A strain difference in the daily rhythm of glyceraldehyde-3-phosphate dehydrogenase activity in the mouse

Journal of Comparative Physiology A - A/J mice differ from C57BL/6J mice in the time of the daily peak of activity of glyceraldehyde-3-phosphate dehydrogenase (GAPD) in thymus and in thyroid....     

Next-generation sequencing to generate interactome datasets

Next-generation sequencing has not been applied to protein-protein interactome network mapping so far because the association between the members of each interacting pair would not be maintained in en masse sequencing. We describe a massively parallel interactome-mapping pipeline, Stitch-seq, that combines PCR stitching with next-generation sequencing and used it to generate a new human interactome dataset. Stitch-seq is applicable to various interaction assays and should help expand interactome network mapping.     

Herpes Simplex Virus Is Equipped with RNA- and Protein-Based Mechanisms To Repress Expression of ATRX, an Effector of Intrinsic Immunity

Intrinsic immunity is a first-line intracellular defense against virus infection, and viruses have evolved mechanisms to counteract it. During herpes simplex virus (HSV) infection, nuclear domain 10 (ND10) components localize adjacent to incoming viral genomes and generate a repressive environment for viral gene expression. Here, we found that the ND10 component, alpha-thalassemia/mental retardation syndrome X-linked (ATRX) protein, is predicted to be a target of HSV-1 miR-H1 and HSV-2 miR-H6. These microRNAs (miRNAs) share a seed sequence and are abundant during lytic infection. Mimics of both miRNAs could deplete endogenous ATRX, and an miR-H1 mimic could repress the expression of a reporter linked to the 3' untranslated region of ATRX mRNA, identifying a cellular mRNA targeted by an HSV miRNA. Interestingly, ATRX protein and its mRNA were depleted in cells lytically infected with HSV, and ATRX protein was also depleted in cells infected with human cytomegalovirus. However, infection with an HSV-1 mutant lacking miR-H1 still resulted in ATRX depletion. This depletion was sensitive to a proteasome inhibitor and was largely ablated by a deletion of the gene encoding the immediate-early ICP0 protein. Additionally, a deletion of the gene encoding the tegument protein Vhs ablated most of the depletion of ATRX mRNA. Thus, HSV is equipped with multiple mechanisms to limit the expression of ATRX. As ATRX is implicated in repression of lytic viral gene expression, our results suggest roles for these different mechanisms during various phases of HSV infection.     

Strategic Habitat Conservation for Beach Mice: Estimating Management Scenario Efficiencies

The Perdido Key beach mouse (Peromyscus polionotus trissyllepsis), Choctawhatchee beach mouse (P. p. allophrys), and St. Andrew beach mouse (P. p. peninsularis) are 3 federally endangered subspecies that inhabit coastal dunes of Alabama and Florida, USA. Conservation opportunities for these subspecies are limited and costly. Consequently, well-targeted efforts are required to achieve their downlisting criteria. To aid the development of targeted management scenarios that are designed to achieve downlisting criteria, we developed a Bayesian network model that uses habitat characteristics to predict the probability of beach mouse presence at a 30-m resolution across a portion of the Florida Panhandle. We then designed alternative management scenarios for a variety of habitat conditions for coastal dunes. Finally, we estimated how much area is needed to achieve the established downlisting criterion (i.e., habitat objective) and the amount of effort needed to achieve the habitat objective (i.e., management efficiency). The results suggest that after 7 years of post-storm recolonization, habitat objectives were met for Perdido Key (within its Florida critical habitat) and Choctawhatchee beach mice. The St. Andrew beach mouse required 5.14 km² of additional critical habitat to be protected and occupied. The St. Andrew beach mouse habitat objective might be achieved by first restoring protected critical habitat to good dune conditions and then protecting or restoring the unprotected critical habitat with the highest predicted probability of beach mouse presence. This scenario provided a 28% increase in management efficiency compared to a scenario that randomly protected or restored undeveloped unprotected critical habitat. In total, when coupled with established downlisting criteria, these quantitative and spatial decision support tools could provide insight into how much habitat is available, how much more is needed, and targeted conservation or restoration efforts that might efficiently achieve habitat objectives. © 2020 The Wildlife Society.     

Temperature response of denitrification rate and greenhouse gas production in agricultural river marginal wetland soils

Soils are predicted to exhibit significant feedback to global warming via the temperature response of greenhouse gas (GHG) production. However, the temperature response of hydromorphic wetland soils is complicated by confounding factors such as oxygen (O₂), nitrate () and soil carbon (C). We examined the effect of a temperature gradient (2–25 °C) on denitrification rates and net nitrous oxide (N₂O), methane (CH₄) production and heterotrophic respiration in mineral (Eutric cambisol and Fluvisol) and organic (Histosol) soil types in a river marginal landscape of the Tamar catchment, Devon, UK, under non‐flooded and flooded with enriched conditions. It was hypothesized that the temperature response is dependent on interactions with ‐enriched flooding, and the physicochemical conditions of these soil types. Denitrification rate (mean, 746 ± 97.3 μg m^?2 h^?1), net N₂O production (mean, 180 ± 26.6 μg m^?2 h^?1) and net CH₄ production (mean, 1065 ± 183 μg m^?2 h^?1) were highest in the organic Histosol, with higher organic matter, ammonium and moisture, and lower concentrations. Heterotrophic respiration (mean, 127 ± 4.6 mg m^?2 h^?1) was not significantly different between soil types and dominated total GHG (CO₂eq) production in all soil types. Generally, the temperature responses of denitrification rate and net N₂O production were exponential, whilst net CH₄ production was unresponsive, possibly due to substrate limitation, and heterotrophic respiration was exponential but limited in summer at higher temperatures. Flooding with increased denitrification rate, net N₂O production and heterotrophic respiration, but a reduction in net CH₄ production suggests inhibition of methanogenesis by or N₂O produced from denitrification. Implications for management and policy are that warming and flood events may promote microbial interactions in soil between distinct microbial communities and increase denitrification of excess with N₂O production contributing to no more than 50% of increases in total GHG production.