56,263 research outputs found
Molecular Evolution in Time Dependent Environments
The quasispecies theory is studied for dynamic replication landscapes. A
meaningful asymptotic quasispecies is defined for periodic time dependencies.
The quasispecies' composition is constantly changing over the oscillation
period. The error threshold moves towards the position of the time averaged
landscape for high oscillation frequencies and follows the landscape closely
for low oscillation frequencies.Comment: 5 pages, 3 figures, Latex, uses Springer documentclass llncs.cl
Molecular Evolution in Collapsing Prestellar Cores
We have investigated the evolution and distribution of molecules in
collapsing prestellar cores via numerical chemical models, adopting the
Larson-Penston solution and its delayed analogues to study collapse. Molecular
abundances and distributions in a collapsing core are determined by the balance
among the dynamical, chemical and adsorption time scales. When the central
density n_H of a prestellar core with the Larson-Penston flow rises to 3 10^6
cm^{-3}, the CCS and CO column densities are calculated to show central holes
of radius 7000 AU and 4000 AU, respectively, while the column density of N2H+
is centrally peaked. These predictions are consistent with observations of
L1544. If the dynamical time scale of the core is larger than that of the
Larson-Penston solution owing to magnetic fields, rotation, or turbulence, the
column densities of CO and CCS are smaller, and their holes are larger than in
the Larson-Penston core with the same central gas density. On the other hand,
N2H+ and NH3 are more abundant in the more slowly collapsing core. Therefore,
molecular distributions can probe the collapse time scale of prestellar cores.
Deuterium fractionation has also been studied via numerical calculations. The
deuterium fraction in molecules increases as a core evolves and molecular
depletion onto grains proceeds. When the central density of the core is n_H=3
10^6 cm^{-3}, the ratio DCO+/HCO+ at the center is in the range 0.06-0.27,
depending on the collapse time scale and adsorption energy; this range is in
reasonable agreement with the observed value in L1544.Comment: 21 pages, 17 figure
Molecular evolution research Annual report
Amino acid syntheses by heating formaldehyde and ammonia mixtures in molecular evolution researc
Selective pressures on genomes in molecular evolution
We describe the evolution of macromolecules as an information transmission
process and apply tools from Shannon information theory to it. This allows us
to isolate three independent, competing selective pressures that we term
compression, transmission, and neutrality selection. The first two affect
genome length: the pressure to conserve resources by compressing the code, and
the pressure to acquire additional information that improves the channel,
increasing the rate of information transmission into each offspring. Noisy
transmission channels (replication with mutations) gives rise to a third
pressure that acts on the actual encoding of information; it maximizes the
fraction of mutations that are neutral with respect to the phenotype. This
neutrality selection has important implications for the evolution of
evolvability. We demonstrate each selective pressure in experiments with
digital organisms.Comment: 16 pages, 3 figures, to be published in J. theor. Biolog
Integrating influenza antigenic dynamics with molecular evolution.
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
A Hierarchical Approach to Protein Molecular Evolution
Biological diversity has evolved despite the essentially infinite complexity
of protein sequence space. We present a hierarchical approach to the efficient
searching of this space and quantify the evolutionary potential of our approach
with Monte Carlo simulations. These simulations demonstrate that non-homologous
juxtaposition of encoded structure is the rate-limiting step in the production
of new tertiary protein folds. Non-homologous ``swapping'' of low energy
secondary structures increased the binding constant of a simulated protein by
relative to base substitution alone. Applications of our approach
include the generation of new protein folds and modeling the molecular
evolution of disease.Comment: 15 pages. 2 figures. LaTeX styl
Molecular evolution of the sheep prion protein gene
Transmissible spongiform encephalopathies (TSEs) are infectious, fatal neurodegenerative diseases characterized by aggregates of modified forms of the prion protein (PrP) in the central nervous system. Well known examples include variant Creutzfeldt-Jakob Disease (vCJD) in humans, BSE in cattle, chronic wasting disease in deer and scrapie in sheep and goats. In humans, sheep and deer, disease susceptibility is determined by host genotype at the prion protein gene (PRNP). Here I examine the molecular evolution of PRNP in ruminants and show that variation in sheep appears to have been maintained by balancing selection, a profoundly different process from that seen in other ruminants. Scrapie eradication programs such as those recently implemented in the UK, USA and elsewhere are based on the assumption that PRNP is under positive selection in response to scrapie. If, as these data suggest, that assumption is wrong, eradication programs will disrupt this balancing selection, and may have a negative impact on the fitness or scrapie resistance of national flocks
Molecular Evolution
Comprised of essays by top scholars in the field, this volume offers detailed overviews of philosophical issues raised by biology
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