149,416 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
Second-generation p-values: improved rigor, reproducibility, & transparency in statistical analyses
Verifying that a statistically significant result is scientifically
meaningful is not only good scientific practice, it is a natural way to control
the Type I error rate. Here we introduce a novel extension of the p-value - a
second-generation p-value - that formally accounts for scientific relevance and
leverages this natural Type I Error control. The approach relies on a
pre-specified interval null hypothesis that represents the collection of effect
sizes that are scientifically uninteresting or are practically null. The
second-generation p-value is the proportion of data-supported hypotheses that
are also null hypotheses. As such, second-generation p-values indicate when the
data are compatible with null hypotheses, or with alternative hypotheses, or
when the data are inconclusive. Moreover, second-generation p-values provide a
proper scientific adjustment for multiple comparisons and reduce false
discovery rates. This is an advance for environments rich in data, where
traditional p-value adjustments are needlessly punitive. Second-generation
p-values promote transparency, rigor and reproducibility of scientific results
by a priori specifying which candidate hypotheses are practically meaningful
and by providing a more reliable statistical summary of when the data are
compatible with alternative or null hypotheses.Comment: 29 pages, 29 page Supplemen
Phenotypic robustness can increase phenotypic variability after non-genetic perturbations in gene regulatory circuits
Non-genetic perturbations, such as environmental change or developmental
noise, can induce novel phenotypes. If an induced phenotype confers a fitness
advantage, selection may promote its genetic stabilization. Non-genetic
perturbations can thus initiate evolutionary innovation. Genetic variation that
is not usually phenotypically visible may play an important role in this
process. Populations under stabilizing selection on a phenotype that is robust
to mutations can accumulate such variation. After non-genetic perturbations,
this variation can become a source of new phenotypes. We here study the
relationship between a phenotype's robustness to mutations and a population's
potential to generate novel phenotypic variation. To this end, we use a
well-studied model of transcriptional regulation circuits. Such circuits are
important in many evolutionary innovations. We find that phenotypic robustness
promotes phenotypic variability in response to non-genetic perturbations, but
not in response to mutation. Our work suggests that non-genetic perturbations
may initiate innovation more frequently in mutationally robust gene expression
traits.Comment: 11 pages, 5 figure
VEGF guides angiogenic sprouting utilizing endothelial tip cell filopodia
Vascular endothelial growth factor (VEGF-A) is a major regulator of blood vessel formation and function. it controls several processes in endothelial cells, such as proliferation, survival, and migration, but it is not known how these are coordinately regulated to result in more complex morphogenetic events, such as tubular sprouting, fusion, and network formation. We show here that VEGF-A controls angiogenic sprouting in the early postnatal retina by guiding filopodial extension from specialized endothelial cells situated at the tips of the vascular sprouts. The tip cells respond to VEGF-A only by guided migration; the proliferative response to VEGF-A occurs in the sprout stalks. These two cellular responses are both mediated by agonistic activity of VEGF-A on VEGF receptor 2. Whereas tip cell migration depends on a gradient of VEGF-A, proliferation is regulated by its concentration. Thus, vessel patterning during retinal angiogenesis depends on the balance between two different qualities of the extracellular VEGF-A distribution, which regulate distinct cellular responses in defined populations of endothelial cells
Does Meaning Evolove?
A common method of improving how well understood a theory is, is by comparing it to another theory which has been better developed. Radical interpretation is a theory which attempts to explain how communication has meaning. Radical interpretation is treated as another time dependent theory and compared to the time dependent theory of biological evolution. Several similarities and differences are uncovered. Biological evolution can be gradual or punctuated. Whether radical interpretation is gradual or punctuated depends on how the question is framed: on the coarse-grained time scale it proceeds gradually, but on the fine-grained time scale it proceeds by punctuated equilibria. Biological evolution proceeds by natural selection, the counterpart to this is the increase in both correspondence and coherence. Exaption, mutations, and spandrels have counterparts metaphor, speech errors, and puns respectively. Homologous and analogs have direct counterparts in specific words. The most important differences originate from the existence of a unit of inheritance (the traditional gene) occurring in biological evolution - there is no such unit in language
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