Subequivalence Relations and Positive-Definite Functions

We study a positive-definite function associated to a measure-preserving equivalence relation on a standard probability space and use it to measure quantitatively the proximity of subequivalence relations. This is combined with a recent co-inducing construction of Epstein to produce new kinds of mixing actions of an arbitrary infinite discrete group and it is also used to show that orbit equivalence of free, measure preserving, mixing actions of non-amenable groups is unclassifiable in a strong sense. Finally, in the case of property (T) groups we discuss connections with invariant percolation on Cayley graphs and the calculation of costs

Expansion of elevational range in a forest pest: Can parasitoids track their hosts?

We are thankful to Karim Senhadji and Ramon Ruiz-Puche for their help during the field work, and to Sara Garcia Morato for her contribution to quantifying rates of parasitism in PPM clutches at the laboratory. Two anonymous referees contributed to improve the manuscript. This study was supported by projects PROPINOL (PN22/2008), GESBOME (P06-RNM-1890) from Junta de Andalucia, REMEDINAL TE-CM (S2018/EMT-4338) from Comunidad de Madrid, ADAPTAMED (LIFE14 CCA/ES/000612) from LIFE program, and GILES (PCIN-2016-150) from the ERANET-LAC H2020 Programme.Gradients in elevation impose changes in environmental conditions, which in turn modulate species distribution and abundance as well as the interactions they maintain. Along the gradient, interacting species (e.g., predators, parasitoids) can respond to changes in different ways. This study aims to investigate how egg parasitism of a forest pest, the pine processionary moth (PPM), Thaumetopoea pityocampa, vary along an elevational gradient (190-2000 m.a.s.l.) in a mountain range of SE Spain, including areas of recent elevational expansion, for a seven years period (2008-2014). We used generalized linear mixed models to ascertain the effect of both elevation and the winter North Atlantic Oscillation (NAO) index (a proxy of interannual climatic conditions) on the rate of parasitism, and the occurrence probabilities of two parasitoid species: a PPM specialist and a generalist species. Since four pine species are stratified along the elevational gradient, we repeated all the analyses separately for lowlands (190-1300 m. a.s.l.) and uplands (1350-2000 m. a.s.l.). Results showed a decrease in both parasitism rate and probability of occurrence of the two main parasitoid species with elevation, although decline was more severe for the specialist species. The effect of elevation was more conspicuous and intense in uplands than in lowlands. Positive NAO winter values, associated with cold and dry winters, reduced the rate of parasitism and the probability of occurrence of the two main parasitoid species-but particularly for the generalist species-as elevation increases. In a context of climate warming, it is crucial to mitigate PPM elevational and latitudinal expansion. Increasing tree diversity at the PPM expansion areas may favor the establishment of parasitoids, which could contribute to synchronizing host- parasitoid interactions and minimize the risk of PPM outbreaks.Junta de Andalucia PN22/2008REMEDINAL TE-CM from Comunidad de Madrid S2018/EMT-4338ADAPTAMED from LIFE program LIFE14 CCA/ES/000612GILES from the ERANET-LAC H2020 Programme PCIN-2016-150Junta de Andalucia P06-RNM-189

Communication between levels of transcriptional control improves robustness and adaptivity

Regulation of eukaryotic gene expression depends on groups of related proteins acting at the levels of chromatin organization, transcriptional initiation, RNA processing, and nuclear transport. However, a unified understanding of how these different levels of transcriptional control interact has been lacking. Here, we combine genome-wide protein–DNA binding data from multiple sources to infer the connections between functional groups of regulators in Saccharomyces cerevisiae. Our resulting transcriptional network uncovers novel biological relationships; supporting experiments confirm new associations between actively transcribed genes and Sir2 and Esc1, two proteins normally linked to silencing chromatin. Analysis of the regulatory network also reveals an elegant architecture for transcriptional control. Using communication theory, we show that most protein regulators prefer to form modules within their functional class, whereas essential proteins maintain the sparse connections between different classes. Moreover, we provide evidence that communication between different regulatory groups improves the robustness and adaptivity of the cell

Genetic diversity and host alternation of the egg parasitoid Oencyrtus pityocampae between the pine processionary moth and caper bug

Research ArticleThe increased use of molecular tools for species identification in recent decades revealed that each of many apparently generalist parasitoids are actually a complex of morphologically similar congeners, most of which have a rather narrow host range. Ooencyrtus pityocampae (OP), an important egg parasitoid of the pine processionary moth (PPM), is considered a generalist parasitoid. OP emerges from PPM eggs after winter hibernation, mainly in spring and early summer, long before the eggs of the next PPM generation occurs. The occurrence of OP in eggs of the variegated caper bug (CB) Stenozygum coloratum in spring and summer suggests that OP populations alternate seasonally between PPM and CB. However, the identity of OP population on CB eggs seemed uncertain; unlike OP-PPM populations, the former displayed apparently high male/female ratios and lack of attraction to the PPM sex pheromone. We studied the molecular identities of the two populations since the morphological identification of the genus Ooencyrtus, and OP in particular, is difficult. Sequencing of COI and ITS2 DNA fragments and AFLP analysis of individuals from both hosts revealed no apparent differences between the OP-PPM and the OP-CB populations for both the Israeli and the Turkish OPs, which therefore supported the possibility of host alternation. Sequencing data extended our knowledge of the genetic structure of OP populations in the Mediterranean area, and revealed clear separation between East and West Mediterranean populations. The overall level of genetic diversity was rather small, with the Israeli population much less diverse than all others; possible explanations for this finding are discussed. The findings support the possibility of utilizing the CB and other hosts for enhancing biological control of the PPMinfo:eu-repo/semantics/publishedVersio

A Src inhibitor regulates the cell cycle of human pluripotent stem cells and improves directed differentiation

Driving human pluripotent stem cells (hPSCs) into specific lineages is an inefficient and challenging process. We show that a potent Src inhibitor, PP1, regulates expression of genes involved in the G1 to S phase transition of the cell cycle, activates proteins in the retinoblastoma family, and subsequently increases the differentiation propensities of hPSCs into all three germ layers. We further demonstrate that genetic suppression of Src regulates the activity of the retinoblastoma protein and enhances the differentiation potential of hPSCs across all germ layers. These positive effects extend beyond the initial germ layer specification and enable efficient differentiation at subsequent stages of differentiation

Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression

Maintenance of pluripotency and specification towards a new cell fate are both dependent on precise interactions between extrinsic signals and transcriptional and epigenetic regulators. Directed methylation of cytosines by the de novo methyltransferases DNMT3A and DNMT3B plays an important role in facilitating proper differentiation, whereas DNMT1 is essential for maintaining global methylation levels in all cell types. Here, we generated single-cell mRNA expression data from wild-type, DNMT3A, DNMT3A/3B and DNMT1 knockout human embryonic stem cells and observed a widespread increase in cellular and transcriptional variability, even with limited changes in global methylation levels in the de novo knockouts. Furthermore, we found unexpected transcriptional repression upon either loss of the de novo methyltransferase DNMT3A or the double knockout of DNMT3A/3B that is further propagated upon differentiation to mesoderm and ectoderm. Taken together, our single-cell RNA-sequencing data provide a high-resolution view into the consequences of depleting the three catalytically active DNMTs in human pluripotent stem cells

Inhibition of 26S Protease Regulatory Subunit 7 (MSS1) Suppresses Neuroinflammation

Recently, researchers have focused on immunosuppression induced by rifampicin. Our previous investigation found that rifampicin was neuroprotective by inhibiting the production of pro-inflammatory mediators, thereby suppressing microglial activation. In this study, using 2-dimensional gel electrophoresis (2-DE) and mass spectrometry (MS), we discovered that 26S protease regulatory subunit 7 (MSS1) was decreased in rifampicin-treated microglia. Western blot analysis verified the downregulation of MSS1 expression by rifampicin. As it is indicated that the modulation of the ubiquitin-26S proteasome system (UPS) with proteasome inhibitors is efficacious for the treatment of neuro-inflammatory disorders, we next hypothesized that silencing MSS1 gene expression might inhibit microglial inflammation. Using RNA interference (RNAi), we showed significant reduction of IkBα degradation and NF-kB activation. The production of lipopolysaccharides-induced pro-inflammatory mediators such as inducible nitric oxide synthase (iNOS), nitric oxide, cyclooxygenase-2, and prostaglandin E2 were also reduced by MSS1 gene knockdown. Taken together, our findings suggested that rifampicin inhibited microglial inflammation by suppressing MSS1 protein production. Silencing MSS1 gene expression decreased neuroinflammation. We concluded that MSS1 inhibition, in addition to anti-inflammatory rifampicin, might represent a novel mechanism for the treatment of neuroinflammatory disorders

Functional Conservation of Nucleosome Formation Selectively Biases Presumably Neutral Molecular Variation in Yeast Genomes

One prominent pattern of mutational frequency, long appreciated in comparative genomics, is the bias of purine/pyrimidine conserving substitutions (transitions) over purine/pyrimidine altering substitutions (transversions). Traditionally, this transitional bias has been thought to be driven by the underlying rates of DNA mutation and/or repair. However, recent sequencing studies of mutation accumulation lines in model organisms demonstrate that substitutions generally do not accumulate at rates that would indicate a transitional bias. These observations have called into question a very basic assumption of molecular evolution; that naturally occurring patterns of molecular variation in noncoding regions accurately reflect the underlying processes of randomly accumulating neutral mutation in nuclear genomes. Here, in Saccharomyces yeasts, we report a very strong inverse association (r = −0.951, P < 0.004) between the genome-wide frequency of substitutions and their average energetic effect on nucleosome formation, as predicted by a structurally based energy model of DNA deformation around the nucleosome core. We find that transitions occurring at sites positioned nearest the nucleosome surface, which are believed to function most importantly in nucleosome formation, alter the deformation energy of DNA to the nucleosome core by only a fraction of the energy changes typical of most transversions. When we examined the same substitutions set against random background sequences as well as an existing study reporting substitutions arising in mutation accumulation lines of Saccharomyces cerevisiae, we failed to find a similar relationship. These results support the idea that natural selection acting to functionally conserve chromatin organization may contribute significantly to genome-wide transitional bias, even in noncoding regions. Because nucleosome core structure is highly conserved across eukaryotes, our observations may also help to further explain locally elevated transition bias at CpG islands, which are known to destabilize nucleosomes at vertebrate promoters

The PADME electromagnetic calorimeter

The PADME experiment, hosted at Laboratori Nazionali di Frascati in Italy, is going to start its data taking in September 2018. It is designed to search for the Dark Photon (indicated by the symbol A′), an hypothetical particle that can explain the Dark Matter elusiveness, possibly produced in the reaction e + e - → A′ γ. Together with the target, the segmented electromagnetic calorimeter is the most important component of the experiment, since it is needed to detect the recoil photon energy and position, in such a way to measure the A′ mass. It will consist of 616 2.1 × 2.1 × 23.0 cm3 BGO crystals arranged in a cylindrical shape and read by HZC photomultipliers with a diameter of 1.9 cm. Here we present the results obtained during the measurements performed on the scintillating units with a radioactive source and test beams, together with an overall description of the entire experiment