The epigenetic regulator Histone Deacetylase 1 promotes transcription of a core neurogenic programme in zebrafish embryos

<p>Abstract</p> <p>Background</p> <p>The epigenetic regulator Histone Deacetylase 1 (Hdac1) is required for specification and patterning of neurones and myelinating glia during development of the vertebrate central nervous system (CNS). This co-ordinating function for Hdac1 is evolutionarily conserved in zebrafish and mouse, but the mechanism of action of Hdac1 in the developing CNS is not well-understood.</p> <p>Results</p> <p>A genome-wide comparative analysis of the transcriptomes of Hdac1-deficient and wild-type zebrafish embryos was performed, which identified an extensive programme of gene expression that is regulated by Hdac1 in the developing embryo. Using time-resolved expression profiling of embryos, we then identified a small subset of 54 genes within the Hdac1-regulated transcriptome that specifically exhibit robust and sustained Hdac1-dependent expression from early neurogenesis onwards. 18 of these 54 stringently Hdac1-regulated genes encode DNA-binding transcription factors that are implicated in promoting neuronal specification and CNS patterning, including the proneural bHLH proteins Ascl1a and Ascl1b, as well as Neurod4 and Neurod. Relatively few genes are strongly repressed by Hdac1 but expression of the Notch target gene <it>her6 </it>is attenuated by Hdac1 in specific sub-regions of the developing CNS, from early stages of neurogenesis onwards. Selected members of the stringently Hdac1-regulated group of genes were tested for Hdac1 binding to their promoter-proximal <it>cis</it>-regulatory elements. Surprisingly, we found that Hdac1 is specifically and stably associated with DNA sequences within the promoter region of <it>ascl1b </it>during neurogenesis, and that this Hdac1-<it>ascl1b </it>interaction is abolished in <it>hdac1 </it>mutant embryos.</p> <p>Conclusions</p> <p>We conclude that Hdac1 regulates histone acetylation and methylation in the developing zebrafish embryo and promotes the sustained, co-ordinate transcription of a small set of transcription factor genes that control expansion and diversification of cell fates within the developing CNS. Our <it>in vivo </it>chromatin immunoprecipitation results also suggest a specific function for Hdac1 in directly regulating transcription of a key member of this group of genes, <it>ascl1b</it>, from the beginning of neurogenesis onwards. Taken together, our observations indicate a novel role for Hdac1 as a positive regulator of gene transcription during development of the vertebrate CNS, in addition to its more well-established function in transcriptional repression.</p

Restriction associated DNA-genotyping at multiple spatial scales in Arabidopsis lyrata reveals signatures of pathogen-mediated selection

Background: Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is unclear whether high throughput genotyping approaches for identification of single nucleotide polymorphisms have sufficient power to detect modes of selection expected to result in reduced genetic differentiation among populations. In this study, we used Arabidopsis lyrata to investigate whether signatures of balancing selection can be detected based on genomic smoothing of Restriction Associated DNA sequencing (RAD-seq) data. We compared how different sampling approaches (both within and between subspecies) and different background levels of polymorphism (inbreeding or outcrossing populations) affected the ability to detect genomic regions showing key signatures of balancing selection, specifically elevated polymorphism, reduced differentiation and shifts towards intermediate allele frequencies. We then tested whether candidate genes associated with disease resistance (R-gene analogs) were detected more frequently in these regions compared to other regions of the genome. Results: We found that genomic regions showing elevated polymorphism contained a significantly higher density of R-gene analogs predicted to be under pathogen-mediated selection than regions of non-elevated polymorphism, and that many of these also showed evidence for an intermediate site-frequency spectrum based on Tajima’s D. However, we found few genomic regions that showed both elevated polymorphism and reduced FST among populations, despite strong background levels of genetic differentiation among populations. This suggests either insufficient power to detect the reduced population structure predicted for genes under balancing selection using sparsely distributed RAD markers, or that other forms of diversifying selection are more common for the R-gene analogs tested. Conclusions: Genome scans based on a small number of individuals sampled from a wide range of populations were sufficient to confirm the relative scarcity of signatures of balancing selection across the genome, but also identified new potential disease resistance candidates within genomic regions showing signatures of balancing selection that would be strong candidates for further sequencing efforts

Systematic and Evolutionary Insights Derived from mtDNA COI Barcode Diversity in the Decapoda (Crustacea: Malacostraca)

Background: Decapods are the most recognizable of all crustaceans and comprise a dominant group of benthic invertebrates of the continental shelf and slope, including many species of economic importance. Of the 17635 morphologically described Decapoda species, only 5.4% are represented by COI barcode region sequences. It therefore remains a challenge to compile regional databases that identify and analyse the extent and patterns of decapod diversity throughout the world. Methodology/Principal Findings: We contributed 101 decapod species from the North East Atlantic, the Gulf of Cadiz and the Mediterranean Sea, of which 81 species represent novel COI records. Within the newly-generated dataset, 3.6% of the species barcodes conflicted with the assigned morphological taxonomic identification, highlighting both the apparent taxonomic ambiguity among certain groups, and the need for an accelerated and independent taxonomic approach. Using the combined COI barcode projects from the Barcode of Life Database, we provide the most comprehensive COI data set so far examined for the Order (1572 sequences of 528 species, 213 genera, and 67 families). Patterns within families show a general predicted molecular hierarchy, but the scale of divergence at each taxonomic level appears to vary extensively between families. The range values of mean K2P distance observed were: within species 0.285% to 1.375%, within genus 6.376% to 20.924% and within family 11.392% to 25.617%. Nucleotide composition varied greatly across decapods, ranging from 30.8 % to 49.4 % GC content. Conclusions/Significance: Decapod biological diversity was quantified by identifying putative cryptic species allowing a rapid assessment of taxon diversity in groups that have until now received limited morphological and systematic examination. We highlight taxonomic groups or species with unusual nucleotide composition or evolutionary rates. Such data are relevant to strategies for conservation of existing decapod biodiversity, as well as elucidating the mechanisms and constraints shaping the patterns observed.FCT - SFRH/BD/25568/ 2006EC FP6 - GOCE-CT-2005-511234 HERMESFCT - PTDC/MAR/69892/2006 LusomarBo

Structural evolutions of a borosilicate glass induced by heavy ions

High-level nuclear waste containment glass is subjected to irradiation-induced stresses whose consequences must be assessed to guarantee the material behavior over time. Alpha decay from the minor actinides confined in the glass structure is responsible for most of the atom displacements. Radiation studies of nuclear glasses have shown some slight evolutions of some macroscopic properties (density, mechanical properties). The understanding of the structural origin of these modifications is important for the modeling of the long term behavior of such materials. A powder of simplified borosilicate glass composition was irradiated by multi energies gold ions to simulate the effect of alpha decay. The irradiation conditions were defined to induce a constant nuclear interaction in the grains of diameter around 2µm. For these irradiations conditions, the hardness of the glass decreased by 35%. Structural characterizations of the pristine and irradiated powders were made by multinuclear (11B, 23Na, 27Al, 29Si) Magic Angle Spinning Nuclear magnetic Resonance (NMR) and RPE to try to identify the structural origins of the macroscopic modification observed. It is observed that the local environment of boron and sodium are highly influenced by the irradiation with an important increase of boron tri-coordinated and a significant modification of the sodium cations organization. The NMR silicon spectra show fewer evolutions but a slight shift is observed that may indicate a less polymerized silicate networ

Steep Glacier Bed Knickpoints Mitigate Inland Thinning in Greenland.

Greenland's outlet glaciers have been a leading source of mass loss and accompanying sea-level rise from the Greenland Ice Sheet (GrIS) over the last 25 years. The dynamic component of outlet glacier mass loss depends on both the ice flux through the terminus and the inland extent of glacier thinning, initiated at the ice-ocean interface. Here, we find limits to the inland spread of thinning that initiates at glacier termini for 141 ocean-terminating outlet glaciers around the GrIS. Inland diffusion of thinning is limited by steep reaches of bed topography that we call "knickpoints." We show that knickpoints exist beneath the majority of outlet glaciers but they are less steep in regions of gentle bed topography, giving glaciers in gentle bed topography the potential to contribute to ongoing and future mass loss from the GrIS by allowing the diffusion of thinning far into the ice sheet interior

Steep Glacier Bed Knickpoints Mitigate Inland Thinning in Greenland.

Greenland's outlet glaciers have been a leading source of mass loss and accompanying sea-level rise from the Greenland Ice Sheet (GrIS) over the last 25 years. The dynamic component of outlet glacier mass loss depends on both the ice flux through the terminus and the inland extent of glacier thinning, initiated at the ice-ocean interface. Here, we find limits to the inland spread of thinning that initiates at glacier termini for 141 ocean-terminating outlet glaciers around the GrIS. Inland diffusion of thinning is limited by steep reaches of bed topography that we call "knickpoints." We show that knickpoints exist beneath the majority of outlet glaciers but they are less steep in regions of gentle bed topography, giving glaciers in gentle bed topography the potential to contribute to ongoing and future mass loss from the GrIS by allowing the diffusion of thinning far into the ice sheet interior

Last-millennium summer-temperature variations in Brianconnais (French Alps) based on a composite tree-ring larch chronology

International audienceWe present a tree-ring-based reconstruction of last millenium summer temperature from Briançonnais in the northern French Alps. The sample material is derived from multi-centennial living trees and also includes larch (Larix decidua Mill.) series from historical construction timbers. The Regional Curve Standardization method was applied to preserve interannual to multicentennial variations in this high-elevation dataset. The proxies are inferred using a linear model and calibrated using the June to August mean temperatures from the last revised version of the HISTALP database spanning the 1760-2003 and adjusted to take into account warm bias before 1850. The transfer function has cross-validated coefficients of correlation (r) of 0.48 (0.42), reductions of error (RE) of 0.21 (0.27) and coefficients of efficiency of 0.20 (0.16). The concordance of the Briançonnais temperature reconstruction with other Alpine records suggests that the transfer function has successfully reconstructed past summer temperature during the last two millennia. Evidence was found of a warm episode between and 900 and 1200AD, and a cold phase between 1500 and 1850AD. These events were possibly correlated to the so-called 'Mediaeval Warm Period' (MWP) and 'Little Ice Age' (LIA). model reconstructed a summer temperature decrease more than 2°C for the LIA compared with the temperature prevailing during the MWP

Cost-effectiveness of home telemonitoring in chronic kidney disease patients at different stages by a pragmatic randomized controlled trial (eNephro): rationale and study design

BACKGROUND:Home telemonitoring has developed considerably over recent years in chronic diseases in order to improve communication between healthcare professionals and patients and to promote early detection of deteriorating health status. In the nephrology setting, home telemonitoring has been evaluated in home dialysis patients but data are scarce concerning chronic kidney disease (CKD) patients before and after renal replacement therapy. The eNephro study is designed to assess the cost effectiveness, clinical/biological impact, and patient perception of a home telemonitoring for CKD patients. Our purpose is to present the rationale, design and organisational aspects of this study.METHODS:eNephro is a pragmatic randomised controlled trial, comparing home telemonitoring versus usual care in three populations of CKD patients: stage 3B/4 (n = 320); stage 5D CKD on dialysis (n = 260); stage 5 T CKD treated with transplantation (n= 260). Five hospitals and three not-for-profit providers managing self-care dialysis situated in three administrative regions in France are participating. The trial began in December 2015, with a scheduled 12-month inclusion period and 12 months follow-up. Outcomes include clinical and biological data (e.g. blood pressure, haemoglobin) collected from patient records, perceived health status (e.g. health related quality of life) collected from self-administered questionnaires, and health expenditure data retrieved from the French health insurance database (SNIIRAM) using a probabilistic matching procedure.DISCUSSION:The hypothesis is that home telemonitoring enables better control of clinical and biological parameters as well as improved perceived health status. This better control should limit emergency consultations and hospitalisations leading to decreased healthcare expenditure, compensating for the financial investment due to the telemedicine system.TRIAL REGISTRATION:This study has been registered at ClinicalTrials.gov under NCT02082093 (date of registration: February 14, 2014)