actin genes comparing nucleotide and amino acid sequences of 20 actin genes. Nucleotide changes resulting in amino acid substitutions (replacement substitutions) ranged from 3–7% for all pairwise comparisons of animal actin genes with the following exceptions. Comparisons between higher animal muscle actin gene sequences and comparisons between higher animal cytoplasmic actin gene sequences indicated <3% divergence. Comparisons between plant and nonplant actin genes revealed, with two exceptions, 11–15% replacement substitution. In the analysis of plant actins, replacement substitution between soybean actin genes SAc1, SAc3, SAc4 and maize actin gene MAc1 ranged from 8–10%, whereas these members within the soybean actin gene family ranged from 6–9% replacement substitution. The rate of sequence divergence of plant actin sequences appears to be similar to that observed for animal actins. Furthermore, these and other data suggest that the plant actin gene family is ancient and that the families of soybean and maize actin genes have diverged from a single common ancestral plant actin gene that originated long before the divergence of monocots and dicots. The soybean actin multigene family encodes at least three classes of actin. These classes each contain a pair of actin genes that have been designated kappa (SAc1, SAc6), lambda (SAc2, SAc4) and mu (SAc3, SAc7). The three classes of soybean actin are more divergent in nucleotide sequence from one another than higher animal cytoplasmic actin is divergent from muscle actin. The location and distribution of amino acid changes were compared between actin proteins from all sources. A comparison of the hydropathy of all actin sequences, except from Oxytricha, indicated a strong similarity in hydropathic character between all plant and nonplant actins despite the greater number of replacement substitutions in plant actins. These protein sequence

  15. Statistical limitations on molecular evolution.

    PubMed

    Perlovsky, Leonid I

    2002-06-01

    Complexity of functions evolving in an evolution process are expected to be limited by the time length of an evolution process among other factors. This paper outlines a general method of deriving function-complexity limitations based on mathematical statistics and independent from details of a biological or genetic mechanism of the evolution of the function. Limitations on the emergence of life are derived, these limitations indicate a possibility of a very fast evolution and are consistent with "RNA world" hypothesis. The discussed method is general and can be used to characterize evolution of more specific biological organism functions and relate functions to genetic structures. The derived general limitations indicate that a co-evolution of multiple functions and species could be a slow process, whereas an evolution of a specific function might proceed very fast, so that no trace of intermediate forms (species) is preserved in fossil records of phenotype or DNA structure; this is consistent with a picture of "punctuated equilibrium". PMID:12023805

  16. Molecular evolution tracks macroevolutionary transitions in Cetacea.

    PubMed

    McGowen, Michael R; Gatesy, John; Wildman, Derek E

    2014-06-01

    Cetacea (whales, dolphins, and porpoises) is a model group for investigating the molecular signature of macroevolutionary transitions. Recent research has begun to reveal the molecular underpinnings of the remarkable anatomical and behavioral transformation in this clade. This shift from terrestrial to aquatic environments is arguably the best-understood major morphological transition in vertebrate evolution. The ancestral body plan and physiology were extensively modified and, in many cases, these crucial changes are recorded in cetacean genomes. Recent studies have highlighted cetaceans as central to understanding adaptive molecular convergence and pseudogene formation. Here, we review current research in cetacean molecular evolution and the potential of Cetacea as a model for the study of other macroevolutionary transitions from a genomic perspective. PMID:24794916

  17. Molecular Evolution of Puumala Hantavirus

    PubMed Central

    Sironen, Tarja; Vaheri, Antti; Plyusnin, Alexander

    2001-01-01

    Puumala virus (PUUV) is a negative-stranded RNA virus in the genus Hantavirus, family Bunyaviridae. In this study, detailed phylogenetic analysis was performed on 42 complete S segment sequences of PUUV originated from several European countries, Russia, and Japan, the largest set available thus far for hantaviruses. The results show that PUUV sequences form seven distinct and well-supported genetic lineages; within these lineages, geographical clustering of genetic variants is observed. The overall phylogeny of PUUV is star-like, suggesting an early split of genetic lineages. The individual PUUV lineages appear to be independent, with the only exception to this being the Finnish and the Russian lineages that are closely connected to each other. Two strains of PUUV-like virus from Japan form the most ancestral lineage diverging from PUUV. Recombination points within the S segment were searched for and evidence for intralineage recombination events was seen in the Finnish, Russian, Danish, and Belgian lineages of PUUV. Molecular clock analysis showed that PUUV is a stable virus, evolving slowly at a rate of 0.7 × 10−7 to 2.2 × 10−6 nt substitutions per site per year. PMID:11689661

  18. Molecular pathogenesis of CLL and its evolution.

    PubMed

    Rodríguez, David; Bretones, Gabriel; Arango, Javier R; Valdespino, Víctor; Campo, Elías; Quesada, Víctor; López-Otín, Carlos

    2015-03-01

    In spite of being the most prevalent adult leukemia in Western countries, the molecular mechanisms driving the establishment and progression of chronic lymphocytic leukemia (CLL) remain largely unknown. In recent years, the use of next-generation sequencing techniques has uncovered new and, in some cases, unexpected driver genes with prognostic and therapeutic value. The mutational landscape of CLL is characterized by high-genetic and epigenetic heterogeneity, low mutation recurrence and a long tail of cases with undefined driver genes. On the other hand, the use of deep sequencing has also revealed high intra-tumor heterogeneity and provided a detailed picture of clonal evolution processes. This phenomenon, in which aberrant DNA methylation can also participate, appears to be tightly associated to poor outcomes and chemo-refractoriness, thus providing a new subject for therapeutic intervention. Hence, and having in mind the limitations derived from the CLL complexity thus described, the application of massively parallel sequencing studies has unveiled a wealth of information that is expected to substantially improve patient staging schemes and CLL clinical management. PMID:25630433

  19. Molecular clocks and the early evolution of metazoan nervous systems.

    PubMed

    Wray, Gregory A

    2015-12-19

    The timing of early animal evolution remains poorly resolved, yet remains critical for understanding nervous system evolution. Methods for estimating divergence times from sequence data have improved considerably, providing a more refined understanding of key divergences. The best molecular estimates point to the origin of metazoans and bilaterians tens to hundreds of millions of years earlier than their first appearances in the fossil record. Both the molecular and fossil records are compatible, however, with the possibility of tiny, unskeletonized, low energy budget animals during the Proterozoic that had planktonic, benthic, or meiofaunal lifestyles. Such animals would likely have had relatively simple nervous systems equipped primarily to detect food, avoid inhospitable environments and locate mates. The appearance of the first macropredators during the Cambrian would have changed the selective landscape dramatically, likely driving the evolution of complex sense organs, sophisticated sensory processing systems, and diverse effector systems involved in capturing prey and avoiding predation. PMID:26554040

  20. Evolution of molecular phenotypes under stabilizing selection

    NASA Astrophysics Data System (ADS)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes.

  1. Molecular evolution of prolactin in primates.

    PubMed

    Wallis, O Caryl; Mac-Kwashie, Akofa O; Makri, Georgia; Wallis, Michael

    2005-05-01

    Pituitary prolactin, like growth hormone (GH) and several other protein hormones, shows an episodic pattern of molecular evolution in which sustained bursts of rapid change contrast with long periods of slow evolution. A period of rapid change occurred in the evolution of prolactin in primates, leading to marked sequence differences between human prolactin and that of nonprimate mammals. We have defined this burst more precisely by sequencing the coding regions of prolactin genes for a prosimian, the slow loris (Nycticebus pygmaeus), and a New World monkey, the marmoset (Callithrix jacchus). Slow loris prolactin is very similar in sequence to pig prolactin, so the episode of rapid change occurred during primate evolution, after the separation of lines leading to prosimians and higher primates. Marmoset prolactin is similar in sequence to human prolactin, so the accelerated evolution occurred before divergence of New World monkeys and Old World monkeys/apes. The burst of change was confined largely to coding sequence (nonsynonymous sites) for mature prolactin and is not marked in other components of the gene sequence. This and the observations that (1) there was no apparent loss of function during the episode of rapid evolution, (2) the rate of evolution slowed toward the basal rate after this burst, and (3) the distribution of substitutions in the prolactin molecule is very uneven support the idea that this episode of rapid change was due to positive adaptive selection. In the slow loris and marmoset there is no evidence for duplication of the prolactin gene, and evidence from another New World monkey (Cebus albifrons) and from the chimpanzee and human genome sequences, suggests that this is the general position in primates, contrasting with the situation for GH genes. The chimpanzee prolactin sequence differs from that of human at two residues and comparison of human and chimpanzee prolactin gene sequences suggests that noncoding regions associated with regulating

  2. Selectionism and Neutralism in Molecular Evolution

    PubMed Central

    Nei, Masatoshi

    2006-01-01

    Charles Darwin proposed that evolution occurs primarily by natural selection, but this view has been controversial from the beginning. Two of the major opposing views have been mutationism and neutralism. Early molecular studies suggested that most amino acid substitutions in proteins are neutral or nearly neutral and the functional change of proteins occurs by a few key amino acid substitutions. This suggestion generated an intense controversy over selectionism and neutralism. This controversy is partially caused by Kimura's definition of neutrality, which was too strict (|2Ns| ≤ 1). If we define neutral mutations as the mutations that do not change the function of gene products appreciably, many controversies disappear because slightly deleterious and slightly advantageous mutations are engulfed by neutral mutations. The ratio of the rate of nonsynonymous nucleotide substitution to that of synonymous substitution is a useful quantity to study positive Darwinian selection operating at highly variable genetic loci, but it does not necessarily detect adaptively important codons. Previously, multigene families were thought to evolve following the model of concerted evolution, but new evidence indicates that most of them evolve by a birth-and-death process of duplicate genes. It is now clear that most phenotypic characters or genetic systems such as the adaptive immune system in vertebrates are controlled by the interaction of a number of multigene families, which are often evolutionarily related and are subject to birth-and-death evolution. Therefore, it is important to study the mechanisms of gene family interaction for understanding phenotypic evolution. Because gene duplication occurs more or less at random, phenotypic evolution contains some fortuitous elements, though the environmental factors also play an important role. The randomness of phenotypic evolution is qualitatively different from allele frequency changes by random genetic drift. However, there is

  3. Molecular evolution of hydrogen peroxide degrading enzymes.

    PubMed

    Zámocký, Marcel; Gasselhuber, Bernhard; Furtmüller, Paul G; Obinger, Christian

    2012-09-15

    For efficient removal of intra- and/or extracellular hydrogen peroxide by dismutation to harmless dioxygen and water (2H(2)O(2) → O(2) + 2H(2)O), nature designed three metalloenzyme families that differ in oligomeric organization, monomer architecture as well as active site geometry and catalytic residues. Here we report on the updated reconstruction of the molecular phylogeny of these three gene families. Ubiquitous typical (monofunctional) heme catalases are found in all domains of life showing a high structural conservation. Their evolution was directed from large subunit towards small subunit proteins and further to fused proteins where the catalase fold was retained but lost its original functionality. Bifunctional catalase-peroxidases were at the origin of one of the two main heme peroxidase superfamilies (i.e. peroxidase-catalase superfamily) and constitute a protein family predominantly present among eubacteria and archaea, but two evolutionary branches are also found in the eukaryotic world. Non-heme manganese catalases are a relatively small protein family with very old roots only present among bacteria and archaea. Phylogenetic analyses of the three protein families reveal features typical (i) for the evolution of whole genomes as well as (ii) for specific evolutionary events including horizontal gene transfer, paralog formation and gene fusion. As catalases have reached a striking diversity among prokaryotic and eukaryotic pathogens, understanding their phylogenetic and molecular relationship and function will contribute to drug design for prevention of diseases of humans, animals and plants. PMID:22330759

  4. Molecular epidemiology, phylogeny and evolution of Legionella.

    PubMed

    Khodr, A; Kay, E; Gomez-Valero, L; Ginevra, C; Doublet, P; Buchrieser, C; Jarraud, S

    2016-09-01

    Legionella are opportunistic pathogens that develop in aquatic environments where they multiply in protozoa. When infected aerosols reach the human respiratory tract they may accidentally infect the alveolar macrophages leading to a severe pneumonia called Legionnaires' disease (LD). The ability of Legionella to survive within host-cells is strictly dependent on the Dot/Icm Type 4 Secretion System that translocates a large repertoire of effectors into the host cell cytosol. Although Legionella is a large genus comprising nearly 60 species that are worldwide distributed, only about half of them have been involved in LD cases. Strikingly, the species Legionella pneumophila alone is responsible for 90% of all LD cases. The present review summarizes the molecular approaches that are used for L. pneumophila genotyping with a major focus on the contribution of whole genome sequencing (WGS) to the investigation of local L. pneumophila outbreaks and global epidemiology studies. We report the newest knowledge regarding the phylogeny and the evolution of Legionella and then focus on virulence evolution of those Legionella species that are known to have the capacity to infect humans. Finally, we discuss the evolutionary forces and adaptation mechanisms acting on the Dot/Icm system itself as well as the role of mobile genetic elements (MGE) encoding T4ASSs and of gene duplications in the evolution of Legionella and its adaptation to different hosts and lifestyles. PMID:27180896

  5. Integrating influenza antigenic dynamics with molecular evolution

    PubMed Central

    Bedford, Trevor; Suchard, Marc A; Lemey, Philippe; Dudas, Gytis; Gregory, Victoria; Hay, Alan J; McCauley, John W; Russell, Colin A; Smith, Derek J; Rambaut, Andrew

    2014-01-01

    Influenza viruses undergo continual antigenic evolution allowing mutant viruses to evade host immunity acquired to previous virus strains. Antigenic phenotype is often assessed through pairwise measurement of cross-reactivity between influenza strains using the hemagglutination inhibition (HI) assay. Here, we extend previous approaches to antigenic cartography, and simultaneously characterize antigenic and genetic evolution by modeling the diffusion of antigenic phenotype over a shared virus phylogeny. Using HI data from influenza lineages A/H3N2, A/H1N1, B/Victoria and B/Yamagata, we determine patterns of antigenic drift across viral lineages, showing that A/H3N2 evolves faster and in a more punctuated fashion than other influenza lineages. We also show that year-to-year antigenic drift appears to drive incidence patterns within each influenza lineage. This work makes possible substantial future advances in investigating the dynamics of influenza and other antigenically-variable pathogens by providing a model that intimately combines molecular and antigenic evolution. DOI: http://dx.doi.org/10.7554/eLife.01914.001 PMID:24497547

  6. The chemical evolution of molecular clouds

    NASA Technical Reports Server (NTRS)

    Iglesias, E.

    1977-01-01

    The nonequilibrium chemistry of dense molecular clouds (10,000 to 1 million hydrogen molecules per cu cm) is studied in the framework of a model that includes the latest published chemical data and most of the recent theoretical advances. In this model the only important external source of ionization is assumed to be high-energy cosmic-ray bombardment; standard charge-transfer reactions are taken into account as well as reactions that transfer charge from molecular ions to trace-metal atoms. Schemes are proposed for the synthesis of such species as NCO, HNCO, and CN. The role played by adsorption and condensation of molecules on the surface of dust grains is investigated, and effects on the chemical evolution of a dense molecular cloud are considered which result from varying the total density or the elemental abundances and from assuming negligible or severe condensation of gaseous species on dust grains. It is shown that the chemical-equilibrium time scale is given approximately by the depletion times of oxygen and nitrogen when the condensation efficiency is negligible; that this time scale is probably in the range from 1 to 4 million years, depending on the elemental composition and initial conditions in the cloud; and that this time scale is insensitive to variations in the total density.

  7. R evolution: Improving perturbative QCD

    NASA Astrophysics Data System (ADS)

    Hoang, André H.; Jain, Ambar; Scimemi, Ignazio; Stewart, Iain W.

    2010-07-01

    Perturbative QCD results in the MS¯ scheme can be dramatically improved by switching to a scheme that accounts for the dominant power law dependence on the factorization scale in the operator product expansion. We introduce the “MSR scheme” which achieves this in a Lorentz and gauge invariant way and has a very simple relation to MS¯. Results in MSR depend on a cutoff parameter R, in addition to the μ of MS¯. R variations can be used to independently estimate (i.) the size of power corrections, and (ii.) higher-order perturbative corrections (much like μ in MS¯). We give two examples at three-loop order, the ratio of mass splittings in the B*-B and D*-D systems, and the Ellis-Jaffe sum rule as a function of momentum transfer Q in deep inelastic scattering. Comparing to data, the perturbative MSR results work well even for Q˜1GeV, and power corrections are reduced compared to MS¯.

  8. R evolution: Improving perturbative QCD

    SciTech Connect

    Hoang, Andre H.; Jain, Ambar; Stewart, Iain W.; Scimemi, Ignazio

    2010-07-01

    Perturbative QCD results in the MS scheme can be dramatically improved by switching to a scheme that accounts for the dominant power law dependence on the factorization scale in the operator product expansion. We introduce the ''MSR scheme'' which achieves this in a Lorentz and gauge invariant way and has a very simple relation to MS. Results in MSR depend on a cutoff parameter R, in addition to the {mu} of MS. R variations can be used to independently estimate (i.) the size of power corrections, and (ii.) higher-order perturbative corrections (much like {mu} in MS). We give two examples at three-loop order, the ratio of mass splittings in the B*-B and D*-D systems, and the Ellis-Jaffe sum rule as a function of momentum transfer Q in deep inelastic scattering. Comparing to data, the perturbative MSR results work well even for Q{approx}1 GeV, and power corrections are reduced compared to MS.

  9. Molecular epidemiology and evolution of fish Novirhabdoviruses

    USGS Publications Warehouse

    Kurath, Gael

    2014-01-01

    The genus Novirhabdoviridae contains several of the important rhabdoviruses that infect fish hosts. There are four established virus species: Infectious hematopoietic necrosis virus (IHNV), Viral hemorrhagic septicemia virus (VHSV), Hirame rhabdovirus(HIRRV), and Snakehead rhabdovirus (SHRV). Viruses of these species vary in host and geographic range, and they have all been studied at the molecular and genomic level. As globally significant pathogens of cultured fish, IHNV and VHSV have been particularly well studied in terms of molecular epidemiology and evolution. Phylogenic analyses of hundreds of field isolates have defined five major genogroups of IHNV and four major genotypes of VHSV worldwide. These phylogenies are informed by the known histories of IHNV and VHSV, each involving a series of viral emergence events that are sometimes associated with host switches, most often into cultured rainbow trout. In general, IHNV has relatively low genetic diversity and a narrow host range, and has been spread from its endemic source in North American to Europe and Asia due to aquaculture activities. In contrast, VHSV has broad host range and high genetic diversity, and the source of emergence events is virus in widespread marine fish reservoirs in the northern Atlantic and Pacific Oceans. Common mechanisms of emergence and host switch events include use of raw feed, proximity to wild fish reservoirs of virus, and geographic translocations of virus or naive fish hosts associated with aquaculture.

  10. Molecular epidemiology and evolution of porcine parvoviruses.

    PubMed

    Streck, André Felipe; Canal, Cláudio Wageck; Truyen, Uwe

    2015-12-01

    Porcine parvovirus (PPV), recently named Ungulate protoparvovirus 1, is considered to be one of the most important causes of reproductive failure in swine. Fetal death, mummification, stillbirths and delayed return to estrus are predominant clinical signs commonly associated with PPV infection in a herd. It has recently been shown that certain parvoviruses exhibit a nucleotide substitution rate close to that commonly determined for RNA viruses. However, the PPV vaccines broadly used in the last 30 years have most likely reduced the genetic diversity of the virus and led to the predominance of strains with a capsid profile distinct from that of the original vaccine-based strains. Furthermore, a number of novel porcine parvovirus species with yet-unknown veterinary relevance and characteristics have been described during the last decade. In this review, an overview of PPV molecular evolution is presented, highlighting characteristics of the various genetic elements, their evolutionary rate and the discovery of new capsid profiles driven by the currently used vaccines. PMID:26453771

  11. High rates of molecular evolution in hantaviruses.

    PubMed

    Ramsden, Cadhla; Melo, Fernando L; Figueiredo, Luiz M; Holmes, Edward C; Zanotto, Paolo M A

    2008-07-01

    Hantaviruses are rodent-borne Bunyaviruses that infect the Arvicolinae, Murinae, and Sigmodontinae subfamilies of Muridae. The rate of molecular evolution in the hantaviruses has been previously estimated at approximately 10(-7) nucleotide substitutions per site, per year (substitutions/site/year), based on the assumption of codivergence and hence shared divergence times with their rodent hosts. If substantiated, this would make the hantaviruses among the slowest evolving of all RNA viruses. However, as hantaviruses replicate with an RNA-dependent RNA polymerase, with error rates in the region of one mutation per genome replication, this low rate of nucleotide substitution is anomalous. Here, we use a Bayesian coalescent approach to estimate the rate of nucleotide substitution from serially sampled gene sequence data for hantaviruses known to infect each of the 3 rodent subfamilies: Araraquara virus (Sigmodontinae), Dobrava virus (Murinae), Puumala virus (Arvicolinae), and Tula virus (Arvicolinae). Our results reveal that hantaviruses exhibit short-term substitution rates of 10(-2) to 10(-4) substitutions/site/year and so are within the range exhibited by other RNA viruses. The disparity between this substitution rate and that estimated assuming rodent-hantavirus codivergence suggests that the codivergence hypothesis may need to be reevaluated. PMID:18417484

  12. Molecular musings in microbial ecology and evolution

    PubMed Central

    2011-01-01

    A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology. The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology. The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology). The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies

  13. Automatic Evolution of Molecular Nanotechnology Designs

    NASA Technical Reports Server (NTRS)

    Globus, Al; Lawton, John; Wipke, Todd; Saini, Subhash (Technical Monitor)

    1998-01-01

    This paper describes strategies for automatically generating designs for analog circuits at the molecular level. Software maps out the edges and vertices of potential nanotechnology systems on graphs, then selects appropriate ones through evolutionary or genetic paradigms.

  14. Molecular clouds. [significance in stellar evolution

    NASA Technical Reports Server (NTRS)

    Thaddeus, P.

    1977-01-01

    An attempt is made to understand star formation in the context of the dense interstellar molecular gas from which stars are made. Attention is given to how molecular observations (e.g., UV spectroscopy and radio 21-cm and recombination line observations) provide data on the physical state of the dense interstellar gas; observations of H II regions, stellar associations, and dark nebulae are discussed. CO clouds are studied with reference to radial velocity, temperature, density, ionization, magnetic field.

  15. Molecular evolution in food allergy diagnosis.

    PubMed

    Barocci, Fiorella; DE Amici, Mara; Marseglia, Gian L

    2016-10-01

    Traditional allergological diagnostics often provide laboratory data that seem to correspond with similar positive results in different patients. However, with technological developments and the introduction of molecular diagnostics, it is possible to extract and highlight the differences in the serological laboratory data, to obtain detailed specificity on the various allergen components in different clinical settings. Allergological diagnostics prove to be increasingly useful in accurately distinguishing "cross-reactivity" and "cosensitization". This aspect is very important especially in patients who are, with a traditional diagnosis, polysensitized. Molecular diagnosis in allergology has expanded its range of applications thanks to the ability to IgE dose specific (in addition to classic total IgE serum) not only to allergens, food and inhalants, but also to the individual protein components which make up the allergenic source. It is essential to establish a correct diagnosis in order to determine the appropriate therapy. Therefore it is crucial to discern whether a patient is truly allergic because he presents specific IgE for molecules of a species or if the positivity is given from the structural homology between the different proteins. Molecular diagnostics emerges as a valuable tool for the discrimination of allergic patients and to differentiate between "true allergies" and "cross-reactivity". Molecular diagnostics should be used in a targeted manner for an accurate assessment and diagnosis, which would also reduce the use of oral challenges, to predict severe reactions and allergy persistence. PMID:26091488

  16. Molecular evolution of the vertebrate mechanosensory cell and ear

    PubMed Central

    Fritzsch, Bernd; Beisel, Kirk W.; Pauley, Sarah; Soukup, Garrett

    2014-01-01

    The molecular basis of mechanosensation, mechanosensory cell development and mechanosensory organ development is reviewed with an emphasis on its evolution. In contrast to eye evolution and development, which apparently modified a genetic program through intercalation of genes between the master control genes on the top (Pax6, Eya1, Six1) of the hierarchy and the structural genes (rhodopsin) at the bottom, the as yet molecularly unknown mechanosensory channel precludes such a firm conclusion for mechanosensors. However, recent years have seen the identification of several structural genes which are involved in mechanosensory tethering and several transcription factors controlling mechanosensory cell and organ development; these warrant the interpretation of available data in very much the same fashion as for eye evolution: molecular homology combined with potential morphological parallelism. This assertion of molecular homology is strongly supported by recent findings of a highly conserved set of microRNAs that appear to be associated with mechanosensory cell development across phyla. The conservation of transcription factors and their regulators fits very well to the known or presumed mechanosensory specializations which can be mostly grouped as variations of a common cellular theme. Given the widespread distribution of the molecular ability to form mechanosensory cells, it comes as no surprise that structurally different mechanosensory organs evolved in different phyla, presenting a variation of a common theme specified by a conserved set of transcription factors in their cellular development. Within vertebrates and arthropods, some mechanosensory organs evolved into auditory organs, greatly increasing sensitivity to sound through modifications of accessory structures to direct sound to the specific sensory epithelia. However, while great attention has been paid to the evolution of these accessory structures in vertebrate fossils, comparatively less attention has

  17. Slow rate of molecular evolution in high-elevation hummingbirds.

    PubMed

    Bleiweiss, R

    1998-01-20

    Estimates of relative rates of molecular evolution from a DNA-hybridization phylogeny for 26 hummingbird species provide evidence for a negative association between elevation and rate of single-copy genome evolution. This effect of elevation on rate remains significant even after taking into account a significant negative association between body mass and molecular rate. Population-level processes do not appear to account for these patterns because (i) all hummingbirds breed within their first year and (ii) the more extensive subdivision and speciation of bird populations living at high elevations predicts a positive association between elevation and rate. The negative association between body mass and molecular rate in other organisms has been attributed to higher mutation rates in forms with higher oxidative metabolism. As ambient oxygen tensions and temperature decrease with elevation, the slow rate of molecular evolution in high-elevation hummingbirds also may have a metabolic basis. A slower rate of single-copy DNA change at higher elevations suggests that the dynamics of molecular evolution cannot be separated from the environmental context. PMID:9435240

  18. A half-century after the molecular clock: new dimensions of molecular evolution.

    PubMed

    Koonin, Eugene V

    2012-08-01

    The EMBO workshop on 'Evolution in the Time of Genomics' took place in May 2012 in the magnificent sixteenth century Palazzo Franchetti near Ponte dell'Accademia in Venice. The meeting focused on phenomena that are not part of the traditional narrative of molecular evolution and which might signal a paradigm shift in the field. PMID:22791022

  19. Functional molecular markers for crop improvement.

    PubMed

    Kage, Udaykumar; Kumar, Arun; Dhokane, Dhananjay; Karre, Shailesh; Kushalappa, Ajjamada C

    2016-10-01

    A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as "foundation for twenty-first century crop improvement", a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as "the holy grail" of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered. PMID:26171816

  20. Molecular evolution of GPCRs: Ghrelin/ghrelin receptors.

    PubMed

    Kaiya, Hiroyuki; Kangawa, Kenji; Miyazato, Mikiya

    2014-06-01

    After the discovery in 1996 of the GH secretagogue-receptor type-1a (GHS-R1a) as an orphan G-protein coupled receptor, many research groups attempted to identify the endogenous ligand. Finally, Kojima and colleagues successfully isolated the peptide ligand from rat stomach extracts, determined its structure, and named it ghrelin. The GHS-R1a is now accepted to be the ghrelin receptor. The existence of the ghrelin system has been demonstrated in many animal classes through biochemical and molecular biological strategies as well as through genome projects. Our work, focused on identifying the ghrelin receptor and its ligand ghrelin in laboratory animals, particularly nonmammalian vertebrates, has provided new insights into the molecular evolution of the ghrelin receptor. In mammals, it is assumed that the ghrelin receptor evolution is in line with the plate tectonics theory. In contrast, the evolution of the ghrelin receptor in nonmammalian vertebrates differs from that of mammals: multiplicity of the ghrelin receptor isoforms is observed in nonmammalian vertebrates only. This multiplicity is due to genome duplication and polyploidization events that particularly occurred in Teleostei. Furthermore, it is likely that the evolution of the ghrelin receptor is distinct from that of its ligand, ghrelin, because only one ghrelin isoform has been detected in all species examined so far. In this review, we summarize current knowledge related to the molecular evolution of the ghrelin receptor in mammalian and nonmammalian vertebrates. PMID:24353285

  1. The Jukes-Cantor Model of Molecular Evolution

    ERIC Educational Resources Information Center

    Erickson, Keith

    2010-01-01

    The material in this module introduces students to some of the mathematical tools used to examine molecular evolution. This topic is standard fare in many mathematical biology or bioinformatics classes, but could also be suitable for classes in linear algebra or probability. While coursework in matrix algebra, Markov processes, Monte Carlo…

  2. Witnessing Phenotypic and Molecular Evolution in the Fruit Fly.

    PubMed

    Heil, Caiti S S; Hunter, Mika J; Noor, Juliet Kf; Miglia, Kathleen; Manzano-Winkler, Brenda; McDermott, Shannon R; Noor, Mohamed Af

    2012-12-01

    This multi-day exercise is designed for a college Genetics and Evolution laboratory to demonstrate concepts of inheritance and phenotypic and molecular evolution using a live model organism, Drosophila simulans. Students set up an experimental fruit fly population consisting of ten white eyed flies and one red eyed fly. Having red eyes is advantageous compared to having white eyes, allowing students to track the spread of this advantageous trait over several generations. Ultimately, the students perform PCR and gel electrophoresis at two neutral markers, one located in close proximity to the eye-color locus, and one located at the other end of the chromosome. Students observe that most flies have red eyes, and these red-eyed flies have lost variation at the near marker, but maintained variation at the far marker, hence observing a "selective sweep" and the "hitchhiking" of a nearby neutral variant. Students literally observe phenotypic and molecular evolution in their classroom! PMID:23459154

  3. The Molecular Evolution of the Qo Motif

    PubMed Central

    Kao, Wei-Chun; Hunte, Carola

    2014-01-01

    Quinol oxidation in the catalytic quinol oxidation site (Qo site) of cytochrome (cyt) bc1 complexes is the key step of the Q cycle mechanism, which laid the ground for Mitchell’s chemiosmotic theory of energy conversion. Bifurcated electron transfer upon quinol oxidation enables proton uptake and release on opposite membrane sides, thus generating a proton gradient that fuels ATP synthesis in cellular respiration and photosynthesis. The Qo site architecture formed by cyt b and Rieske iron–sulfur protein (ISP) impedes harmful bypass reactions. Catalytic importance is assigned to four residues of cyt b formerly described as PEWY motif in the context of mitochondrial complexes, which we now denominate Qo motif as comprehensive evolutionary sequence analysis of cyt b shows substantial natural variance of the motif with phylogenetically specific patterns. In particular, the Qo motif is identified as PEWY in mitochondria, α- and ε-Proteobacteria, Aquificae, Chlorobi, Cyanobacteria, and chloroplasts. PDWY is present in Gram-positive bacteria, Deinococcus–Thermus and haloarchaea, and PVWY in β- and γ-Proteobacteria. PPWF only exists in Archaea. Distinct patterns for acidophilic organisms indicate environment-specific adaptations. Importantly, the presence of PDWY and PEWY is correlated with the redox potential of Rieske ISP and quinone species. We propose that during evolution from low to high potential electron-transfer systems in the emerging oxygenic atmosphere, cyt bc1 complexes with PEWY as Qo motif prevailed to efficiently use high potential ubiquinone as substrate, whereas cyt b with PDWY operate best with low potential Rieske ISP and menaquinone, with the latter being the likely composition of the ancestral cyt bc1 complex. PMID:25115012

  4. Giant Molecular Cloud Structure and Evolution

    NASA Technical Reports Server (NTRS)

    Hollenbach, David (Technical Monitor); Bodenheimer, P. H.

    2003-01-01

    Bodenheimer and Burkert extended earlier calculations of cloud core models to study collapse and fragmentation. The initial condition for an SPH collapse calculation is the density distribution of a Bonnor-Ebert sphere, with near balance between turbulent plus thermal energy and gravitational energy. The main parameter is the turbulent Mach number. For each Mach number several runs are made, each with a different random realization of the initial turbulent velocity field. The turbulence decays on a dynamical time scale, leading the cloud into collapse. The collapse proceeds isothermally until the density has increased to about 10(exp 13) g cm(exp -3). Then heating is included in the dense regions. The nature of the fragmentation is investigated. About 15 different runs have been performed with Mach numbers ranging from 0.3 to 3.5 (the typical value observed in molecular cloud cores is 0.7). The results show a definite trend of increasing multiplicity with increasing Mach number (M), with the number of fragments approximately proportional to (1 + M). In general, this result agrees with that of Fisher, Klein, and McKee who published three cases with an AMR grid code. However our results show that there is a large spread about this curve. For example, for M=0.3 one case resulted in no fragmentation while a second produced three fragments. Thus it is not only the value of M but also the details of the superposition of the various velocity modes that play a critical role in the formation of binaries. Also, the simulations produce a wide range of separations (10-1000 AU) for the multiple systems, in rough agreement with observations. These results are discussed in two conference proceedings.

  5. Molecular evolution of nitrate reductase genes.

    PubMed

    Zhou, J; Kleinhofs, A

    1996-04-01

    To understand the evolutionary mechanisms and relationships of nitrate reductases (NRs), the nucleotide sequences encoding 19 nitrate reductase (NR) genes from 16 species of fungi, algae, and higher plants were analyzed. The NR genes examined show substantial sequence similarity, particularly within functional domains, and large variations in GC content at the third codon position and intron number. The intron positions were different between the fungi and plants, but conserved within these groups. The overall and nonsynonymous substitution rates among fungi, algae, and higher plants were estimated to be 4.33 x 10(-10) and 3.29 x 10(-10) substitutions per site per year. The three functional domains of NR genes evolved at about one-third of the rate of the N-terminal and the two hinge regions connecting the functional domains. Relative rate tests suggested that the nonsynonymous substitution rates were constant among different lineages, while the overall nucleotide substitution rates varied between some lineages. The phylogenetic trees based on NR genes correspond well with the phylogeny of the organisms determined from systematics and other molecular studies. Based on the nonsynonymous substitution rate, the divergence time of monocots and dicots was estimated to be about 340 Myr when the fungi-plant or algae-higher plant divergence times were used as reference points and 191 Myr when the rice-barley divergence time was used as a reference point. These two estimates are consistent with other estimates of divergence times based on these reference points. The lack of consistency between these two values appears to be due to the uncertainty of the reference times. PMID:8642612

  6. Improved molecular tools for sugar cane biotechnology.

    PubMed

    Kinkema, Mark; Geijskes, Jason; Delucca, Paulo; Palupe, Anthony; Shand, Kylie; Coleman, Heather D; Brinin, Anthony; Williams, Brett; Sainz, Manuel; Dale, James L

    2014-03-01

    Sugar cane is a major source of food and fuel worldwide. Biotechnology has the potential to improve economically-important traits in sugar cane as well as diversify sugar cane beyond traditional applications such as sucrose production. High levels of transgene expression are key to the success of improving crops through biotechnology. Here we describe new molecular tools that both expand and improve gene expression capabilities in sugar cane. We have identified promoters that can be used to drive high levels of gene expression in the leaf and stem of transgenic sugar cane. One of these promoters, derived from the Cestrum yellow leaf curling virus, drives levels of constitutive transgene expression that are significantly higher than those achieved by the historical benchmark maize polyubiquitin-1 (Zm-Ubi1) promoter. A second promoter, the maize phosphonenolpyruvate carboxylate promoter, was found to be a strong, leaf-preferred promoter that enables levels of expression comparable to Zm-Ubi1 in this organ. Transgene expression was increased approximately 50-fold by gene modification, which included optimising the codon usage of the coding sequence to better suit sugar cane. We also describe a novel dual transcriptional enhancer that increased gene expression from different promoters, boosting expression from Zm-Ubi1 over eightfold. These molecular tools will be extremely valuable for the improvement of sugar cane through biotechnology. PMID:24150836

  7. HIV-1 evolution: frustrating therapies, but disclosing molecular mechanisms

    PubMed Central

    Das, Atze T.; Berkhout, Ben

    2010-01-01

    Replication of HIV-1 under selective pressure frequently results in the evolution of virus variants that replicate more efficiently under the applied conditions. For example, in patients on antiretroviral therapy, such evolution can result in variants that are resistant to the HIV-1 inhibitors, thus frustrating the therapy. On the other hand, virus evolution can help us to understand the molecular mechanisms that underlie HIV-1 replication. For example, evolution of a defective virus mutant can result in variants that overcome the introduced defect by restoration of the original sequence or by the introduction of additional mutations in the viral genome. Analysis of the evolution pathway can reveal the requirements of the element under study and help to understand its function. Analysis of the escape routes may generate new insight in the viral life cycle and result in the identification of unexpected biological mechanisms. We have developed in vitro HIV-1 evolution into a systematic research tool that allows the study of different aspects of the viral replication cycle. We will briefly review this method of forced virus evolution and provide several examples that illustrate the power of this approach. PMID:20478891

  8. Social parasitism and the molecular basis of phenotypic evolution.

    PubMed

    Cini, Alessandro; Patalano, Solenn; Segonds-Pichon, Anne; Busby, George B J; Cervo, Rita; Sumner, Seirian

    2015-01-01

    Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer-Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization. PMID:25741361

  9. Social parasitism and the molecular basis of phenotypic evolution

    PubMed Central

    Cini, Alessandro; Patalano, Solenn; Segonds-Pichon, Anne; Busby, George B. J.; Cervo, Rita; Sumner, Seirian

    2015-01-01

    Contrasting phenotypes arise from similar genomes through a combination of losses, gains, co-option and modifications of inherited genomic material. Understanding the molecular basis of this phenotypic diversity is a fundamental challenge in modern evolutionary biology. Comparisons of the genes and their expression patterns underlying traits in closely related species offer an unrivaled opportunity to evaluate the extent to which genomic material is reorganized to produce novel traits. Advances in molecular methods now allow us to dissect the molecular machinery underlying phenotypic diversity in almost any organism, from single-celled entities to the most complex vertebrates. Here we discuss how comparisons of social parasites and their free-living hosts may provide unique insights into the molecular basis of phenotypic evolution. Social parasites evolve from a eusocial ancestor and are specialized to exploit the socially acquired resources of their closely-related eusocial host. Molecular comparisons of such species pairs can reveal how genomic material is re-organized in the loss of ancestral traits (i.e., of free-living traits in the parasites) and the gain of new ones (i.e., specialist traits required for a parasitic lifestyle). We define hypotheses on the molecular basis of phenotypes in the evolution of social parasitism and discuss their wider application in our understanding of the molecular basis of phenotypic diversity within the theoretical framework of phenotypic plasticity and shifting reaction norms. Currently there are no data available to test these hypotheses, and so we also provide some proof of concept data using the paper wasp social parasite/host system (Polistes sulcifer—Polistes dominula). This conceptual framework and first empirical data provide a spring-board for directing future genomic analyses on exploiting social parasites as a route to understanding the evolution of phenotypic specialization. PMID:25741361

  10. Widespread convergence in toxin resistance by predictable molecular evolution

    PubMed Central

    Ujvari, Beata; Casewell, Nicholas R.; Sunagar, Kartik; Arbuckle, Kevin; Wüster, Wolfgang; Lo, Nathan; O’Meally, Denis; Beckmann, Christa; King, Glenn F.; Deplazes, Evelyne; Madsen, Thomas

    2015-01-01

    The question about whether evolution is unpredictable and stochastic or intermittently constrained along predictable pathways is the subject of a fundamental debate in biology, in which understanding convergent evolution plays a central role. At the molecular level, documented examples of convergence are rare and limited to occurring within specific taxonomic groups. Here we provide evidence of constrained convergent molecular evolution across the metazoan tree of life. We show that resistance to toxic cardiac glycosides produced by plants and bufonid toads is mediated by similar molecular changes to the sodium-potassium-pump (Na+/K+-ATPase) in insects, amphibians, reptiles, and mammals. In toad-feeding reptiles, resistance is conferred by two point mutations that have evolved convergently on four occasions, whereas evidence of a molecular reversal back to the susceptible state in varanid lizards migrating to toad-free areas suggests that toxin resistance is maladaptive in the absence of selection. Importantly, resistance in all taxa is mediated by replacements of 2 of the 12 amino acids comprising the Na+/K+-ATPase H1–H2 extracellular domain that constitutes a core part of the cardiac glycoside binding site. We provide mechanistic insight into the basis of resistance by showing that these alterations perturb the interaction between the cardiac glycoside bufalin and the Na+/K+-ATPase. Thus, similar selection pressures have resulted in convergent evolution of the same molecular solution across the breadth of the animal kingdom, demonstrating how a scarcity of possible solutions to a selective challenge can lead to highly predictable evolutionary responses. PMID:26372961

  11. Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects.

    PubMed

    Chenuil, Anne; Anne, Chenuil

    2006-05-01

    The use of molecular genetic markers (MGMs) has become widespread among evolutionary biologists, and the methods of analysis of genetic data improve rapidly, yet an organized framework in which scientists can work is lacking. Elements of molecular evolution are summarized to explain the origin of variation at the DNA level, its measures, and the relationships linking genetic variability to the biological parameters of the studied organisms. MGM are defined by two components: the DNA region(s) screened, and the technique used to reveal its variation. Criteria of choice belong to three categories: (1) the level of variability, (2) the nature of the information (e.g. dominance vs. codominance, ploidy, ... ) which must be determined according to the biological question and (3) some practical criteria which mainly depend on the equipment of the laboratory and experience of the scientist. A three-step procedure is proposed for drawing up MGMs suitable to answer given biological questions, and compiled data are organized to guide the choice at each step: (1) choice, determined by the biological question, of the level of variability and of the criteria of the nature of information, (2) choice of the DNA region and (3) choice of the technique. PMID:16850217

  12. [The genotyping and molecular evolution of varicella-zoster virus].

    PubMed

    Jiang, Long-Feng; Gan, Lin; Chen, Jing-Xian; Wang, Ming-Li

    2012-09-01

    Varicella-zoster virus (VZV, Human herpesvirus 3) is a member of the family Herpesviridae, and is classified as alpha-subfamily along with HSV-1 and HSV-2. VZV is the causative agent of chicken pox (varicella) mostly in children, after which it establishes latency in the sensory ganglia with the potential to reactivate at a later time to cause shingles (zoster). Increasing molecular epidemiological studies in recent years have been performed to monitor the mutations in VZV genome, discriminate vaccine virus from wild type virus, study the phylogeny of VZV strains throughout the world, and understand the evolution of the different clades of VZV. The progress has great impact on the fields of epidemiology, virology and bioinformatics. In this review, the currently available data concerning the geographic distribution and molecular evolution of VZV clades are discussed. PMID:23233938

  13. [The molecular evolution of rice stress-related genes].

    PubMed

    Song, Xiaojun; Xie, Kaibin; Zhang, Yanping; Jin, Ping

    2014-10-01

    In the processes of evolution, plants have formed a perfect regulation system to tolerate adverse environmental conditions. However, there has not been any report about the molecular evolution of rice stress-related genes. We derived a family of 22 stress-related genes in rice from Plant Stress Gene Database, and analyzed it by bioinformatics and comparative genome method. The results showed that these genes are relatively conservative in low organisms, and their copy numbers increase along with the environmental changes and the evolution. We also found four conserved sequence motifs and three other specific motifs. We propose that these motifs are closely associated with the function of rice stress-related genes. The analysis of selection pressure showed that about 50% rice stress-related genes have positive selection sites, although they were subject to a strong purifying selection. Positive selection sites might be very significant for plants to adapt to environmental changes. PMID:25406251

  14. Reconstructing phylogenies and phenotypes: a molecular view of human evolution.

    PubMed

    Bradley, Brenda J

    2008-04-01

    This review broadly summarizes how molecular biology has contributed to our understanding of human evolution. Molecular anthropology began in the 1960s with immunological comparisons indicating that African apes and humans were closely related and, indeed, shared a common ancestor as recently as 5 million years ago. Although initially dismissed, this finding has proven robust and numerous lines of molecular evidence now firmly place the human-ape divergence at 4-8 Ma. Resolving the trichotomy among humans, chimpanzees and gorillas took a few more decades. Despite the readily apparent physical similarities shared by African apes to the exclusion of modern humans (body hair, knuckle-walking, thin tooth enamel), the molecular support for a human-chimpanzee clade is now overwhelming. More recently, whole genome sequencing and gene mapping have shifted the focus of molecular anthropology from phylogenetic analyses to phenotypic reconstruction and functional genomics. We are starting to identify the genetic basis of the morphological, physiological and behavioural traits that distinguish modern humans from apes and apes from other primates. Most notably, recent comparative genomic analyses strongly indicate that the marked differences between modern humans and chimpanzees are likely due more to changes in gene regulation than to modifications of the genes themselves, an idea first proposed over 30 years ago. Almost weekly, press releases describe newly identified genes and regulatory elements that seem to have undergone strong positive selection along the human lineage. Loci involved in speech (e.g. FOXP2), brain development (e.g. ASPM), and skull musculature (e.g. MYH16) have been of particular interest, but some surprising candidate loci (e.g. those involved in auditory capabilities) have emerged as well. Exciting new research avenues, such as the Neanderthal Genome Project, promise that molecular analyses will continue to provide novel insights about our evolution

  15. Flight loss linked to faster molecular evolution in insects

    PubMed Central

    Mitterboeck, T. Fatima; Adamowicz, Sarah J.

    2013-01-01

    The loss of flight ability has occurred thousands of times independently during insect evolution. Flight loss may be linked to higher molecular evolutionary rates because of reductions in effective population sizes (Ne) and relaxed selective constraints. Reduced dispersal ability increases population subdivision, may decrease geographical range size and increases (sub)population extinction risk, thus leading to an expected reduction in Ne. Additionally, flight loss in birds has been linked to higher molecular rates of energy-related genes, probably owing to relaxed selective constraints on energy metabolism. We tested for an association between insect flight loss and molecular rates through comparative analysis in 49 phylogenetically independent transitions spanning multiple taxa, including moths, flies, beetles, mayflies, stick insects, stoneflies, scorpionflies and caddisflies, using available nuclear and mitochondrial protein-coding DNA sequences. We estimated the rate of molecular evolution of flightless (FL) and related flight-capable lineages by ratios of non-synonymous-to-synonymous substitutions (dN/dS) and overall substitution rates (OSRs). Across multiple instances of flight loss, we show a significant pattern of higher dN/dS ratios and OSRs in FL lineages in mitochondrial but not nuclear genes. These patterns may be explained by relaxed selective constraints in FL ectotherms relating to energy metabolism, possibly in combination with reduced Ne. PMID:23884090

  16. Molecular evolution of the lysophosphatidic acid acyltransferase (LPAAT) gene family.

    PubMed

    Körbes, Ana Paula; Kulcheski, Franceli Rodrigues; Margis, Rogério; Margis-Pinheiro, Márcia; Turchetto-Zolet, Andreia Carina

    2016-03-01

    Lysophosphatidic acid acyltransferases (LPAATs) perform an essential cellular function by controlling the production of phosphatidic acid (PA), a key intermediate in the synthesis of membrane, signaling and storage lipids. Although LPAATs have been extensively explored by functional and biotechnological studies, little is known about their molecular evolution and diversification. We performed a genome-wide analysis using data from several plants and animals, as well as other eukaryotic and prokaryotic species, to identify LPAAT genes and analyze their evolutionary history. We used phylogenetic and molecular evolution analysis to test the hypothesis of distinct origins for these genes. The reconstructed phylogeny supported the ancient origin of some isoforms (plant LPAAT1 and LPAATB; animal AGPAAT1/2), while others emerged more recently (plant LPAAT2/3/4/5; AGPAAT3/4/5/8). Additionally, the hypothesis of endosymbiotic origin of the plastidic isoform LPAAT1 was confirmed. LPAAT genes from plants and animals mainly experienced strong purifying selection pressures with limited functional divergence after the species-specific duplications. Gene expression analyses of LPAAT isoforms in model plants demonstrated distinct LPAAT expression patterns in these organisms. The results showed that distinct origins followed by diversification of the LPAAT genes shaped the evolution of TAG biosynthesis. The expression pattern of individual genes may be responsible for adaptation into multiple ecological niches. PMID:26721558

  17. Molecular evolution of haemagglutinin (H) gene in measles virus.

    PubMed

    Kimura, Hirokazu; Saitoh, Mika; Kobayashi, Miho; Ishii, Haruyuki; Saraya, Takeshi; Kurai, Daisuke; Tsukagoshi, Hiroyuki; Shirabe, Komei; Nishina, Atsuyoshi; Kozawa, Kunihisa; Kuroda, Makoto; Takeuchi, Fumihiko; Sekizuka, Tsuyoshi; Minakami, Hisanori; Ryo, Akihide; Takeda, Makoto

    2015-01-01

    We studied the molecular evolution of the haemagglutinin (H) gene (full length) in all genotypes (24 genotypes, 297 strains) of measles virus (MeV). The gene's evolutionary timescale was estimated by the Bayesian Markov chain Monte Carlo (MCMC) method. We also analysed positive selection sites. The MCMC tree indicated that the MeV H gene diverged from the rinderpest virus (same genus) about 250 years ago and that 24 MeV genotypes formed 3 lineages dating back to a 1915 ancestor (95% highest posterior density [HPD] 1882-1941) with relatively rapid evolution (mean rate: 9.02 × 10(-4) substitutions/site/year). The 3 lineages diverged in 1915 (lineage 1, 95% HPD 1882-1941), 1954 (lineage 2, 95% HPD 1937-1969), and 1940 (lineage 3, 95% HPD 1927-1952). These 24 genotypes may have diverged and emerged between the 1940s and 1990 s. Selective pressure analysis identified many negative selection sites on the H protein but only a few positive selection sites, suggesting strongly operated structural and/or functional constraint of changes on the H protein. Based on the molecular evolution of H gene, an ancestor MeV of the 24 genotypes emerged about 100 years ago and the structure of H protein has been well conserved. PMID:26130388

  18. Molecular hyperdiversity and evolution in very large populations

    PubMed Central

    Cutter, Asher D.; Jovelin, Richard; Dey, Alivia

    2014-01-01

    The genomic density of sequence polymorphisms critically affects the sensitivity of inferences about ongoing sequence evolution, function, and demographic history. Most animal and plant genomes have relatively low densities of polymorphisms, but some species are hyperdiverse with neutral nucleotide heterozygosity exceeding 5%. Eukaryotes with extremely large populations, mimicking bacterial and viral populations, present novel opportunities for studying molecular evolution in sexually-reproducing taxa with complex development. In particular, hyperdiverse species can help answer controversial questions about the evolution of genome complexity, the limits of natural selection, modes of adaptation, and subtleties of the mutation process. However, such systems have some inherent complications and here we identify topics in need of theoretical developments. Close relatives of the model organisms Caenorhabditis elegans and Drosophila melanogaster provide known examples of hyperdiverse eukaryotes, encouraging functional dissection of resulting molecular evolutionary patterns. We recommend how best to exploit hyperdiverse populations for analysis, for example, in quantifying the impact of non-crossover recombination in genomes and for determining the identity and micro-evolutionary selective pressures on non-coding regulatory elements. PMID:23506466

  19. Molecular evolution of WDR62, a gene that regulates neocorticogenesis

    PubMed Central

    Pervaiz, Nashaiman; Abbasi, Amir Ali

    2016-01-01

    Human brain evolution is characterized by dramatic expansion in cerebral cortex size. WDR62 (WD repeat domain 62) is one of the important gene in controlling human cortical development. Mutations in WDR62 lead to primary microcephaly, a neurodevelopmental disease characterized by three to four fold reduction in cerebral cortex size of affected individuals. This study analyzes comparative protein evolutionary rate to provide a useful insight into the molecular evolution of WDR62 and hence pinpointed human specific amino acid replacements. Comparative analysis of human WDR62 with two archaic humans (Neanderthals and Denisovans) and modern human populations revealed that five hominin specific amino acid residues (human specific amino acids shared with two archaic humans) might have been accumulated in the common ancestor of extinct archaic humans and modern humans about 550,000–765,000 years ago. Collectively, the data demonstrates an acceleration of WDR62 sequence evolution in hominin lineage and suggests that the ability of WDR62 protein to mediate the neurogenesis has been altered in the course of hominin evolution. PMID:27114917

  20. Molecular evolution of WDR62, a gene that regulates neocorticogenesis.

    PubMed

    Pervaiz, Nashaiman; Abbasi, Amir Ali

    2016-09-01

    Human brain evolution is characterized by dramatic expansion in cerebral cortex size. WDR62 (WD repeat domain 62) is one of the important gene in controlling human cortical development. Mutations in WDR62 lead to primary microcephaly, a neurodevelopmental disease characterized by three to four fold reduction in cerebral cortex size of affected individuals. This study analyzes comparative protein evolutionary rate to provide a useful insight into the molecular evolution of WDR62 and hence pinpointed human specific amino acid replacements. Comparative analysis of human WDR62 with two archaic humans (Neanderthals and Denisovans) and modern human populations revealed that five hominin specific amino acid residues (human specific amino acids shared with two archaic humans) might have been accumulated in the common ancestor of extinct archaic humans and modern humans about 550,000-765,000 years ago. Collectively, the data demonstrates an acceleration of WDR62 sequence evolution in hominin lineage and suggests that the ability of WDR62 protein to mediate the neurogenesis has been altered in the course of hominin evolution. PMID:27114917

  1. A Tale of Two Crocoducks: Creationist Misuses of Molecular Evolution

    NASA Astrophysics Data System (ADS)

    Hofmann, James R.

    2014-10-01

    Although some creationist objections to evolutionary biology are simplistic and thus are easily refuted, when more technical arguments become widespread it is important for science educators to explain the relevant science in a straightforward manner. An interesting case study is provided by misguided allegations about how cytochrome c data pertain to molecular evolution. The most common of these misrepresentations bears a striking similarity to a particularly glaring misunderstanding of what should be expected of a transitional form in a fossil sequence. Although evangelist Kirk Cameron's ridiculous injunction of a hypothetical `crocoduck' as an example of a potential transitional form is frequently invoked to illustrate the ignorance of many critics of evolutionary science, a strikingly analogous argument was applied to cytochrome c data by biochemist Michael Denton in 1985. The details of this analogy are worth exploring to clarify the fallacy of the widely circulated molecular argument.

  2. [Evolution and systematics of nematodes based on molecular investigation].

    PubMed

    Okulewicz, Anna; Perec, Agnieszka

    2004-01-01

    Evolution and systematics of nematodes based on molecular investigation. The use of molecular phylogenetics to examine the interrelationships between animal parasites, free-living nematodes, and plant parasites versus traditional classification based on morphological-ecological characters was discussed and reviewed. Distinct differences were observed between parasitic nematodes and free-living ones. Within the former group, animal parasites turned out to be distinctly different from plant parasites. Using small subunit of ribosomal RNA gene sequence from a wide range of nematodes, there is a possibility to compare animal-parasitic, plant-parasitic and free-living taxa. Nowadays the parasitic nematodes expressed sequence tag (EST) project is currently generating sequence information to provide a new source of data to examine the evolutionary history of this taxonomic group. PMID:16859012

  3. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  4. Application of Molecular Genetics and Transformation to Barley Improvement

    Technology Transfer Automated Retrieval System (TEKTRAN)

    This chapter of the new barley monograph summarizes current applications of molecular genetics and transformation to barley improvement. The chapter describes recent applications of molecular markers including association genetics, QTL mapping and marker assisted selection in barley programs, and in...

  5. The interface of protein structure, protein biophysics, and molecular evolution

    PubMed Central

    Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

    2012-01-01

    Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

  6. The evolution of human populations: a molecular perspective.

    PubMed

    Ayala, F J; Escalante, A A

    1996-02-01

    Human evolution exhibits repeated speciations and conspicuous morphological change: from Australopithecus to Homo habilis, H. erectus, and H. sapiens; and from their hominoid ancestor to orangutans, gorillas, chimpanzees, and humans. Theories of founder-event speciation propose that speciation often occurs as a consequence of population bottlenecks, down to one or very few individual pairs. Proponents of punctuated equilibrium claim in addition that founder-event speciation results in rapid morphological change. The major histocompatibility complex (MHC) consists of several very polymorphic gene loci. The genealogy of 19 human alleles of the DQB1 locus coalesces more than 30 million years ago, before the divergence of apes and Old World monkeys. Many human alleles are more closely related to pongid and cercopithecoid alleles than to other human alleles. Using the theory of gene coalescence, we estimate that these polymorphisms require human populations of the order of N = 100,000 individuals for the last several million years. This conclusion is confirmed by computer simulations showing the rate of decay of the polymorphisms over time. Computer simulations indicate, in addition, that in human evolution no bottlenecks have occurred with fewer than several thousand individuals. We evaluate studies of mtDNA, Y-chromosome, and microsatellite autosomal polymorphisms and conclude that they are consistent with the MHC result that no narrow population bottlenecks have occurred in human evolution. The available molecular information favors a recent African origin of modern humans, who spread out of Africa approximately 100,000 to 200,000 years ago. PMID:8673287

  7. Statistical mechanics of quasispecies theories of molecular evolution

    NASA Astrophysics Data System (ADS)

    Munoz Tavera, Enrique

    This thesis presents a statistical mechanical analysis of different formulations of quasispecies theory of molecular evolution. These theories, characterized by two different families of models, the Crow-Kimura and the Eigen model, constitute a microscopie description of evolution. These models are most often used for RNA viruses, where a phase transition is predicted, in agreement with experiments, between an organized or quasispecies phase, and a disordered non-selective phase when the mutation rate exceeds a critical value. The methods of statistical mechanics, in particular field-theoretic methods, are employed to obtain analytic solutions to four problems relevant to biological interest. The first chapter presents the study of evolution under a multiple-peak fitness landscape, with biological applications in the study of the proliferation of viruses or cancer under the control of drugs or the immune system. The second chapter studies the effect of incorporating different forms of horizontal gene transfer and two-parent recombination to the classical formulation of quasispecies models. As an example, we study the effect of the sign of epistasis of the fitness landscape on the advantage or disadvantage of recombination for the mean fitness. The third chapter considers the relaxation of the purine/pyrimidine assumption in the classical formulation of the models, by formulating and solving the parallel and Eigen models in the context of a four-letter alphabet. The fourth and final chapter studies finite population effects, both in the presence and in the absence of horizontal gene transfer.

  8. Rhodopsin Molecular Evolution in Mammals Inhabiting Low Light Environments

    PubMed Central

    Zhao, Huabin; Ru, Binghua; Teeling, Emma C.; Faulkes, Christopher G.; Zhang, Shuyi; Rossiter, Stephen J.

    2009-01-01

    The ecological radiation of mammals to inhabit a variety of light environments is largely attributed to adaptive changes in their visual systems. Visual capabilities are conferred by anatomical features of the eyes as well as the combination and properties of their constituent light sensitive pigments. To test whether evolutionary switches to different niches characterized by dim-light conditions coincided with molecular adaptation of the rod pigment rhodopsin, we sequenced the rhodopsin gene in twenty-two mammals including several bats and subterranean mole-rats. We compared these to thirty-seven published mammal rhodopsin sequences, from species with divergent visual ecologies, including nocturnal, diurnal and aquatic groups. All taxa possessed an intact functional rhodopsin; however, phylogenetic tree reconstruction recovered a gene tree in which rodents were not monophyletic, and also in which echolocating bats formed a monophyletic group. These conflicts with the species tree appear to stem from accelerated evolution in these groups, both of which inhabit low light environments. Selection tests confirmed divergent selection pressures in the clades of subterranean rodents and bats, as well as in marine mammals that live in turbid conditions. We also found evidence of divergent selection pressures among groups of bats with different sensory modalities based on vision and echolocation. Sliding window analyses suggest most changes occur in transmembrane domains, particularly obvious within the pinnipeds; however, we found no obvious pattern between photopic niche and predicted spectral sensitivity based on known critical amino acids. This study indicates that the independent evolution of rhodopsin vision in ecologically specialised groups of mammals has involved molecular evolution at the sequence level, though such changes might not mediate spectral sensitivity directly. PMID:20016835

  9. Molecular Recognition of the Catalytic Zinc(II) Ion in MMP-13: Structure-Based Evolution of an Allosteric Inhibitor to Dual Binding Mode Inhibitors with Improved Lipophilic Ligand Efficiencies

    PubMed Central

    Fischer, Thomas; Riedl, Rainer

    2016-01-01

    Matrix metalloproteinases (MMPs) are a class of zinc dependent endopeptidases which play a crucial role in a multitude of severe diseases such as cancer and osteoarthritis. We employed MMP-13 as the target enzyme for the structure-based design and synthesis of inhibitors able to recognize the catalytic zinc ion in addition to an allosteric binding site in order to increase the affinity of the ligand. Guided by molecular modeling, we optimized an initial allosteric inhibitor by addition of linker fragments and weak zinc binders for recognition of the catalytic center. Furthermore we improved the lipophilic ligand efficiency (LLE) of the initial inhibitor by adding appropriate zinc binding fragments to lower the clogP values of the inhibitors, while maintaining their potency. All synthesized inhibitors showed elevated affinity compared to the initial hit, also most of the novel inhibitors displayed better LLE. Derivatives with carboxylic acids as the zinc binding fragments turned out to be the most potent inhibitors (compound 3 (ZHAWOC5077): IC50 = 134 nM) whereas acyl sulfonamides showed the best lipophilic ligand efficiencies (compound 18 (ZHAWOC5135): LLE = 2.91). PMID:26938528

  10. Molecular Recognition of the Catalytic Zinc(II) Ion in MMP-13: Structure-Based Evolution of an Allosteric Inhibitor to Dual Binding Mode Inhibitors with Improved Lipophilic Ligand Efficiencies.

    PubMed

    Fischer, Thomas; Riedl, Rainer

    2016-01-01

    Matrix metalloproteinases (MMPs) are a class of zinc dependent endopeptidases which play a crucial role in a multitude of severe diseases such as cancer and osteoarthritis. We employed MMP-13 as the target enzyme for the structure-based design and synthesis of inhibitors able to recognize the catalytic zinc ion in addition to an allosteric binding site in order to increase the affinity of the ligand. Guided by molecular modeling, we optimized an initial allosteric inhibitor by addition of linker fragments and weak zinc binders for recognition of the catalytic center. Furthermore we improved the lipophilic ligand efficiency (LLE) of the initial inhibitor by adding appropriate zinc binding fragments to lower the clogP values of the inhibitors, while maintaining their potency. All synthesized inhibitors showed elevated affinity compared to the initial hit, also most of the novel inhibitors displayed better LLE. Derivatives with carboxylic acids as the zinc binding fragments turned out to be the most potent inhibitors (compound 3 (ZHAWOC5077): IC50 = 134 nM) whereas acyl sulfonamides showed the best lipophilic ligand efficiencies (compound 18 (ZHAWOC5135): LLE = 2.91). PMID:26938528

  11. Supernova Feedback in Molecular Clouds: Global Evolution and Dynamics

    NASA Astrophysics Data System (ADS)

    Körtgen, Bastian; Seifried, Daniel; Banerjee, Robi; Vázquez-Semadeni, Enrique; Zamora-Avilés, Manuel

    2016-04-01

    We use magnetohydrodynamical simulations of converging warm neutral medium flows to analyse the formation and global evolution of magnetised and turbulent molecular clouds subject to supernova feedback from massive stars. We show that supernova feedback alone fails to disrupt entire, gravitationally bound, molecular clouds, but is able to disperse small-sized (˜10 pc) regions on timescales of less than 1 Myr. Efficient radiative cooling of the supernova remnant as well as strong compression of the surrounding gas result in non-persistent energy and momentum input from the supernovae. However, if the time between subsequent supernovae is short and they are clustered, large hot bubbles form that disperse larger regions of the parental cloud. On longer timescales, supernova feedback increases the amount of gas with moderate temperatures (T ≈ 300 - 3000 K). Despite its inability to disrupt molecular clouds, supernova feedback leaves a strong imprint on the star formation process. We find an overall reduction of the star formation efficiency by a factor of 2 and of the star formation rate by roughly factors of 2-4.

  12. Supernova feedback in molecular clouds: global evolution and dynamics

    NASA Astrophysics Data System (ADS)

    Körtgen, Bastian; Seifried, Daniel; Banerjee, Robi; Vázquez-Semadeni, Enrique; Zamora-Avilés, Manuel

    2016-07-01

    We use magnetohydrodynamical simulations of converging warm neutral medium flows to analyse the formation and global evolution of magnetized and turbulent molecular clouds subject to supernova feedback from massive stars. We show that supernova feedback alone fails to disrupt entire, gravitationally bound, molecular clouds, but is able to disperse small-sized (˜10 pc) regions on time-scales of less than 1 Myr. Efficient radiative cooling of the supernova remnant as well as strong compression of the surrounding gas result in non-persistent energy and momentum input from the supernovae. However, if the time between subsequent supernovae is short and they are clustered, large hot bubbles form that disperse larger regions of the parental cloud. On longer time-scales, supernova feedback increases the amount of gas with moderate temperatures (T ≈ 300-3000 K). Despite its inability to disrupt molecular clouds, supernova feedback leaves a strong imprint on the star formation process. We find an overall reduction of the star formation efficiency by a factor of 2 and of the star formation rate by roughly factors of 2-4.

  13. MOLECULAR GAS EVOLUTION ACROSS A SPIRAL ARM IN M51

    SciTech Connect

    Egusa, Fumi; Scoville, Nick; Koda, Jin

    2011-01-10

    We present sensitive and high angular resolution CO(1-0) data obtained by the Combined Array for Research in Millimeter-wave Astronomy observations toward the nearby grand-design spiral galaxy M51. The angular resolution of 0.''7 corresponds to 30 pc, which is similar to the typical size of giant molecular clouds (GMCs), and the sensitivity is also high enough to detect typical GMCs. Within the 1' field of view centered on a spiral arm, a number of GMC-scale structures are detected as clumps. However, only a few clumps are found to be associated with each giant molecular association (GMA) and more than 90% of the total flux is resolved out in our data. Considering the high sensitivity and resolution of our data, these results indicate that GMAs are not mere confusion with GMCs but plausibly smooth structures. In addition, we have found that the most massive clumps are located downstream of the spiral arm, which suggests that they are at a later stage of molecular cloud evolution across the arm and plausibly are cores of GMAs. By comparing with H{alpha} and Pa{alpha} images, most of these cores are found to have nearby star-forming regions. We thus propose an evolutionary scenario for the interstellar medium, in which smaller molecular clouds collide to form smooth GMAs at spiral arm regions and then star formation is triggered in the GMA cores. Our new CO data have revealed the internal structure of GMAs at GMC scales, finding the most massive substructures on the downstream side of the arm in close association with the brightest H II regions.

  14. Electrocatalytic hydrogen evolution in acidic water with molecular cobalt tetraazamacrocycles.

    PubMed

    McCrory, Charles C L; Uyeda, Christopher; Peters, Jonas C

    2012-02-15

    A series of water-soluble molecular cobalt complexes of tetraazamacrocyclic ligands are reported for the electrocatalytic production of H(2) from pH 2.2 aqueous solutions. The comparative data reported for this family of complexes shed light on their relative efficiencies for hydrogen evolution in water. Rotating disk electrode voltammetry data are presented for each of the complexes discussed, as are data concerning their respective pH-dependent electrocatalytic activity. In particular, two diimine-dioxime complexes were identified as exhibiting catalytic onset at comparatively low overpotentials relative to other reported homogeneous cobalt and nickel electrocatalysts in aqueous solution. These complexes are stable at pH 2.2 and produce hydrogen with high Faradaic efficiency in bulk electrolysis experiments over time intervals ranging from 2 to 24 h. PMID:22280515

  15. Application of Improved Grammatical Evolution to Santa Fe Trail Problems

    NASA Astrophysics Data System (ADS)

    Kuroda, Takuya; Iwasawa, Hiroto; Awgichew, Tewodros; Kita, Eisuke

    Grammatical Evolution (GE) is one of the evolutionary algorithms, which can deal with the rules with tree structure by one-dimensional chromosome. Syntax rules are defined in Backus Naur Form (BNF) to translate binary number (genotype) to function or program (phenotype). In this study, three algorithms are introduced for improving the convergence speed. First, an original GE are compared with Genetic Programming (GP) in the function identification problem. Next, the improved GE algorithms are applied to Santa Fe Trail problem. The results show that the improved schemes are effective for improving the convergence speed.

  16. Molecular Evolution and Structural Features of IRAK Family Members

    PubMed Central

    Gosu, Vijayakumar; Basith, Shaherin; Durai, Prasannavenkatesh; Choi, Sangdun

    2012-01-01

    The interleukin-1 receptor-associated kinase (IRAK) family comprises critical signaling mediators of the TLR/IL-1R signaling pathways. IRAKs are Ser/Thr kinases. There are 4 members in the vertebrate genome (IRAK1, IRAK2, IRAKM, and IRAK4) and an IRAK homolog, Pelle, in insects. IRAK family members are highly conserved in vertebrates, but the evolutionary relationship between IRAKs in vertebrates and insects is not clear. To investigate the evolutionary history and functional divergence of IRAK members, we performed extensive bioinformatics analysis. The phylogenetic relationship between IRAK sequences suggests that gene duplication events occurred in the evolutionary lineage, leading to early vertebrates. A comparative phylogenetic analysis with insect homologs of IRAKs suggests that the Tube protein is a homolog of IRAK4, unlike the anticipated protein, Pelle. Furthermore, the analysis supports that an IRAK4-like kinase is an ancestral protein in the metazoan lineage of the IRAK family. Through functional analysis, several potentially diverged sites were identified in the common death domain and kinase domain. These sites have been constrained during evolution by strong purifying selection, suggesting their functional importance within IRAKs. In summary, our study highlighted the molecular evolution of the IRAK family, predicted the amino acids that contributed to functional divergence, and identified structural variations among the IRAK paralogs that may provide a starting point for further experimental investigations. PMID:23166766

  17. Molecular Evolution of the Capsid Gene in Norovirus Genogroup I.

    PubMed

    Kobayashi, Miho; Yoshizumi, Shima; Kogawa, Sayaka; Takahashi, Tomoko; Ueki, Yo; Shinohara, Michiyo; Mizukoshi, Fuminori; Tsukagoshi, Hiroyuki; Sasaki, Yoshiko; Suzuki, Rieko; Shimizu, Hideaki; Iwakiri, Akira; Okabe, Nobuhiko; Shirabe, Komei; Shinomiya, Hiroto; Kozawa, Kunihisa; Kusunoki, Hideki; Ryo, Akihide; Kuroda, Makoto; Katayama, Kazuhiko; Kimura, Hirokazu

    2015-01-01

    We studied the molecular evolution of the capsid gene in all genotypes (genotypes 1-9) of human norovirus (NoV) genogroup I. The evolutionary time scale and rate were estimated by the Bayesian Markov chain Monte Carlo (MCMC) method. We also performed selective pressure analysis and B-cell linear epitope prediction in the deduced NoV GI capsid protein. Furthermore, we analysed the effective population size of the virus using Bayesian skyline plot (BSP) analysis. A phylogenetic tree by MCMC showed that NoV GI diverged from the common ancestor of NoV GII, GIII, and GIV approximately 2,800 years ago with rapid evolution (about 10(-3) substitutions/site/year). Some positive selection sites and over 400 negative selection sites were estimated in the deduced capsid protein. Many epitopes were estimated in the deduced virus capsid proteins. An epitope of GI.1 may be associated with histo-blood group antigen binding sites (Ser377, Pro378, and Ser380). Moreover, BSP suggested that the adaptation of NoV GI strains to humans was affected by natural selection. The results suggested that NoV GI strains evolved rapidly and date back to many years ago. Additionally, the virus may have undergone locally affected natural selection in the host resulting in its adaptation to humans. PMID:26338545

  18. Genetic Diversity and Molecular Evolution of Chinese Waxy Maize Germplasm

    PubMed Central

    Zheng, Hongjian; Wang, Hui; Yang, Hua; Wu, Jinhong; Shi, Biao; Cai, Run; Xu, Yunbi; Wu, Aizhong; Luo, Lijun

    2013-01-01

    Waxy maize (Zea mays L. var. certaina Kulesh), with many excellent characters in terms of starch composition and economic value, has grown in China for a long history and its production has increased dramatically in recent decades. However, the evolution and origin of waxy maize still remains unclear. We studied the genetic diversity of Chinese waxy maize including typical landraces and inbred lines by SSR analysis and the results showed a wide genetic diversity in the Chinese waxy maize germplasm. We analyzed the origin and evolution of waxy maize by sequencing 108 samples, and downloading 52 sequences from GenBank for the waxy locus in a number of accessions from genus Zea. A sharp reduction of nucleotide diversity and significant neutrality tests (Tajima’s D and Fu and Li’s F*) were observed at the waxy locus in Chinese waxy maize but not in nonglutinous maize. Phylogenetic analysis indicated that Chinese waxy maize originated from the cultivated flint maize and most of the modern waxy maize inbred lines showed a distinct independent origin and evolution process compared with the germplasm from Southwest China. The results indicated that an agronomic trait can be quickly improved to meet production demand by selection. PMID:23818949

  19. Sex speeds adaptation by altering the dynamics of molecular evolution.

    PubMed

    McDonald, Michael J; Rice, Daniel P; Desai, Michael M

    2016-03-10

    Sex and recombination are pervasive throughout nature despite their substantial costs. Understanding the evolutionary forces that maintain these phenomena is a central challenge in biology. One longstanding hypothesis argues that sex is beneficial because recombination speeds adaptation. Theory has proposed several distinct population genetic mechanisms that could underlie this advantage. For example, sex can promote the fixation of beneficial mutations either by alleviating interference competition (the Fisher-Muller effect) or by separating them from deleterious load (the ruby in the rubbish effect). Previous experiments confirm that sex can increase the rate of adaptation, but these studies did not observe the evolutionary dynamics that drive this effect at the genomic level. Here we present the first, to our knowledge, comparison between the sequence-level dynamics of adaptation in experimental sexual and asexual Saccharomyces cerevisiae populations, which allows us to identify the specific mechanisms by which sex speeds adaptation. We find that sex alters the molecular signatures of evolution by changing the spectrum of mutations that fix, and confirm theoretical predictions that it does so by alleviating clonal interference. We also show that substantially deleterious mutations hitchhike to fixation in adapting asexual populations. In contrast, recombination prevents such mutations from fixing. Our results demonstrate that sex both speeds adaptation and alters its molecular signature by allowing natural selection to more efficiently sort beneficial from deleterious mutations. PMID:26909573

  20. Evolution of Molecular Clouds in a Hot Plasma

    NASA Astrophysics Data System (ADS)

    Vieser, Wolfgang; Hensler, Gerhard

    We are performing 2D hydrodynamic simulations to examine the evaporation and condensation of molecular clouds in the hot phase of the interstellar medium due to heat conduction. Heat conduction is a process that may not be neglected for clouds which are embedded in a hot gas, High-Velocity-Clouds falling through the hot galactic halo or clouds in a galactic chimney. The evolution of cold and dense clouds with different masses and radii is calculated in the subsonic streaming of a hot rarefied plasma. Our code includes self-gravity, heating and cooling effects and heat conduction by electrons. Simulations with and without heat conduction show significant differences. Heat conduction provides a possibility to stabilize clouds agains hydrodynamic instabilities. Molecular clouds become able to survive significantly longer in a violent stream of hot gas. Additionally, this hot gas condensates onto the cloud's surface and is mixed very efficiently with the cloud material. Therefore, heat conduction is an important process, which has to be considered in order to explain the existence and metallicity of clouds in a stream of hot gas.

  1. Evolution of Molecular Alignment in a Background Plasma

    NASA Astrophysics Data System (ADS)

    Pearson, Andrew; Antonsen, Thomas

    2008-11-01

    We study numerically the behavior of rotational revivals in a molecular gas when subject to the fluctuating electric field of a background plasma. We model a molecule as a rigid rotor and couple it to an electric field using permanent and induced multipole interactions. The evolution of the density matrix for the molecule is calculated for a short, intense laser pulse, followed by a fluctuating electric field. A broad superposition of angular momentum eigenstates of a molecule is created by the laser field, and the result is a set of recurring peaks in the probability density for observing a particular orientation -- the so-called 'rotational revivals.' Experimentally, this effect is manifest as a variation in the refractive index of the gas [1]. The fluctuating field is created using the dressed particle method, and the result is a loss of coherence between the phases of the basis states of the molecule, which causes a decreasing amplitude for subsequent alignment peaks. Modern short-pulse lasers operate with sufficient intensity to make this effect relevant to experiments in molecular alignment. This work was supported by the Department of Energy.[1] Y.-H. Chen et. al., Optics Express Vol. 15, No. 18, 11341 (2007)

  2. The first molecular phylogeny of Strepsiptera (Insecta) reveals an early burst of molecular evolution correlated with the transition to endoparasitism.

    PubMed

    McMahon, Dino P; Hayward, Alexander; Kathirithamby, Jeyaraney

    2011-01-01

    A comprehensive model of evolution requires an understanding of the relationship between selection at the molecular and phenotypic level. We investigate this in Strepsiptera, an order of endoparasitic insects whose evolutionary biology is poorly studied. We present the first molecular phylogeny of Strepsiptera, and use this as a framework to investigate the association between parasitism and molecular evolution. We find evidence of a significant burst in the rate of molecular evolution in the early history of Strepsiptera. The evolution of morphological traits linked to parasitism is significantly correlated with the pattern in molecular rate. The correlated burst in genotypic-phenotypic evolution precedes the main phase of strepsipteran diversification, which is characterised by the return to a low and even molecular rate, and a period of relative morphological stability. These findings suggest that the transition to endoparasitism led to relaxation of selective constraint in the strepsipteran genome. Our results indicate that a parasitic lifestyle can affect the rate of molecular evolution, although other causal life-history traits correlated with parasitism may also play an important role. PMID:21738621

  3. Evolution of the atomic and molecular gas content of galaxies

    NASA Astrophysics Data System (ADS)

    Popping, Gergö; Somerville, Rachel S.; Trager, Scott C.

    2014-08-01

    We study the evolution of atomic and molecular gas in galaxies in semi-analytic models of galaxy formation that include new modelling of the partitioning of cold gas in galactic discs into atomic, molecular, and ionized phases. We adopt two scenarios for the formation of molecules: one pressure based and one metallicity based. We find that both recipes successfully reproduce the gas fractions and gas-to-stellar mass ratios of H I and H2 in local galaxies, as well as the H I and H2 disc sizes up to z ≤ 2. We reach good agreement with the locally observed H I and H2 mass function, although both recipes slightly overpredict the low-mass end of the H I mass function. Both of our models predict that the high-mass end of the H I mass function remains nearly constant at redshifts z < 2.0. The metallicity-based recipe yields a higher cosmic density of cold gas and much lower cosmic H2 fraction over the entire redshift range probed than the pressure-based recipe. These strong differences in H I mass function and cosmic density between the two recipes are driven by low-mass galaxies (log (M*/M⊙) ≤ 7) residing in low-mass haloes (log (Mvir/M⊙) ≤ 10). Both recipes predict that galaxy gas fractions remain high from z ˜ 6to3 and drop rapidly at lower redshift. The galaxy H2 fractions show a similar trend, but drop even more rapidly. We provide predictions for the CO J = 1-0 luminosity of galaxies, which will be directly comparable with observations with sub-mm and radio instruments.

  4. Molecular evolution of the MAGUK family in metazoan genomes

    PubMed Central

    te Velthuis, Aartjan JW; Admiraal, Jeroen F; Bagowski, Christoph P

    2007-01-01

    Background Development, differentiation and physiology of metazoans all depend on cell to cell communication and subsequent intracellular signal transduction. Often, these processes are orchestrated via sites of specialized cell-cell contact and involve receptors, adhesion molecules and scaffolding proteins. Several of these scaffolding proteins important for synaptic and cellular junctions belong to the large family of membrane-associated guanylate kinases (MAGUK). In order to elucidate the origin and the evolutionary history of the MAGUKs we investigated full-length cDNA, EST and genomic sequences of species in major phyla. Results Our results indicate that at least four of the seven MAGUK subfamilies were present in early metazoan lineages, such as Porifera. We employed domain sequence and structure based methods to infer a model for the evolutionary history of the MAGUKs. Notably, the phylogenetic trees for the guanylate kinase (GK)-, the PDZ- and the SH3-domains all suggested a matching evolutionary model which was further supported by molecular modeling of the 3D structures of different GK domains. We found no MAGUK in plants, fungi or other unicellular organisms, which suggests that the MAGUK core structure originated early in metazoan history. Conclusion In summary, we have characterized here the molecular and structural evolution of the large MAGUK family. Using the MAGUKs as an example, our results show that it is possible to derive a highly supported evolutionary model for important multidomain families by analyzing encoded protein domains. It further suggests that larger superfamilies encoded in the different genomes can be analyzed in a similar manner. PMID:17678554

  5. Chemical evolution of giant molecular clouds in simulations of galaxies

    NASA Astrophysics Data System (ADS)

    Richings, Alexander J.; Schaye, Joop

    2016-08-01

    We present an analysis of giant molecular clouds (GMCs) within hydrodynamic simulations of isolated, low-mass (M* ˜ 109 M⊙) disc galaxies. We study the evolution of molecular abundances and the implications for CO emission and the XCO conversion factor in individual clouds. We define clouds either as regions above a density threshold n_{H, min} = 10 {cm}^{-3}, or using an observationally motivated CO intensity threshold of 0.25 {K} {km} {s}^{-1}. Our simulations include a non-equilibrium chemical model with 157 species, including 20 molecules. We also investigate the effects of resolution and pressure floors (i.e. Jeans limiters). We find cloud lifetimes up to ≈ 40 Myr, with a median of 13 Myr, in agreement with observations. At one-tenth solar metallicity, young clouds ( ≲ 10-15 Myr) are underabundant in H2 and CO compared to chemical equilibrium, by factors of ≈3 and one to two orders of magnitude, respectively. At solar metallicity, GMCs reach chemical equilibrium faster (within ≈ 1 Myr). We also compute CO emission from individual clouds. The mean CO intensity, ICO, is strongly suppressed at low dust extinction, Av, and possibly saturates towards high Av, in agreement with observations. The ICO-Av relation shifts towards higher Av for higher metallicities and, to a lesser extent, for stronger UV radiation. At one-tenth solar metallicity, CO emission is weaker in young clouds ( ≲ 10-15 Myr), consistent with the underabundance of CO. Consequently, XCO decreases by an order of magnitude from 0 to 15 Myr, albeit with a large scatter.

  6. Chemical evolution of giant molecular clouds in simulations of galaxies

    NASA Astrophysics Data System (ADS)

    Richings, Alexander J.; Schaye, Joop

    2016-08-01

    We present an analysis of Giant Molecular Clouds (GMCs) within hydrodynamic simulations of isolated, low-mass (M* ~ 10^9 M_sol) disc galaxies. We study the evolution of molecular abundances and the implications for CO emission and the X_CO conversion factor in individual clouds. We define clouds either as regions above a density threshold n_H,min = 10 cm^-3, or using an observationally motivated CO intensity threshold of 0.25 K km s^-1. Our simulations include a non-equilibrium chemical model with 157 species, including 20 molecules. We also investigate the effects of resolution and pressure floors (i.e. Jeans limiters). We find cloud lifetimes up to ~40 Myr, with a median of 13 Myr, in agreement with observations. At one tenth solar metallicity, young clouds (<10-15 Myr) are underabundant in H2 and CO compared to chemical equilibrium, by factors of ~3 and 1-2 orders of magnitude, respectively. At solar metallicity, GMCs reach chemical equilibrium faster (within ~1 Myr). We also compute CO emission from individual clouds. The mean CO intensity, I_CO, is strongly suppressed at low dust extinction, A_v, and possibly saturates towards high A_v, in agreement with observations. The I_CO - A_v relation shifts towards higher A_v for higher metallicities and, to a lesser extent, for stronger UV radiation. At one tenth solar metallicity, CO emission is weaker in young clouds (<10-15 Myr), consistent with the underabundance of CO. Consequently, X_CO decreases by an order of magnitude from 0 to 15 Myr, albeit with a large scatter.

  7. The Structure and Evolution of Self-Gravitating Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Holliman, John Herbert, II

    1995-01-01

    We present a theoretical formalism to evaluate the structure of molecular clouds and to determine precollapse conditions in star-forming regions. Models consist of pressure-bounded, self-gravitating spheres of a single -fluid ideal gas. We treat the case without rotation. The analysis is generalized to consider states in hydrostatic equilibrium maintained by multiple pressure components. Individual pressures vary with density as P_i(r) ~ rho^{gamma {rm p},i}(r), where gamma_{rm p},i is the polytropic index. Evolution depends additionally on whether conduction occurs on a dynamical time scale and on the adiabatic index gammai of each component, which is modified to account for the effects of any thermal coupling to the environment of the cloud. Special attention is given to properly representing the major contributors to dynamical support in molecular clouds: the pressures due to static magnetic fields, Alfven waves, and thermal motions. Straightforward adjustments to the model allow us to treat the intrinsically anisotropic support provided by the static fields. We derive structure equations, as well as perturbation equations for performing a linear stability analysis. The analysis provides insight on the nature of dynamical motions due to collapse from an equilibrium state and estimates the mass of condensed objects that form in such a process. After presenting a set of general results, we describe models of star-forming regions that include the major pressure components. We parameterize the extent of ambipolar diffusion. The analysis contributes to the physical understanding of several key results from observations of these regions. Commonly observed quantities are explicitly cross-referenced with model results. We theoretically determine density and linewidth profiles on scales ranging from that of molecular cloud cores to that of giant molecular clouds (GMCs). The model offers an explanation of the mean pressures in GMCs, which are observed to be high relative

  8. galaxy formation and evolution with an improved SPH code

    NASA Astrophysics Data System (ADS)

    Zhu, Qirong; Li, Y.

    2014-01-01

    We present the results with an updated version of Gadget-3. Our improvements over the original version include both modifications on SPH algorithms and physical processes relevant to galaxy formation and evolution. A smoother kernel is used to reduce the noise of force calculation. Discontinuities and sub-sonic turbulence are treated with a time dependent conduction term and a time dependent viscosity term. The new code successfully handles the KH/RT instabilities. A new set of metal dependent cooling/heating functions is computed self-consistently to account for the ionizing UV background from galaxies and QSOs. Meanwhile we also updated the star formation model and black hole accretion model. With all of these improvement, our code can produce more realistic disk galaxies compared to previous work. Future simulations with this new code will give us more reliable results and enable us to better understand galaxy formation and evolution in greater detail and accuracy.

  9. Improved Differential Evolution for Combined Heat and Power Economic Dispatch

    NASA Astrophysics Data System (ADS)

    Jena, C.; Basu, M.; Panigrahi, C. K.

    2016-04-01

    This paper presents an improved differential evolution to solve non-smooth non-convex combined heat and power economic dispatch (CHPED) problem. Valve-point loading and prohibited operating zones of conventional thermal generators are taken into account. Differential evolution (DE) exploits the differences of randomly sampled pairs of objective vectors for its mutation process. Consequently the variation between vectors will outfit the objective function toward the optimization process and therefore provides efficient global optimization capability. However, although DE is shown to be precise, fast as well as robust, its search efficiency will be impaired during solution process with fast descending diversity of population. This paper proposes Gaussian random variable instead of scaling factor which improves search efficiency. The effectiveness of the proposed method has been verified on four test systems. The results of the proposed approach are compared with those obtained by other evolutionary methods. It is found that the proposed improved differential evolution based approach is able to provide better solution.

  10. Molecular mechanisms of cobalt-catalyzed hydrogen evolution

    PubMed Central

    Marinescu, Smaranda C.; Winkler, Jay R.; Gray, Harry B.

    2012-01-01

    Several cobalt complexes catalyze the evolution of hydrogen from acidic solutions, both homogeneously and at electrodes. The detailed molecular mechanisms of these transformations remain unresolved, largely owing to the fact that key reactive intermediates have eluded detection. One method of stabilizing reactive intermediates involves minimizing the overall reaction free-energy change. Here, we report a new cobalt(I) complex that reacts with tosylic acid to evolve hydrogen with a driving force of just 30 meV/Co. Protonation of CoI produces a transient CoIII-H complex that was characterized by nuclear magnetic resonance spectroscopy. The CoIII-H intermediate decays by second-order kinetics with an inverse dependence on acid concentration. Analysis of the kinetics suggests that CoIII-H produces hydrogen by two competing pathways: a slower homolytic route involving two CoIII-H species and a dominant heterolytic channel in which a highly reactive CoII-H transient is generated by CoI reduction of CoIII-H. PMID:22949704

  11. Dynamical Evolution of Supernova Remnants Breaking Through Molecular Clouds

    NASA Astrophysics Data System (ADS)

    Cho, Wankee; Kim, Jongsoo; Koo, Bon-Chul

    2015-04-01

    We carry out three-dimensional hydrodynamic simulations of the supernova remnants (SNRs) produced inside molecular clouds (MCs) near their surface using the HLL code tep{har83}. We explore the dynamical evolution and the X-ray morphology of SNRs after breaking through the MC surface for ranges of the explosion depths below the surface and the density ratios of the clouds to the intercloud media (ICM). We find that if an SNR breaks out through an MC surface in its Sedov stage, the outermost dense shell of the remnant is divided into several layers. The divided layers are subject to the Rayleigh-Taylor instability and fragmented. On the other hand, if an SNR breaks through an MC after the remnant enters the snowplow phase, the radiative shell is not divided to layers. We also compare the predictions of previous analytic solutions for the expansion of SNRs in stratified media with our one-dimensional simulations. Moreover, we produce synthetic X-ray surface brightness in order to research the center-bright X-ray morphology shown in thermal composite SNRs. In the late stages, a breakout SNR shows the center-bright X-ray morphology inside an MC in our results. We apply our model to the observational results of the X-ray morphology of the thermal composite SNR 3C 391.

  12. Modification of pancreatic lipase properties by directed molecular evolution.

    PubMed

    Colin, Damien Yann; Deprez-Beauclair, Paule; Silva, Noella; Infantes, Lourdes; Kerfelec, Brigitte

    2010-05-01

    Cystic fibrosis is associated with pancreatic insufficiency and acidic intraluminal conditions that limit the action of pancreatic enzyme replacement therapy, especially that of lipase. Directed evolution combined with rational design was used in the aim of improving the performances of the human pancreatic lipase at acidic pH. We set up a method for screening thousands of lipase variants for activity at low pH. A single round of random mutagenesis yielded one lipase variant with an activity at acidic pH enhanced by approximately 50% on medium- and long-chain triglycerides. Sequence analysis revealed two substitutions (E179G/N406S) located in specific regions, the hydrophobic groove accommodating the sn-1 chain of the triglyceride (E179G) and the surface loop that is likely to mediate lipase/colipase interaction in the presence of lipids (N406S). Interestingly, these two substitutions shifted the chain-length specificity of lipase toward medium- and long-chain triglycerides. Combination of those two mutations with a promising one at the entrance of the catalytic cavity (K80E) negatively affected the lipase activity at neutral pH but not that at acidic pH. Our results provide a basis for the design of improved lipase at acidic pH and identify for the first time key residues associated with chain-length specificity. PMID:20150178

  13. Improved molecular barcodes by lifetime discrimination

    NASA Astrophysics Data System (ADS)

    Hall, Daniel B.; Lawrence, William G.

    2009-02-01

    Individual microspheres labeled with a unique barcode and a surface-bound probe are able to provide multiplexed biological assays in a convenient and high-throughput format. Typically, barcodes are created by impregnating microspheres with several colors of fluorophores mixed at different intensity levels. The number of barcodes is limited to hundreds primarily due to variability in fluorophore loading and difficulties in compensating for signal crosstalk. We constructed a molecular barcode based on differences in lifetimes rather than intensities. Lifetime-based measurements have an advantage in that signal from neighboring channels is reduced (because signal intensities are equal) and may be mathematically deconvoluted. The excited state lifetime of quantum dots (QDs) was systematically altered by attaching a variable number of quencher molecules to the surface. We have synthesized a series of ten QDs with distinguishable lifetimes all emitting at the same wavelength. The QDs were loaded into microspheres to determine the expected signal intensities. The uncertainty in lifetimes as a function of the interrogation time was determined. An acceptable standard deviation (3%) was obtained with a measurement time of approximately 10-30 μsec. Currently, we are expanding these studies to include multiple wavelengths and determining the maximal number of barcodes for a given spectral window.

  14. Molecular Imaging and Contrast Agent Database (MICAD): Evolution and Progress

    PubMed Central

    Chopra, Arvind; Shan, Liang; Eckelman, W. C.; Leung, Kam; Latterner, Martin; Bryant, Stephen H.; Menkens, Anne

    2011-01-01

    The purpose of writing this review is to showcase the Molecular Imaging and Contrast Agent Database (MICAD; www.micad.nlm.nih.gov) to students, researchers and clinical investigators interested in the different aspects of molecular imaging. This database provides freely accessible, current, online scientific information regarding molecular imaging (MI) probes and contrast agents (CA) used for positron emission tomography, single-photon emission computed tomography, magnetic resonance imaging, x-ray/computed tomography, optical imaging and ultrasound imaging. Detailed information on >1000 agents in MICAD is provided in a chapter format and can be accessed through PubMed. Lists containing >4250 unique MI probes and CAs published in peer-reviewed journals and agents approved by the United States Food and Drug Administration (FDA) as well as a CSV file summarizing all chapters in the database can be downloaded from the MICAD homepage. Users can search for agents in MICAD on the basis of imaging modality, source of signal/contrast, agent or target category, preclinical or clinical studies, and text words. Chapters in MICAD describe the chemical characteristics (structures linked to PubChem), the in vitro and in vivo activities and other relevant information regarding an imaging agent. All references in the chapters have links to PubMed. A Supplemental Information Section in each chapter is available to share unpublished information regarding an agent. A Guest Author Program is available to facilitate rapid expansion of the database. Members of the imaging community registered with MICAD periodically receive an e-mail announcement (eAnnouncement) that lists new chapters uploaded to the database. Users of MICAD are encouraged to provide feedback, comments or suggestions for further improvement of the database by writing to the editors at: micad@nlm.nih.gov PMID:21989943

  15. Multiple cellular origins and molecular evolution of intrahepatic cholangiocarcinoma.

    PubMed

    Wei, Miaoyan; Lü, Lisheng; Lin, Peiyi; Chen, Zhisheng; Quan, Zhiwei; Tang, Zhaohui

    2016-09-01

    Intrahepatic cholangiocarcinoma (ICC) is an aggressive malignancy associated with unfavorable prognosis and for which no effective treatments are available. Its molecular pathogenesis is poorly understood. Genome-wide sequencing and high-throughput technologies have provided critical insights into the molecular basis of ICC while sparking a heated debate on the cellular origin. Cancer exhibits variabilities in origin, progression and cell biology. Recent evidence suggests that ICC has multiple cellular origins, including differentiated hepatocytes; intrahepatic biliary epithelial cells (IBECs)/cholangiocytes; pluripotent stem cells, such as hepatic stem/progenitor cells (HPCs) and biliary tree stem/progenitor cells (BTSCs); and peribiliary gland (PBG). However, both somatic mutagenesis and epigenomic features are highly cell type-specific. Multiple cellular origins may have profoundly different genomic landscapes and key signaling pathways, driving phenotypic variation and thereby posing significant challenges to personalized medicine in terms of achieving the optimal drug response and patient outcome. Considering this information, we have summarized the latest experimental evidence and relevant literature to provide an up-to-date view of the cellular origin of ICC, which will contribute to establishment of a hierarchical model of carcinogenesis and allow for improvement of the anatomical-based classification of ICC. These new insights have important implications for both the diagnosis and treatment of ICC patients. PMID:26940139

  16. Decoding the molecular evolution of human cognition using comparative genomics

    PubMed Central

    Usui, Noriyoshi; Co, Marissa; Konopka, Genevieve

    2014-01-01

    Identification of genetic and molecular factors responsible for the specialized cognitive abilities of humans is expected to provide important insights into the mechanisms responsible for disorders of cognition such as autism, schizophrenia, and Alzheimer’s disease. Here, we discuss the use of comparative genomics for identifying salient genes and gene networks that may underlie cognition. We focus on the comparison of human and non-human primate brain gene expression and the utility of building gene co-expression networks for prioritizing hundreds of genes that differ in expression among the species queried. We also discuss the importance and methods for functional studies of individual genes identified. Together, this integration of comparative genomics with cellular and animal models should provide improved systems for developing effective therapeutics for disorders of cognition. PMID:25247723

  17. Molecular evolution of SRP cycle components: functional implications.

    PubMed Central

    Althoff, S; Selinger, D; Wise, J A

    1994-01-01

    Signal recognition particle (SRP) is a cytoplasmic ribonucleoprotein that targets a subset of nascent presecretory proteins to the endoplasmic reticulum membrane. We have considered the SRP cycle from the perspective of molecular evolution, using recently determined sequences of genes or cDNAs encoding homologs of SRP (7SL) RNA, the Srp54 protein (Srp54p), and the alpha subunit of the SRP receptor (SR alpha) from a broad spectrum of organisms, together with the remaining five polypeptides of mammalian SRP. Our analysis provides insight into the significance of structural variation in SRP RNA and identifies novel conserved motifs in protein components of this pathway. The lack of congruence between an established phylogenetic tree and size variation in 7SL homologs implies the occurrence of several independent events that eliminated more than half the sequence content of this RNA during bacterial evolution. The apparently non-essential structures are domain I, a tRNA-like element that is constant in archaea, varies in size among eucaryotes, and is generally missing in bacteria, and domain III, a tightly base-paired hairpin that is present in all eucaryotic and archeal SRP RNAs but is invariably absent in bacteria. Based on both structural and functional considerations, we propose that the conserved core of SRP consists minimally of the 54 kDa signal sequence-binding protein complexed with the loosely base-paired domain IV helix of SRP RNA, and is also likely to contain a homolog of the Srp68 protein. Comparative sequence analysis of the methionine-rich M domains from a diverse array of Srp54p homologs reveals an extended region of amino acid identity that resembles a recently identified RNA recognition motif. Multiple sequence alignment of the G domains of Srp54p and SR alpha homologs indicates that these two polypeptides exhibit significant similarity even outside the four GTPase consensus motifs, including a block of nine contiguous amino acids in a location

  18. MOLECULAR CLOUD EVOLUTION. III. ACCRETION VERSUS STELLAR FEEDBACK

    SciTech Connect

    Vazquez-Semadeni, Enrique; ColIn, Pedro; Gomez, Gilberto C.; Ballesteros-Paredes, Javier; Watson, Alan W. E-mail: p.colin@crya.unam.m E-mail: alan@astro.unam.m

    2010-06-01

    We numerically investigate the effect of feedback from the ionization heating from massive stars on the evolution of giant molecular clouds (GMCs) and their star formation efficiency (SFE), which we treat as an instantaneous, time-dependent quantity. We follow the GMCs' evolution from their formation to advanced star-forming stages. After an initial period of contraction, the collapsing clouds begin forming stars, whose feedback evaporates part of the clouds' mass, opposing the continuing accretion from the infalling gas. Our results are as follows: (1) in the presence of feedback, the clouds attain levels of the SFE that are consistent at all times with observational determinations for regions of comparable star formation rates. (2) However, the dense gas mass is larger in general in the presence of feedback, while the total mass (dense gas + stars) is nearly insensitive to the presence of feedback, suggesting that it is determined mainly by the accretion, while the feedback inhibits mainly the conversion of dense gas to stars, because it acts directly to reheat and disperse the gas that is directly on its way to forming stars. (3) The factor by which the SFE is reduced upon the inclusion of feedback is a decreasing function of the cloud's mass, for clouds of size {approx}10 pc. This naturally explains the larger observed SFEs of massive-star-forming regions. (4) The clouds may attain a pseudo-virialized state, with a value of the virial mass very similar to the actual cloud mass. However, this state differs from true virialization in that the clouds, rather than being equilibrium entities, are the centers of a larger-scale collapse, in which accretion replenishes the mass consumed by star formation. (5) The higher-density regions within the clouds are in a similar situation, accreting gas infalling from the less-dense, more extended regions of the clouds. (6) The density probability density functions of the regions containing the clouds in general exhibit a shape

  19. Morphology Evolution of Molecular Weight Dependent P3HT: PCBM Solar Cells

    NASA Astrophysics Data System (ADS)

    Liu, Feng; Chen, Dian; Briseno, Alejandro; Russell, Thomas

    2011-03-01

    Effective strategies to maximize the performance of bulk heterojunction (BHJ) photovoltaic devices have to be developed and understood to realize their full potential. In BHJ solar cells, the morphology of the active layer is a critical issue to improve device efficiency. In this work, we choose poly(3-hexyl-thiophene) (P3HT) and phenyl-C61-butyric acid methyl ester (PCBM) system to study the morphology evolution. Different molecular weight P3HTs were synthesized by using Grignard Metathesis (GRIM)~method. In device optimization, polymer with a molecular weight between 20k-30k shows the highest efficiency. It was observed that the as-spun P3HT: PCBM (1:1) blends do not have high order by GISAXS. Within a few seconds of thermal annealing at 150& circ; the crystallinity of P3HT increaased substantially and the polymer chains adopted an edge-on orientation. An-bicontinous morphology was also developed within this short thermal treatment. The in situ GISAXS experiment showed that P3HT of high molecular weight was more easily crystallized from a slowly evaporated chlorobenzene solution and their edge-on orientation is much more obvious than for the lower molecular weight P3HTs. DSC was used to study the thermal properties of P3HTs and P3HT: PCBM blend. The χ of P3HT-PCBM was also calculated by using melting point depression method.

  20. An improved molecular assay for Tritrichomonas foetus.

    PubMed

    Grahn, R A; BonDurant, R H; van Hoosear, K A; Walker, R L; Lyons, L A

    2005-01-01

    Tritrichomonas foetus (T. foetus) is the causative agent of bovine trichomonosis, a sexually transmitted disease leading to abortion (from 1 to 8 months gestation), infertility, and occasional pyometra. The annual losses to the U.S. beef industry are estimated to be in the hundreds of millions of dollars. Currently, the "gold standard" diagnostic test for trichomonosis in most countries is the cultivation of live organisms from reproductive secretions. The cultured organisms can then be followed by PCR assays with primers that amplify T. foetus to the exclusion of all other trichomonad species. Thus, negative results present as null data, indistinguishable from failed PCR amplification during T. foetus specific amplification. Our newly developed assay improves previously developed PCR based techniques by using diagnostic size variants from within the internal transcribed spacer 1 (ITS1) region that is between the 18S rRNA and 5.8S rRNA subunits. This new PCR assay amplifies trichomonad DNA from a variety of genera and positively identifies the causative agent in the bovine trichomonad infection. This approach eliminates false negatives found in some current assays as well as identifying the causative agent of trichomonad infection. Additionally, our assay incorporates a fluorescently labeled primer enabling high sensitivity and rapid assessment of the specific trichomonad species. Moreover, electrophoretic separation of amplified samples can be outsourced, thus eliminating the need for diagnostic laboratories to purchase expensive analysis equipment. PMID:15619373

  1. Molecular Specificity, Convergence and Constraint Shape Adaptive Evolution in Nutrient-Poor Environments

    PubMed Central

    Hong, Jungeui; Gresham, David

    2014-01-01

    One of the central goals of evolutionary biology is to explain and predict the molecular basis of adaptive evolution. We studied the evolution of genetic networks in Saccharomyces cerevisiae (budding yeast) populations propagated for more than 200 generations in different nitrogen-limiting conditions. We find that rapid adaptive evolution in nitrogen-poor environments is dominated by the de novo generation and selection of copy number variants (CNVs), a large fraction of which contain genes encoding specific nitrogen transporters including PUT4, DUR3 and DAL4. The large fitness increases associated with these alleles limits the genetic heterogeneity of adapting populations even in environments with multiple nitrogen sources. Complete identification of acquired point mutations, in individual lineages and entire populations, identified heterogeneity at the level of genetic loci but common themes at the level of functional modules, including genes controlling phosphatidylinositol-3-phosphate metabolism and vacuole biogenesis. Adaptive strategies shared with other nutrient-limited environments point to selection of genetic variation in the TORC1 and Ras/PKA signaling pathways as a general mechanism underlying improved growth in nutrient-limited environments. Within a single population we observed the repeated independent selection of a multi-locus genotype, comprised of the functionally related genes GAT1, MEP2 and LST4. By studying the fitness of individual alleles, and their combination, as well as the evolutionary history of the evolving population, we find that the order in which these mutations are acquired is constrained by epistasis. The identification of repeatedly selected variation at functionally related loci that interact epistatically suggests that gene network polymorphisms (GNPs) may be a frequent outcome of adaptive evolution. Our results provide insight into the mechanistic basis by which cells adapt to nutrient-limited environments and suggest that

  2. Patterns of molecular evolution of RNAi genes in social and socially parasitic bumblebees.

    PubMed

    Helbing, Sophie; Lattorff, H Michael G

    2016-08-01

    The high frequency of interactions amongst closely related individuals in social insect colonies enhances pathogen transmission. Group-mediated behavior supporting immune defenses tends to decrease selection acting on immune genes. Along with low effective population sizes this might result in relaxed constraint and rapid evolution of immune system genes. Here, we show that antiviral siRNA genes show high rates of molecular evolution with argonaute 2, armitage and maelstrom evolving faster in social bumblebees compared to their socially parasitic cuckoo bumblebees that lack a worker caste. RNAi genes show frequent positive selection at the codon level additionally supported by the occurrence of parallel evolution. Their evolutionary rate is linked to their pathway specific position with genes directly interacting with viruses showing the highest rates of molecular evolution. We suggest that higher pathogen load in social insects indeed drives the molecular evolution of immune genes including antiviral siRNA, if not compensated by behavior. PMID:27117935

  3. A molecular description of the evolution of resistance

    NASA Technical Reports Server (NTRS)

    Ordoukhanian, P.; Joyce, G. F.

    1999-01-01

    BACKGROUND: In vitro evolution has been used to obtain nucleic acid molecules with interesting functional properties. The evolution process usually is carried out in a stepwise manner, involving successive rounds of selection, amplification and mutation. Recently, a continuous in vitro evolution system was devised for RNAs that catalyze the ligation of oligonucleotide substrates, allowing the evolution of catalytic function to be studied in real time. RESULTS: Continuous in vitro evolution of an RNA ligase ribozyme was carried out in the presence of a DNA enzyme that was capable of cleaving, and thereby inactivating, the ribozyme. The DNA concentration was increased steadily over 33.5 hours of evolution, reaching a final concentration that would have been sufficient to inactivate the starting population in one second. The evolved population of ribozymes developed resistance to the DNA enzyme, reducing their vulnerability to cleavage by 2000-fold but retaining their own catalytic function. Based on sequencing and kinetic analysis of the ribozymes, two mechanisms are proposed for this resistance. One involves three nucleotide substitutions, together with two compensatory mutations, that alter the site at which the DNA enzyme binds the ribozyme. The other involves enhancement of the ribozyme's ability to bind its own substrate in a way that protects it from cleavage by the DNA enzyme. CONCLUSIONS: The ability to direct the evolution of an enzyme's biochemical properties in response to the behavior of another macromolecule provides insight into the evolution of resistance and may be useful in developing enzymes with novel or enhanced function.

  4. Improved Precursor Directed Biosynthesis in E. coli via Directed Evolution

    PubMed Central

    Lee, Ho Young; Harvey, Colin J.B.; Cane, David E.; Khosla, Chaitan

    2010-01-01

    Erythromycin and related macrolide antibiotics are widely used polyketide natural products. We have evolved an engineered biosynthetic pathway in Escherichia coli that yields erythromycin analogs from simple synthetic precursors. Multiple rounds of mutagenesis and screening led to the identification of new mutant strains with improved efficiency for precursor directed biosynthesis. Genetic and biochemical analysis suggested that the phenotypically relevant alterations in these mutant strains were localized exclusively to the host-vector system, and not to the polyketide synthase. We also demonstrate the utility of this improved system through engineered biosynthesis of a novel alkynyl erythromycin derivative with comparable antibacterial activity to its natural counterpart. In addition to reinforcing the power of directed evolution for engineering macrolide biosynthesis, our studies have identified a new lead substance for investigating structure-function relationships in the bacterial ribosome. PMID:21081955

  5. Molecular diversity and functional evolution of scorpion potassium channel toxins.

    PubMed

    Zhu, Shunyi; Peigneur, Steve; Gao, Bin; Luo, Lan; Jin, Di; Zhao, Yong; Tytgat, Jan

    2011-02-01

    Scorpion toxins affecting K(+) channels (KTxs) represent important pharmacological tools and potential drug candidates. Here, we report molecular characterization of seven new KTxs in the scorpion Mesobuthus eupeus by cDNA cloning combined with biochemical approaches. Comparative modeling supports that all these KTxs share a conserved cysteine-stabilized α-helix/β-sheet structural motif despite the differences in protein sequence and size. We investigated functional diversification of two orthologous α-KTxs (MeuTXKα1 from M. eupeus and BmP01 from Mesobuthus martensii) by comparing their K(+) channel-blocking activities. Pharmacologically, MeuTXKα1 selectively blocked Kv1.3 channel with nanomolar affinity (IC(50), 2.36 ± 0.9 nM), whereas only 35% of Kv1.1 currents were inhibited at 3 μM concentration, showing more than 1271-fold selectivity for Kv1.3 over Kv1.1. This peptide displayed a weak effect on Drosophila Shaker channel and no activity on Kv1.2, Kv1.4, Kv1.5, Kv1.6, and human ether-a-go-go-related gene (hERG) K(+) channels. Although BmB01 and MeuTXKα1 have a similar channel spectrum, their affinity and selectivity for these channels largely varies. In comparison with MeuTXKα1, BmP01 only exhibits a submicromolar affinity (IC(50), 133.72 ± 10.98 nM) for Kv1.3, showing 57-fold less activity than MeuTXKα1. Moreover, it lacks the ability to distinguish between Kv1.1 and Kv1.3. We also found that MeuTXKα1 inhibited the proliferation of activated T cells induced by phorbol myristate acetate and ionomycin at micromolar concentrations. Our results demonstrate that accelerated evolution drives affinity variations of orthologous α-KTxs on Kv channels and indicate that MeuTXKα1 is a promising candidate to develop an immune modulation agent for human autoimmune diseases. PMID:20889474

  6. DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution.

    PubMed

    Xia, Xuhua

    2013-07-01

    Since its first release in 2001 as mainly a software package for phylogenetic analysis, data analysis for molecular biology and evolution (DAMBE) has gained many new functions that may be classified into six categories: 1) sequence retrieval, editing, manipulation, and conversion among more than 20 standard sequence formats including MEGA, NEXUS, PHYLIP, GenBank, and the new NeXML format for interoperability, 2) motif characterization and discovery functions such as position weight matrix and Gibbs sampler, 3) descriptive genomic analysis tools with improved versions of codon adaptation index, effective number of codons, protein isoelectric point profiling, RNA and protein secondary structure prediction and calculation of minimum folding energy, and genomic skew plots with optimized window size, 4) molecular phylogenetics including sequence alignment, testing substitution saturation, distance-based, maximum parsimony, and maximum-likelihood methods for tree reconstructions, testing the molecular clock hypothesis with either a phylogeny or with relative-rate tests, dating gene duplication and speciation events, choosing the best-fit substitution models, and estimating rate heterogeneity over sites, 5) phylogeny-based comparative methods for continuous and discrete variables, and 6) graphic functions including secondary structure display, optimized skew plot, hydrophobicity plot, and many other plots of amino acid properties along a protein sequence, tree display and drawing by dragging nodes to each other, and visual searching of the maximum parsimony tree. DAMBE features a graphic, user-friendly, and intuitive interface and is freely available from http://dambe.bio.uottawa.ca (last accessed April 16, 2013). PMID:23564938

  7. Molecular co-catalyst accelerating hole transfer for enhanced photocatalytic H2 evolution

    PubMed Central

    Bi, Wentuan; Li, Xiaogang; Zhang, Lei; Jin, Tao; Zhang, Lidong; Zhang, Qun; Luo, Yi; Wu, Changzheng; Xie, Yi

    2015-01-01

    In artificial photocatalysis, sluggish kinetics of hole transfer and the resulting high-charge recombination rate have been the Achilles' heel of photocatalytic conversion efficiency. Here we demonstrate water-soluble molecules as co-catalysts to accelerate hole transfer for improved photocatalytic H2 evolution activity. Trifluoroacetic acid (TFA), by virtue of its reversible redox couple TFA·/TFA−, serves as a homogeneous co-catalyst that not only maximizes the contact areas between co-catalysts and reactants but also greatly promotes hole transfer. Thus K4Nb6O17 nanosheet catalysts achieve drastically increased photocatalytic H2 production rate in the presence of TFA, up to 32 times with respect to the blank experiment. The molecular co-catalyst represents a new, simple and highly effective approach to suppress recombination of photogenerated charges, and has provided fertile new ground for creating high-efficiency photosynthesis systems, avoiding use of noble-metal co-catalysts. PMID:26486863

  8. Molecular co-catalyst accelerating hole transfer for enhanced photocatalytic H2 evolution

    NASA Astrophysics Data System (ADS)

    Bi, Wentuan; Li, Xiaogang; Zhang, Lei; Jin, Tao; Zhang, Lidong; Zhang, Qun; Luo, Yi; Wu, Changzheng; Xie, Yi

    2015-10-01

    In artificial photocatalysis, sluggish kinetics of hole transfer and the resulting high-charge recombination rate have been the Achilles' heel of photocatalytic conversion efficiency. Here we demonstrate water-soluble molecules as co-catalysts to accelerate hole transfer for improved photocatalytic H2 evolution activity. Trifluoroacetic acid (TFA), by virtue of its reversible redox couple TFA./TFA-, serves as a homogeneous co-catalyst that not only maximizes the contact areas between co-catalysts and reactants but also greatly promotes hole transfer. Thus K4Nb6O17 nanosheet catalysts achieve drastically increased photocatalytic H2 production rate in the presence of TFA, up to 32 times with respect to the blank experiment. The molecular co-catalyst represents a new, simple and highly effective approach to suppress recombination of photogenerated charges, and has provided fertile new ground for creating high-efficiency photosynthesis systems, avoiding use of noble-metal co-catalysts.

  9. The Eyes Have It: A Problem-Based Learning Exercise in Molecular Evolution

    ERIC Educational Resources Information Center

    White, Harold B.

    2007-01-01

    Molecular evolution provides an interesting context in which to use problem-based learning because it integrates a variety of topics in biology, biochemistry, and molecular biology. This three-stage problem for advanced students deals with the structure, multiple functions, and properties of lactate dehydrogenase isozymes, and the related…

  10. Molecular activities, biosynthesis and evolution of triterpenoid saponins.

    PubMed

    Augustin, Jörg M; Kuzina, Vera; Andersen, Sven B; Bak, Søren

    2011-04-01

    Saponins are bioactive compounds generally considered to be produced by plants to counteract pathogens and herbivores. Besides their role in plant defense, saponins are of growing interest for drug research as they are active constituents of several folk medicines and provide valuable pharmacological properties. Accordingly, much effort has been put into unraveling the modes of action of saponins, as well as in exploration of their potential for industrial processes and pharmacology. However, the exploitation of saponins for bioengineering crop plants with improved resistances against pests as well as circumvention of laborious and uneconomical extraction procedures for industrial production from plants is hampered by the lack of knowledge and availability of genes in saponin biosynthesis. Although the ability to produce saponins is rather widespread among plants, a complete synthetic pathway has not been elucidated in any single species. Current conceptions consider saponins to be derived from intermediates of the phytosterol pathway, and predominantly enzymes belonging to the multigene families of oxidosqualene cyclases (OSCs), cytochromes P450 (P450s) and family 1 UDP-glycosyltransferases (UGTs) are thought to be involved in their biosynthesis. Formation of unique structural features involves additional biosynthetical enzymes of diverse phylogenetic background. As an example of this, a serine carboxypeptidase-like acyltransferase (SCPL) was recently found to be involved in synthesis of triterpenoid saponins in oats. However, the total number of identified genes in saponin biosynthesis remains low as the complexity and diversity of these multigene families impede gene discovery based on sequence analysis and phylogeny. This review summarizes current knowledge of triterpenoid saponin biosynthesis in plants, molecular activities, evolutionary aspects and perspectives for further gene discovery. PMID:21333312

  11. The Evolution and Origin of Animal Toll-Like Receptor Signaling Pathway Revealed by Network-Level Molecular Evolutionary Analyses

    PubMed Central

    Qin, Sheng; Chen, Liming; Ma, Fei

    2012-01-01

    Genes carry out their biological functions through pathways in complex networks consisting of many interacting molecules. Studies on the effect of network architecture on the evolution of individual proteins will provide valuable information for understanding the origin and evolution as well as functional conservation of signaling pathways. However, the relationship between the network architecture and the individual protein sequence evolution is yet little known. In current study, we carried out network-level molecular evolution analysis on TLR (Toll-like receptor ) signaling pathway, which plays an important role in innate immunity in insects and mammals, and we found that: 1) The selection constraint of genes was negatively correlated with its position along TLR signaling pathway; 2) all genes in TLR signaling pathway were highly conserved and underwent strong purifying selection; 3) the distribution of selective pressure along the pathway was driven by differential nonsynonymous substitution levels; 4) The TLR signaling pathway might present in a common ancestor of sponges and eumetazoa, and evolve via the TLR, IKK, IκB and NF-κB genes underwent duplication events as well as adaptor molecular enlargement, and gene structure and conservation motif of NF-κB genes shifted in their evolutionary history. Our results will improve our understanding on the evolutionary history of animal TLR signaling pathway as well as the relationship between the network architecture and the sequences evolution of individual protein. PMID:23236523

  12. Evolution of cyanobacterial morphotypes: Taxa required for improved phylogenomic approaches.

    PubMed

    Schirrmeister, Bettina E; Anisimova, Maria; Antonelli, Alexandre; Bagheri, Homayoun C

    2011-07-01

    Within prokaryotes cyanobacteria represent one of the oldest and morphologically most diverse phyla on Earth. The rise of oxygen levels in the atmosphere 2.32-2.45 billion years ago is assigned to the photosynthetic activity of ancestors from this phylum. Subsequently cyanobacteria were able to adapt to various habitats evolving a comprehensive set of different morphotypes. In a recent study we showed that this evolution is not a gradual transition from simple unicellular to more complex multicellular forms as often assumed. Instead complexity was lost several times and regained at least once. An understanding of the genetic basis of these transitions would be further strengthened by phylogenomic approaches. However, considering that new methods for phylogenomic analyses are emerging, it is unfortunate that genomes available today are comprised of an unbalanced sampling of taxa. We propose avenues to remedy this by identifying taxa that would improve the representation of phylogenetic diversity in this phylum. PMID:21966561

  13. MOLECULAR PHYLOGENY AND EVOLUTION OF MOSQUITO PARASTIC MICROSPORIDIA (MICROSPORIDIA: AMBLYOSPORIDAE)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Amblyospora and related species were isolated from mosquitoes, black flies and copepods and the small subunit ribosomal DNA gene was sequenced. The comparative phylogenetic analysis for this study shows co-evolution agreement between the mosquito host genera and Amblyospora parasite species with a ...

  14. "Eve" in Africa: Human Evolution Meets Molecular Biology.

    ERIC Educational Resources Information Center

    Seager, Robert D.

    1990-01-01

    Presented is a discussion of recent evidence on the evolution of human forms on earth gathered and evaluated using mitochondrial DNA techniques. Theories regarding the possibility that a common female ancestor existed in Africa about 200,000 years ago are discussed. A list of teaching aids is provided. (CW)

  15. On the Stability and Evolution of Isolated Molecular Clouds

    NASA Technical Reports Server (NTRS)

    Langer, W.; Nelson, R.

    1998-01-01

    We present the results of three dimensional hydrodynamic models of evolving, isolated, low mass, quiescent clouds and Bok gobules, where the interstellar radiation field plays an important role in the thermal and chemical evolution, and thermal pressure provides dominant support against gravitational collapse.

  16. Extracellular Matrix Molecular Remodeling in Human Liver Fibrosis Evolution

    PubMed Central

    Baiocchini, Andrea; Montaldo, Claudia; Conigliaro, Alice; Grimaldi, Alessio; Correani, Virginia; Mura, Francesco; Ciccosanti, Fabiola; Rotiroti, Nicolina; Brenna, Alessia; Montalbano, Marzia; D’Offizi, Gianpiero; Capobianchi, Maria Rosaria; Alessandro, Riccardo; Piacentini, Mauro; Schininà, Maria Eugenia; Maras, Bruno; Del Nonno, Franca; Tripodi, Marco; Mancone, Carmine

    2016-01-01

    Chronic liver damage leads to pathological accumulation of ECM proteins (liver fibrosis). Comprehensive characterization of the human ECM molecular composition is essential for gaining insights into the mechanisms of liver disease. To date, studies of ECM remodeling in human liver diseases have been hampered by the unavailability of purified ECM. Here, we developed a decellularization method to purify ECM scaffolds from human liver tissues. Histological and electron microscopy analyses demonstrated that the ECM scaffolds, devoid of plasma and cellular components, preserved the three-dimensional ECM structure and zonal distribution of ECM components. This method has been then applied on 57 liver biopsies of HCV-infected patients at different stages of liver fibrosis according to METAVIR classification. Label-free nLC-MS/MS proteomics and computation biology were performed to analyze the ECM molecular composition in liver fibrosis progression, thus unveiling protein expression signatures specific for the HCV-related liver fibrotic stages. In particular, the ECM molecular composition of liver fibrosis was found to involve dynamic changes in matrix stiffness, flexibility and density related to the dysregulation of predominant collagen, elastic fibers and minor components with both structural and signaling properties. This study contributes to the understanding of the molecular bases underlying ECM remodeling in liver fibrosis and suggests new molecular targets for fibrolytic strategies. PMID:26998606

  17. Temporal scaling of molecular evolution in primates and other mammals.

    PubMed

    Gingerich, P D

    1986-05-01

    Molecular clocks are routinely tested for linearity using a relative rate test and routinely calibrated against the geological time scale using a single or average paleontologically determined time of divergence between living taxa. The relative rate test is a test of parallel rate equality, not a test of rate constancy. Temporal scaling provides a test of rates, where scaling coefficients of 1.0 (isochrony) represent stochastic rate constancy. The fossil record of primates and other mammals is now known in sufficient detail to provide several independent divergence times for major taxonomic groups. Molecular difference should scale negatively or isochronically (scaling coefficients less than 1.0) with divergence time: where two or more divergence times are available, molecular difference appears to scale positively (scaling coefficient greater than 1.0). A minimum of four divergence times are required for adequate statistical power in testing the linear model: scaling is significantly nonlinear and positive in six of 11 published investigations meeting this criterion. All groups studied show some slowdown in rates of molecular change over Cenozoic time. The break from constant or increasing rates during the Mesozoic to decreasing rates during the Cenozoic appears to coincide with extraordinary diversification of placental mammals at the beginning of this era. High rates of selectively neutral molecular change may be concentrated in such discrete events of evolutionary diversification. PMID:3444400

  18. Photocatalytic hydrogen evolution with ruthenium polypyridine sensitizers: unveiling the key factors to improve efficiencies.

    PubMed

    Deponti, Elisa; Natali, Mirco

    2016-05-31

    Photochemical hydrogen evolution studies aimed at evaluating new molecular catalysts have usually exploited Ru(bpy)3(2+) (where bpy = 2,2'-bipyridine) as the reference photosensitizer, thanks to its suitable optical and redox properties. In principle, an additional improvement of the photocatalytic performances can be achieved also by a careful adjustment of the photophysical and/or electrochemical characteristics of the ruthenium-based sensitizer. Herein we describe homogeneous molecular systems for photocatalytic hydrogen evolution composed of a series of ruthenium polypyridine complexes as the photosensitizers (), a cobaloxime catalyst, and ascorbic acid as the sacrificial electron donor. Suitable functionalizations of the 4,4' positions of bipyridine ligands have been addressed in order to modify the redox properties of the chromophores rather than their optical ones. A careful and detailed kinetic characterization of the relevant processes at the basis of hydrogen evolving photocatalysis has been addressed to rationalize the observed behavior. The results show that the ruthenium complex involving two 2,2'-bipyridines and one 4,4'-dimethyl-2,2'-bipyridine () may outperform the standard Ru(bpy)3(2+) (), combining the right balance of structural and redox properties, thus posing as an alternative benchmark photosensitizer for the study of new hydrogen evolving catalysts. PMID:27165725

  19. Evolution and Molecular Control of Hybrid Incompatibility in Plants.

    PubMed

    Chen, Chen; E, Zhiguo; Lin, Hong-Xuan

    2016-01-01

    Postzygotic reproductive isolation (RI) plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice. Recent progress suggests that hybrid incompatibility is a by-product of co-evolution either with "parasitic" selfish elements in the genome or with invasive microbes in the natural environment. We discuss the environmental influences on the expression of hybrid incompatibility and the possible effects of environment-dependent hybrid incompatibility on sympatric speciation. We also discuss the role of domestication on the evolution of hybrid incompatibilities. PMID:27563306

  20. Evolution and Molecular Control of Hybrid Incompatibility in Plants

    PubMed Central

    Chen, Chen; E, Zhiguo; Lin, Hong-Xuan

    2016-01-01

    Postzygotic reproductive isolation (RI) plays an important role in speciation. According to the stage at which it functions and the symptoms it displays, postzygotic RI can be called hybrid inviability, hybrid weakness or necrosis, hybrid sterility, or hybrid breakdown. In this review, we summarized new findings about hybrid incompatibilities in plants, most of which are from studies on Arabidopsis and rice. Recent progress suggests that hybrid incompatibility is a by-product of co-evolution either with “parasitic” selfish elements in the genome or with invasive microbes in the natural environment. We discuss the environmental influences on the expression of hybrid incompatibility and the possible effects of environment-dependent hybrid incompatibility on sympatric speciation. We also discuss the role of domestication on the evolution of hybrid incompatibilities. PMID:27563306

  1. Structural limits for evolutive capacities in complex molecular systems.

    PubMed

    Bergareche, A M; Ostolaza, J F

    1990-01-01

    The possibilities of evolution for a system with and without a code of translation from nucleic acids into proteins are evaluated. Our interest is mainly centred on the enzymatic RNA case since this molecule has, at the same time, reproductive and functional properties. After scanning the evolutive capacities of the enzymatic RNAs, including the possibility to play the role of "synthetase" which would match nucleic acids with amino acids as a transition step towards a code, we will try to show that due to their own functional limitative factors, the matching system (code) is necessary. This would be the only way to transform the formal complexity--complexity which has not entered into action before the translation process--into functional information to drive the instructive self-reproductive process. Once this stage is reached, the system could evolve without a limit. PMID:1707552

  2. Exploiting models of molecular evolution to efficiently direct protein engineering.

    PubMed

    Cole, Megan F; Gaucher, Eric A

    2011-02-01

    Directed evolution and protein engineering approaches used to generate novel or enhanced biomolecular function often use the evolutionary sequence diversity of protein homologs to rationally guide library design. To fully capture this sequence diversity, however, libraries containing millions of variants are often necessary. Screening libraries of this size is often undesirable due to inaccuracies of high-throughput assays, costs, and time constraints. The ability to effectively cull sequence diversity while still generating the functional diversity within a library thus holds considerable value. This is particularly relevant when high-throughput assays are not amenable to select/screen for certain biomolecular properties. Here, we summarize our recent attempts to develop an evolution-guided approach, Reconstructing Evolutionary Adaptive Paths (REAP), for directed evolution and protein engineering that exploits phylogenetic and sequence analyses to identify amino acid substitutions that are likely to alter or enhance function of a protein. To demonstrate the utility of this technique, we highlight our previous work with DNA polymerases in which a REAP-designed small library was used to identify a DNA polymerase capable of accepting non-standard nucleosides. We anticipate that the REAP approach will be used in the future to facilitate the engineering of biopolymers with expanded functions and will thus have a significant impact on the developing field of 'evolutionary synthetic biology'. PMID:21132281

  3. Improved Infrastucture for Cdms and JPL Molecular Spectroscopy Catalogues

    NASA Astrophysics Data System (ADS)

    Endres, Christian; Schlemmer, Stephan; Drouin, Brian; Pearson, John; Müller, Holger S. P.; Schilke, P.; Stutzki, Jürgen

    2014-06-01

    Over the past years a new infrastructure for atomic and molecular databases has been developed within the framework of the Virtual Atomic and Molecular Data Centre (VAMDC). Standards for the representation of atomic and molecular data as well as a set of protocols have been established which allow now to retrieve data from various databases through one portal and to combine the data easily. Apart from spectroscopic databases such as the Cologne Database for Molecular Spectroscopy (CDMS), the Jet Propulsion Laboratory microwave, millimeter and submillimeter spectral line catalogue (JPL) and the HITRAN database, various databases on molecular collisions (BASECOL, KIDA) and reactions (UMIST) are connected. Together with other groups within the VAMDC consortium we are working on common user tools to simplify the access for new customers and to tailor data requests for users with specified needs. This comprises in particular tools to support the analysis of complex observational data obtained with the ALMA telescope. In this presentation requests to CDMS and JPL will be used to explain the basic concepts and the tools which are provided by VAMDC. In addition a new portal to CDMS will be presented which has a number of new features, in particular meaningful quantum numbers, references linked to data points, access to state energies and improved documentation. Fit files are accessible for download and queries to other databases are possible.

  4. Evolution & Phylogenetic Analysis: Classroom Activities for Investigating Molecular & Morphological Concepts

    ERIC Educational Resources Information Center

    Franklin, Wilfred A.

    2010-01-01

    In a flexible multisession laboratory, students investigate concepts of phylogenetic analysis at both the molecular and the morphological level. Students finish by conducting their own analysis on a collection of skeletons representing the major phyla of vertebrates, a collection of primate skulls, or a collection of hominid skulls.

  5. Molecular Evolution of the Plant SLT Protein Family

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The products of the sodium/lithium tolerance (Slt) genes are proteins that have molecular chaperone activity in vitro. The results from extensive database analyses indicate that SLT-orthologous proteins are present only in seed plants (Spermatopsida). Herein we describe the sequence analysis of th...

  6. Adaptive Evolution of Synthetic Cooperating Communities Improves Growth Performance

    PubMed Central

    Zhang, Xiaolin; Reed, Jennifer L.

    2014-01-01

    Symbiotic interactions between organisms are important for human health and biotechnological applications. Microbial mutualism is a widespread phenomenon and is important in maintaining natural microbial communities. Although cooperative interactions are prevalent in nature, little is known about the processes that allow their initial establishment, govern population dynamics and affect evolutionary processes. To investigate cooperative interactions between bacteria, we constructed, characterized, and adaptively evolved a synthetic community comprised of leucine and lysine Escherichia coli auxotrophs. The co-culture can grow in glucose minimal medium only if the two auxotrophs exchange essential metabolites — lysine and leucine (or its precursors). Our experiments showed that a viable co-culture using these two auxotrophs could be established and adaptively evolved to increase growth rates (by ∼3 fold) and optical densities. While independently evolved co-cultures achieved similar improvements in growth, they took different evolutionary trajectories leading to different community compositions. Experiments with individual isolates from these evolved co-cultures showed that changes in both the leucine and lysine auxotrophs improved growth of the co-culture. Interestingly, while evolved isolates increased growth of co-cultures, they exhibited decreased growth in mono-culture (in the presence of leucine or lysine). A genome-scale metabolic model of the co-culture was also constructed and used to investigate the effects of amino acid (leucine or lysine) release and uptake rates on growth and composition of the co-culture. When the metabolic model was constrained by the estimated leucine and lysine release rates, the model predictions agreed well with experimental growth rates and composition measurements. While this study and others have focused on cooperative interactions amongst community members, the adaptive evolution of communities with other types of

  7. The Coevolution of Phycobilisomes: Molecular Structure Adapting to Functional Evolution

    PubMed Central

    Shi, Fei; Qin, Song; Wang, Yin-Chu

    2011-01-01

    Phycobilisome is the major light-harvesting complex in cyanobacteria and red alga. It consists of phycobiliproteins and their associated linker peptides which play key role in absorption and unidirectional transfer of light energy and the stability of the whole complex system, respectively. Former researches on the evolution among PBPs and linker peptides had mainly focused on the phylogenetic analysis and selective evolution. Coevolution is the change that the conformation of one residue is interrupted by mutation and a compensatory change selected for in its interacting partner. Here, coevolutionary analysis of allophycocyanin, phycocyanin, and phycoerythrin and covariation analysis of linker peptides were performed. Coevolution analyses reveal that these sites are significantly correlated, showing strong evidence of the functional and structural importance of interactions among these residues. According to interprotein coevolution analysis, less interaction was found between PBPs and linker peptides. Our results also revealed the correlations between the coevolution and adaptive selection in PBS were not directly related, but probably demonstrated by the sites coupled under physical-chemical interactions. PMID:21904470

  8. Molecular phylogeny, biogeography, and habitat preference evolution of marsupials.

    PubMed

    Mitchell, Kieren J; Pratt, Renae C; Watson, Laura N; Gibb, Gillian C; Llamas, Bastien; Kasper, Marta; Edson, Janette; Hopwood, Blair; Male, Dean; Armstrong, Kyle N; Meyer, Matthias; Hofreiter, Michael; Austin, Jeremy; Donnellan, Stephen C; Lee, Michael S Y; Phillips, Matthew J; Cooper, Alan

    2014-09-01

    Marsupials exhibit great diversity in ecology and morphology. However, compared with their sister group, the placental mammals, our understanding of many aspects of marsupial evolution remains limited. We use 101 mitochondrial genomes and data from 26 nuclear loci to reconstruct a dated phylogeny including 97% of extant genera and 58% of modern marsupial species. This tree allows us to analyze the evolution of habitat preference and geographic distributions of marsupial species through time. We found a pattern of mesic-adapted lineages evolving to use more arid and open habitats, which is broadly consistent with regional climate and environmental change. However, contrary to the general trend, several lineages subsequently appear to have reverted from drier to more mesic habitats. Biogeographic reconstructions suggest that current views on the connectivity between Australia and New Guinea/Wallacea during the Miocene and Pliocene need to be revised. The antiquity of several endemic New Guinean clades strongly suggests a substantially older period of connection stretching back to the Middle Miocene and implies that New Guinea was colonized by multiple clades almost immediately after its principal formation. PMID:24881050

  9. Molecular cytogenetic dissection of human chromosomes 3 and 21 evolution

    PubMed Central

    Müller, S.; Stanyon, R.; Finelli, P.; Archidiacono, N.; Wienberg, J.

    2000-01-01

    Chromosome painting in placental mammalians illustrates that genome evolution is marked by chromosomal synteny conservation and that the association of chromosomes 3 and 21 may be the largest widely conserved syntenic block known for mammals. We studied intrachromosomal rearrangements of the syntenic block 3/21 by using probes derived from chromosomal subregions with a resolution of up to 10–15 Mbp. We demonstrate that the rearrangements visualized by chromosome painting, mostly translocations, are only a fraction of the actual chromosomal changes that have occurred during evolution. The ancestral segment order for both primates and carnivores is still found in some species in both orders. From the ancestral primate/carnivore condition an inversion is needed to derive the pig homolog, and a fission of chromosome 21 and a pericentric inversion is needed to derive the Bornean orangutan condition. Two overlapping inversions in the chromosome 3 homolog then would lead to the chromosome form found in humans and African apes. This reconstruction of the origin of human chromosome 3 contrasts with the generally accepted scenario derived from chromosome banding in which it was proposed that only one pericentric inversion was needed. From the ancestral form for Old World primates (now found in the Bornean orangutan) a pericentric inversion and centromere shift leads to the chromosome ancestral for all Old World monkeys. Intrachromosomal rearrangements, as shown here, make up a set of potentially plentiful and informative markers that can be used for phylogenetic reconstruction and a more refined comparative mapping of the genome. PMID:10618396

  10. Molecular Evolution of the TET Gene Family in Mammals

    PubMed Central

    Akahori, Hiromichi; Guindon, Stéphane; Yoshizaki, Sumio; Muto, Yoshinori

    2015-01-01

    Ten-eleven translocation (TET) proteins, a family of Fe2+- and 2-oxoglutarate-dependent dioxygenases, are involved in DNA demethylation. They also help regulate various cellular functions. Three TET paralogs have been identified (TET1, TET2, and TET3) in humans. This study focuses on the evolution of mammalian TET genes. Distinct patterns in TET1 and TET2 vs. TET3 were revealed by codon-based tests of positive selection. Results indicate that TET1 and TET2 genes have experienced positive selection more frequently than TET3 gene, and that the majority of codon sites evolved under strong negative selection. These findings imply that the selective pressure on TET3 may have been relaxed in several lineages during the course of evolution. Our analysis of convergent amino acid substitutions also supports the different evolutionary dynamics among TET gene subfamily members. All of the five amino acid sites that are inferred to have evolved under positive selection in the catalytic domain of TET2 are localized at the protein’s outer surface. The adaptive changes of these positively selected amino acid sites could be associated with dynamic interactions between other TET-interacting proteins, and positive selection thus appears to shift the regulatory scheme of TET enzyme function. PMID:26633372

  11. 'Molecules and monkeys': George Gaylord Simpson and the challenge of molecular evolution.

    PubMed

    Aronson, Jay D

    2002-01-01

    In this paper, I analyze George Gaylord Simpson's response to the molecularization of evolutionary biology from his unique perspective as a paleontologist. I do so by exploring his views on early attempts to reconstruct phylogenetic relationships among primates using molecular data. Particular attention is paid to Simpson's role in the evolutionary synthesis of the 1930s and 1940s, as well as his concerns about the rise of molecular biology as a powerful discipline and world-view in the 1960s. I argue that Simpson's belief in the supremacy of natural selection as the primary driving force of evolution, as well as his view that biology was a historical science that seeks ultimate causes and highlights contingency, prevented him from acknowledging that the study of molecular evolution was an inherently valuable part of the life sciences. PMID:15045833

  12. Molecular phylogeny analysis of fiddler crabs: test of the hypothesis of increasing behavioral complexity in evolution.

    PubMed Central

    Sturmbauer, C; Levinton, J S; Christy, J

    1996-01-01

    The current phylogenetic hypothesis for the evolution and biogeography of fiddler crabs relies on the assumption that complex behavioral traits are assumed to also be evolutionary derived. Indo-west Pacific fiddler crabs have simpler reproductive social behavior and are more marine and were thought to be ancestral to the more behaviorally complex and more terrestrial American species. It was also hypothesized that the evolution of more complex social and reproductive behavior was associated with the colonization of the higher intertidal zones. Our phylogenetic analysis, based upon a set of independent molecular characters, however, demonstrates how widely entrenched ideas about evolution and biogeography led to a reasonable, but apparently incorrect, conclusion about the evolutionary trends within this pantropical group of crustaceans. Species bearing the set of "derived traits" are phylogenetically ancestral, suggesting an alternative evolutionary scenario: the evolution of reproductive behavioral complexity in fiddler crabs may have arisen multiple times during their evolution. The evolution of behavioral complexity may have arisen by coopting of a series of other adaptations for high intertidal living and antipredator escape. A calibration of rates of molecular evolution from populations on either side of the Isthmus of Panama suggest a sequence divergence rate for 16S rRNA of 0.9% per million years. The divergence between the ancestral clade and derived forms is estimated to be approximately 22 million years ago, whereas the divergence between the American and Indo-west Pacific is estimated to be approximately 17 million years ago. Images Fig. 1 PMID:11607711

  13. Molecular genetics and the evolution of ultraviolet vision in vertebrates

    PubMed Central

    Shi, Yongsheng; Radlwimmer, F. Bernhard; Yokoyama, Shozo

    2001-01-01

    Despite the biological importance of UV vision, its molecular bases are not well understood. Here, we present evidence that UV vision in vertebrates is determined by eight specific amino acids in the UV pigments. Amino acid sequence analyses show that contemporary UV pigments inherited their UV sensitivities from the vertebrate ancestor by retaining most of these eight amino acids. In the avian lineage, the ancestral pigment lost UV sensitivity, but some descendants regained it by one amino acid change. Our results also strongly support the hypothesis that UV pigments have an unprotonated Schiff base-linked chromophore. PMID:11573008

  14. [Molecular Mechanism and Malignant Clonal Evolution of Multiple Myeloma].

    PubMed

    Ding, Fei; Zhu, Ping; Wu, Xue-Qiang

    2015-10-01

    Almost all patients with multiple myeloma (MM) have chromosomal translocation which can result in genetic variation. There are mainly five types of chromosomal translocations, involving the IGH gene translocation to 11q13 (CCND1), 4p16 (FGFR/MMSET), 16q23 (MAF), 6p21 (CCND3) and 20q11 (MAFB). It is possible that all IGH translocations converge on a common cell cycle signal pathway. Some MM develops through a multistep transformation from monoclonal gammopathy of undetermined significance (MGUS) to smoldering MM (SMM) and eventually to MM and plasma cell leukemia (PCL). Similarly to what Darwin proposed in the mid-19th century-random genetic variation and natural selection in the context of limited resources, MM clonal evolution follow branching and nonlinear mode. The failure of MM treatment is usually related with the minimal subclone which is hardly found at newlydiagnosed. PMID:26524068

  15. Molecular networks and the evolution of human cognitive specializations

    PubMed Central

    Fontenot, Miles; Konopka, Genevieve

    2014-01-01

    Inroads into elucidating the origins of human cognitive specializations have taken many forms, including genetic, genomic, anatomical, and behavioral assays that typically compare humans to non-human primates. While the integration of all of these approaches is essential for ultimately understanding human cognition, here, we review the usefulness of coexpression network analysis for specifically addressing this question. An increasing number of studies have incorporated coexpression networks into brain expression studies comparing species, disease versus control tissue, brain regions, or developmental time periods. A clearer picture has emerged of the key genes driving brain evolution, as well as the developmental and regional contributions of gene expression patterns important for normal brain development and those misregulated in cognitive diseases. PMID:25212263

  16. Molecular evolution of peste des petits ruminants virus.

    PubMed

    Muniraju, Murali; Munir, Muhammad; Parthiban, AravindhBabu R; Banyard, Ashley C; Bao, Jingyue; Wang, Zhiliang; Ayebazibwe, Chrisostom; Ayelet, Gelagay; El Harrak, Mehdi; Mahapatra, Mana; Libeau, Geneviève; Batten, Carrie; Parida, Satya

    2014-12-01

    Despite safe and efficacious vaccines against peste des petits ruminants virus (PPRV), this virus has emerged as the cause of a highly contagious disease with serious economic consequences for small ruminant agriculture across Asia, the Middle East, and Africa. We used complete and partial genome sequences of all 4 lineages of the virus to investigate evolutionary and epidemiologic dynamics of PPRV. A Bayesian phylogenetic analysis of all PPRV lineages mapped the time to most recent common ancestor and initial divergence of PPRV to a lineage III isolate at the beginning of 20th century. A phylogeographic approach estimated the probability for root location of an ancestral PPRV and individual lineages as being Nigeria for PPRV, Senegal for lineage I, Nigeria/Ghana for lineage II, Sudan for lineage III, and India for lineage IV. Substitution rates are critical parameters for understanding virus evolution because restrictions in genetic variation can lead to lower adaptability and pathogenicity. PMID:25418782

  17. Molecular evolution and phylogeny of dengue-4 viruses.

    PubMed

    Lanciotti, R S; Gubler, D J; Trent, D W

    1997-09-01

    Nucleotide sequences of the envelope protein genes of 19 geographically and temporally distinct dengue (DEN)-4 viruses were determined. Nucleic acid sequence comparison revealed that the identity among the DEN-4 viruses was greater than 92%. Similarity among deduced amino acids was between 96 and 100%; in most cases identical amino acid substitutions occurred among viruses from similar geographical regions. Alignment of nucleic acid sequences followed by parsimony analysis generated phylogenetic trees, which indicated that geographically independent evolution of DEN-4 viruses had occurred. DEN-4 viruses were separated into two genetically distinct subtypes (genotypes). Genotype-1 contains viruses from the Philippines, Thailand and Sri Lanka; genotype-2 consists of viruses from Indonesia, Tahiti, the Caribbean Islands (Puerto Rico, Dominica) and Central and South America. PMID:9292015

  18. Glutamine synthetase gene evolution: a good molecular clock.

    PubMed Central

    Pesole, G; Bozzetti, M P; Lanave, C; Preparata, G; Saccone, C

    1991-01-01

    Glutamine synthetase (EC 6.3.1.2) gene evolution in various animals, plants, and bacteria was evaluated by a general stationary Markov model. The evolutionary process proved to be unexpectedly regular even for a time span as long as that between the divergence of prokaryotes from eukaryotes. This enabled us to draw phylogenetic trees for species whose phylogeny cannot be easily reconstructed from the fossil record. Our calculation of the times of divergence of the various organelle-specific enzymes led us to hypothesize that the pea and bean chloroplast genes for these enzymes originated from the duplication of nuclear genes as a result of the different metabolic needs of the various species. Our data indicate that the duplication of plastid glutamine synthetase genes occurred long after the endosymbiotic events that produced the organelles themselves. PMID:1671172

  19. Gibberellin Receptor GID1: Gibberellin Recognition and Molecular Evolution

    NASA Astrophysics Data System (ADS)

    Kato, Hiroaki; Sato, Tomomi; Ueguchi-Tanaka, Miyako

    Gibberellins (GAs) are phytohormones essential for many developmental processes in plants. We analyzed the crystal structure of a nuclear GA receptor, GIBBERELLIN INSENSITIVE DWARF 1 (GID1) from Oryza sativa. As it was proposed from the sequence similarity, the overall structure of GID1 shows an α/β-hydrolase fold similar to that of the hormone-sensitive lipases (HSLs) except for an amino-terminal lid. The GA-binding site corresponds to the substrate-binding site of HSLs. Almost residues assigned for GA binding showed very little or no activity when they were replaced with Ala. The substitution of the residues corresponding to those of the lycophyte GID1s caused an increase in the binding affinity for GA34, a 2β-hydroxylated GA4. These findings indicate that GID1 originated from HSL and was tinkered to have the specificity for bioactive GAs in the course of plant evolution.

  20. Structure, molecular evolution, and hydrolytic specificities of largemouth bass pepsins.

    PubMed

    Miura, Yoko; Suzuki-Matsubara, Mieko; Kageyama, Takashi; Moriyama, Akihiko

    2016-02-01

    The nucleotide sequences of largemouth bass pepsinogens (PG1, 2 and 3) were determined after molecular cloning of the respective cDNAs. Encoded PG1, 2 and 3 were classified as fish pepsinogens A1, A2 and C, respectively. Molecular evolutionary analyses show that vertebrate pepsinogens are classified into seven monophyletic groups, i.e. pepsinogens A, F, Y (prochymosins), C, B, and fish pepsinogens A and C. Regarding the primary structures, extensive deletion was obvious in S'1 loop residues in fish pepsin A as well as tetrapod pepsin Y. This deletion resulted in a decrease in hydrophobic residues in the S'1 site. Hydrolytic specificities of bass pepsins A1 and A2 were investigated with a pepsin substrate and its variants. Bass pepsins preferred both hydrophobic/aromatic residues and charged residues at the P'1 sites of substrates, showing the dual character of S'1 sites. Thermodynamic analyses of bass pepsin A2 showed that its activation Gibbs energy change (∆G(‡)) was lower than that of porcine pepsin A. Several sites of bass pepsin A2 moiety were found to be under positive selection, and most of them are located on the surface of the molecule, where they are involved in conformational flexibility. The broad S'1 specificity and flexible structure of bass pepsin A2 are thought to cause its high proteolytic activity. PMID:26627128

  1. Molecular tools in understanding the evolution of Vibrio cholerae

    PubMed Central

    Rahaman, Md. Habibur; Islam, Tarequl; Colwell, Rita R.; Alam, Munirul

    2015-01-01

    Vibrio cholerae, the etiological agent of cholera, has been a scourge for centuries. Cholera remains a serious health threat for developing countries and has been responsible for millions of deaths globally over the past 200 years. Identification of V. cholerae has been accomplished using a variety of methods, ranging from phenotypic strategies to DNA based molecular typing and currently whole genomic approaches. This array of methods has been adopted in epidemiological investigations, either singly or in the aggregate, and more recently for evolutionary analyses of V. cholerae. Because the new technologies have been developed at an ever increasing pace, this review of the range of fingerprinting strategies, their relative advantages and limitations, and cholera case studies was undertaken. The task was challenging, considering the vast amount of the information available. To assist the study, key references representative of several areas of research are provided with the intent to provide readers with a comprehensive view of recent advances in the molecular epidemiology of V. cholerae. Suggestions for ways to obviate many of the current limitations of typing techniques are also provided. In summary, a comparative report has been prepared that includes the range from traditional typing to whole genomic strategies. PMID:26500613

  2. The molecular evolution of the vertebrate behavioural repertoire.

    PubMed

    Grant, Seth G N

    2016-01-01

    How the sophisticated vertebrate behavioural repertoire evolved remains a major question in biology. The behavioural repertoire encompasses the set of individual behavioural components that an organism uses when adapting and responding to changes in its external world. Although unicellular organisms, invertebrates and vertebrates share simple reflex responses, the fundamental mechanisms that resulted in the complexity and sophistication that is characteristic of vertebrate behaviours have only recently been examined. A series of behavioural genetic experiments in mice and humans support a theory that posited the importance of synapse proteome expansion in generating complexity in the behavioural repertoire. Genome duplication events, approximately 550 Ma, produced expansion in the synapse proteome that resulted in increased complexity in synapse signalling mechanisms that regulate components of the behavioural repertoire. The experiments demonstrate the importance to behaviour of the gene duplication events, the diversification of paralogues and sequence constraint. They also confirm the significance of comparative proteomic and genomic studies that identified the molecular origins of synapses in unicellular eukaryotes and the vertebrate expansion in proteome complexity. These molecular mechanisms have general importance for understanding the repertoire of behaviours in different species and for human behavioural disorders arising from synapse gene mutations. PMID:26598730

  3. The molecular evolution of the vertebrate behavioural repertoire

    PubMed Central

    2016-01-01

    How the sophisticated vertebrate behavioural repertoire evolved remains a major question in biology. The behavioural repertoire encompasses the set of individual behavioural components that an organism uses when adapting and responding to changes in its external world. Although unicellular organisms, invertebrates and vertebrates share simple reflex responses, the fundamental mechanisms that resulted in the complexity and sophistication that is characteristic of vertebrate behaviours have only recently been examined. A series of behavioural genetic experiments in mice and humans support a theory that posited the importance of synapse proteome expansion in generating complexity in the behavioural repertoire. Genome duplication events, approximately 550 Ma, produced expansion in the synapse proteome that resulted in increased complexity in synapse signalling mechanisms that regulate components of the behavioural repertoire. The experiments demonstrate the importance to behaviour of the gene duplication events, the diversification of paralogues and sequence constraint. They also confirm the significance of comparative proteomic and genomic studies that identified the molecular origins of synapses in unicellular eukaryotes and the vertebrate expansion in proteome complexity. These molecular mechanisms have general importance for understanding the repertoire of behaviours in different species and for human behavioural disorders arising from synapse gene mutations. PMID:26598730

  4. Improving Molecular Level Chemical Speciation of Organic Aerosols

    NASA Astrophysics Data System (ADS)

    Worton, D. R.; Decker, M.; Isaacman, G. A.; Chan, A.; Wilson, K. R.; Goldstein, A. H.

    2013-12-01

    A substantial fraction of fine mode aerosols are organic with the majority formed in the atmosphere through oxidation of gas phase compounds emitted from a variety of natural and man-made sources. As a result, organic aerosols are comprised of thousands of individual organic species whose complexity increases exponentially with carbon number and degree of atmospheric oxidation. Chemical characterization of individual compounds present in this complex mixture provides information on sources and transformation processes that are critical for apportioning organic carbon from an often convoluted mixture of sources and to constrain oxidation mechanisms needed for atmospheric models. These compounds also affect the physical and optical properties of the aerosol but the vast majority remain unidentified and missing from published mass spectral libraries because of difficulties in separating and identifying them. We have developed improved methodologies for chemical identification in order to better understand complex environmental mixtures. Our approach has been to combine two-dimensional gas chromatography with high resolution time of flight mass spectrometry (GC×GC-HRTOFMS) and both traditional electron ionization (EI) and vacuum ultraviolet (VUV) photoionization. GC×GC provides improved separation of individual compounds over traditional one dimensional GC and minimizes co-elution of peaks resulting in mass spectra that are virtually free of interferences. VUV ionization is a ';soft' ionization technique that reduces fragmentation and enhances the abundance of the parent or molecular ion, which when combined with high resolution mass spectrometry can provide molecular formulas for chromatographic peaks. We demonstrate our methodology by applying it to identify more than 500 individual compounds in aerosol filter samples collected at Blodgett Forest, a rural site in the Sierra Nevada Mountains. Using the EI NIST mass spectral library and molecular formulas determined

  5. Molecular Evolution of the Oxygen-Binding Hemerythrin Domain

    PubMed Central

    Alvarez-Carreño, Claudia; Becerra, Arturo; Lazcano, Antonio

    2016-01-01

    Background The evolution of oxygenic photosynthesis during Precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. Four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins) are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in marine invertebrates but further research has made it clear that it is present in the three domains of life, strongly suggesting that its origin predated the emergence of eukaryotes. Results Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histidine, histidine, glutamic acid) cation-binding domain. Oxygen-binding hemerythrin homologs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 eukaryotic genomes. Overall, oxygen-binding hemerythrin homologues were found in the same proportion as single-domain and as long protein sequences. The associated functions of protein domains in long hemerythrin sequences can be classified in three major groups: signal transduction, phosphorelay response regulation, and protein binding. This suggests that in many organisms the reversible oxygen-binding capacity was incorporated in signaling pathways. A maximum-likelihood tree of oxygen-binding hemerythrin homologues revealed a complex evolutionary history in which lateral gene transfer, duplications and gene losses appear to have played an important role. Conclusions Hemerythrin is an ancient protein domain with a complex evolutionary history. The distinctive iron-binding coordination site of oxygen-binding hemerythrins evolved first in prokaryotes, very likely prior to the divergence of Firmicutes and Proteobacteria, and spread into many bacterial, archaeal and eukaryotic species. The later

  6. Molecular evolution and in vitro characterization of Botryllus histocompatibility factor.

    PubMed

    Taketa, Daryl A; Nydam, Marie L; Langenbacher, Adam D; Rodriguez, Delany; Sanders, Erin; De Tomaso, Anthony W

    2015-10-01

    Botryllus schlosseri is a colonial ascidian with a natural ability to anastomose with another colony to form a vascular and hematopoietic chimera. In order to fuse, two individuals must share at least one allele at the highly polymorphic fuhc locus. Otherwise, a blood-based inflammatory response will occur resulting in a melanin scar at the sites of interaction. The single-locus genetic control of allorecognition makes B. schlosseri an attractive model to study the underlying molecular mechanisms. Over the past decade, several candidate genes involved in allorecognition have been identified, but how they ultimately contribute to allorecognition outcome remains poorly understood. Here, we report our initial molecular characterization of a recently identified candidate allodeterminant called Botryllus histocompatibility factor (bhf). bhf, both on a DNA and protein level, is the least polymorphic protein in the fuhc locus studied so far and, unlike other known allorecognition determinants, does not appear to be under any form of balancing or directional selection. Additionally, we identified a second isoform through mRNA-Seq and an EST assembly library which is missing exon 3, resulting in a C-terminally truncated form. We report via whole-mount fluorescent in situ hybridization that a subset of cells co-express bhf and cfuhc(sec). Finally, we observed BHF's localization in HEK293T at the cytoplasmic side of the plasma membrane in addition to the nucleus via a nuclear localization signal. Given the localization data thus far, we hypothesize that BHF may function as a scaffolding protein in a complex with other Botryllus proteins, rather than functioning as an allorecognition determinant. PMID:26359175

  7. Vibration-mediated Kondo transport in molecular junctions: conductance evolution during mechanical stretching

    PubMed Central

    Rakhmilevitch, David

    2015-01-01

    Summary The vibration-mediated Kondo effect attracted considerable theoretical interest during the last decade. However, due to lack of extensive experimental demonstrations, the fine details of the phenomenon were not addressed. Here, we analyze the evolution of vibration-mediated Kondo effect in molecular junctions during mechanical stretching. The described analysis reveals the different contributions of Kondo and inelastic transport. PMID:26734532

  8. Epistasis and the Dynamics of Reversion in Molecular Evolution.

    PubMed

    McCandlish, David M; Shah, Premal; Plotkin, Joshua B

    2016-07-01

    Recent studies of protein evolution contend that the longer an amino acid substitution is present at a site, the less likely it is to revert to the amino acid previously occupying that site. Here we study this phenomenon of decreasing reversion rates rigorously and in a much more general context. We show that, under weak mutation and for arbitrary fitness landscapes, reversion rates decrease with time for any site that is involved in at least one epistatic interaction. Specifically, we prove that, at stationarity, the hazard function of the distribution of waiting times until reversion is strictly decreasing for any such site. Thus, in the presence of epistasis, the longer a particular character has been absent from a site, the less likely the site will revert to its prior state. We also explore several examples of this general result, which share a common pattern whereby the probability of having reverted increases rapidly at short times to some substantial value before becoming almost flat after a few substitutions at other sites. This pattern indicates a characteristic tendency for reversion to occur either almost immediately after the initial substitution or only after a very long time. PMID:27194749

  9. Phylogeography and molecular evolution of potato virus Y.

    PubMed

    Cuevas, José M; Delaunay, Agnès; Visser, Johan C; Bellstedt, Dirk U; Jacquot, Emmanuel; Elena, Santiago F

    2012-01-01

    Potato virus Y (PVY) is an important plant pathogen, whose host range includes economically important crops such as potato, tobacco, tomato, and pepper. PVY presents three main strains (PVY(O), PVY(N) and PVY(C)) and several recombinant forms. PVY has a worldwide distribution, yet the mechanisms that promote and maintain its population structure and genetic diversity are still unclear. In this study, we used a pool of 77 complete PVY genomes from isolates collected worldwide. After removing the effect of recombination in our data set, we used bayesian techniques to study the influence of geography and host species in both PVY population structure and dynamics. We have also performed selection and covariation analyses to identify evolutionarily relevant amino acid residues. Our results show that both geographic and host-driven adaptations explain PVY diversification. Furthermore, purifying selection is the main force driving PVY evolution, although some indications of positive selection accounted for the diversification of the different strains. Interestingly, the analysis of P3N-PIPO, a recently described gene in potyviruses, seems to show a variable length among the isolates analyzed, and this variability is explained, in part, by host-driven adaptation. PMID:22655074

  10. Molecular evolution of the capsid gene in human norovirus genogroup II

    PubMed Central

    Kobayashi, Miho; Matsushima, Yuki; Motoya, Takumi; Sakon, Naomi; Shigemoto, Naoki; Okamoto-Nakagawa, Reiko; Nishimura, Koichi; Yamashita, Yasutaka; Kuroda, Makoto; Saruki, Nobuhiro; Ryo, Akihide; Saraya, Takeshi; Morita, Yukio; Shirabe, Komei; Ishikawa, Mariko; Takahashi, Tomoko; Shinomiya, Hiroto; Okabe, Nobuhiko; Nagasawa, Koo; Suzuki, Yoshiyuki; Katayama, Kazuhiko; Kimura, Hirokazu

    2016-01-01

    Capsid protein of norovirus genogroup II (GII) plays crucial roles in host infection. Although studies on capsid gene evolution have been conducted for a few genotypes of norovirus, the molecular evolution of norovirus GII is not well understood. Here we report the molecular evolution of all GII genotypes, using various bioinformatics techniques. The time-scaled phylogenetic tree showed that the present GII strains diverged from GIV around 1630CE at a high evolutionary rate (around 10−3 substitutions/site/year), resulting in three lineages. The GII capsid gene had large pairwise distances (maximum > 0.39). The effective population sizes of the present GII strains were large (>102) for about 400 years. Positive (20) and negative (over 450) selection sites were estimated. Moreover, some linear and conformational B-cell epitopes were found in the deduced GII capsid protein. These results suggested that norovirus GII strains rapidly evolved with high divergence and adaptation to humans. PMID:27384324

  11. Karyotypic evolution in the Galliformes: an examination of the process of karyotypic evolution by comparison of the molecular cytogenetic findings with the molecular phylogeny.

    PubMed

    Shibusawa, M; Nishibori, M; Nishida-Umehara, C; Tsudzuki, M; Masabanda, J; Griffin, D K; Matsuda, Y

    2004-01-01

    To define the process of karyotypic evolution in the Galliformes on a molecular basis, we conducted genome-wide comparative chromosome painting for eight species, i.e. silver pheasant (Lophura nycthemera), Lady Amherst's pheasant (Chrysolophus amherstiae), ring-necked pheasant (Phasianus colchicus), turkey (Meleagris gallopavo), Western capercaillie (Tetrao urogallus), Chinese bamboo-partridge (Bambusicola thoracica) and common peafowl (Pavo cristatus) of the Phasianidae, and plain chachalaca (Ortalis vetula) of the Cracidae, with chicken DNA probes of chromosomes 1-9 and Z. Including our previous data from five other species, chicken (Gallus gallus), Japanese quail (Coturnix japonica) and blue-breasted quail (Coturnix chinensis) of the Phasianidae, guinea fowl (Numida meleagris) of the Numididae and California quail (Callipepla californica) of the Odontophoridae, we represented the evolutionary changes of karyotypes in the 13 species of the Galliformes. In addition, we compared the cytogenetic data with the molecular phylogeny of the 13 species constructed with the nucleotide sequences of the mitochondrial cytochrome b gene, and discussed the process of karyotypic evolution in the Galliformes. Comparative chromosome painting confirmed the previous data on chromosome rearrangements obtained by G-banding analysis, and identified several novel chromosome rearrangements. The process of the evolutionary changes of macrochromosomes in the 13 species was in good accordance with the molecular phylogeny, and the ancestral karyotype of the Galliformes is represented. PMID:15218250

  12. Are Molecular Alphabets Universal Enabling Factors for the Evolution of Complex Life?

    NASA Astrophysics Data System (ADS)

    Dunn, Ian S.

    2013-12-01

    Terrestrial biosystems depend on macromolecules, and this feature is often considered as a likely universal aspect of life. While opinions differ regarding the importance of small-molecule systems in abiogenesis, escalating biological functional demands are linked with increasing complexity in key molecules participating in biosystem operations, and many such requirements cannot be efficiently mediated by relatively small compounds. It has long been recognized that known life is associated with the evolution of two distinct molecular alphabets (nucleic acid and protein), specific sequence combinations of which serve as informational and functional polymers. In contrast, much less detailed focus has been directed towards the potential universal need for molecular alphabets in constituting complex chemically-based life, and the implications of such a requirement. To analyze this, emphasis here is placed on the generalizable replicative and functional characteristics of molecular alphabets and their concatenates. A primary replicative alphabet based on the simplest possible molecular complementarity can potentially enable evolutionary processes to occur, including the encoding of secondarily functional alphabets. Very large uniquely specified (`non-alphabetic') molecules cannot feasibly underlie systems capable of the replicative and evolutionary properties which characterize complex biosystems. Transitions in the molecular evolution of alphabets can be related to progressive bridging of barriers which enable higher levels of biosystem organization. It is thus highly probable that molecular alphabets are an obligatory requirement for complex chemically-based life anywhere in the universe. In turn, reference to molecular alphabets should be usefully applied in current definitions of life.

  13. Are molecular alphabets universal enabling factors for the evolution of complex life?

    PubMed

    Dunn, Ian S

    2013-12-01

    Terrestrial biosystems depend on macromolecules, and this feature is often considered as a likely universal aspect of life. While opinions differ regarding the importance of small-molecule systems in abiogenesis, escalating biological functional demands are linked with increasing complexity in key molecules participating in biosystem operations, and many such requirements cannot be efficiently mediated by relatively small compounds. It has long been recognized that known life is associated with the evolution of two distinct molecular alphabets (nucleic acid and protein), specific sequence combinations of which serve as informational and functional polymers. In contrast, much less detailed focus has been directed towards the potential universal need for molecular alphabets in constituting complex chemically-based life, and the implications of such a requirement. To analyze this, emphasis here is placed on the generalizable replicative and functional characteristics of molecular alphabets and their concatenates. A primary replicative alphabet based on the simplest possible molecular complementarity can potentially enable evolutionary processes to occur, including the encoding of secondarily functional alphabets. Very large uniquely specified ('non-alphabetic') molecules cannot feasibly underlie systems capable of the replicative and evolutionary properties which characterize complex biosystems. Transitions in the molecular evolution of alphabets can be related to progressive bridging of barriers which enable higher levels of biosystem organization. It is thus highly probable that molecular alphabets are an obligatory requirement for complex chemically-based life anywhere in the universe. In turn, reference to molecular alphabets should be usefully applied in current definitions of life. PMID:24510462

  14. Molecular evolution and functional characterisation of haplotypes of an important rubber biosynthesis gene in Hevea brasiliensis.

    PubMed

    Uthup, T K; Rajamani, A; Ravindran, M; Saha, T

    2016-07-01

    Hydroxy-methylglutaryl coenzyme-A synthase (HMGS) is a rate-limiting enzyme in the cytoplasmic isoprenoid biosynthesis pathway leading to natural rubber production in Hevea brasiliensis (rubber). Analysis of the structural variants of this gene is imperative to understand their functional significance in rubber biosynthesis so that they can be properly utilised for ongoing crop improvement programmes in Hevea. We report here allele richness and diversity of the HMGS gene in selected popular rubber clones. Haplotypes consisting of single nucleotide polymorphisms (SNPs) from the coding and non-coding regions with a high degree of heterozygosity were identified. Segregation and linkage disequilibrium analysis confirmed that recombination is the major contributor to the generation of allelic diversity, rather than point mutations. The evolutionarily conserved nature of some SNPs was identified by comparative DNA sequence analysis of HMGS orthologues from diverse taxa, demonstrating the molecular evolution of rubber biosynthesis genes in general. In silico three-dimensional structural studies highlighting the structural positioning of non-synonymous SNPs from different HMGS haplotypes revealed that the ligand-binding site on the enzyme remains impervious to the reported sequence variations. In contrast, gene expression results indicated the possibility of association between specific haplotypes and HMGS expression in Hevea clones, which may have a downstream impact up to the level of rubber production. Moreover, haplotype diversity of the HMGS gene and its putative association with gene expression can be the basis for further genetic association studies in rubber. Furthermore, the data also show the role of SNPs in the evolution of candidate genes coding for functional traits in plants. PMID:26787454

  15. Molecular evolution of GPCRs: Melanocortin/melanocortin receptors.

    PubMed

    Dores, Robert M; Londraville, Richard L; Prokop, Jeremy; Davis, Perry; Dewey, Nathan; Lesinski, Natalie

    2014-06-01

    The melanocortin receptors (MCRs) are a family of G protein-coupled receptors that are activated by melanocortin ligands derived from the proprotein, proopiomelanocortin (POMC). During the radiation of the gnathostomes, the five receptors have become functionally segregated (i.e. melanocortin 1 receptor (MC1R), pigmentation regulation; MC2R, glucocorticoid synthesis; MC3R and MC4R, energy homeostasis; and MC5R, exocrine gland physiology). A focus of this review is the role that ligand selectivity plays in the hypothalamus/pituitary/adrenal-interrenal (HPA-I) axis of teleosts and tetrapods as a result of the exclusive ligand selectivity of MC2R for the ligand ACTH. A second focal point of this review is the roles that the accessory proteins melanocortin 2 receptor accessory protein 1 (MRAP1) and MRAP2 are playing in, respectively, the HPA-I axis (MC2R) and the regulation of energy homeostasis by neurons in the hypothalamus (MC4R) of teleosts and tetrapods. In addition, observations are presented on trends in the ligand selectivity parameters of cartilaginous fish, teleost, and tetrapod MC1R, MC3R, MC4R, and MC5R paralogs, and the modeling of the HFRW motif of ACTH(1-24) when compared with α-MSH. The radiation of the MCRs during the evolution of the gnathostomes provides examples of how the physiology of endocrine and neuronal circuits can be shaped by ligand selectivity, the intersession of reverse agonists (agouti-related peptides (AGRPs)), and interactions with accessory proteins (MRAPs). PMID:24868105

  16. Distribution and molecular evolution of bacillus anthracis genotypes in Namibia.

    PubMed

    Beyer, Wolfgang; Bellan, Steve; Eberle, Gisela; Ganz, Holly H; Getz, Wayne M; Haumacher, Renate; Hilss, Karen A; Kilian, Werner; Lazak, Judith; Turner, Wendy C; Turnbull, Peter C B

    2012-01-01

    The recent development of genetic markers for Bacillus anthracis has made it possible to monitor the spread and distribution of this pathogen during and between anthrax outbreaks. In Namibia, anthrax outbreaks occur annually in the Etosha National Park (ENP) and on private game and livestock farms. We genotyped 384 B. anthracis isolates collected between 1983-2010 to identify the possible epidemiological correlations of anthrax outbreaks within and outside the ENP and to analyze genetic relationships between isolates from domestic and wild animals. The isolates came from 20 animal species and from the environment and were genotyped using a 31-marker multi-locus-VNTR-analysis (MLVA) and, in part, by twelve single nucleotide polymorphism (SNP) markers and four single nucleotide repeat (SNR) markers. A total of 37 genotypes (GT) were identified by MLVA, belonging to four SNP-groups. All GTs belonged to the A-branch in the cluster- and SNP-analyses. Thirteen GTs were found only outside the ENP, 18 only within the ENP and 6 both inside and outside. Genetic distances between isolates increased with increasing time between isolations. However, genetic distance between isolates at the beginning and end of the study period was relatively small, indicating that while the majority of GTs were only found sporadically, three genetically close GTs, accounting for more than four fifths of all the ENP isolates, appeared dominant throughout the study period. Genetic distances among isolates were significantly greater for isolates from different host species, but this effect was small, suggesting that while species-specific ecological factors may affect exposure processes, transmission cycles in different host species are still highly interrelated. The MLVA data were further used to establish a model of the probable evolution of GTs within the endemic region of the ENP. SNR-analysis was helpful in correlating an isolate with its source but did not elucidate epidemiological

  17. Molecular Breeding for Improved Second Generation Bioenergy Crops.

    PubMed

    Allwright, Mike R; Taylor, Gail

    2016-01-01

    There is increasing urgency to develop and deploy sustainable sources of energy to reduce our global dependency on finite, high-carbon fossil fuels. Lignocellulosic feedstocks, used in power and liquid fuel generation, are valuable sources of non-food plant biomass. They are cultivated with minimal inputs on marginal or degraded lands to prevent competition with arable agriculture and offer significant potential for sustainable intensification (the improvement of yield without the necessity for additional inputs) through advanced molecular breeding. This article explores progress made in next generation sequencing, advanced genotyping, association genetics, and genetic modification in second generation bioenergy production. Using poplar as an exemplar where most progress has been made, a suite of target traits is also identified giving insight into possible routes for crop improvement and deployment in the immediate future. PMID:26541073

  18. Directed molecular evolution to design advanced red fluorescent proteins

    PubMed Central

    Subach, Fedor V; Piatkevich, Kiryl D; Verkhusha, Vladislav V

    2015-01-01

    Fluorescent proteins have become indispensable imaging tools for biomedical research. continuing progress in fluorescence imaging, however, requires probes with additional colors and properties optimized for emerging techniques. Here we summarize strategies for development of red-shifted fluorescent proteins. We discuss possibilities for knowledge-based rational design based on the photochemistry of fluorescent proteins and the position of the chromophore in protein structure. We consider advances in library design by mutagenesis, protein expression systems and instrumentation for high-throughput screening that should yield improved fluorescent proteins for advanced imaging applications. PMID:22127219

  19. Molecular evolution of HR, a gene that regulates the postnatal cycle of the hair follicle

    PubMed Central

    Abbasi, Amir Ali

    2011-01-01

    Hair is a unique mammalian trait that is absent in all other animal forms. Hairlessness is rare in mammals and humans are exceptional among primates in lacking dense layer of hair covering. HR was the first gene identified to be implicated in hair-cycle regulation. Point mutations in HR lead to congenital human hair loss, which results in the complete loss of body and scalp hairs. HR functions are indispensable for initiation of postnatal hair follicular cycling. This study investigates the phylogenetic history and analyzes the protein evolutionary rate to provide useful insight into the molecular evolution of HR. The data demonstrates an acceleration of HR sequence evolution in human branch and suggests that the ability of HR protein to mediate postnatal hair-cycling has been altered in the course of human evolution. In particular those residues were pinpointed which should be regarded as target of positive Darwinian selection during human evolution. PMID:22355551

  20. Molecular systematics and evolution of the Cyanocorax jays.

    PubMed

    Bonaccorso, Elisa; Peterson, A Townsend; Navarro-Sigüenza, Adolfo G; Fleischer, Robert C

    2010-03-01

    Phylogenetic relationships were studied in the genus Cyanocorax (Aves: Corvidae) and related genera, Psilorhinus and Calocitta, a diverse group of New World jays distributed from the southern United States south to Argentina. Although the ecology and behavior of some species in the group have been studied extensively, lack of a molecular phylogeny has precluded rigorous interpretations in an evolutionary framework. Given the diverse combinations of plumage coloration, size, and morphology, the taxonomy of the group has been inconsistent and understanding of biogeographic patterns problematic. Moreover, plumage similarity between two geographically disjuct species, the Tufted jay (Cyanocorax dickeyi) from western Mexico and the White-tailed jay (C. mystacalis) from western Ecuador and Peru, has puzzled ornithologists for decades. Here, a phylogeny of all species in the three genera is presented, based on study of two mitochondrial and three nuclear genes. Phylogenetic trees revealed the non-monophyly of Cyanocorax, and the division of the whole assemblage in two groups: "Clade A" containing Psilorhinus morio, both species in Calocitta,Cyanocorax violaceus, C. caeruleus, C. cristatellus, and C. cyanomelas, and "Clade B" consisting of the remaining species in Cyanocorax. Relationships among species in Clade A were ambiguous and, in general, not well resolved. Within Clade B, analyses revealed the monophyly of the "Cissilopha" jays and showed no evidence for a sister relationship between C. mystacalis and C. dickeyi. The phylogenetic complexity of lineages in the group suggests several complications for the understanding biogeographic patterns, as well as for proposing a taxonomy that is consistent with morphological variation. Although multiple taxonomic arrangements are possible, recommendations are for recognizing only one genus, Cyanocorax, with Psilorhinus and Calocitta as synonyms. PMID:19931623

  1. Reconstructing web evolution and spider diversification in the molecular era

    PubMed Central

    Blackledge, Todd A.; Scharff, Nikolaj; Coddington, Jonathan A.; Szüts, Tamas; Wenzel, John W.; Hayashi, Cheryl Y.; Agnarsson, Ingi

    2009-01-01

    The evolutionary diversification of spiders is attributed to spectacular innovations in silk. Spiders are unique in synthesizing many different kinds of silk, and using silk for a variety of ecological functions throughout their lives, particularly to make prey-catching webs. Here, we construct a broad higher-level phylogeny of spiders combining molecular data with traditional morphological and behavioral characters. We use this phylogeny to test the hypothesis that the spider orb web evolved only once. We then examine spider diversification in relation to different web architectures and silk use. We find strong support for a single origin of orb webs, implying a major shift in the spinning of capture silk and repeated loss or transformation of orb webs. We show that abandonment of costly cribellate capture silk correlates with the 2 major diversification events in spiders (1). Replacement of cribellate silk by aqueous silk glue may explain the greater diversity of modern orb-weaving spiders (Araneoidea) compared with cribellate orb-weaving spiders (Deinopoidea) (2). Within the “RTA clade,” which is the sister group to orb-weaving spiders and contains half of all spider diversity, >90% of species richness is associated with repeated loss of cribellate silk and abandonment of prey capture webs. Accompanying cribellum loss in both groups is a release from substrate-constrained webs, whether by aerially suspended webs, or by abandoning webs altogether. These behavioral shifts in silk and web production by spiders thus likely played a key role in the dramatic evolutionary success and ecological dominance of spiders as predators of insects. PMID:19289848

  2. The Diversity and Molecular Evolution of B-Cell Receptors during Infection.

    PubMed

    Hoehn, Kenneth B; Fowler, Anna; Lunter, Gerton; Pybus, Oliver G

    2016-05-01

    B-cell receptors (BCRs) are membrane-bound immunoglobulins that recognize and bind foreign proteins (antigens). BCRs are formed through random somatic changes of germline DNA, creating a vast repertoire of unique sequences that enable individuals to recognize a diverse range of antigens. After encountering antigen for the first time, BCRs undergo a process of affinity maturation, whereby cycles of rapid somatic mutation and selection lead to improved antigen binding. This constitutes an accelerated evolutionary process that takes place over days or weeks. Next-generation sequencing of the gene regions that determine BCR binding has begun to reveal the diversity and dynamics of BCR repertoires in unprecedented detail. Although this new type of sequence data has the potential to revolutionize our understanding of infection dynamics, quantitative analysis is complicated by the unique biology and high diversity of BCR sequences. Models and concepts from molecular evolution and phylogenetics that have been applied successfully to rapidly evolving pathogen populations are increasingly being adopted to study BCR diversity and divergence within individuals. However, BCR dynamics may violate key assumptions of many standard evolutionary methods, as they do not descend from a single ancestor, and experience biased mutation. Here, we review the application of evolutionary models to BCR repertoires and discuss the issues we believe need be addressed for this interdisciplinary field to flourish. PMID:26802217

  3. The Diversity and Molecular Evolution of B-Cell Receptors during Infection

    PubMed Central

    Hoehn, Kenneth B.; Fowler, Anna; Lunter, Gerton; Pybus, Oliver G.

    2016-01-01

    B-cell receptors (BCRs) are membrane-bound immunoglobulins that recognize and bind foreign proteins (antigens). BCRs are formed through random somatic changes of germline DNA, creating a vast repertoire of unique sequences that enable individuals to recognize a diverse range of antigens. After encountering antigen for the first time, BCRs undergo a process of affinity maturation, whereby cycles of rapid somatic mutation and selection lead to improved antigen binding. This constitutes an accelerated evolutionary process that takes place over days or weeks. Next-generation sequencing of the gene regions that determine BCR binding has begun to reveal the diversity and dynamics of BCR repertoires in unprecedented detail. Although this new type of sequence data has the potential to revolutionize our understanding of infection dynamics, quantitative analysis is complicated by the unique biology and high diversity of BCR sequences. Models and concepts from molecular evolution and phylogenetics that have been applied successfully to rapidly evolving pathogen populations are increasingly being adopted to study BCR diversity and divergence within individuals. However, BCR dynamics may violate key assumptions of many standard evolutionary methods, as they do not descend from a single ancestor, and experience biased mutation. Here, we review the application of evolutionary models to BCR repertoires and discuss the issues we believe need be addressed for this interdisciplinary field to flourish. PMID:26802217

  4. Parasitic plants have increased rates of molecular evolution across all three genomes

    PubMed Central

    2013-01-01

    Background Theoretical models and experimental evidence suggest that rates of molecular evolution could be raised in parasitic organisms compared to non-parasitic taxa. Parasitic plants provide an ideal test for these predictions, as there are at least a dozen independent origins of the parasitic lifestyle in angiosperms. Studies of a number of parasitic plant lineages have suggested faster rates of molecular evolution, but the results of some studies have been mixed. Comparative analysis of all parasitic plant lineages, including sequences from all three genomes, is needed to examine the generality of the relationship between rates of molecular evolution and parasitism in plants. Results We analysed DNA sequence data from the mitochondrial, nuclear and chloroplast genomes for 12 independent evolutionary origins of parasitism in angiosperms. We demonstrated that parasitic lineages have a faster rate of molecular evolution than their non-parasitic relatives in sequences for all three genomes, for both synonymous and nonsynonymous substitutions. Conclusions Our results prove that raised rates of molecular evolution are a general feature of parasitic plants, not confined to a few taxa or specific genes. We discuss possible causes for this relationship, including increased positive selection associated with host-parasite arms races, relaxed selection, reduced population size or repeated bottlenecks, increased mutation rates, and indirect causal links with generation time and body size. We find no evidence that faster rates are due to smaller effective populations sizes or changes in selection pressure. Instead, our results suggest that parasitic plants have a higher mutation rate than their close non-parasitic relatives. This may be due to a direct connection, where some aspect of the parasitic lifestyle drives the evolution of raised mutation rates. Alternatively, this pattern may be driven by an indirect connection between rates and parasitism: for example, parasitic

  5. Directed evolution improves the fibrinolytic activity of nattokinase from Bacillus natto.

    PubMed

    Yongjun, Cai; Wei, Bao; Shujun, Jiang; Meizhi, Weng; Yan, Jia; Yan, Yin; Zhongliang, Zheng; Goulin, Zou

    2011-12-01

    Nattokinase (subtilisin NAT, NK) is a relatively effective microbial fibrinolytic enzyme that has been identified and characterized from Bacillus natto. In the current report, DNA family shuffling was used to improve the fibrinolytic activity of nattokinase. Three homologous genes from B. natto AS 1.107, Bacillus amyloliquefaciens CICC 20164 and Bacillus licheniformis CICC 10092 were shuffled to generate a mutant library. A plate-based method was used to screen the mutant libraries for improved activity. After three rounds of DNA shuffling, one desirable mutant with 16 amino acid substitutions was obtained. The mutant enzyme was purified and characterized. The kinetic measurements showed that the catalytic efficiency of the mutant NK was approximately 2.3 times higher than that of the wild-type nattokinase. In addition, the molecular modeling analysis suggested that the mutations affect the enzymatic function by changing the surface conformation of the substrate-binding pocket. The current study shows that the evolution of nattokinase with improved fibrinolytic activity by DNA family shuffling is feasible and provides useful references to facilitate the application of nattokinase in thrombolytic therapy. PMID:22029857

  6. High molecular weight insulating polymers can improve the performance of molecular solar cells

    NASA Astrophysics Data System (ADS)

    Huang, Ye; Wen, Wen; Kramer, Edward; Bazan, Guillermo

    2014-03-01

    Solution-processed molecular semiconductors for the fabrication of solar cells have emerged as a competitive alternative to their conjugated polymer counterparts, primarily because such materials systems exhibit no batch-to-batch variability, can be purified to a greater extent and offer precisely defined chemical structures. Highest power conversion efficiencies (PCEs) have been achieved through a combination of molecular design and the application of processing methods that optimize the bulk heterojunction (BHJ) morphology. However, one finds that the methods used for controlling structural order, for example the use of high boiling point solvent additives, have been inspired by examination of the conjugated polymer literature. It stands to reason that a different class of morphology modifiers should be sought that address challenges unique to molecular films, including difficulties in obtaining thicker films and avoiding the dewetting of active photovoltaic layers. Here we show that the addition of small quantities of high molecular weight polystyrene (PS) is a very simple to use and economically viable additive that improves PCE. Remarkably, the PS spontaneously accumulates away from the electrodes as separate domains that do not interfere with charge extraction and collection or with the arrangement of the donor and acceptor domains in the BHJ blend.

  7. A Simple, General Result for the Variance of Substitution Number in Molecular Evolution

    PubMed Central

    Houchmandzadeh, Bahram; Vallade, Marcel

    2016-01-01

    The number of substitutions (of nucleotides, amino acids, etc.) that take place during the evolution of a sequence is a stochastic variable of fundamental importance in the field of molecular evolution. Although the mean number of substitutions during molecular evolution of a sequence can be estimated for a given substitution model, no simple solution exists for the variance of this random variable. We show in this article that the computation of the variance is as simple as that of the mean number of substitutions for both short and long times. Apart from its fundamental importance, this result can be used to investigate the dispersion index R, that is, the ratio of the variance to the mean substitution number, which is of prime importance in the neutral theory of molecular evolution. By investigating large classes of substitution models, we demonstrate that although R≥1, to obtain R significantly larger than unity necessitates in general additional hypotheses on the structure of the substitution model. PMID:27189545

  8. DNA Re-EvolutioN: a game for learning molecular genetics and evolution.

    PubMed

    Miralles, Laura; Moran, Paloma; Dopico, Eduardo; Garcia-Vazquez, Eva

    2013-01-01

    Evolution is a main concept in biology, but not many students understand how it works. In this article we introduce the game DNA Re-EvolutioN as an active learning tool that uses genetic concepts (DNA structure, transcription and translation, mutations, natural selection, etc.) as playing rules. Students will learn about molecular evolution while playing a game that mixes up theory and entertainment. The game can be easily adapted to different educational levels. The main goal of this play is to arrive at the end of the game with the longest protein. Students play with pawns and dices, a board containing hypothetical events (mutations, selection) that happen to molecules, "Evolution cards" with indications for DNA mutations, prototypes of a DNA and a mRNA chain with colored "nucleotides" (plasticine balls), and small pieces simulating t-RNA with aminoacids that will serve to construct a "protein" based on the DNA chain. Students will understand how changes in DNA affect the final protein product and may be subjected to positive or negative selection, using a didactic tool funnier than classical theory lectures and easier than molecular laboratory experiments: a flexible and feasible game to learn and enjoy molecular evolution at no-cost. The game was tested by majors and non-majors in genetics from 13 different countries and evaluated with pre- and post-tests obtaining very positive results. PMID:24259334

  9. Modelling the chemical evolution of molecular clouds as a function of metallicity

    NASA Astrophysics Data System (ADS)

    Penteado, E. M.; Cuppen, H. M.; Rocha-Pinto, H. J.

    2014-04-01

    The Galaxy is in continuous elemental evolution. Since new elements produced by dying stars are delivered to the interstellar medium, the formation of new generations of stars and planetary systems is influenced by this metal enrichment. We aim to study the role of the metallicity on the gas phase chemistry of the interstellar medium. Using a system of coupled ordinary differential equations to model the chemical reactions, we simulate the evolution of the abundance of molecules in the gas phase for different initial interstellar elemental compositions. These varying initial elemental compositions consider the change in the `elemental abundances' predicted by a self-consistent model of the elemental evolution of the Galaxy. As far as we are aware, this is the first attempt to combine elemental evolution of the Galaxy and chemical evolution of molecular clouds. The metallicity was found to have a strong effect on the overall gas phase composition. With decreasing metallicity, the number of long carbon chains was found to increase, the time-scale on which small molecular species are increases, and the main form of oxygen changed from O and CO to O2. These effects were found to be mainly due to the change in electron, H_3^+, and atomic oxygen abundance.

  10. Protein engineering of conger eel galectins by tracing of molecular evolution using probable ancestral mutants

    PubMed Central

    2010-01-01

    Background Conger eel galectins, congerin I (ConI) and congerin II (ConII), show the different molecular characteristics resulting from accelerating evolution. We recently reconstructed a probable ancestral form of congerins, Con-anc. It showed properties similar to those of ConII in terms of thermostability and carbohydrate recognition specificity, although it shares a higher sequence similarity with ConI than ConII. Results In this study, we have focused on the different amino acid residues between Con-anc and ConI, and have performed the protein engineering of Con-anc through site-directed mutagenesis, followed by the molecular evolution analysis of the mutants. This approach revealed the functional importance of loop structures of congerins: (1) N- and C-terminal and loop 5 regions that are involved in conferring a high thermostability to ConI; (2) loops 3, 5, and 6 that are responsible for stronger binding of ConI to most sugars; and (3) loops 5 and 6, and Thr38 residue in loop 3 contribute the specificity of ConI toward lacto-N-fucopentaose-containing sugars. Conclusions Thus, this methodology, with tracing of the molecular evolution using ancestral mutants, is a powerful tool for the analysis of not only the molecular evolutionary process, but also the structural elements of a protein responsible for its various functions. PMID:20152053

  11. DNA barcoding and molecular evolution of mosquito vectors of medical and veterinary importance.

    PubMed

    Murugan, Kadarkarai; Vadivalagan, Chithravel; Karthika, Pushparaj; Panneerselvam, Chellasamy; Paulpandi, Manickam; Subramaniam, Jayapal; Wei, Hui; Aziz, Al Thabiani; Alsalhi, Mohamad Saleh; Devanesan, Sandhanasamy; Nicoletti, Marcello; Paramasivan, Rajaiah; Parajulee, Megha N; Benelli, Giovanni

    2016-01-01

    Mosquitoes (Diptera: Culicidae) are a key threat for millions of people worldwide, since they act as vectors for devastating pathogens and parasites. The standard method of utilisation of morphological characters becomes challenging due to various factors such as phenotypical variations. We explored the complementary approach of CO1 gene-based identification, analysing ten species of mosquito vectors belonging to three genera, Aedes, Culex and Anopheles from India. Analysed nucleotide sequences were found without pseudo genes and indels; they match with high similarity in nucleotide Basic Local Alignment Search Tool (BLASTn) search. The partial CO1 sequence of Anopheles niligricus was the first time record submitted to National Center for Biotechnology Information (NCBI). Mean intra- and interspecies divergence was found to be 1.30 and 3.83 %, respectively. The congeneric divergence was three times higher than the conspecifics. Deep intraspecific divergence was noted in three of the species, and the reason could be explained more accurately in the future by improving the sample size across different locations. The transitional and transversional substitutions were tested individually. Ts and Tv substitutions in all the 1st, 2nd and 3rd codons were estimated to be (0.44, 99.51), (40.35, 59.66) and (59.16, 40.84), respectively. Saturation of the sequences was resolved, since both the Ts and Tv exhibited a linear relationship suggesting that the sequences were not saturated. NJ and ML tree analysis showed that the individuals of the same species clustered together based on the CO1 sequence similarity, regardless of their collection site and geographic location. Overall, this study adds basic knowledge to molecular evolution of mosquito vectors of medical and veterinary importance and may be useful to improve biotechnological tools employed in Culicidae control programmes. PMID:26358100

  12. A molecular time-scale for eukaryote evolution recalibrated with the continuous microfossil record

    PubMed Central

    Berney, Cédric; Pawlowski, Jan

    2006-01-01

    Recent attempts to establish a molecular time-scale of eukaryote evolution failed to provide a congruent view on the timing of the origin and early diversification of eukaryotes. The major discrepancies in molecular time estimates are related to questions concerning the calibration of the tree. To limit these uncertainties, we used here as a source of calibration points the rich and continuous microfossil record of dinoflagellates, diatoms and coccolithophorids. We calibrated a small-subunit ribosomal RNA tree of eukaryotes with four maximum and 22 minimum time constraints. Using these multiple calibration points in a Bayesian relaxed molecular clock framework, we inferred that the early radiation of eukaryotes occurred near the Mesoproterozoic–Neoproterozoic boundary, about 1100 million years ago. Our results indicate that most Proterozoic fossils of possible eukaryotic origin cannot be confidently assigned to extant lineages and should therefore not be used as calibration points in molecular dating. PMID:16822745

  13. Correcting for Purifying Selection: An Improved Human Mitochondrial Molecular Clock

    PubMed Central

    Soares, Pedro; Ermini, Luca; Thomson, Noel; Mormina, Maru; Rito, Teresa; Röhl, Arne; Salas, Antonio; Oppenheimer, Stephen; Macaulay, Vincent; Richards, Martin B.

    2009-01-01

    There is currently no calibration available for the whole human mtDNA genome, incorporating both coding and control regions. Furthermore, as several authors have pointed out recently, linear molecular clocks that incorporate selectable characters are in any case problematic. We here confirm a modest effect of purifying selection on the mtDNA coding region and propose an improved molecular clock for dating human mtDNA, based on a worldwide phylogeny of > 2000 complete mtDNA genomes and calibrating against recent evidence for the divergence time of humans and chimpanzees. We focus on a time-dependent mutation rate based on the entire mtDNA genome and supported by a neutral clock based on synonymous mutations alone. We show that the corrected rate is further corroborated by archaeological dating for the settlement of the Canary Islands and Remote Oceania and also, given certain phylogeographic assumptions, by the timing of the first modern human settlement of Europe and resettlement after the Last Glacial Maximum. The corrected rate yields an age of modern human expansion in the Americas at ∼15 kya that—unlike the uncorrected clock—matches the archaeological evidence, but continues to indicate an out-of-Africa dispersal at around 55–70 kya, 5–20 ky before any clear archaeological record, suggesting the need for archaeological research efforts focusing on this time window. We also present improved rates for the mtDNA control region, and the first comprehensive estimates of positional mutation rates for human mtDNA, which are essential for defining mutation models in phylogenetic analyses. PMID:19500773

  14. The Evolution of School Improvement from the Classroom Teacher's Perspective.

    ERIC Educational Resources Information Center

    Thompson, Marci; Mitchell, Deborah

    2002-01-01

    Highlights changes that have occurred since 1992 at Elm Dale Elementary School (Greenfield, Wisconsin) through the school improvement process. Describes how teachers have become involved in and developed ownership of the improvement process, and how they have learned to analyze data. Asserts that the school improvement process has changed the…

  15. Morphological and Molecular Evolution Are Not Linked in Lamellodiscus (Plathyhelminthes, Monogenea)

    PubMed Central

    Poisot, Timothée; Verneau, Olivier; Desdevises, Yves

    2011-01-01

    Lamellodiscus Johnston & Tiegs 1922 (Monogenea, Diplectanidae) is a genus of common parasites on the gills of sparid fishes. Here we show that this genus is probably undergoing a fast molecular diversification, as reflected by the important genetic variability observed within three molecular markers (partial nuclear 18S rDNA, Internal Transcribed Spacer 1, and mitonchondrial Cytochrome Oxidase I). Using an updated phylogeny of this genus, we show that molecular and morphological evolution are weakly correlated, and that most of the morphologically defined taxonomical units are not consistent with the molecular data. We suggest that Lamellodiscus morphology is probably constrained by strong environmental (host-induced) pressure, and discuss why this result can apply to other taxa. Genetic variability within nuclear 18S and mitochondrial COI genes are compared for several monogenean genera, as this measure may reflect the level of diversification within a genus. Overall our results suggest that cryptic speciation events may occur within Lamellodiscus, and discuss the links between morphological and molecular evolution. PMID:22022582

  16. The pattern of mammalian evolution and the relative rate of molecular evolution

    SciTech Connect

    Easteal, S. )

    1990-01-01

    The rates of nucleotide substitution at four genes in four orders of eutherian mammals are compared in relative rate tests using marsupial orthologs for reference. There is no evidence of systematic variation in evolutionary rate among the orders. The sequences are used to reconstruct the phylogeny of the orders using maximum likelihood, parsimony and compatibility methods. A branching order of rodent then ungulate then primate and lagomorph is overwhelmingly indicated. The nodes of the nucleotide based cladograms are widely separated in relation to the total lengths of the branches. The assumption of a star phylogeny that underlies Kimura's test for molecular evolutionary rate variation is shown to be invalid for eutherian mammals. Excess variance in nucleotide or amino acid differences between mammalian orders, above that predicted by neutral theory is explained better by variation in divergence time than by variation in evolutionary rate.

  17. Book review: Darwinian agriculture: How understanding evolution can improve agriculture by R. Ford Dennison

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Agricultural research continually seeks to increase productivity while protecting soil, water and genetic resources. The book Darwinian Agriculture: How Understanding Evolution Can Improve Agriculture, by R. Ford Dennison, delivers a thought-provoking view of how principles of ecology and evolution ...

  18. Molecular dynamics study of nanoparticle evolution in a background gas under laser ablation conditions

    NASA Astrophysics Data System (ADS)

    Gouriet, K.; Zhigilei, L. V.; Itina, T. E.

    2009-03-01

    Long-time evolution of nanoparticles produced by short laser interactions is investigated for different materials. To better understand the mechanisms of the nanoparticle formation at a microscopic level, we use molecular dynamics (MD) simulations to analyse the evolution of a cluster in the presence of a background gas with different parameters (density and temperature). In particular, we compare the simulation results obtained for materials with different interaction potentials (Morse, Lennard-Jones, and Embedded Atom Model). Attention is focused on the evaporation and condensation processes of a cluster with different size and initial temperature. As a result of the MD calculations, we determinate the influence of both cluster properties and background gas parameters on the nanoparticle evolution. The role of the interaction potential is discussed based on the results of the simulations.

  19. A new model for biological effects of radiation and the driven force of molecular evolution

    NASA Astrophysics Data System (ADS)

    Wada, Takahiro; Manabe, Yuichiro; Nakajima, Hiroo; Tsunoyama, Yuichi; Bando, Masako

    We proposed a new mathematical model to estimate biological effects of radiation, which we call Whack-A-Mole (WAM) model. A special feature of WAM model is that it involves the dose rate of radiation as a key ingredient. We succeeded to reproduce the experimental data of various species concerning the radiation induced mutation frequencies. From the analysis of the mega-mouse experiments, we obtained the mutation rate per base-pair per year for mice which is consistent with the so-called molecular clock in evolution genetics, 10-9 mutation/base-pair/year. Another important quantity is the equivalent dose rate for the whole spontaneous mutation, deff. The value of deff for mice is 1.1*10-3 Gy/hour which is much larger than the dose rate of natural radiation (10- (6 - 7) Gy/hour) by several orders of magnitude. We also analyzed Drosophila data and obtained essentially the same numbers. This clearly indicates that the natural radiation is not the dominant driving force of the molecular evolution, but we should look for other factors, such as miscopy of DNA in duplication process. We believe this is the first quantitative proof of the small contribution of the natural radiation in the molecular evolution.

  20. Molecular evolution of H9N2 avian influenza viruses in Israel.

    PubMed

    Davidson, Irit; Fusaro, Alice; Heidari, Alireza; Monne, Isabella; Cattoli, Giovanni

    2014-06-01

    While the previous phylogenetic analyses of AIV H9N2 in Israel had mainly focused on phylogenetics and on describing different virus introductions into the country, for the first time, the H9N2-HA gene evolutionary history has been examined taking into account its origin, evolution and phylodynamics. The present study reveals the Israeli H9N2 molecular evolution rate, the virus molecular clock and skyline plot. The molecular skyline plot showed two major increments in population diversity sizes, the first which had occurred in 2003, the second between the end of 2007 and the first half of 2008. Between 2004 and 2007 the population size had proved to be constant. The two peaks correspond to the appearance of the 3rd and 4th major genetic groups, as well as to the introduction of two H9N2 vaccines. The mean evolution rate was 6.123 E-3 substitutions/site/year, typical of avian influenza viruses. The time interval from the most recent common ancestor was 12.3 years, corresponding to the year 2000, when H9N2 was first isolated in Israel. PMID:24469467

  1. Effect of colliding plasmas dynamics, evolution, and stagnation on carbon molecular formation

    NASA Astrophysics Data System (ADS)

    Al-Shboul, Khaled F.

    carbon plasmas generated by 40fs pulses of 800 nm radiation from a femtosecond Ti:Sapphire laser. The results show that the molecular species spatial extension and lifetime are directly correlated to the evolution of excited ions in the presence of an ambient gas. Compared to ns graphite LPPs where carbon dimers are represented by complex intensity contours, the contours of fs laser plumes showed more uniform C2 emission. Chapter 6 of this thesis show that graphite colliding plasmas can be used for generating stagnation layer as a potential source for cluster production and as an alternative to introducing ambient gas for decelerating or controlling the plume dynamics. In this study, it was found that C2 dimer emission intensity improved significantly using the colliding scheme compared to conventional single laser ablation plumes. In chapter 7, a special colliding plasma experimental scheme was designed to study fusion reactor plasma facing component material ablation. A special experimental setup was designed where the laser is split into two perpendicular line-like beams focused onto a hemi-circular targets composed of varied elements. Single plume and stagnation layer dynamics of candidate fusion wall materials, viz., carbon and tungsten, and other materials, viz., aluminum, and molybdenum were investigated. The results highlight different characteristics of tungsten and carbon colliding plasmas under similar conditions. While tungsten plumes did not show stagnation clouds at the colliding zone, an intense stagnation layer formed from carbon colliding plumes. This stagnation layer, which may be a source of nanoparticles and aerosols generation, could limit the reactor performance by slowing down the repetition rate. (Abstract shortened by UMI.)

  2. An Improved Differential Evolution Solution for Software Project Scheduling Problem

    PubMed Central

    Biju, A. C.; Victoire, T. Aruldoss Albert; Mohanasundaram, Kumaresan

    2015-01-01

    This paper proposes a differential evolution (DE) method for the software project scheduling problem (SPSP). The interest on finding a more efficient solution technique for SPSP is always a topic of interest due to the fact of ever growing challenges faced by the software industry. The curse of dimensionality is introduced in the scheduling problem by ever increasing software assignments and the number of staff who handles it. Thus the SPSP is a class of NP-hard problem, which requires a rigorous solution procedure which guarantees a reasonably better solution. Differential evolution is a direct search stochastic optimization technique that is fairly fast and reasonably robust. It is also capable of handling nondifferentiable, nonlinear, and multimodal objective functions like SPSP. This paper proposes a refined DE where a new mutation mechanism is introduced. The superiority of the proposed method is experimented and demonstrated by solving the SPSP on 50 random instances and the results are compared with some of the techniques in the literature. PMID:26495419

  3. Improved estimates of coordinate error for molecular replacement

    SciTech Connect

    Oeffner, Robert D.; Bunkóczi, Gábor; McCoy, Airlie J.; Read, Randy J.

    2013-11-01

    A function for estimating the effective root-mean-square deviation in coordinates between two proteins has been developed that depends on both the sequence identity and the size of the protein and is optimized for use with molecular replacement in Phaser. A top peak translation-function Z-score of over 8 is found to be a reliable metric of when molecular replacement has succeeded. The estimate of the root-mean-square deviation (r.m.s.d.) in coordinates between the model and the target is an essential parameter for calibrating likelihood functions for molecular replacement (MR). Good estimates of the r.m.s.d. lead to good estimates of the variance term in the likelihood functions, which increases signal to noise and hence success rates in the MR search. Phaser has hitherto used an estimate of the r.m.s.d. that only depends on the sequence identity between the model and target and which was not optimized for the MR likelihood functions. Variance-refinement functionality was added to Phaser to enable determination of the effective r.m.s.d. that optimized the log-likelihood gain (LLG) for a correct MR solution. Variance refinement was subsequently performed on a database of over 21 000 MR problems that sampled a range of sequence identities, protein sizes and protein fold classes. Success was monitored using the translation-function Z-score (TFZ), where a TFZ of 8 or over for the top peak was found to be a reliable indicator that MR had succeeded for these cases with one molecule in the asymmetric unit. Good estimates of the r.m.s.d. are correlated with the sequence identity and the protein size. A new estimate of the r.m.s.d. that uses these two parameters in a function optimized to fit the mean of the refined variance is implemented in Phaser and improves MR outcomes. Perturbing the initial estimate of the r.m.s.d. from the mean of the distribution in steps of standard deviations of the distribution further increases MR success rates.

  4. Improved molecular collision models for nonequilibrium rarefied gases

    NASA Astrophysics Data System (ADS)

    Parsons, Neal

    The Direct Simulation Monte Carlo (DSMC) method typically used to model thermochemical nonequilibrium rarefied gases requires accurate total collision cross sections, reaction probabilities, and molecular internal energy exchange models. However, the baseline total cross sections are often determined from extrapolations of relatively low-temperature viscosity data, reaction probabilities are defined such that experimentally determined equilibrium reaction rates are replicated, and internal energy relaxation models are phenomenological in nature. Therefore, these models have questionable validity in modeling strongly nonequilibrium gases with temperatures greater than those possible in experimental test facilities. To rectify this deficiency, the Molecular Dynamics/Quasi-Classical Trajectories (MD/QCT) method can be used to accurately compute total collision cross sections, reaction probabilities, and internal energy exchange models based on first principles for hypervelocity collision conditions. In this thesis, MD/QCT-based models were used to improve simulations of two unique nonequilibrium rarefied gas systems: the Ionian atmosphere and hypersonic shocks in Earth's atmosphere. The Jovian plasma torus flows over Io at ≈ 57 km/s, inducing high-speed collisions between atmospheric SO2 and the hypervelocity plasma's O atoms and ions. The DSMC method is well-suited to model the rarefied atmosphere, so MD/QCT studies are therefore conducted to improve DSMC collision models of the critical SO2-O collision pair. The MD/QCT trajectory simulations employed a new potential energy surface that was developed using a ReaxFF fit to a set of ab initio calculations. Compared to the MD/QCT results, the baseline DSMC models are found to significantly under-predict total cross sections, use reaction probabilities that are unrealistically high, and give unphysical internal energies above the dissociation energy for non-reacting inelastic collisions and under-predicts post

  5. From the ultrasonic to the infrared: molecular evolution and the sensory biology of bats.

    PubMed

    Jones, Gareth; Teeling, Emma C; Rossiter, Stephen J

    2013-01-01

    Great advances have been made recently in understanding the genetic basis of the sensory biology of bats. Research has focused on the molecular evolution of candidate sensory genes, genes with known functions [e.g., olfactory receptor (OR) genes] and genes identified from mutations associated with sensory deficits (e.g., blindness and deafness). For example, the FoxP2 gene, underpinning vocal behavior and sensorimotor coordination, has undergone diversification in bats, while several genes associated with audition show parallel amino acid substitutions in unrelated lineages of echolocating bats and, in some cases, in echolocating dolphins, representing a classic case of convergent molecular evolution. Vision genes encoding the photopigments rhodopsin and the long-wave sensitive opsin are functional in bats, while that encoding the short-wave sensitive opsin has lost functionality in rhinolophoid bats using high-duty cycle laryngeal echolocation, suggesting a sensory trade-off between investment in vision and echolocation. In terms of olfaction, bats appear to have a distinctive OR repertoire compared with other mammals, and a gene involved in signal transduction in the vomeronasal system has become non-functional in most bat species. Bitter taste receptors appear to have undergone a "birth-and death" evolution involving extensive gene duplication and loss, unlike genes coding for sweet and umami tastes that show conservation across most lineages but loss in vampire bats. Common vampire bats have also undergone adaptations for thermoperception, via alternative splicing resulting in the evolution of a novel heat-sensitive channel. The future for understanding the molecular basis of sensory biology is promising, with great potential for comparative genomic analyses, studies on gene regulation and expression, exploration of the role of alternative splicing in the generation of proteomic diversity, and linking genetic mechanisms to behavioral consequences. PMID:23755015

  6. Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata.

    PubMed

    Maurer-Alcalá, Xyrus X; Katz, Laura A

    2016-01-01

    The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a "heteromeric" macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into "gene-sized" chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a "gene bank" that facilitates rapid changes in expression of genes required only in specific life history stages. By using "nonmodel" organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features. PMID:27189988

  7. From the ultrasonic to the infrared: molecular evolution and the sensory biology of bats

    PubMed Central

    Jones, Gareth; Teeling, Emma C.; Rossiter, Stephen J.

    2013-01-01

    Great advances have been made recently in understanding the genetic basis of the sensory biology of bats. Research has focused on the molecular evolution of candidate sensory genes, genes with known functions [e.g., olfactory receptor (OR) genes] and genes identified from mutations associated with sensory deficits (e.g., blindness and deafness). For example, the FoxP2 gene, underpinning vocal behavior and sensorimotor coordination, has undergone diversification in bats, while several genes associated with audition show parallel amino acid substitutions in unrelated lineages of echolocating bats and, in some cases, in echolocating dolphins, representing a classic case of convergent molecular evolution. Vision genes encoding the photopigments rhodopsin and the long-wave sensitive opsin are functional in bats, while that encoding the short-wave sensitive opsin has lost functionality in rhinolophoid bats using high-duty cycle laryngeal echolocation, suggesting a sensory trade-off between investment in vision and echolocation. In terms of olfaction, bats appear to have a distinctive OR repertoire compared with other mammals, and a gene involved in signal transduction in the vomeronasal system has become non-functional in most bat species. Bitter taste receptors appear to have undergone a “birth-and death” evolution involving extensive gene duplication and loss, unlike genes coding for sweet and umami tastes that show conservation across most lineages but loss in vampire bats. Common vampire bats have also undergone adaptations for thermoperception, via alternative splicing resulting in the evolution of a novel heat-sensitive channel. The future for understanding the molecular basis of sensory biology is promising, with great potential for comparative genomic analyses, studies on gene regulation and expression, exploration of the role of alternative splicing in the generation of proteomic diversity, and linking genetic mechanisms to behavioral consequences. PMID

  8. Nuclear Architecture and Patterns of Molecular Evolution Are Correlated in the Ciliate Chilodonella uncinata

    PubMed Central

    Maurer-Alcalá, Xyrus X.; Katz, Laura A.

    2016-01-01

    The relationship between nuclear architecture and patterns of molecular evolution in lineages across the eukaryotic tree of life is not well understood, partly because molecular evolution is traditionally explored as changes in base pairs along a linear sequence without considering the context of nuclear position of chromosomes. The ciliate Chilodonella uncinata is an ideal system to address the relationship between nuclear architecture and patterns of molecular evolution as the somatic macronucleus of this ciliate is composed of a peripheral DNA-rich area (orthomere) and a DNA-poor central region (paramere) to form a “heteromeric” macronucleus. Moreover, because the somatic chromosomes of C. uncinata are highly processed into “gene-sized” chromosomes (i.e., nanochromosomes), we can assess fine-scale relationships between location and sequence evolution. By combining fluorescence microscopy and analyses of transcriptome data from C. uncinata, we find that highly expressed genes have the greatest codon usage bias and are enriched in DNA-poor regions. In contrast, genes with less biased sequences tend to be concentrated in DNA abundant areas, at least during vegetative growth. Our analyses are consistent with recent work in plants and animals where nuclear architecture plays a role in gene expression. At the same time, the unusual localization of nanochromosomes suggests that the highly structured nucleus in C. uncinata may create a “gene bank” that facilitates rapid changes in expression of genes required only in specific life history stages. By using “nonmodel” organisms like C. uncinata, we can explore the universality of eukaryotic features while also providing examples of novel properties (i.e., the presence of a gene bank) that build from these features. PMID:27189988

  9. Improving Glyphosate Oxidation Activity of Glycine Oxidase from Bacillus cereus by Directed Evolution

    PubMed Central

    Zhan, Tao; Zhang, Kai; Chen, Yangyan; Lin, Yongjun; Wu, Gaobing; Zhang, Lili; Yao, Pei; Shao, Zongze; Liu, Ziduo

    2013-01-01

    Glyphosate, a broad spectrum herbicide widely used in agriculture all over the world, inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, and glycine oxidase (GO) has been reported to be able to catalyze the oxidative deamination of various amines and cleave the C-N bond in glyphosate. Here, in an effort to improve the catalytic activity of the glycine oxidase that was cloned from a glyphosate-degrading marine strain of Bacillus cereus (BceGO), we used a bacteriophage T7 lysis-based method for high-throughput screening of oxidase activity and engineered the gene encoding BceGO by directed evolution. Six mutants exhibiting enhanced activity toward glyphosate were screened from two rounds of error-prone PCR combined with site directed mutagenesis, and the beneficial mutations of the six evolved variants were recombined by DNA shuffling. Four recombinants were generated and, when compared with the wild-type BceGO, the most active mutant B3S1 showed the highest activity, exhibiting a 160-fold increase in substrate affinity, a 326-fold enhancement in catalytic efficiency against glyphosate, with little difference between their pH and temperature stabilities. The role of these mutations was explored through structure modeling and molecular docking, revealing that the Arg51 mutation is near the active site and could be an important residue contributing to the stabilization of glyphosate binding, while the role of the remaining mutations is unclear. These results provide insight into the application of directed evolution in optimizing glycine oxidase function and have laid a foundation for the development of glyphosate-tolerant crops. PMID:24223901

  10. Evolution of planetary nebulae. I. An improved synthetic model

    NASA Astrophysics Data System (ADS)

    Marigo, P.; Girardi, L.; Groenewegen, M. A. T.; Weiss, A.

    2001-11-01

    We present a new synthetic model to follow the evolution of a planetary nebula (PN) and its central star, starting from the onset of AGB phase up to the white dwarf cooling sequence. The model suitably combines various analytical prescriptions to account for different (but inter-related) aspects of planetary nebulae, such as: the dynamical evolution of the primary shell and surrounding ejecta, the photoionisation of H and He by the central star, the nebular emission of a few relevant optical lines (e.g. Hβ ; He II lambda 4686; [O III] lambda 5007). Particular effort has been put into the analytical description of dynamical effects such as the three-winds interaction and the shell thickening due to ionisation (i.e. the thin-shell approximation is relaxed), that are nowadays considered important aspects of the PN evolution. Predictions of the synthetic model are tested by comparison with both findings of hydrodynamical calculations, and observations of Galactic PNe. The sensitiveness of the results to the model parameters (e.g. transition time, mass of the central star, H-/He-burning tracks, etc.) is also discussed. We briefly illustrate the systematic differences that are expected in the luminosities and lifetimes of PNe with either H- or He-burning central stars, which result in different ``detection probabilities'' across the H-R diagram, in both Hβ and [OIII] lambda5007 lines. Adopting reasonable values of the model parameters, we are able to reproduce, in a satisfactory way, many general properties of PNe, like the ionised mass-nebular radius relationship, the trends of a few main nebular line ratios, and the observed ranges of nebular shell thicknesses, electron densities, and expansion velocities. The models naturally predict also the possible transitions from optically-thick to optically-thin configurations (and vice versa). In this context, our analysis indicates that the condition of optical thinness to the H continuum plays an important role in producing

  11. Recent insertion/deletion (reINDEL) mutations: increasing awareness to boost molecular-based research in ecology and evolution

    PubMed Central

    Schlick-Steiner, Birgit C; Arthofer, Wolfgang; Moder, Karl; Steiner, Florian M

    2015-01-01

    Today, the comparative analysis of DNA molecules mainly uses information inferred from nucleotide substitutions. Insertion/deletion (INDEL) mutations, in contrast, are largely considered uninformative and discarded, due to our lacking knowledge on their evolution. However, including rather than discarding INDELs would be relevant to any research area in ecology and evolution that uses molecular data. As a practical approach to better understanding INDEL evolution in general, we propose the study of recent INDEL (reINDEL) mutations – mutations where both ancestral and derived state are seen in the sample. The precondition for reINDEL identification is knowledge about the pedigree of the individuals sampled. Sound reINDEL knowledge will allow the improved modeling needed for including INDELs in the downstream analysis of molecular data. Both microsatellites, currently still the predominant marker system in the analysis of populations, and sequences generated by next-generation sequencing, a promising and rapidly developing range of technologies, offer the opportunity for reINDEL identification. However, a 2013 sample of animal microsatellite studies contained unexpectedly few reINDELs identified. As most likely explanation, we hypothesize that reINDELs are underreported rather than absent and that this underreporting stems from common reINDEL unawareness. If our hypothesis applies, increased reINDEL awareness should allow gathering data rapidly. We recommend the routine reporting of either the absence or presence of reINDELs together with standardized key information on the nature of mutations when they are detected and the use of the keyword “reINDEL” to increase visibility in both instances of successful and unsuccessful search. PMID:25628861

  12. Molecular representation of molar domain (volume), evolution equations, and linear constitutive relations for volume transport.

    PubMed

    Eu, Byung Chan

    2008-09-01

    In the traditional theories of irreversible thermodynamics and fluid mechanics, the specific volume and molar volume have been interchangeably used for pure fluids, but in this work we show that they should be distinguished from each other and given distinctive statistical mechanical representations. In this paper, we present a general formula for the statistical mechanical representation of molecular domain (volume or space) by using the Voronoi volume and its mean value that may be regarded as molar domain (volume) and also the statistical mechanical representation of volume flux. By using their statistical mechanical formulas, the evolution equations of volume transport are derived from the generalized Boltzmann equation of fluids. Approximate solutions of the evolution equations of volume transport provides kinetic theory formulas for the molecular domain, the constitutive equations for molar domain (volume) and volume flux, and the dissipation of energy associated with volume transport. Together with the constitutive equation for the mean velocity of the fluid obtained in a previous paper, the evolution equations for volume transport not only shed a fresh light on, and insight into, irreversible phenomena in fluids but also can be applied to study fluid flow problems in a manner hitherto unavailable in fluid dynamics and irreversible thermodynamics. Their roles in the generalized hydrodynamics will be considered in the sequel. PMID:19044872

  13. Molecular evolution of the capsid gene in human norovirus genogroup II.

    PubMed

    Kobayashi, Miho; Matsushima, Yuki; Motoya, Takumi; Sakon, Naomi; Shigemoto, Naoki; Okamoto-Nakagawa, Reiko; Nishimura, Koichi; Yamashita, Yasutaka; Kuroda, Makoto; Saruki, Nobuhiro; Ryo, Akihide; Saraya, Takeshi; Morita, Yukio; Shirabe, Komei; Ishikawa, Mariko; Takahashi, Tomoko; Shinomiya, Hiroto; Okabe, Nobuhiko; Nagasawa, Koo; Suzuki, Yoshiyuki; Katayama, Kazuhiko; Kimura, Hirokazu

    2016-01-01

    Capsid protein of norovirus genogroup II (GII) plays crucial roles in host infection. Although studies on capsid gene evolution have been conducted for a few genotypes of norovirus, the molecular evolution of norovirus GII is not well understood. Here we report the molecular evolution of all GII genotypes, using various bioinformatics techniques. The time-scaled phylogenetic tree showed that the present GII strains diverged from GIV around 1630CE at a high evolutionary rate (around 10(-3) substitutions/site/year), resulting in three lineages. The GII capsid gene had large pairwise distances (maximum > 0.39). The effective population sizes of the present GII strains were large (>10(2)) for about 400 years. Positive (20) and negative (over 450) selection sites were estimated. Moreover, some linear and conformational B-cell epitopes were found in the deduced GII capsid protein. These results suggested that norovirus GII strains rapidly evolved with high divergence and adaptation to humans. PMID:27384324

  14. Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes

    PubMed Central

    Fischbach, Michael A.; Lai, Jonathan R.; Roche, Eric D.; Walsh, Christopher T.; Liu, David R.

    2007-01-01

    Nonribosomal peptides (NRPs) are produced by NRP synthetase (NRPS) enzymes that function as molecular assembly lines. The modular architecture of NRPSs suggests that a domain responsible for activating a building block could be replaced with a domain from a foreign NRPS to create a chimeric assembly line that produces a new variant of a natural NRP. However, such chimeric NRPS modules are often heavily impaired, impeding efforts to create novel NRP variants by swapping domains from different modules or organisms. Here we show that impaired chimeric NRPSs can be functionally restored by directed evolution. Using rounds of mutagenesis coupled with in vivo screens for NRP production, we rapidly isolated variants of two different chimeric NRPSs with ≈10-fold improvements in enzyme activity and product yield, including one that produces new derivatives of the potent NRP/polyketide antibiotic andrimid. Because functional restoration in these examples required only modest library sizes (103 to 104 clones) and three or fewer rounds of screening, our approach may be widely applicable even for NRPSs from genetically challenging hosts. PMID:17620609

  15. Molecular Evolution of Dengue Viruses: Contributions of Phylogenetics to Understanding the History and Epidemiology of the Preeminent Arboviral Disease

    PubMed Central

    Weaver, Scott C.; Vasilakis, Nikos

    2013-01-01

    Dengue viruses (DENV) are the most important arboviral pathogens in tropical and subtropical regions throughout the world, putting at risk of infection nearly a third of the global human population. Evidence from the historical record suggests a long association between these viruses and humans. The transmission of DENV includes a sylvatic, enzootic cycle between nonhuman primates and arboreal mosquitoes of the genus Aedes, and an urban, endemic/epidemic cycle between Aedes aegypti, a mosquito with larval development in peridomestic water containers, and human reservoir hosts. DENV are members of the genus Flavivirus in the Family Flaviviridae and comprise of 4 antigenically distinct serotypes (DENV-1-4). Although they are nearly identical epidemiologically, the 4 DENV serotypes are genetically quite distinct. Utilization of phylogenetic analyses based on partial and/or complete genomic sequences has elucidated the origins, epidemiology (genetic diversity, transmission dynamics and epidemic potential), and the forces that shape DENV molecular evolution (rates of evolution, selection pressures, population sizes, putative recombination and evolutionary constraints) in nature. In this review, we examine how phylogenetics have improved understanding of DENV population dynamics and sizes at various stages of infection and transmission, and how this information may influence pathogenesis and improve our ability to understand and predict DENV emergence. PMID:19460319

  16. Molecular evolution and adaptation of the mitochondrial cytochrome b gene in the subgenus Martes.

    PubMed

    Li, B; Malyarchuk, B; He, X B; Derenko, M

    2013-01-01

    Martes species represent a typical example of rapid evolutionary radiation and a recent speciation event. To identify regions of the genome that experienced adaptive evolution, which might provide clues to their functional importance and may be informative about the features that make each species unique, we sought evidence of molecular adaptation in the mitochondrial DNA (mtDNA) cytochrome b gene in the subgenus Martes. Complete sequences of the cytochrome b gene were obtained from 87 samples, including 49 sables, 28 pine martens, and 10 stone martens, and were combined with mtDNA sequences of other true martens, such as M. melampus and M. americana. Analysis of the cytochrome b gene variation in true martens has shown that the evolution of this gene is under negative selection. In contrast, positive selection on the cytochrome b protein has been detected by means of the software TreeSAAP using a phylogenetic reconstruction of Martes taxa. Signatures of adaptive variation in cytochrome b were restricted to the transmembrane domains, which likely function as proton pumps. We compared results of different methods for testing selection and molecular adaptation, and we supposed that the radical changes of the cytochrome b amino acid residues in the subgenus Martes may be the result of molecular adaptation to specific environmental conditions coupled with species dispersals. PMID:24085456

  17. The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure

    PubMed Central

    Allen, Benjamin; Sample, Christine; Dementieva, Yulia; Medeiros, Ruben C.; Paoletti, Christopher; Nowak, Martin A.

    2015-01-01

    Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a “molecular clock” to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution. PMID:25719560

  18. Hepatitis C virus molecular evolution: Transmission, disease progression and antiviral therapy

    PubMed Central

    Preciado, Maria Victoria; Valva, Pamela; Escobar-Gutierrez, Alejandro; Rahal, Paula; Ruiz-Tovar, Karina; Yamasaki, Lilian; Vazquez-Chacon, Carlos; Martinez-Guarneros, Armando; Carpio-Pedroza, Juan Carlos; Fonseca-Coronado, Salvador; Cruz-Rivera, Mayra

    2014-01-01

    Hepatitis C virus (HCV) infection represents an important public health problem worldwide. Reduction of HCV morbidity and mortality is a current challenge owned to several viral and host factors. Virus molecular evolution plays an important role in HCV transmission, disease progression and therapy outcome. The high degree of genetic heterogeneity characteristic of HCV is a key element for the rapid adaptation of the intrahost viral population to different selection pressures (e.g., host immune responses and antiviral therapy). HCV molecular evolution is shaped by different mechanisms including a high mutation rate, genetic bottlenecks, genetic drift, recombination, temporal variations and compartmentalization. These evolutionary processes constantly rearrange the composition of the HCV intrahost population in a staging manner. Remarkable advances in the understanding of the molecular mechanism controlling HCV replication have facilitated the development of a plethora of direct-acting antiviral agents against HCV. As a result, superior sustained viral responses have been attained. The rapidly evolving field of anti-HCV therapy is expected to broad its landscape even further with newer, more potent antivirals, bringing us one step closer to the interferon-free era. PMID:25473152

  19. Molecular evolution and antigenic variation of European brown hare syndrome virus (EBHSV).

    PubMed

    Lopes, Ana M; Capucci, Lorenzo; Gavier-Widén, Dolores; Le Gall-Reculé, Ghislaine; Brocchi, Emiliana; Barbieri, Ilaria; Quéméner, Agnès; Le Pendu, Jacques; Geoghegan, Jemma L; Holmes, Edward C; Esteves, Pedro J; Abrantes, Joana

    2014-11-01

    European brown hare syndrome virus (EBHSV) is the aetiological agent of European brown hare syndrome (EBHS), a disease affecting Lepus europaeus and Lepus timidus first diagnosed in Sweden in 1980. To characterize EBHSV evolution we studied hare samples collected in Sweden between 1982 and 2008. Our molecular clock dating is compatible with EBHSV emergence in the 1970s. Phylogenetic analysis revealed two lineages: Group A persisted until 1989 when it apparently suffered extinction; Group B emerged in the mid-1980s and contains the most recent strains. Antigenic differences exist between groups, with loss of reactivity of some MAbs over time, which are associated with amino acid substitutions in recognized epitopes. A role for immune selection is also supported by the presence of positively selected codons in exposed regions of the capsid. Hence, EBHSV evolution is characterized by replacement of Group A by Group B viruses, suggesting that the latter possess a selective advantage. PMID:25155199

  20. Molecular evolution of Dmrt1 accompanies change of sex-determining mechanisms in reptilia

    PubMed Central

    Janes, Daniel E.; Organ, Christopher L.; Stiglec, Rami; O'Meally, Denis; Sarre, Stephen D.; Georges, Arthur; Graves, Jennifer A. M.; Valenzuela, Nicole; Literman, Robert A.; Rutherford, Kim; Gemmell, Neil; Iverson, John B.; Tamplin, Jeffrey W.; Edwards, Scott V.; Ezaz, Tariq

    2014-01-01

    In reptiles, sex-determining mechanisms have evolved repeatedly and reversibly between genotypic and temperature-dependent sex determination. The gene Dmrt1 directs male determination in chicken (and presumably other birds), and regulates sex differentiation in animals as distantly related as fruit flies, nematodes and humans. Here, we show a consistent molecular difference in Dmrt1 between reptiles with genotypic and temperature-dependent sex determination. Among 34 non-avian reptiles, a convergently evolved pair of amino acids encoded by sequence within exon 2 near the DM-binding domain of Dmrt1 distinguishes species with either type of sex determination. We suggest that this amino acid shift accompanied the evolution of genotypic sex determination from an ancestral condition of temperature-dependent sex determination at least three times among reptiles, as evident in turtles, birds and squamates. This novel hypothesis describes the evolution of sex-determining mechanisms as turnover events accompanied by one or two small mutations. PMID:25540158

  1. Plant hemoglobins: a molecular fossil record for the evolution of oxygen transport.

    PubMed

    Hoy, Julie A; Robinson, Howard; Trent, James T; Kakar, Smita; Smagghe, Benoit J; Hargrove, Mark S

    2007-08-01

    The evolution of oxygen transport hemoglobins occurred on at least two independent occasions. The earliest event led to myoglobin and red blood cell hemoglobin in animals. In plants, oxygen transport "leghemoglobins" evolved much more recently. In both events, pentacoordinate heme sites capable of inert oxygen transfer evolved from hexacoordinate hemoglobins that have unrelated functions. High sequence homology between hexacoordinate and pentacoordinate hemoglobins in plants has poised them for potential structural analysis leading to a molecular understanding of this important evolutionary event. However, the lack of a plant hexacoordinate hemoglobin structure in the exogenously ligand-bound form has prevented such comparison. Here we report the crystal structure of the cyanide-bound hexacoordinate hemoglobin from barley. This presents the first opportunity to examine conformational changes in plant hexacoordinate hemoglobins upon exogenous ligand binding, and reveals structural mechanisms for stabilizing the high-energy pentacoordinate heme conformation critical to the evolution of reversible oxygen binding hemoglobins. PMID:17560601

  2. PAL: an object-oriented programming library for molecular evolution and phylogenetics.

    PubMed

    Drummond, A; Strimmer, K

    2001-07-01

    Phylogenetic Analysis Library (PAL) is a collection of Java classes for use in molecular evolution and phylogenetics. PAL provides a modular environment for the rapid construction of both special-purpose and general analysis programs. PAL version 1.1 consists of 145 public classes or interfaces in 13 packages, including classes for models of character evolution, maximum-likelihood estimation, and the coalescent, with a total of more than 27000 lines of code. The PAL project is set up as a collaborative project to facilitate contributions from other researchers. AVAILIABILTY: The program is free and is available at http://www.pal-project.org. It requires Java 1.1 or later. PAL is licensed under the GNU General Public License. PMID:11448888

  3. Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution

    PubMed Central

    Skinner, Michael K.

    2015-01-01

    Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of environmental factors cannot directly alter DNA sequence. Epigenetic mechanisms directly regulate genetic processes and can be dramatically altered by environmental factors. Therefore, environmental epigenetics provides a molecular mechanism to directly alter phenotypic variation generationally. Lamarck proposed in 1802 the concept that environment can directly alter phenotype in a heritable manner. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process. Therefore, environment can on a molecular level influence the phenotypic variation directly. The ability of environmental epigenetics to alter phenotypic and genotypic variation directly can significantly impact natural selection. Neo-Lamarckian concept can facilitate neo-Darwinian evolution. A unified theory of evolution is presented to describe the integration of environmental epigenetic and genetic aspects of evolution. PMID:25917417

  4. Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness

    PubMed Central

    Peña, Matthew I.; Van Itallie, Elizabeth; Bennett, Matthew R.; Shamoo, Yousif

    2010-01-01

    Evolution by natural selection is the driving force behind the endless variation we see in nature, yet our understanding of how changes at the molecular level give rise to different phenotypes and altered fitness at the population level remains inadequate. The reproductive fitness of an organism is the most basic metric that describes the chance that an organism will succeed or fail in its environment and it depends upon a complex network of inter- and intramolecular interactions. A deeper understanding of the quantitative relationships relating molecular evolution to adaptation, and consequently fitness, can guide our understanding of important issues in biomedicine such as drug resistance and the engineering of new organisms with applications to biotechnology. We have developed the “weak link” approach to determine how changes in molecular structure and function can relate to fitness and evolutionary outcomes. By replacing adenylate kinase (AK), an essential gene, in a thermophile with a homologous AK from a mesophile we have created a maladapted weak link that produces a temperature-sensitive phenotype. The recombinant strain adapts to nonpermissive temperatures through point mutations to the weak link that increase both stability and activity of the enzyme AK at higher temperatures. Here, we propose a fitness function relating enzyme activity to growth rate and use it to create a dynamic model of a population of bacterial cells. Using metabolic control analysis we show that the growth rate exhibits thresholdlike behavior, saturating at high enzyme activity as other reactions in the energy metabolism pathway become rate limiting. The dynamic model accurately recapitulates observed evolutionary outcomes. These findings suggest that in vitro enzyme kinetic data, in combination with metabolic network analysis, can be used to create fitness functions and dynamic models of evolution within simple metabolic systems. PMID:20590336

  5. Evolution of a single gene highlights the complexity underlying molecular descriptions of fitness

    NASA Astrophysics Data System (ADS)

    Peña, Matthew I.; Van Itallie, Elizabeth; Bennett, Matthew R.; Shamoo, Yousif

    2010-06-01

    Evolution by natural selection is the driving force behind the endless variation we see in nature, yet our understanding of how changes at the molecular level give rise to different phenotypes and altered fitness at the population level remains inadequate. The reproductive fitness of an organism is the most basic metric that describes the chance that an organism will succeed or fail in its environment and it depends upon a complex network of inter- and intramolecular interactions. A deeper understanding of the quantitative relationships relating molecular evolution to adaptation, and consequently fitness, can guide our understanding of important issues in biomedicine such as drug resistance and the engineering of new organisms with applications to biotechnology. We have developed the "weak link" approach to determine how changes in molecular structure and function can relate to fitness and evolutionary outcomes. By replacing adenylate kinase (AK), an essential gene, in a thermophile with a homologous AK from a mesophile we have created a maladapted weak link that produces a temperature-sensitive phenotype. The recombinant strain adapts to nonpermissive temperatures through point mutations to the weak link that increase both stability and activity of the enzyme AK at higher temperatures. Here, we propose a fitness function relating enzyme activity to growth rate and use it to create a dynamic model of a population of bacterial cells. Using metabolic control analysis we show that the growth rate exhibits thresholdlike behavior, saturating at high enzyme activity as other reactions in the energy metabolism pathway become rate limiting. The dynamic model accurately recapitulates observed evolutionary outcomes. These findings suggest that in vitro enzyme kinetic data, in combination with metabolic network analysis, can be used to create fitness functions and dynamic models of evolution within simple metabolic systems.

  6. Water oxidation catalysis upon evolution of molecular Co(III) cubanes in aqueous media.

    PubMed

    Genoni, Andrea; La Ganga, Giuseppina; Volpe, Andrea; Puntoriero, Fausto; Di Valentin, Marilena; Bonchio, Marcella; Natali, Mirco; Sartorel, Andrea

    2015-01-01

    The increasing global energy demand has stimulated great recent efforts in investigating new solutions for artificial photosynthesis, a potential source of clean and renewable solar fuel. In particular, according to the generally accepted modular approach aimed at optimising separately the different compartments of the entire process, many studies have focused on the development of catalytic systems for water oxidation to oxygen. While in recent years there have been many reports on new catalytic systems, the mechanism and the active intermediates operating the catalysis have been less investigated. Well-defined, molecular catalysts, constituted by transition metals stabilised by a suitable ligand pool, could help in solving this aspect. However, in some cases molecular species have been shown to evolve to active metal oxides that constitute the other side of this catalysis dichotomy. In this paper, we address the evolution of tetracobalt(III) cubanes, stabilised by a pyridine/acetate ligand pool, to active species that perform water oxidation to oxygen. Primary evolution of the cubane in aqueous solution is likely initiated by removal of an acetate bridge, opening the coordination sphere of the cobalt centres. This cobalt derivative, where the pristine ligands still impact on the reactivity, shows enhanced electron transfer rates to Ru(bpy)3(3+) (hole scavenging) within a photocatalytic cycle with Ru(bpy)3(2+) as the photosensitiser and S2O8(2-) as the electron sink. A more accentuated evolution occurs under continuous irradiation, where Electron Paramagnetic Resonance (EPR) spectroscopy reveals the formation of Co(ii) intermediates, likely contributing to the catalytic process that evolves oxygen. All together, these results confirm the relevant effect of molecular species, in particular in fostering the rate of the electron transfer processes involved in light activated cycles, pivotal in the design of a photoactive device. PMID:26400662

  7. Non-unity molecular heritability demonstrated by continuous evolution in vitro

    NASA Technical Reports Server (NTRS)

    Schmitt, T.; Lehman, N.

    1999-01-01

    INTRODUCTION: When catalytic RNA is evolved in vitro, the molecule's chemical reactivity is usually the desired selection target. Sometimes the phenotype of a particular RNA molecule cannot be unambiguously determined from its genotype, however. This can occur if a nucleotide sequence can adopt multiple folded states, an example of non-unity heritability (i.e. one genotype gives rise to more than one phenotype). In these cases, more rounds of selection are required to achieve a phenotypic shift. We tested the influence of non-unity heritability at the molecular level by selecting for variants of a ligase ribozyme via continuous evolution. RESULTS: During 20 bursts of continuous evolution of a 152-nucleotide ligase ribozyme in which the Mg2+ concentration was periodically lowered, a nine-error variant of the starting 'wild-type' molecule became dominant in the last eight bursts. This variant appears to be more active than the wild type. Kinetic analyses of the mutant suggest that it may not possess a higher first-order catalytic rate constant, however. Examination of the multiple RNA conformations present under the continuous evolution conditions suggests that the mutant is superior to the wild type because it is less likely to misfold into inactive conformers. CONCLUSIONS: The evolution of genotypes that are more likely to exhibit a particular phenotype is an epiphenomenon usually ascribed only to complex living systems. We show that this can occur at the molecular level, demonstrating that in vitro systems may have more life-like characteristics than previously thought, and providing additional support for an RNA world.

  8. Evolution.

    ERIC Educational Resources Information Center

    Mayr, Ernst

    1978-01-01

    Traces the history of evolution theory from Lamarck and Darwin to the present. Discusses natural selection in detail. Suggests that, besides biological evolution, there is also a cultural evolution which is more rapid than the former. (MA)

  9. Collinearly-improved BK evolution meets the HERA data

    NASA Astrophysics Data System (ADS)

    Iancu, E.; Madrigal, J. D.; Mueller, A. H.; Soyez, G.; Triantafyllopoulos, D. N.

    2015-11-01

    In a previous publication, we have established a collinearly-improved version of the Balitsky-Kovchegov (BK) equation, which resums to all orders the radiative corrections enhanced by large double transverse logarithms. Here, we study the relevance of this equation as a tool for phenomenology, by confronting it to the HERA data. To that aim, we first improve the perturbative accuracy of our resummation, by including two classes of single-logarithmic corrections: those generated by the first non-singular terms in the DGLAP splitting functions and those expressing the one-loop running of the QCD coupling. The equation thus obtained includes all the next-to-leading order corrections to the BK equation which are enhanced by (single or double) collinear logarithms. We then use numerical solutions to this equation to fit the HERA data for the electron-proton reduced cross-section at small Bjorken x. We obtain good quality fits for physically acceptable initial conditions. Our best fit, which shows a good stability up to virtualities as large as Q2 = 400 GeV2 for the exchanged photon, uses as an initial condition the running-coupling version of the McLerran-Venugopalan model, with the QCD coupling running according to the smallest dipole prescription.

  10. An improved version of the Green's function molecular dynamics method

    NASA Astrophysics Data System (ADS)

    Kong, Ling Ti; Denniston, Colin; Müser, Martin H.

    2011-02-01

    This work presents an improved version of the Green's function molecular dynamics method (Kong et al., 2009; Campañá and Müser, 2004 [1,2]), which enables one to study the elastic response of a three-dimensional solid to an external stress field by taking into consideration only atoms near the surface. In the previous implementation, the effective elastic coefficients measured at the Γ-point were altered to reduce finite size effects: their eigenvalues corresponding to the acoustic modes were set to zero. This scheme was found to work well for simple Bravais lattices as long as only atoms within the last layer were treated as Green's function atoms. However, it failed to function as expected in all other cases. It turns out that a violation of the acoustic sum rule for the effective elastic coefficients at Γ (Kong, 2010 [3]) was responsible for this behavior. In the new version, the acoustic sum rule is enforced by adopting an iterative procedure, which is found to be physically more meaningful than the previous one. In addition, the new algorithm allows one to treat lattices with bases and the Green's function slab is no longer confined to one layer. New version program summaryProgram title: FixGFC/FixGFMD v1.12 Catalogue identifier: AECW_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AECW_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 206 436 No. of bytes in distributed program, including test data, etc.: 4 314 850 Distribution format: tar.gz Programming language: C++ Computer: All Operating system: Linux Has the code been vectorized or parallelized?: Yes. Code has been parallelized using MPI directives. RAM: Depends on the problem Classification: 7.7 External routines: LAMMPS ( http://lammps.sandia.gov/), MPI ( http

  11. Evolution of shear banding flows in metallic glasses characterized by molecular dynamics

    NASA Astrophysics Data System (ADS)

    Yao, Li; Luan, Yingwei

    2016-06-01

    To reveal the evolution of shear banding flows, one-dimensional nanostructure metallic glass composites have been studied with molecular dynamics. The inherent size determines the initial thickness of shear bands, and the subsequent broadening can be restricted to some extent. The vortex-like flows evoke the atomic motion perpendicular to the shear plane, which accelerates the interatomic diffusion. The reduction of local strain rate causes the flow softening for monolithic Cu-Zr glass, but the participation of Cu-atoms in the shear banding flow gradually leads to the shear hardening for the composites.

  12. Thiol-catalyzed formation of lactate and glycerate from glyceraldehyde. [significance in molecular evolution

    NASA Technical Reports Server (NTRS)

    Weber, A. L.

    1983-01-01

    The rate of lactate formation from glyceraldehyde, catalyzed by N-acetyl-cysteine at ambient temperature in aqueous sodium phosphate (pH 7.0), is more rapid at higher sodium phosphate concentrations and remains essentially the same in the presence and absence of oxygen. The dramatic increase in the rate of glycerate formation that is brought about by this thiol, N-acetylcysteine, is accompanied by commensurate decreases in the rates of glycolate and formate production. It is suggested that the thiol-dependent formation of lactate and glycerate occurs by way of their respective thioesters. Attention is given to the significance of these reactions in the context of molecular evolution.

  13. Molecular structure matching by simulated annealing. II. An exploration of the evolution of configuration landscape problems.

    PubMed

    Barakat, M T; Dean, P M

    1990-09-01

    This paper considers some of the landscape problems encountered in matching molecules by simulated annealing. Although the method is in theory ergodic, the global minimum in the objective function is not always encountered. Factors inherent in the molecular data that lead the trajectory of the minimization away from its optimal route are analysed. Segments comprised of the C alpha atoms of dihydrofolate reductase are used as test data. The evolution of a reverse ordering landscape problem is examined in detail. Where such patterns in the data could lead to incorrect matches, the problem can in part be circumvented by assigning an initial random ordering to the molecules. PMID:2280267

  14. Spatiotemporal evolution of plasma molecular emission following laser ablation of explosive analogs

    NASA Astrophysics Data System (ADS)

    Merten, Jonathan; Jones, Matthew; Sheppard, Cheyenne; Parigger, Christian; Allen, Susan

    2013-05-01

    The spatial and temporal evolution of the CN molecular emission following laser ablation of a TNT analog (3- nitrobenzoic acid) has been studied along with ablation of targets that contain neither nitro groups nor C-N bonds. At a fluence of ~104 J/cm2, behavior indicative of the ablation of native CN bonds has been observed in samples containing no native CN bonds. The recorded data show significant plasma background emissions that pose difficulties for direct spectral imaging. Spatially resolved images suggest that some of the observed phenomena are simply the result of the interaction of the plasma and the observation volume of the collection optics.

  15. Genetic diversity and molecular evolution of arabis mosaic virus based on the CP gene sequence.

    PubMed

    Gao, Fangluan; Lin, Wuzhen; Shen, Jianguo; Liao, Furong

    2016-04-01

    Arabis mosaic virus (ArMV) is a virus with a wide host range. In this study, the genetic diversity of ArMV and the molecular mechanisms underlying its evolution were investigated using the coat protein (CP) sequence. Of the 33 ArMV isolates studied, three were found to be recombinants. The other 30 recombination-free ArMV isolates could be separated into two major lineages with a significant F ST value (0.384) and tended to cluster according to their geographical origin. Different evolutionary constraints were detected for the two linages, pointing to a role of natural selection in the differentiation of ArMV. PMID:26758729

  16. Molecular basis for convergent evolution of glutamate recognition by pentameric ligand-gated ion channels

    PubMed Central

    Lynagh, Timothy; Beech, Robin N.; Lalande, Maryline J.; Keller, Kevin; Cromer, Brett A.; Wolstenholme, Adrian J.; Laube, Bodo

    2015-01-01

    Glutamate is an indispensable neurotransmitter, triggering postsynaptic signals upon recognition by postsynaptic receptors. We questioned the phylogenetic position and the molecular details of when and where glutamate recognition arose in the glutamate-gated chloride channels. Experiments revealed that glutamate recognition requires an arginine residue in the base of the binding site, which originated at least three distinct times according to phylogenetic analysis. Most remarkably, the arginine emerged on the principal face of the binding site in the Lophotrochozoan lineage, but 65 amino acids upstream, on the complementary face, in the Ecdysozoan lineage. This combined experimental and computational approach throws new light on the evolution of synaptic signalling. PMID:25708000

  17. [Molecular evolution of ciliates (Ciliophora) and some related groups of protozoans].

    PubMed

    Lukashenko, N P

    2009-08-01

    The review summarizes current evidence, including the findings related to molecular phylogeny of ciliates (type Ciliophora) and some related groups of protozoans. Based on comparison of the sequences of genes encoding various ribosomal RNAs (rRNAs), the phylogenetic relationships in seven out of eight known classes of ciliates are discussed. The events related to early branching of the eukaryotic tree are briefly presented. The evolutionary history of amitochondrial protists ids considered with regard to reductionistic evolution and archeozoic hypothesis. The phylogenetic relationships among ciliates and sister groups of apicomplexans and dinoflagellates are considered. PMID:19769290

  18. Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws

    PubMed Central

    Šmajs, David; Norris, Steven J.; Weinstock, George M.

    2013-01-01

    Pathogenic uncultivable treponemes, similar to syphilis-causing Treponema pallidum subspecies pallidum, include T. pallidum ssp. pertenue, T. pallidum ssp. endemicum and Treponema carateum, which cause yaws, bejel and pinta, respectively. Genetic analyses of these pathogens revealed striking similarity among these bacteria and also a high degree of similarity to the rabbit pathogen, T. paraluiscuniculi, a treponeme not infectious to humans. Genome comparisons between pallidum and non-pallidum treponemes revealed genes with potential involvement in human infectivity, whereas comparisons between pallidum and pertenue treponemes identified genes possibly involved in the high invasivity of syphilis treponemes. Genetic variability within syphilis strains is considered as the basis of syphilis molecular epidemiology with potential to detect more virulent strains, whereas genetic variability within a single strain is related to its ability to elude the immune system of the host. Genome analyses also shed light on treponemal evolution and on chromosomal targets for molecular diagnostics of treponemal infections. PMID:22198325

  19. Molecular engineering of a cobalt-based electrocatalytic nanomaterial for H₂ evolution under fully aqueous conditions.

    PubMed

    Andreiadis, Eugen S; Jacques, Pierre-André; Tran, Phong D; Leyris, Adeline; Chavarot-Kerlidou, Murielle; Jousselme, Bruno; Matheron, Muriel; Pécaut, Jacques; Palacin, Serge; Fontecave, Marc; Artero, Vincent

    2013-01-01

    The viability of a hydrogen economy depends on the design of efficient catalytic systems based on earth-abundant elements. Innovative breakthroughs for hydrogen evolution based on molecular tetraimine cobalt compounds have appeared in the past decade. Here we show that such a diimine-dioxime cobalt catalyst can be grafted to the surface of a carbon nanotube electrode. The resulting electrocatalytic cathode material mediates H(2) generation (55,000 turnovers in seven hours) from fully aqueous solutions at low-to-medium overpotentials. This material is remarkably stable, which allows extensive cycling with preservation of the grafted molecular complex, as shown by electrochemical studies, X-ray photoelectron spectroscopy and scanning electron microscopy. This clearly indicates that grafting provides an increased stability to these cobalt catalysts, and suggests the possible application of these materials in the development of technological devices. PMID:23247177

  20. Genetic diversity in Treponema pallidum: implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws.

    PubMed

    Smajs, David; Norris, Steven J; Weinstock, George M

    2012-03-01

    Pathogenic uncultivable treponemes, similar to syphilis-causing Treponema pallidum subspecies pallidum, include T. pallidum ssp. pertenue, T. pallidum ssp. endemicum and Treponema carateum, which cause yaws, bejel and pinta, respectively. Genetic analyses of these pathogens revealed striking similarity among these bacteria and also a high degree of similarity to the rabbit pathogen, Treponema paraluiscuniculi, a treponeme not infectious to humans. Genome comparisons between pallidum and non-pallidum treponemes revealed genes with potential involvement in human infectivity, whereas comparisons between pallidum and pertenue treponemes identified genes possibly involved in the high invasivity of syphilis treponemes. Genetic variability within syphilis strains is considered as the basis of syphilis molecular epidemiology with potential to detect more virulent strains, whereas genetic variability within a single strain is related to its ability to elude the immune system of the host. Genome analyses also shed light on treponemal evolution and on chromosomal targets for molecular diagnostics of treponemal infections. PMID:22198325

  1. Evolution of Molecular and Atomic Gas Phases in the Milky Way

    NASA Astrophysics Data System (ADS)

    Koda, Jin; Scoville, Nick; Heyer, Mark

    2016-06-01

    We analyze radial and azimuthal variations of the phase balance between the molecular and atomic interstellar medium (ISM) in the Milky Way (MW) using archival CO(J = 1-0) and HI 21 cm data. In particular, the azimuthal variations—between the spiral arm and interarm regions—are analyzed without any explicit definition of the spiral arm locations. We show that the molecular gas mass fraction, i.e., {f}{{mol}}={{{Σ }}}{{{H}}2}/({{{Σ }}}{HI}+{{{Σ }}}{{{H}}2}), varies predominantly in the radial direction: starting from ∼ 100% at the center, remaining ≳ 50% to R∼ 6 {{kpc}} and decreasing to ∼10%–20% at R=8.5 {{kpc}} when averaged over the whole disk thickness (from ∼100% to ≳60%, then to ∼50% in the midplane). Azimuthal, arm-interarm variations are secondary: only ∼ 20% in the globally molecule-dominated inner MW, but becoming larger, ∼40%–50%, in the atom-dominated outskirts. This suggests that in the inner MW the gas remains highly molecular ({f}{{mol}}\\gt 50%) as it moves from an interarm region into a spiral arm and back into the next interarm region. Stellar feedback does not dissociate molecules much, and the coagulation and fragmentation of molecular clouds dominate the evolution of the ISM at these radii. The trend differs in the outskirts where the gas phase is globally atomic ({f}{{mol}}\\lt 50%). The HI and H2 phases cycle through spiral arm passage there. These different regimes of ISM evolution are also seen in external galaxies (e.g., the LMC, M33, and M51). We explain the radial gradient of {f}{{mol}} using a simple flow continuity model. The effects of spiral arms on this analysis are illustrated in the Appendix.

  2. Evolution of Molecular and Atomic Gas Phases in the Milky Way

    NASA Astrophysics Data System (ADS)

    Koda, Jin; Scoville, Nick; Heyer, Mark

    2016-06-01

    We analyze radial and azimuthal variations of the phase balance between the molecular and atomic interstellar medium (ISM) in the Milky Way (MW) using archival CO(J = 1-0) and HI 21 cm data. In particular, the azimuthal variations—between the spiral arm and interarm regions—are analyzed without any explicit definition of the spiral arm locations. We show that the molecular gas mass fraction, i.e., {f}{{mol}}={{{Σ }}}{{{H}}2}/({{{Σ }}}{HI}+{{{Σ }}}{{{H}}2}), varies predominantly in the radial direction: starting from ˜ 100% at the center, remaining ≳ 50% to R˜ 6 {{kpc}} and decreasing to ˜10%–20% at R=8.5 {{kpc}} when averaged over the whole disk thickness (from ˜100% to ≳60%, then to ˜50% in the midplane). Azimuthal, arm-interarm variations are secondary: only ˜ 20% in the globally molecule-dominated inner MW, but becoming larger, ˜40%–50%, in the atom-dominated outskirts. This suggests that in the inner MW the gas remains highly molecular ({f}{{mol}}\\gt 50%) as it moves from an interarm region into a spiral arm and back into the next interarm region. Stellar feedback does not dissociate molecules much, and the coagulation and fragmentation of molecular clouds dominate the evolution of the ISM at these radii. The trend differs in the outskirts where the gas phase is globally atomic ({f}{{mol}}\\lt 50%). The HI and H2 phases cycle through spiral arm passage there. These different regimes of ISM evolution are also seen in external galaxies (e.g., the LMC, M33, and M51). We explain the radial gradient of {f}{{mol}} using a simple flow continuity model. The effects of spiral arms on this analysis are illustrated in the Appendix.

  3. Anticipatory dynamics of biological systems: from molecular quantum states to evolution

    NASA Astrophysics Data System (ADS)

    Igamberdiev, Abir U.

    2015-08-01

    Living systems possess anticipatory behaviour that is based on the flexibility of internal models generated by the system's embedded description. The idea was suggested by Aristotle and is explicitly introduced to theoretical biology by Rosen. The possibility of holding the embedded internal model is grounded in the principle of stable non-equilibrium (Bauer). From the quantum mechanical view, this principle aims to minimize energy dissipation in expense of long relaxation times. The ideas of stable non-equilibrium were developed by Liberman who viewed living systems as subdivided into the quantum regulator and the molecular computer supporting coherence of the regulator's internal quantum state. The computational power of the cell molecular computer is based on the possibility of molecular rearrangements according to molecular addresses. In evolution, the anticipatory strategies are realized both as a precession of phylogenesis by ontogenesis (Berg) and as the anticipatory search of genetic fixation of adaptive changes that incorporates them into the internal model of genetic system. We discuss how the fundamental ideas of anticipation can be introduced into the basic foundations of theoretical biology.

  4. Major Radiations in the Evolution of Caviid Rodents: Reconciling Fossils, Ghost Lineages, and Relaxed Molecular Clocks

    PubMed Central

    Pérez, María Encarnación; Pol, Diego

    2012-01-01

    Background Caviidae is a diverse group of caviomorph rodents that is broadly distributed in South America and is divided into three highly divergent extant lineages: Caviinae (cavies), Dolichotinae (maras), and Hydrochoerinae (capybaras). The fossil record of Caviidae is only abundant and diverse since the late Miocene. Caviids belongs to Cavioidea sensu stricto (Cavioidea s.s.) that also includes a diverse assemblage of extinct taxa recorded from the late Oligocene to the middle Miocene of South America (“eocardiids”). Results A phylogenetic analysis combining morphological and molecular data is presented here, evaluating the time of diversification of selected nodes based on the calibration of phylogenetic trees with fossil taxa and the use of relaxed molecular clocks. This analysis reveals three major phases of diversification in the evolutionary history of Cavioidea s.s. The first two phases involve two successive radiations of extinct lineages that occurred during the late Oligocene and the early Miocene. The third phase consists of the diversification of Caviidae. The initial split of caviids is dated as middle Miocene by the fossil record. This date falls within the 95% higher probability distribution estimated by the relaxed Bayesian molecular clock, although the mean age estimate ages are 3.5 to 7 Myr older. The initial split of caviids is followed by an obscure period of poor fossil record (refered here as the Mayoan gap) and then by the appearance of highly differentiated modern lineages of caviids, which evidentially occurred at the late Miocene as indicated by both the fossil record and molecular clock estimates. Conclusions The integrated approach used here allowed us identifying the agreements and discrepancies of the fossil record and molecular clock estimates on the timing of the major events in cavioid evolution, revealing evolutionary patterns that would not have been possible to gather using only molecular or paleontological data alone. PMID

  5. Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis.

    PubMed

    Gong, Yu-Nong; Yang, Shu-Li; Shih, Shin-Ru; Huang, Yhu-Chering; Chang, Pi-Yueh; Huang, Chung-Guei; Kao, Kuo-Chin; Hu, Han-Chung; Liu, Yi-Chun; Tsao, Kuo-Chien

    2016-08-01

    Human enterovirus D68 (EV-D68) was first reported in the United States in 1962; thereafter, a few cases were reported from 1970 to 2005, but 2 outbreaks occurred in the Philippines (2008) and the United States (2014). However, little is known regarding the molecular evolution of this globally reemerging virus due to a lack of whole-genome sequences and analyses. Here, all publically available sequences including 147 full and 1248 partial genomes from GenBank were collected and compared at the clade and subclade level; 11 whole genomes isolated in Taiwan (TW) in 2014 were also added to the database. Phylogenetic trees were constructed to identify a new subclade, B3, and represent clade circulations among strains. Nucleotide sequence identities of the VP1 gene were 94% to 95% based on a comparison of subclade B3 to B1 and B2 and 87% to 91% when comparing A, C, and D. The patterns of clade circulation need to be clarified to improve global monitoring of EV-D68, even though this virus showed lower diversity among clades compared with the common enterovirus EV-71. Notably, severe cases isolated from Taiwan and China in 2014 were found in subclade B3. One severe case from Taiwan occurred in a female patient with underlying angioimmunoblastic T-cell lymphoma, from whom a bronchoalveolar lavage specimen was obtained. Although host factors play a key role in disease severity, we cannot exclude the possibility that EV-D68 may trigger clinical symptoms or death. To further investigate the genetic diversity of EV-D68, we reported 34 amino acid (aa) polymorphisms identified by comparing subclade B3 to B1 and B2. Clade D strains had a 1-aa deletion and a 2-aa insertion in the VP1 gene, and 1 of our TW/2014 strains had a shorter deletion in the 5' untranslated region than a previously reported deletion. In summary, a new subclade, genetic indels, and polymorphisms in global strains were discovered elucidating evolutionary and epidemiological trends of EV-D68, and 11 genomes were

  6. Molecular evolution and the global reemergence of enterovirus D68 by genome-wide analysis

    PubMed Central

    Gong, Yu-Nong; Yang, Shu-Li; Shih, Shin-Ru; Huang, Yhu-Chering; Chang, Pi-Yueh; Huang, Chung-Guei; Kao, Kuo-Chin; Hu, Han-Chung; Liu, Yi-Chun; Tsao, Kuo-Chien

    2016-01-01

    Abstract Human enterovirus D68 (EV-D68) was first reported in the United States in 1962; thereafter, a few cases were reported from 1970 to 2005, but 2 outbreaks occurred in the Philippines (2008) and the United States (2014). However, little is known regarding the molecular evolution of this globally reemerging virus due to a lack of whole-genome sequences and analyses. Here, all publically available sequences including 147 full and 1248 partial genomes from GenBank were collected and compared at the clade and subclade level; 11 whole genomes isolated in Taiwan (TW) in 2014 were also added to the database. Phylogenetic trees were constructed to identify a new subclade, B3, and represent clade circulations among strains. Nucleotide sequence identities of the VP1 gene were 94% to 95% based on a comparison of subclade B3 to B1 and B2 and 87% to 91% when comparing A, C, and D. The patterns of clade circulation need to be clarified to improve global monitoring of EV-D68, even though this virus showed lower diversity among clades compared with the common enterovirus EV-71. Notably, severe cases isolated from Taiwan and China in 2014 were found in subclade B3. One severe case from Taiwan occurred in a female patient with underlying angioimmunoblastic T-cell lymphoma, from whom a bronchoalveolar lavage specimen was obtained. Although host factors play a key role in disease severity, we cannot exclude the possibility that EV-D68 may trigger clinical symptoms or death. To further investigate the genetic diversity of EV-D68, we reported 34 amino acid (aa) polymorphisms identified by comparing subclade B3 to B1 and B2. Clade D strains had a 1-aa deletion and a 2-aa insertion in the VP1 gene, and 1 of our TW/2014 strains had a shorter deletion in the 5′ untranslated region than a previously reported deletion. In summary, a new subclade, genetic indels, and polymorphisms in global strains were discovered elucidating evolutionary and epidemiological trends of EV-D68, and 11

  7. Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup

    PubMed Central

    2009-01-01

    Background Genes with sex-biased expression often show rapid molecular evolution between species. Previous population genetic and comparative genomic studies of Drosophila melanogaster and D. simulans revealed that male-biased genes have especially high rates of adaptive evolution. To test if this is also the case for other lineages within the melanogaster group, we investigated gene expression in D. ananassae, a species that occurs in structured populations in tropical and subtropical regions. We used custom-made microarrays and published microarray data to characterize the sex-biased expression of 129 D. ananassae genes whose D. melanogaster orthologs had been classified previously as male-biased, female-biased, or unbiased in their expression and had been studied extensively at the population-genetic level. For 43 of these genes we surveyed DNA sequence polymorphism in a natural population of D. ananassae and determined divergence to the sister species D. atripex and D. phaeopleura. Results Sex-biased expression is generally conserved between D. melanogaster and D. ananassae, with the majority of genes exhibiting the same bias in the two species. However, about one-third of the genes have either gained or lost sex-biased expression in one of the species and a small proportion of genes (~4%) have changed bias from one sex to the other. The male-biased genes of D. ananassae show evidence of positive selection acting at the protein level. However, the signal of adaptive protein evolution for male-biased genes is not as strong in D. ananassae as it is in D. melanogaster and is limited to genes with conserved male-biased expression in both species. Within D. ananassae, a significant signal of adaptive evolution is also detected for female-biased and unbiased genes. Conclusions Our findings extend previous observations of widespread adaptive protein evolution to an independent Drosophila lineage, the D. ananassae subgroup. However, the rate of adaptive evolution is

  8. Molecular evolution of fever, thrombocytopenia and leukocytopenia virus (FTLSV) based on whole-genome sequences.

    PubMed

    Liu, Licheng; Chen, Weijun; Yang, Yinhui; Jiang, Yongqiang

    2016-04-01

    FTLSV is a novel bunyavirus that was discovered in 2007 in the Henan province of China and has reported case fatality rates of up to 30%. Despite the high case fatality rate, knowledge of the evolution and molecular epidemiology of FTLSV is limited. In this study, detailed phylogenetic analyses were performed on whole-genome sequences to examine the virus's evolutionary rates, estimate dates of common ancestry, and determine the population dynamics and selection pressure for FTLSV. The evolutionary rates of FTLSV were estimated to be 2.28×10(-4), 2.42×10(-4) and 1.19×10(-4) nucleotide substitutions/site/year for the S, M and L segments, respectively. The most recent ancestor of the viruses existed approximately 182-294years ago. Evidence of RNA segment reassortment was found in FTLSV. A Bayesian skyline plot showed that after a period of genetic stability following high variability, the FTLSV population appeared to have contracted it. Selection pressures were estimated and revealed an abundance of negatively selected sites and sparse positively selected sites. These data will be valuable in understanding the evolution and molecular epidemiology of FTLSV, eventually helping to determine mechanisms of emergence and pathogenicity and the level of the virus's threat to public health. PMID:26748010

  9. Molecular Evolution of Aralkylamine N-Acetyltransferase in Fish: A Genomic Survey.

    PubMed

    Li, Jia; You, Xinxin; Bian, Chao; Yu, Hui; Coon, Steven L; Shi, Qiong

    2016-01-01

    All living organisms synchronize biological functions with environmental changes; melatonin plays a vital role in regulating daily and seasonal variations. Due to rhythmic activity of the timezyme aralkylamine N-acetyltransferase (AANAT), the blood level of melatonin increases at night and decreases during daytime. Whereas other vertebrates have a single form of AANAT, bony fishes possess various isoforms of aanat genes, though the reasons are still unclear. Here, we have taken advantage of multiple unpublished teleost aanat sequences to explore and expand our understanding of the molecular evolution of aanat in fish. Our results confirm that two rounds of whole-genome duplication (WGD) led to the existence of three fish isoforms of aanat, i.e., aanat1a, aanat1b, and aanat2; in addition, gene loss led to the absence of some forms from certain special fish species. Furthermore, we suggest the different roles of two aanat1s in amphibious mudskippers, and speculate that the loss of aanat1a, may be related to terrestrial vision change. Several important sites of AANAT proteins and regulatory elements of aanat genes were analyzed for structural comparison and functional forecasting, respectively, which provides insights into the molecular evolution of the differences between AANAT1 and AANAT2. PMID:26729109

  10. Molecular evolution of the nuclear von Willebrand factor gene in mammals and the phylogeny of rodents.

    PubMed

    Huchon, D; Catzeflis, F M; Douzery, E J

    1999-05-01

    Nucleotide sequences of exon 28 of the von Willebrand Factor (vWF) were analyzed for a representative sampling of rodent families and eutherian orders, with one marsupial sequence as outgroup. The aim of this study was to test if inclusion of an increased taxonomic diversity in molecular analyses would shed light on three uncertainties concerning rodent phylogeny: (1) relationships between rodent families, (2) Rodentia monophyly, and (3) the sister group relationship of rodents and lagomorphs. The results did not give evidence of any particular rodent pattern of molecular evolution relative to a general eutherian pattern. Base compositions and rates of evolution of vWF sequences of rodents were in the range of placental variation. The 10 rodent families studied here cluster in five clades: Hystricognathi, Sciuridae and Aplodontidae (Sciuroidea), Muridae, Dipodidae, and Gliridae. Among hystricognaths, the following conclusions are drawn: a single colonization event in South America by Caviomorpha, a paraphyly of Old World and New World porcupines, and an African origin for Old World porcupines. Despite a broader taxonomic sampling diversity, we did not obtain a robust answer to the question of Rodentia monophyly, but in the absence of any other alternative, we cannot reject the hypothesis of a single origin of rodents. Moreover, the phylogenetic position of Lagomorpha remains totally unsettled. PMID:10335651

  11. Molecular Evolution of Aralkylamine N-Acetyltransferase in Fish: A Genomic Survey

    PubMed Central

    Li, Jia; You, Xinxin; Bian, Chao; Yu, Hui; Coon, Steven L.; Shi, Qiong

    2015-01-01

    All living organisms synchronize biological functions with environmental changes; melatonin plays a vital role in regulating daily and seasonal variations. Due to rhythmic activity of the timezyme aralkylamine N-acetyltransferase (AANAT), the blood level of melatonin increases at night and decreases during daytime. Whereas other vertebrates have a single form of AANAT, bony fishes possess various isoforms of aanat genes, though the reasons are still unclear. Here, we have taken advantage of multiple unpublished teleost aanat sequences to explore and expand our understanding of the molecular evolution of aanat in fish. Our results confirm that two rounds of whole-genome duplication (WGD) led to the existence of three fish isoforms of aanat, i.e., aanat1a, aanat1b, and aanat2; in addition, gene loss led to the absence of some forms from certain special fish species. Furthermore, we suggest the different roles of two aanat1s in amphibious mudskippers, and speculate that the loss of aanat1a, may be related to terrestrial vision change. Several important sites of AANAT proteins and regulatory elements of aanat genes were analyzed for structural comparison and functional forecasting, respectively, which provides insights into the molecular evolution of the differences between AANAT1 and AANAT2. PMID:26729109

  12. Molecular heterochrony and the evolution of sociality in bumblebees (Bombus terrestris)

    PubMed Central

    Woodard, S. Hollis; Bloch, Guy M.; Band, Mark R.; Robinson, Gene E.

    2014-01-01

    Sibling care is a hallmark of social insects, but its evolution remains challenging to explain at the molecular level. The hypothesis that sibling care evolved from ancestral maternal care in primitively eusocial insects has been elaborated to involve heterochronic changes in gene expression. This elaboration leads to the prediction that workers in these species will show patterns of gene expression more similar to foundress queens, who express maternal care behaviour, than to established queens engaged solely in reproductive behaviour. We tested this idea in bumblebees (Bombus terrestris) using a microarray platform with approximately 4500 genes. Unlike the wasp Polistes metricus, in which support for the above prediction has been obtained, we found that patterns of brain gene expression in foundress and queen bumblebees were more similar to each other than to workers. Comparisons of differentially expressed genes derived from this study and gene lists from microarray studies in Polistes and the honeybee Apis mellifera yielded a shared set of genes involved in the regulation of related social behaviours across independent eusocial lineages. Together, these results suggest that multiple independent evolutions of eusociality in the insects might have involved different evolutionary routes, but nevertheless involved some similarities at the molecular level. PMID:24552837

  13. The tempo and mode of molecular evolution of Mycobacterium tuberculosis at patient-to-patient scale.

    PubMed

    Schürch, Anita C; Kremer, Kristin; Kiers, Albert; Daviena, Olaf; Boeree, Martin J; Siezen, Roland J; Smith, Noel H; van Soolingen, Dick

    2010-01-01

    A total of six polymorphisms were identified by comparing the genomes of the first and the last isolate of a well-characterized transmission chain of Mycobacterium tuberculosis involving five patients over a 12 and a half year period. The six polymorphisms consisted of four single nucleotide changes (SNPs), a tandem repeat polymorphism (TRP) and a previously identified IS6110 transposition event. These polymorphic sites were surveyed in each of the isolates from the five patients in the transmission chain. Surprisingly, five of the six polymorphisms accumulated in a single patient in the transmission chain; this patient had been non-compliant to tuberculosis treatment. This first insight into the tempo and mode of molecular evolution in M. tuberculosis at the patient-to-patient level suggests that the molecular evolution of the pathogen in vivo is characterized by periods of relative genomic stability followed by bursts of mutation. Whatever the mechanism for the accumulation of mutations, this observation may have profound consequences for the application of vaccines and therapeutic drugs, the management and treatment of disease outbreaks of M. tuberculosis, the most important bacterial pathogen of humans. PMID:19835997

  14. Continuous directed evolution of DNA-binding proteins to improve TALEN specificity.

    PubMed

    Hubbard, Basil P; Badran, Ahmed H; Zuris, John A; Guilinger, John P; Davis, Kevin M; Chen, Liwei; Tsai, Shengdar Q; Sander, Jeffry D; Joung, J Keith; Liu, David R

    2015-10-01

    Nucleases containing programmable DNA-binding domains can alter the genomes of model organisms and have the potential to become human therapeutics. Here we present DNA-binding phage-assisted continuous evolution (DB-PACE) as a general approach for the laboratory evolution of DNA-binding activity and specificity. We used this system to generate transcription activator-like effectors nucleases (TALENs) with broadly improved DNA cleavage specificity, establishing DB-PACE as a versatile approach for improving the accuracy of genome-editing agents. PMID:26258293

  15. Continuous directed evolution of DNA-binding proteins to improve TALEN specificity

    PubMed Central

    Hubbard, Basil P.; Badran, Ahmed H.; Zuris, John A.; Guilinger, John P.; Davis, Kevin M.; Chen, Liwei; Tsai, Shengdar Q.; Sander, Jeffry D.; Joung, J. Keith; Liu, David R.

    2015-01-01

    Nucleases containing programmable DNA-binding domains can alter the genomes of model organisms and have the potential to become human therapeutics. Here we present DNA-binding phage-assisted continuous evolution (DB-PACE) as a general approach for the laboratory evolution of DNA-binding activity and specificity. We used this system to generate TALE nucleases with broadly improved DNA cleavage specificity, establishing DB-PACE as a versatile approach for improving the accuracy of genome-editing agents. PMID:26258293

  16. Molecular tools and bumble bees: revealing hidden details of ecology and evolution in a model system.

    PubMed

    Woodard, S Hollis; Lozier, Jeffrey D; Goulson, David; Williams, Paul H; Strange, James P; Jha, Shalene

    2015-06-01

    Bumble bees are a longstanding model system for studies on behaviour, ecology and evolution, due to their well-studied social lifestyle, invaluable role as wild and managed pollinators, and ubiquity and diversity across temperate ecosystems. Yet despite their importance, many aspects of bumble bee biology have remained enigmatic until the rise of the genetic and, more recently, genomic eras. Here, we review and synthesize new insights into the ecology, evolution and behaviour of bumble bees that have been gained using modern genetic and genomic techniques. Special emphasis is placed on four areas of bumble bee biology: the evolution of eusociality in this group, population-level processes, large-scale evolutionary relationships and patterns, and immunity and resistance to pesticides. We close with a prospective on the future of bumble bee genomics research, as this rapidly advancing field has the potential to further revolutionize our understanding of bumble bees, particularly in regard to adaptation and resilience. Worldwide, many bumble bee populations are in decline. As such, throughout the review, connections are drawn between new molecular insights into bumble bees and our understanding of the causal factors involved in their decline. Ongoing and potential applications to bumble bee management and conservation are also included to demonstrate how genetics- and genomics-enabled research aids in the preservation of this threatened group. PMID:25865395

  17. Molecular Evolution of Drosophila Germline Stem Cell and Neural Stem Cell Regulating Genes

    PubMed Central

    Choi, Jae Young; Aquadro, Charles F.

    2015-01-01

    Here, we study the molecular evolution of a near complete set of genes that had functional evidence in the regulation of the Drosophila germline and neural stem cell. Some of these genes have previously been shown to be rapidly evolving by positive selection raising the possibility that stem cell genes as a group have elevated signatures of positive selection. Using recent Drosophila comparative genome sequences and population genomic sequences of Drosophila melanogaster, we have investigated both long- and short-term evolution occurring across these two different stem cell systems, and compared them with a carefully chosen random set of genes to represent the background rate of evolution. Our results showed an excess of genes with evidence of a recent selective sweep in both germline and neural stem cells in D. melanogaster. However compared with their control genes, both stem cell systems had no significant excess of genes with long-term recurrent positive selection in D. melanogaster, or across orthologous sequences from the melanogaster group. The evidence of long-term positive selection was limited to a subset of genes with specific functions in both the germline and neural stem cell system. PMID:26507797

  18. Molecular evolution of the brain size regulator genes CDK5RAP2 and CENPJ.

    PubMed

    Evans, Patrick D; Vallender, Eric J; Lahn, Bruce T

    2006-06-21

    Primary microcephaly is a developmental defect of the brain characterized by severely reduced brain size but an absence of other overt abnormalities. Mutations in several loci have been linked to primary microcephaly. The underlying genes for two of these were recently identified as CDK5RAP2 and CENPJ. Here, we focus on CDK5RAP2 and show that the protein evolutionary rate of this gene is significantly higher in primates than rodents or carnivores. We further show that the evolutionary rate within primates is particularly high in the human and chimpanzee terminal branches. Thus, the pattern of molecular evolution seen in CDK5RAP2 appears to parallel, at least approximately, that seen in two other previously identified primary microcephaly genes, microcephalin and ASPM. We also briefly discuss CENPJ, which similarly exhibits higher rate of protein evolution in primates as compared to rodents and carnivores. Together, the evolutionary patterns of all four presently known primary microcephaly genes are consistent with the hypothesis that genes regulating brain size during development might also play a role in brain evolution in primates and especially humans. PMID:16631324

  19. Near-Neutrality: the Leading Edge of the Neutral Theory of Molecular Evolution

    PubMed Central

    Hughes, Austin L.

    2009-01-01

    The nearly-neutral theory represents a development of Kimura’s Neutral Theory of Molecular Evolution that makes testable predictions that go beyond a mere null model. Recent evidence has strongly supported several of these predictions, including the prediction that slightly deleterious variants will accumulate in a species that has undergone a severe bottleneck or in cases where recombination is reduced or absent. Because bottlenecks often occur in speciation and slightly deleterious mutations in coding regions will usually be nonsynonymous, we should expect that the ratio of nonsynonymous to synonymous fixed differences between species should often exceed the ratio of nonsynonymous to synonymous polymorphisms within species. Numerous data support this prediction, although they have often been wrongly interpreted as evidence for positive Darwinian selection. The use of conceptually flawed tests for positive selection has become widespread in recent years, seriously harming the quest for an understanding of genome evolution. When properly analyzed, many (probably most) claimed cases of positive selection will turn out to involve the fixation of slightly deleterious mutations by genetic drift in bottlenecked populations. Slightly deleterious variants are a transient feature of evolution in the long term, but they have had substantial impact on contemporary species, including our own. PMID:18559820

  20. Molecular phylogenetics of the Anolis onca series: a case history in retrograde evolution revisited.

    PubMed

    Nicholson, Kirsten E; Mijares-Urrutia, Abraham; Larson, Allan

    2006-09-15

    Anoles of the Anolis onca series represent a dramatic case of retrograde evolution, exhibiting great reduction (A. annectens) and loss (A. onca) of the subdigital pads considered a key innovation for the evolutionary radiation of anoles in arboreal environments. We present a molecular phylogenetic analysis of these anoles and their closest known relatives (A. auratus, A. lineatus, A. meridionalis, and A. nitens) using new mitochondrial DNA sequence data from the ND2 gene, five tRNA genes (tRNA(Trp), tRNA(Ala), tRNA(Asn), tRNA(Cys), tRNA(Tyr)), the origin of light-strand replication, and a portion of the CO1 gene (1,446 aligned base positions, 612 parsimony informative). Our results confirm monophyly of the A. onca series and suggest an evolutionary separation of approximately 10 million years between A. annectens and A. onca. Evolution of subdigital structure in this series illustrates ectopic expression of developmental programs that replace flexible subdigital lamellae of the toepad with rigid, keeled scales resembling dorsal digital scales. Our phylogenetic results indicate that narrowing of the toepad in A. auratus evolved separately from toepad reduction in the A. onca series. Expansion of the subdigital lamellae along the phalanges in A. auratus appears to compensate constriction of lamellae by digital narrowing, maintaining greater climbing capability in this species. Toepad evolution in the lineage ancestral to A. auratus features changes of the same developmental modules as the A. onca series but in the opposite direction. Large molecular distances between geographic populations of A. auratus indicate that its derived toepad structure is at least 9 million years old. PMID:16506231

  1. Tryptophanyl-tRNA synthetase Urzyme: a model to recapitulate molecular evolution and investigate intramolecular complementation.

    PubMed

    Pham, Yen; Kuhlman, Brian; Butterfoss, Glenn L; Hu, Hao; Weinreb, Violetta; Carter, Charles W

    2010-12-01

    We substantiate our preliminary description of the class I tryptophanyl-tRNA synthetase minimal catalytic domain with details of its construction, structure, and steady-state kinetic parameters. Generating that active fragment involved deleting 65% of the contemporary enzyme, including the anticodon-binding domain and connecting peptide 1, CP1, a 74-residue internal segment from within the Rossmann fold. We used protein design (Rosetta), rather than phylogenetic sequence alignments, to identify mutations to compensate for the severe loss of modularity, thus restoring stability, as evidenced by renaturation described previously and by 70-ns molecular dynamics simulations. Sufficient solubility to enable biochemical studies was achieved by expressing the redesigned Urzyme as a maltose-binding protein fusion. Michaelis-Menten kinetic parameters from amino acid activation assays showed that, compared with the native full-length enzyme, TrpRS Urzyme binds ATP with similar affinity. This suggests that neither of the two deleted structural modules has a strong influence on ground-state ATP binding. However, tryptophan has 10(3) lower affinity, and the Urzyme has comparably reduced specificity relative to the related amino acid, tyrosine. Molecular dynamics simulations revealed how CP1 may contribute significantly to cognate amino acid specificity. As class Ia editing domains are nested within the CP1, this finding suggests that this module enhanced amino acid specificity continuously, throughout their evolution. We call this type of reconstructed protein catalyst an Urzyme (Ur prefix indicates original, primitive, or earliest). It establishes a model for recapitulating very early steps in molecular evolution in which fitness may have been enhanced by accumulating entire modules, rather than by discrete amino acid sequence changes. PMID:20864539

  2. Molecular bases and improvement of heat tolerance in crop plants

    Technology Transfer Automated Retrieval System (TEKTRAN)

    High temperature is a major constraint to crop productivity, causing substantial reductions in yield and quality, and expected to become a more devastating factor due to global warming. A better understanding of molecular mechanisms of tolerance to high temperatures is necessary for designing and de...

  3. Engineering and Evolution of Molecular Chaperones and Protein Disaggregases with Enhanced Activity

    PubMed Central

    Mack, Korrie L.; Shorter, James

    2016-01-01

    Cells have evolved a sophisticated proteostasis network to ensure that proteins acquire and retain their native structure and function. Critical components of this network include molecular chaperones and protein disaggregases, which function to prevent and reverse deleterious protein misfolding. Nevertheless, proteostasis networks have limits, which when exceeded can have fatal consequences as in various neurodegenerative disorders, including Parkinson's disease and amyotrophic lateral sclerosis. A promising strategy is to engineer proteostasis networks to counter challenges presented by specific diseases or specific proteins. Here, we review efforts to enhance the activity of individual molecular chaperones or protein disaggregases via engineering and directed evolution. Remarkably, enhanced global activity or altered substrate specificity of various molecular chaperones, including GroEL, Hsp70, ClpX, and Spy, can be achieved by minor changes in primary sequence and often a single missense mutation. Likewise, small changes in the primary sequence of Hsp104 yield potentiated protein disaggregases that reverse the aggregation and buffer toxicity of various neurodegenerative disease proteins, including α-synuclein, TDP-43, and FUS. Collectively, these advances have revealed key mechanistic and functional insights into chaperone and disaggregase biology. They also suggest that enhanced chaperones and disaggregases could have important applications in treating human disease as well as in the purification of valuable proteins in the pharmaceutical sector. PMID:27014702

  4. Engineering and Evolution of Molecular Chaperones and Protein Disaggregases with Enhanced Activity.

    PubMed

    Mack, Korrie L; Shorter, James

    2016-01-01

    Cells have evolved a sophisticated proteostasis network to ensure that proteins acquire and retain their native structure and function. Critical components of this network include molecular chaperones and protein disaggregases, which function to prevent and reverse deleterious protein misfolding. Nevertheless, proteostasis networks have limits, which when exceeded can have fatal consequences as in various neurodegenerative disorders, including Parkinson's disease and amyotrophic lateral sclerosis. A promising strategy is to engineer proteostasis networks to counter challenges presented by specific diseases or specific proteins. Here, we review efforts to enhance the activity of individual molecular chaperones or protein disaggregases via engineering and directed evolution. Remarkably, enhanced global activity or altered substrate specificity of various molecular chaperones, including GroEL, Hsp70, ClpX, and Spy, can be achieved by minor changes in primary sequence and often a single missense mutation. Likewise, small changes in the primary sequence of Hsp104 yield potentiated protein disaggregases that reverse the aggregation and buffer toxicity of various neurodegenerative disease proteins, including α-synuclein, TDP-43, and FUS. Collectively, these advances have revealed key mechanistic and functional insights into chaperone and disaggregase biology. They also suggest that enhanced chaperones and disaggregases could have important applications in treating human disease as well as in the purification of valuable proteins in the pharmaceutical sector. PMID:27014702

  5. Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics

    PubMed Central

    Tárraga, Joaquín; Medina, Ignacio; Arbiza, Leonardo; Huerta-Cepas, Jaime; Gabaldón, Toni; Dopazo, Joaquín; Dopazo, Hernán

    2007-01-01

    Phylemon is an online platform for phylogenetic and evolutionary analyses of molecular sequence data. It has been developed as a web server that integrates a suite of different tools selected among the most popular stand-alone programs in phylogenetic and evolutionary analysis. It has been conceived as a natural response to the increasing demand of data analysis of many experimental scientists wishing to add a molecular evolution and phylogenetics insight into their research. Tools included in Phylemon cover a wide yet selected range of programs: from the most basic for multiple sequence alignment to elaborate statistical methods of phylogenetic reconstruction including methods for evolutionary rates analyses and molecular adaptation. Phylemon has several features that differentiates it from other resources: (i) It offers an integrated environment that enables the direct concatenation of evolutionary analyses, the storage of results and handles required data format conversions, (ii) Once an outfile is produced, Phylemon suggests the next possible analyses, thus guiding the user and facilitating the integration of multi-step analyses, and (iii) users can define and save complete pipelines for specific phylogenetic analysis to be automatically used on many genes in subsequent sessions or multiple genes in a single session (phylogenomics). The Phylemon web server is available at http://phylemon.bioinfo.cipf.es. PMID:17452346

  6. Molecular corridors and parameterizations of volatility in the evolution of organic aerosols

    NASA Astrophysics Data System (ADS)

    Li, Y.; Pöschl, U.; Shiraiwa, M.

    2015-10-01

    The formation and aging of organic aerosols (OA) proceed through multiple steps of chemical reaction and mass transport in the gas and particle phases, which is challenging for the interpretation of field measurements and laboratory experiments as well as accurate representation of OA evolution in atmospheric aerosol models. Based on data from over 30 000 compounds, we show that organic compounds with a wide variety of functional groups fall into molecular corridors, characterized by a tight inverse correlation between molar mass and volatility. We developed parameterizations to predict the volatility of organic compounds containing oxygen, nitrogen and sulfur from the elemental composition that can be measured by soft-ionization high-resolution mass spectrometry. Field measurement data from new particle formation events, biomass burning, cloud/fog processing, and indoor environments were mapped into molecular corridors to characterize the chemical nature of the observed OA components. We found that less oxidized indoor OA are constrained to a corridor of low molar mass and high volatility, whereas highly oxygenated compounds in atmospheric water extend to high molar mass and low volatility. Among the nitrogen- and sulfur-containing compounds identified in atmospheric aerosols, amines tend to exhibit low molar mass and high volatility, whereas organonitrates and organosulfates follow high O : C corridors extending to high molar mass and low volatility. We suggest that the consideration of molar mass and molecular corridors can help to constrain volatility and particle phase state in the modeling of OA particularly for nitrogen- and sulfur-containing compounds.

  7. Improving Food Safety by Understanding the Evolution of Egg-contaminating Salmonella Enteritidis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Improving Food Safety by Understanding the Evolution of Egg-contaminating Salmonella Enteritidis Jean Guard, Veterinary Medical Officer U. S. Department of Agriculture, Athens, GA USA (jean.guard@ars.usda.gov) The curious case of egg contamination by Salmonella enterica serovar Enteritidis S. ...

  8. Molecular Corridor Based Approach for Description of Evolution of Secondary Organic Aerosols

    NASA Astrophysics Data System (ADS)

    Li, Y., Sr.; Poeschl, U.; Shiraiwa, M.

    2015-12-01

    Organic aerosol is ubiquitous in the atmosphere and its major component is secondary organic aerosol (SOA). Formation and evolution of SOA is a complex process involving coupled chemical reactions and mass transport in the gas and particle phases (Shiraiwa et al., 2014). Current air quality models do not embody the full spectrum of reaction and transport processes, nor do they identify the dominant rate-limiting steps in SOA formation, resulting in the significant underprediction of observed SOA concentrations, which precludes reliable quantitative predictions of aerosols and their environmental impacts. Recently, it has been suggested that the SOA chemical evolution can be represented well by "molecular corridor" with a tight inverse correlation between molar mass and volatility of SOA oxidation products (Shiraiwa et al., 2014). Here we further analyzed the structure, molar mass and volatility of 31,000 unique organic compounds. These compounds include oxygenated organic compounds as well as nitrogen- and sulfur-containing organics such as amines, organonitrates, and organosulfates. Results show that most of those compounds fall into this two-dimensional (2-D) space, which is constrained by two boundary lines corresponding to the volatility of n -alkanes CnH2n+2 and sugar alcohols CnH2n+2On. A method to predict the volatility of nitrogen- and sulfur- containing compounds is developed based on those 31,000 organic compounds. It is shown that the volatility can be well predicted as a function of chemical composition numbers, providing a way to apply this 2-D space to organic compounds observed in real atmosphere. A comprehensive set of observation data from laboratory experiments, field campaigns and indoor measurements is mapped to the molecular corridor. This 2-D space can successfully grasp the properties of organic compounds formed in different atmospheric conditions. The molecular corridor represents a new framework in which chemical and physical properties as

  9. PyEvolve: a toolkit for statistical modelling of molecular evolution

    PubMed Central

    Butterfield, Andrew; Vedagiri, Vivek; Lang, Edward; Lawrence, Cath; Wakefield, Matthew J; Isaev, Alexander; Huttley, Gavin A

    2004-01-01

    Background Examining the distribution of variation has proven an extremely profitable technique in the effort to identify sequences of biological significance. Most approaches in the field, however, evaluate only the conserved portions of sequences – ignoring the biological significance of sequence differences. A suite of sophisticated likelihood based statistical models from the field of molecular evolution provides the basis for extracting the information from the full distribution of sequence variation. The number of different problems to which phylogeny-based maximum likelihood calculations can be applied is extensive. Available software packages that can perform likelihood calculations suffer from a lack of flexibility and scalability, or employ error-prone approaches to model parameterisation. Results Here we describe the implementation of PyEvolve, a toolkit for the application of existing, and development of new, statistical methods for molecular evolution. We present the object architecture and design schema of PyEvolve, which includes an adaptable multi-level parallelisation schema. The approach for defining new methods is illustrated by implementing a novel dinucleotide model of substitution that includes a parameter for mutation of methylated CpG's, which required 8 lines of standard Python code to define. Benchmarking was performed using either a dinucleotide or codon substitution model applied to an alignment of BRCA1 sequences from 20 mammals, or a 10 species subset. Up to five-fold parallel performance gains over serial were recorded. Compared to leading alternative software, PyEvolve exhibited significantly better real world performance for parameter rich models with a large data set, reducing the time required for optimisation from ~10 days to ~6 hours. Conclusion PyEvolve provides flexible functionality that can be used either for statistical modelling of molecular evolution, or the development of new methods in the field. The toolkit can be

  10. Improving the performance of molecular dynamics simulations on parallel clusters.

    PubMed

    Borstnik, Urban; Hodoscek, Milan; Janezic, Dusanka

    2004-01-01

    In this article a procedure is derived to obtain a performance gain for molecular dynamics (MD) simulations on existing parallel clusters. Parallel clusters use a wide array of interconnection technologies to connect multiple processors together, often at different speeds, such as multiple processor computers and networking. It is demonstrated how to configure existing programs for MD simulations to efficiently handle collective communication on parallel clusters with processor interconnections of different speeds. PMID:15032512