3,350 research outputs found
The maintenance of sex in bacteria is ensured by its potential to reload genes
Why sex is maintained in nature is a fundamental question in biology. Natural
genetic transformation (NGT) is a sexual process by which bacteria actively
take up exogenous DNA and use it to replace homologous chromosomal sequences.
As it has been demonstrated, the role of NGT in repairing deleterious mutations
under constant selection is insufficient for its survival, and the lack of
other viable explanations have left no alternative except that DNA uptake
provides nucleotides for food. Here we develop a novel simulation approach for
the long-term dynamics of genome organization (involving the loss and
acquisition of genes) in a bacterial species consisting of a large number of
spatially distinct populations subject to independently fluctuating ecological
conditions. Our results show that in the presence of weak inter-population
migration NGT is able to subsist as a mechanism to reload locally lost,
intermittently selected genes from the collective gene pool of the species
through DNA uptake from migrants. Reloading genes and combining them with those
in locally adapted genomes allow individual cells to re-adapt faster to
environmental changes. The machinery of transformation survives under a wide
range of model parameters readily encompassing real-world biological
conditions. These findings imply that the primary role of NGT is not to serve
the cell with food, but to provide homologous sequences for restoring genes
that have disappeared from or become degraded in the local population.Comment: 16 pages with 3 color figures. Manuscript accepted for publication in
Genetics (www.genetics.org
On the validity of the 5-dimensional Birkhoff theorem: The tale of an exceptional case
The 5-dimensional (5d) Birkhoff theorem gives the class of 5d vacuum
space-times containing spatial hypersurfaces with cosmological symmetries. This
theorem is violated by the 5d vacuum Gergely-Maartens (GM) space-time, which is
not a representant of the above class, but contains the static Einstein brane
as embedded hypersurface. We prove that the 5d Birkhoff theorem is still
satisfied in a weaker sense: the GM space-time is related to the degenerated
horizon metric of certain black-hole space-times of the allowed class. This
result resembles the connection between the Bertotti-Robinson space-time and
the horizon region of the extremal Reissner-Nordstrom space-time in general
relativity.Comment: 13 pages; v2: title amended, to be published in Classical and Quantum
Gravit
Effect Of Orius insidiosus (Hemiptera: Anthocoridae) And Spinosad (Conserve®) On Western Flower Thrips, Frankliniella occidentalis (Thysanoptera: Thripidae), Populations In Transvaal Daisy Flowers
Western flower thrips (WFT), Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), is a major insect pest of greenhouse-grown horticultural crops. Greenhouse producers typically apply insecticides to suppress WFT populations. However, continual reliance on insecticides can lead to the development of resistant in WFT populations. The insidious flower bug, Orius insidiosus (Say) (Hemiptera: Anthocoridae), is a commercially available predatory bug of WFT that offers an alternative to using insecticides for WFT suppression. Therefore, we investigated the efficacy of one or two O. insidiosus adults compared to spray applications of the standard insecticide, spinosad (Conserve®) in suppressing WFT adult populations in transvaal daisy (Gerbera jamesonii), cut-flowers under greenhouse conditions. Percent adult WFT mortality was significantly lower when one or two O. insidiosus adults were released into the flowers (mean range: 32 to 34%; n=747), compared to the untreated and water control (8 to 9%; n=431). The highest percent mortality of WFT adults was associated with the spinosad (Conserve®) treatment (100%; n= 203)
Non-uniform Braneworld Stars: an Exact Solution
The first exact interior solution to Einstein's field equations for a static
and non-uniform braneworld star with local and non-local bulk terms is
presented. It is shown that the bulk Weyl scalar is always
negative inside the stellar distribution, in consequence it reduces both the
effective density and the effective pressure. It is found that the anisotropy
generated by bulk gravity effect has an acceptable physical behaviour inside
the distribution. Using a Reissner-N\"{o}rdstrom-like exterior solution, the
effects of bulk gravity on pressure and density are found through matching
conditions.Comment: 22 pages, 3 figures, version to be published in International Journal
of Modern Physics D (IJMPD
A Spherically Symmetric Closed Universe as an Example of a 2D Dilatonic Model
We study the two-dimensional (2D) dilatonic model describing a massless
scalar field minimally coupled to the spherically reduced Einstein-Hilbert
gravity. The general solution of this model is given in the case when a Killing
vector is present. When interpreted in four dimensions, the solution describes
either a static or a homogeneous collision of incoming and outgoing null dust
streams with spherical symmetry. The homogeneous Universe is closed.Comment: 5 pages, 2 figures, to appear in Physical Review
The geometry of the Barbour-Bertotti theories II. The three body problem
We present a geometric approach to the three-body problem in the
non-relativistic context of the Barbour-Bertotti theories. The Riemannian
metric characterizing the dynamics is analyzed in detail in terms of the
relative separations. Consequences of a conformal symmetry are exploited and
the sectional curvatures of geometrically preferred surfaces are computed. The
geodesic motions are integrated. Line configurations, which lead to curvature
singularities for , are investigated. None of the independent scalars
formed from the metric and curvature tensor diverges there.Comment: 16 pages, 2 eps figures, to appear in Classical and Quantum Gravit
Efficient Exploration of the Space of Reconciled Gene Trees
Gene trees record the combination of gene level events, such as duplication,
transfer and loss, and species level events, such as speciation and extinction.
Gene tree-species tree reconciliation methods model these processes by drawing
gene trees into the species tree using a series of gene and species level
events. The reconstruction of gene trees based on sequence alone almost always
involves choosing between statistically equivalent or weakly distinguishable
relationships that could be much better resolved based on a putative species
tree. To exploit this potential for accurate reconstruction of gene trees the
space of reconciled gene trees must be explored according to a joint model of
sequence evolution and gene tree-species tree reconciliation.
Here we present amalgamated likelihood estimation (ALE), a probabilistic
approach to exhaustively explore all reconciled gene trees that can be
amalgamated as a combination of clades observed in a sample of trees. We
implement ALE in the context of a reconciliation model, which allows for the
duplication, transfer and loss of genes. We use ALE to efficiently approximate
the sum of the joint likelihood over amalgamations and to find the reconciled
gene tree that maximizes the joint likelihood.
We demonstrate using simulations that gene trees reconstructed using the
joint likelihood are substantially more accurate than those reconstructed using
sequence alone. Using realistic topologies, branch lengths and alignment sizes,
we demonstrate that ALE produces more accurate gene trees even if the model of
sequence evolution is greatly simplified. Finally, examining 1099 gene families
from 36 cyanobacterial genomes we find that joint likelihood-based inference
results in a striking reduction in apparent phylogenetic discord, with 24%, 59%
and 46% percent reductions in the mean numbers of duplications, transfers and
losses.Comment: Manuscript accepted pending revision in Systematic Biolog
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