Role of heat shock related genes in the physiological response of Arabidopsis thaliana to anoxia

Heat shock proteins (Hsps) are involved in the physiological responses of all living organisms to a large variety of abiotic stress. Anoxic stress is charachterized by a decreasing in the energy and redox state of the cell, and in the production of oxygen reactive species. Hsps and other genes typically related to heat shock appear to be importantly expressed following oxygen deprivation % (both at the protein and at the transcript level) and a significant overlapping between anoxic and heat shock response in the transcriptomic response exists. Upstream most of this genes heat shock transcription factor A2, an important transcription factor involved in acclimation to heat stress and in many different abiotic stress, seems to be a key regulator in the anoxic tolerance, as Arabidopsis thaliana seedlings tolerance is altered negatively or positively respectively in plants deficient or overexpressing this TF. We suggests that at least part of importance of hsfA2 and some heat shock related genes is related to the defense from oxidative damage due to the reactive oxygen species produced during anoxic or hypoxic stress

Action-Perception Matching in Human Cultural Evolution: Updates from the Cognitive Science Debate

Analyses of action-perception matching mechanisms, such as the Mirror Neuron System (MNS), have been prominent in evolutionary accounts of human cognition. Some scholars have interpreted data on the MNS to suggest that the human capacity to acquire and transmit cultural information is a learned product of cultural evolution (the Culture not Biology Account of cultural learning). Others have interpreted results related to the MNS to suggest that cultural learning in humans result from both cultural and biological evolution (the Culture per biology Account of cultural learning). In this paper, we analyse action-perception matching mechanisms considering evolutionary models and novel experimental findings about the MNS. We review the Culture not biology account plausibility within evolutionary theory and argue that as it stands this account is theoretically unsound. We finally argue for the plausibility of the Biology per culture account and discuss how it paves the way to further neurobiological investigations about the evolution of our capacity to learn, understand and transmit cultural information

Turning Vice into Virtue : Using Batch-Effects to Detect Errors in Large Genomic Data Sets

It is often unavoidable to combine data from different sequencing centers or sequencing platforms when compiling data sets with a large number of individuals. However, the different data are likely to contain specific systematic errors that will appear as SNPs. Here, we devise a method to detect systematic errors in combined data sets. To measure quality differences between individual genomes, we study pairs of variants that reside on different chromosomes and co-occur in individuals. The abundance of these pairs of variants in different genomes is then used to detect systematic errors due to batch effects. Applying our method to the 1000 Genomes data set, we find that coding regions are enriched for errors, where similar to 1% of the higher frequency variants are predicted to be erroneous, whereas errors outside of coding regions are much rarer (Peer reviewe

Unveiling diffusion pattern and structural impact of the most invasive SARS-CoV-2 spike mutation

SARS-CoV-2 epidemics quickly propagated worldwide, sorting virus genomic variants in newly established propagules of infections. Stochasticity in transmission within and between countries or an actual selective advantage could explain the global high frequency reached by some genomic variants. Using statistical analyses, demographic reconstructions, and molecular dynamics simulations, we show that the globally invasive G614 spike variant i) underwent a significant demographic expansion in most countries not explained by stochastic effects nor by overrepresentation in clinical samples; ii) increases the spike S1/S2 furin-like site conformational plasticity (short-range effect), and iii) modifies the internal motion of the receptor-binding domain affecting its cross-connection with other functional domains (long-range effect). Our results support the hypothesis of a selective advantage at the basis of the spread of the G614 variant, which we suggest may be due to structural modification of the spike protein at the S1/S2 proteolytic site, and provides structural information to guide the design of variant-specific drugs

Shared community effects and the non-genetic maternal environment shape cortisol levels in wild chimpanzees

Mechanisms of inheritance remain poorly defined for many fitness-mediating traits, especially in long-lived animals with protracted development. Using 6,123 urinary samples from 170 wild chimpanzees, we examined the contributions of genetics, non-genetic maternal effects, and shared community effects on variation in cortisol levels, an established predictor of survival in long-lived primates. Despite evidence for consistent individual variation in cortisol levels across years, between-group effects were more influential and made an overwhelming contribution to variation in this trait. Focusing on within-group variation, non-genetic maternal effects accounted for 8% of the individual differences in average cortisol levels, significantly more than that attributable to genetic factors, which was indistinguishable from zero. These maternal effects are consistent with a primary role of a shared environment in shaping physiology. For chimpanzees, and perhaps other species with long life histories, community and maternal effects appear more relevant than genetic inheritance in shaping key physiological traits.Additional co-authors: Klaus Zuberbuehler, Linda Vigilant, Tobias Deschner, Roman M. Wittig & Catherine Crockfor

The Heat-Inducible Transcription Factor HsfA2 Enhances Anoxia Tolerance in Arabidopsis[W]

Anoxia induces several heat shock proteins, and a mild heat pretreatment can acclimatize Arabidopsis (Arabidopsis thaliana) seedlings to subsequent anoxic treatment. In this study, we analyzed the response of Arabidopsis seedlings to anoxia, heat, and combined heat + anoxia stress. A significant overlap between the anoxic and the heat responses was observed by whole-genome microarray analysis. Among the transcription factors induced by both heat and anoxia, the heat shock factor A2 (HsfA2), known to be involved in Arabidopsis acclimation to heat and to other abiotic stresses, was strongly induced by anoxia. Heat-dependent acclimation to anoxia is lost in an HsfA2 knockout mutant (hsfa2) as well as in a double mutant for the constitutively expressed HsfA1a/HsfA1b (hsfA1a/1b), indicating that these three heat shock factors cooperate to confer anoxia tolerance. Arabidopsis seedlings that overexpress HsfA2 showed an increased expression of several known targets of this transcription factor and were markedly more tolerant to anoxia as well as to submergence. Anoxia failed to induce HsfA2 target proteins in wild-type seedlings, while overexpression of HsfA2 resulted in the production of HsfA2 targets under anoxia, correlating well with the low anoxia tolerance experiments. These results indicate that there is a considerable overlap between the molecular mechanisms of heat and anoxia tolerance and that HsfA2 is a player in these mechanisms

Data from: Neandertal and Denisovan DNA from Pleistocene sediments

Multiple sequence alignment files This submission contains multiple sequence alignment files used for phylogenetic reconstructions. Sequences reconstructed from sediments are denominated by the site and layer of origin. The comparative data (identical in all files) is identified by the name of the individual and the accession code of its mtDNA sequence. MSA_sedimentDNA.zipAlthough a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples we detect Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility to detect the presence of hominin groups at sites and in areas where no skeletal remains are found.Peer reviewe

Neandertal and Denisovan DNA from Pleistocene sediments

Although a rich record of Pleistocene human-associated archaeological assemblages exists, the scarcity of hominin fossils often impedes the understanding of which hominins occupied a site. Using targeted enrichment of mitochondrial DNA, we show that cave sediments represent a rich source of ancient mammalian DNA that often includes traces of hominin DNA, even at sites and in layers where no hominin remains have been discovered. By automation-assisted screening of numerous sediment samples, we detected Neandertal DNA in eight archaeological layers from four caves in Eurasia. In Denisova Cave, we retrieved Denisovan DNA in a Middle Pleistocene layer near the bottom of the stratigraphy. Our work opens the possibility of detecting the presence of hominin groups at sites and in areas where no skeletal remains are found