Back from a Predicted Climatic Extinction of an Island Endemic: A Future for the Corsican Nuthatch

The Corsican Nuthatch (Sitta whiteheadi) is red-listed as vulnerable to extinction by the IUCN because of its endemism, reduced population size, and recent decline. A further cause is the fragmentation and loss of its spatially-restricted favourite habitat, the Corsican pine (Pinus nigra laricio) forest. In this study, we aimed at estimating the potential impact of climate change on the distribution of the Corsican Nuthatch using species distribution models. Because this species has a strong trophic association with the Corsican and Maritime pines (P. nigra laricio and P. pinaster), we first modelled the current and future potential distribution of both pine species in order to use them as habitat variables when modelling the nuthatch distribution. However, the Corsican pine has suffered large distribution losses in the past centuries due to the development of anthropogenic activities, and is now restricted to mountainous woodland. As a consequence, its realized niche is likely significantly smaller than its fundamental niche, so that a projection of the current distribution under future climatic conditions would produce misleading results. To obtain a predicted pine distribution at closest to the geographic projection of the fundamental niche, we used available information on the current pine distribution associated to information on the persistence of isolated natural pine coppices. While common thresholds (maximizing the sum of sensitivity and specificity) predicted a potential large loss of the Corsican Nuthatch distribution by 2100, the use of more appropriate thresholds aiming at getting closer to the fundamental distribution of the Corsican pine predicted that 98% of the current presence points should remain potentially suitable for the nuthatch and its range could be 10% larger in the future. The habitat of the endemic Corsican Nuthatch is therefore more likely threatened by an increasing frequency and intensity of wildfires or anthropogenic activities than by climate change

HIV Evolution in Early Infection: Selection Pressures, Patterns of Insertion and Deletion, and the Impact of APOBEC

The pattern of viral diversification in newly infected individuals provides information about the host environment and immune responses typically experienced by the newly transmitted virus. For example, sites that tend to evolve rapidly across multiple early-infection patients could be involved in enabling escape from common early immune responses, could represent adaptation for rapid growth in a newly infected host, or could represent reversion from less fit forms of the virus that were selected for immune escape in previous hosts. Here we investigated the diversification of HIV-1 env coding sequences in 81 very early B subtype infections previously shown to have resulted from transmission or expansion of single viruses (n = 78) or two closely related viruses (n = 3). In these cases, the sequence of the infecting virus can be estimated accurately, enabling inference of both the direction of substitutions as well as distinction between insertion and deletion events. By integrating information across multiple acutely infected hosts, we find evidence of adaptive evolution of HIV-1 env and identify a subset of codon sites that diversified more rapidly than can be explained by a model of neutral evolution. Of 24 such rapidly diversifying sites, 14 were either i) clustered and embedded in CTL epitopes that were verified experimentally or predicted based on the individual's HLA or ii) in a nucleotide context indicative of APOBEC-mediated G-to-A substitutions, despite having excluded heavily hypermutated sequences prior to the analysis. In several cases, a rapidly evolving site was embedded both in an APOBEC motif and in a CTL epitope, suggesting that APOBEC may facilitate early immune escape. Ten rapidly diversifying sites could not be explained by CTL escape or APOBEC hypermutation, including the most frequently mutated site, in the fusion peptide of gp41. We also examined the distribution, extent, and sequence context of insertions and deletions, and we provide evidence that the length variation seen in hypervariable loop regions of the envelope glycoprotein is a consequence of selection and not of mutational hotspots. Our results provide a detailed view of the process of diversification of HIV-1 following transmission, highlighting the role of CTL escape and hypermutation in shaping viral evolution during the establishment of new infections

Utilizing associational resistance for biocontrol: impacted by temperature, supported by indirect defence

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Inhibition of MLC Phosphorylation Restricts Replication of Influenza Virus—A Mechanism of Action for Anti-Influenza Agents

Influenza A viruses are a severe threat worldwide, causing large epidemics that kill thousands every year. Prevention of influenza infection is complicated by continuous viral antigenic changes. Newer anti-influenza agents include MEK/ERK and protein kinase C inhibitors; however, the downstream effectors of these pathways have not been determined. In this study, we identified a common mechanism for the inhibitory effects of a significant group of anti-influenza agents. Our studies showed that influenza infection activates a series of signaling pathways that converge to induce myosin light chain (MLC) phosphorylation and remodeling of the actin cytoskeleton. Inhibiting MLC phosphorylation by blocking RhoA/Rho kinase, phospholipase C/protein kinase C, and HRas/Raf/MEK/ERK pathways with the use of genetic or chemical manipulation leads to the inhibition of influenza proliferation. In contrast, the induction of MLC phosphorylation enhances influenza proliferation, as does activation of the HRas/Raf/MEK/ERK signaling pathway. This effect is attenuated by inhibiting MLC phosphorylation. Additionally, in intracellular trafficking studies, we found that the nuclear export of influenza ribonucleoprotein depends on MLC phosphorylation. Our studies provide evidence that modulation of MLC phosphorylation is an underlying mechanism for the inhibitory effects of many anti-influenza compounds

Cerebrospinal fluid biomarker candidates associated with human WNV neuroinvasive disease

During the last decade, the epidemiology of WNV in humans has changed in the southern regions of Europe, with high incidence of West Nile fever (WNF) cases, but also of West Nile neuroinvasive disease (WNND). The lack of human vaccine or specific treatment against WNV infection imparts a pressing need to characterize indicators associated with neurological involvement. By its intimacy with central nervous system (CNS) structures, modifications in the cerebrospinal fluid (CSF) composition could accurately reflect CNS pathological process. Until now, few studies investigated the association between imbalance of CSF elements and severity of WNV infection. The aim of the present study was to apply the iTRAQ technology in order to identify the CSF proteins whose abundances are modified in patients with WNND. Forty-seven proteins were found modified in the CSF of WNND patients as compared to control groups, and most of them are reported for the first time in the context of WNND. On the basis of their known biological functions, several of these proteins were associated with inflammatory response. Among them, Defensin-1 alpha (DEFA1), a protein reported with anti-viral effects, presente

Low-Pathogenic Avian Influenza Viruses in Wild House Mice

Background: Avian influenza viruses are known to productively infect a number of mammal species, several of which are commonly found on or near poultry and gamebird farms. While control of rodent species is often used to limit avian influenza virus transmission within and among outbreak sites, few studies have investigated the potential role of these species in outbreak dynamics. Methodology/Principal Findings: We trapped and sampled synanthropic mammals on a gamebird farm in Idaho, USA that had recently experienced a low pathogenic avian influenza outbreak. Six of six house mice (Mus musculus) caught on the outbreak farm were presumptively positive for antibodies to type A influenza. Consequently, we experimentally infected groups of naïve wild-caught house mice with five different low pathogenic avian influenza viruses that included three viruses derived from wild birds and two viruses derived from chickens. Virus replication was efficient in house mice inoculated with viruses derived from wild birds and more moderate for chicken-derived viruses. Mean titers (EID50 equivalents/mL) across all lung samples from seven days of sampling (three mice/day) ranged from 103.89 (H3N6) to 105.06 (H4N6) for the wild bird viruses and 102.08 (H6N2) to 102.85 (H4N8) for the chicken-derived viruses. Interestingly, multiple regression models indicated differential replication between sexes, with significantly (p\u3c0.05) higher concentrations of avian influenza RNA found in females compared with males. Conclusions/Significance: Avian influenza viruses replicated efficiently in wild-caught house mice without adaptation, indicating mice may be a risk pathway for movement of avian influenza viruses on poultry and gamebird farms. Differential virus replication between males and females warrants further investigation to determine the generality of this result in avian influenza disease dynamics

Ancient DNA reveals that bowhead whale lineages survived Late Pleistocene climate change and habitat shifts

The climatic changes of the glacial cycles are thought to have been a major driver of population declines and species extinctions. However, studies to date have focused on terrestrial fauna and there is little understanding of how marine species responded to past climate change. Here we show that a true Arctic species, the bowhead whale (Balaena mysticetus), shifted its range and tracked its core suitable habitat northwards during the rapid climate change of the Pleistocene–Holocene transition. Late Pleistocene lineages survived into the Holocene and effective female population size increased rapidly, concurrent with a threefold increase in core suitable habitat. This study highlights that responses to climate change are likely to be species specific and difficult to predict. We estimate that the core suitable habitat of bowhead whales will be almost halved by the end of this century, potentially influencing future population dynamics

Methane bursts as a trigger for intermittent lake-forming climates on post-Noachian Mars

Lakes existed on Mars later than 3.6 billion years ago, according to sedimentary evidence for deltaic deposition. The observed fluviolacustrine deposits suggest that individual lake-forming climates persisted for at least several thousand years (assuming dilute flow). But the lake watersheds’ little-weathered soils indicate a largely dry climate history, with intermittent runoff events. Here we show that these observational constraints, although inconsistent with many previously proposed triggers for lake-forming climates, are consistent with a methane burst scenario. In this scenario, chaotic transitions in mean obliquity drive latitudinal shifts in temperature and ice loading that destabilize methane clathrate. Using numerical simulations, we find that outgassed methane can build up to atmospheric levels sufficient for lake-forming climates, if methane clathrate initially occupies more than 4% of the total volume in which it is thermodynamically stable. Such occupancy fractions are consistent with methane production by water–rock reactions due to hydrothermal circulation on early Mars. We further estimate that photochemical destruction of atmospheric methane curtails the duration of individual lake-forming climates to less than a million years, consistent with observations. We conclude that methane bursts represent a potential pathway for intermittent excursions to a warm, wet climate state on early Mars