Variant‐specific and reciprocal Hsp40 functions in Hsp104‐mediated prion elimination

The amyloid‐based prions of Saccharomyces cerevisiae are heritable aggregates of misfolded proteins, passed to daughter cells following fragmentation by molecular chaperones including the J‐protein Sis1, Hsp70 and Hsp104. Overexpression of Hsp104 efficiently cures cell populations of the prion [PSI⁺] by an alternative Sis1‐dependent mechanism that is currently the subject of significant debate. Here, we broadly investigate the role of J‐proteins in this process by determining the impact of amyloid polymorphisms (prion variants) on the ability of well‐studied Sis1 constructs to compensate for Sis1 and ask whether any other S. cerevisiae cytosolic J‐proteins are also required for this process. Our comprehensive screen, examining all 13 members of the yeast cytosolic/nuclear J‐protein complement, uncovered significant variant‐dependent genetic evidence for a role of Apj1 (antiprion DnaJ) in this process. For strong, but not weak [PSI⁺] variants, depletion of Apj1 inhibits Hsp104‐mediated curing. Overexpression of either Apj1 or Sis1 enhances curing, while overexpression of Ydj1 completely blocks it. We also demonstrated that Sis1 was the only J‐protein necessary for the propagation of at least two weak [PSI⁺] variants and no J‐protein alteration, or even combination of alterations, affected the curing of weak [PSI⁺] variants, suggesting the possibility of biochemically distinct, variant‐specific Hsp104‐mediated curing mechanisms.     

A RAPID ASSESSMENT APPROACH FOR EVALUATING SILVER CARP GENDER

Silver carp Hypophthalmichthys molitrix were introduced into the U.S. to control water quality in aquaculture ponds. From this point of origin, silver carp escaped into nearby rivers through multiple flood events. Because of their documented negative effects on native biota, silver carp have been labeled as problematic. Therefore, evaluating the biology and ecology of these non-indigenous species is critical. Multiple parameters are needed to evaluate silver carp populations(length, weight, age, and sex). Furthermore, developing methods for rapidly acquiring these data are needed. In relation to sex determination, sexual dimorphism was observed where males exhibit distinct pectoral fin ray features. Specifically, males have pronounced ridges or a "rough patch" on the dorsal surface of pectoral fins. Therefore, to test if this was an applicable way of determining silver carp gender; silver carp were collected from Midwestern U.S. rivers(N=2015) in the fall of 2011(N=870), spring of 2012(N=645), winter of 2013—2014(N=202) and summer2015(N=323) via electrofishing. For each silver carp collected, presence(e.g., rough patch) or absence(e.g.,smooth) of pronounced ridges on the top side of the pectoral fins was recorded, and an incision was made in the body cavity to identify gender. Based on the results of our evaluation, gender was correctly identified over99% of the time(2006 out of 2015) based on the pectoral fin dimorphism. In the samples taken in the winter of 2013—2014 and summer of 2015, accuracy for silver carp shorter than 300 mm and longer than 800 mm was 53.7%(19 out of 41) while accuracy for silver carp between 300 mm and 800 mm total length was 98.9%(289 out of 292). This study provides a rapid assessment approach for evaluating silver carp gender.     

Control of RAB7 activity and localization through the retromer‐TBC1D5 complex enables RAB7‐dependent mitophagy

Retromer is an endosomal multi‐protein complex that organizes the endocytic recycling of a vast range of integral membrane proteins. Here, we establish an additional retromer function in controlling the activity and localization of the late endosomal small GTPase RAB7. Surprisingly, we found that RAB7 not only decorates late endosomes or lysosomes, but is also present on the endoplasmic reticulum, trans‐Golgi network, and mitochondrial membranes, a localization that is maintained by retromer and the retromer‐associated RAB7‐specific GAP TBC1D5. In the absence of either TBC1D5 or retromer, RAB7 activity state and localization are no longer controlled and hyperactivated RAB7 expands over the entire lysosomal domain. This lysosomal accumulation of hyperactivated RAB7 results in a striking loss of RAB7 mobility and overall depletion of the inactive RAB7 pool on endomembranes. Functionally, we establish that this control of RAB7 activity is not required for the recycling of retromer‐dependent cargoes, but instead enables the correct sorting of the autophagy related transmembrane protein ATG9a and autophagosome formation around damaged mitochondria during Parkin‐mediated mitophagy.     

Adaptation genomics: The angel is in the details

This article comments on : Genome‐wide signatures of flowering adaptation to climate temperature: Regional analyses in a highly diverse native range of Arabidopsis thaliana     

Zinc preconditioning protects against renal ischaemia reperfusion injury in a preclinical sheep large animal model

Ischaemia–reperfusion injury (IRI) during various surgical procedures, including partial nephrectomy for kidney cancer or renal transplantation, is a major cause of acute kidney injury and chronic kidney disease. Currently there are no drugs or methods for protecting human organs, including the kidneys, against the peril of IRI. The aim of this study was therefore to investigate the reno-protective effect of Zn²⁺ preconditioning in a clinically relevant large animal sheep model of IRI. Further the reno-protective effectiveness of Zn²⁺ preconditioning was tested on normal human kidney cell lines HK-2 and HEK293. Anaesthetised sheep were subjected to uninephrectomy and 60 min of renal ischaemia followed by reperfusion. Sheep were preconditioned with intravenous injection of zinc chloride prior to occlusion. Serum creatinine and urea were measured before ischaemia and for 7 days after reperfusion. HK-2 and HEK293 cells were subjected to in vitro IRI using the oxygen- and glucose-deprivation model. Zn²⁺ preconditioning reduced ischaemic burden determined by creatinine and urea rise over time by ~?70% in sheep. Zn²⁺ preconditioning also increased the survival of normal human kidney cells subjected to cellular stress such as hypoxia, hydrogen peroxide injury, and serum starvation. Overall, our protocol incorporating specific Zn²⁺ dosage, number of dosages (two), time of injection (24 and 4 h prior), mode of Zn²⁺ delivery (IV) and testing of efficacy in a rat model, a large preclinical sheep model of IRI and cells of human origin has laid the foundation for assessment of the benefit of Zn²⁺ preconditioning for human applications.     

Longitudinal data methods for evaluating genome-by-epigenome interactions in families

Background

Longitudinal measurement is commonly employed in health research and provides numerous benefits for understanding disease and trait progression over time. More broadly, it allows for proper treatment of correlated responses within clusters. We evaluated 3 methods for analyzing genome-by-epigenome interactions with longitudinal outcomes from family data.

Results

Linear mixed-effect models, generalized estimating equations, and quadratic inference functions were used to test a pharmacoepigenetic effect in 200 simulated posttreatment replicates. Adjustment for baseline outcome provided greater power and more accurate control of Type I error rates than computation of a pre-to-post change score.

Conclusions

Comparison of all modeling approaches indicated a need for bias correction in marginal models and similar power for each method, with quadratic inference functions providing a minor decrement in power compared to generalized estimating equations and linear mixed-effects models.

     

Genetic diversity of a hitchhiker and prized food source in the Anthropocene: the Asian green mussel <Emphasis Type="Italic">Perna viridis</Emphasis> (Mollusca,Mytilidae)

Insight into a species’ native and introduced range is essential in understanding the invasion process. Genetic diversity, propagule pressure and environmental conditions all have been recognised as playing a determinant role in invasion success. Here, we aimed to investigate the genetic diversity and population genetic structure (using the COI mtDNA gene region and 22 nDNA microsatellite markers) of the Asian green mussel Perna viridis within its potential native range in Asia and at introduced locations in the USA and the Caribbean. We also analyse genetic data from vessel intercepts and an incursion. By doing so, we aimed to identify genetic signatures that could allow to track vessel samples to their source and provide further insight into potential high-risk invasive populations or areas. Three top hierarchical clusters were identified using the individual-based Bayesian clustering method in STRUCTURE, corresponding to populations in three world regions: (1) USA and Caribbean, (2) India and (3) Southeast Asia. Within Southeast Asia, additional analysis indicate a shallow genetic differentiation of three subgroups consisting of (3a) Thailand, (3b) Taiwan and Hong-Kong, and (3c) a cluster of Singapore–Indonesia samples. Overall, the population structure found in this study suggests that the markers used could be useful in identifying source populations, particularly between the three mains world regions. Most surprisingly however, this study shows that the genetic diversity of samples collected from vessel intercepts and incursions did not differ significantly from established populations in Southeast Asia. In this region, in addition to the high vessel connectivity and number of P. viridis transported, all sampled populations are likely to pose a comparable risk in terms of genetic diversity. The present work represents the most comprehensive population genetic study of P. viridis, and the first to address the potential genetic introduction risk posed by populations of this species. The information and genetic markers in this study constitute a valuable addition to the tools already used to infer on potential high-risk source populations of P. viridis. They should therefore prove useful for biosecurity surveillance and management actions directed at this species.