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Register a new userMutagenesis and Background Neutron Radiation
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Authors
Augusto Gonzalez
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We suggest a possible correlation between the ionization events caused by the background neutron radiation and the experimental data on mutations with damage in the DNA repair mechanism, coming from the Long Term Evolution Experiment in E. Coli populations.
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B cell receptor sequences diversify through mutations introduced by purpose-built cellular machinery. A recent paper has concluded that a templated mutagenesis process is a major contributor to somatic hypermutation, and therefore immunoglobulin diversification, in mice and humans. In this proposed process, mutations in the immunoglobulin locus are introduced by copying short segments from other immunoglobulin genes. If true, this would overturn decades of research on B cell diversification, and would require a complete re-write of computational methods to analyze B cell data for these species. In this paper, we re-evaluate the templated mutagenesis hypothesis. By applying the original inferential method using potential donor templates absent from B cell genomes, we obtain estimates of the methodss false positive rates. We find false positive rates of templated mutagenesis in murine and human immunoglobulin loci that are similar to or even higher than the original rate inferences, and by considering the bases used in substitution we find evidence that if templated mutagenesis occurs, it is at a low rate. We also show that the statistically significant results in the original paper can easily result from a slight misspecification of the null model.
We provide quantitative estimates on the size and the structure of the epistatic space defined in the main article, Dynamical Correlations in the escape strategy of Influenza A virus, EPL 101 68003.
A tragedy of the commons (TOC) occurs when individuals acting in their own self-interest deplete commonly-held resources, leading to a worse outcome than had they cooperated. Over time, the depletion of resources can change incentives for subsequent actions. Here, we investigate long-term feedback between game and environment across a continuum of incentives in an individual-based framework. We identify payoff-dependent transition rules that lead to oscillatory TOC-s in stochastic simulations and the mean field limit. Further extending the stochastic model, we find that spatially explicit interactions can lead to emergent, localized dynamics, including the propagation of cooperative wave fronts and cluster formation of both social context and resources. These dynamics suggest new mechanisms underlying how TOCs arise and how they might be averted.
The stabilizing effects of local enrichment are revisited. Diffusively coupled host-parasitoid and predator-prey metapopulations are shown to admit a stable fixed point, limit cycle or stable torus with a rich bifurcation structure. A linear toy model that yields many of the basic qualitative features of this system is presented. The further nonlinear complications are analyzed in the framework of the marginally stable Lotka-Volterra model, and the continuous time analog of the unstable, host-parasitoid Nicholson-Bailey model. The dependence of the results on the migration rate and level of spatial variations is examined, and the possibility of nonlocal effect of enrichment, where local enrichment induces stable oscillations at a distance, is studied. A simple method for basic estimation of the relative importance of this effect in experimental systems is presented and exemplified.
Mediterranean ecosystems such as those found in California, Central Chile, Southern Europe, and Southwest Australia host numerous, diverse, fire-adapted micro-ecosystems. These micro-ecosystems are as diverse as mountainous conifer to desert-like chaparral communities. Over the last few centuries, human intervention, invasive species, and climate warming have drastically affected the composition and health of Mediterranean ecosystems on almost every continent. Increased fuel load from fire suppression policies and the continued range expansion of non-native insects and plants, some driven by long-term drought, produced the deadliest wildfire season on record in 2018. As a consequence of these fires, a large number of structures are destroyed, releasing household chemicals into the environment as uncontrolled toxins. The mobilization of these materials can lead to health risks and disruption in both human and natural systems. This article identifies drivers that led to a structural weakening of the mosaic of fire-adapted ecosystems in California, and subsequently increased the risk of destructive and explosive wildfires throughout the state. Under a new climate regime, managing the impacts on systems moving out-of-phase with natural processes may protect lives and ensure the stability of ecosystem services.
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