Investigating chromatin accessibility during development and differentiation by ATAC-sequencing to guide the identification of cis-regulatory elements

Mapping accessible chromatin across time scales can give insights into its dynamic nature, for example during cellular differentiation and tissue or organism development. Analysis of such data can be utilised to identify functional cis-regulatory elements (CRE) and transcription factor binding sites and, when combined with transcriptomics, can reveal gene regulatory networks (GRNs) of expressed genes. Chromatin accessibility mapping is a powerful approach and can be performed using ATAC-sequencing (ATAC-seq), whereby Tn5 transposase inserts sequencing adaptors into genomic DNA to identify differentially accessible regions of chromatin in different cell populations. It requires low sample input and can be performed and analysed relatively quickly compared with other methods. The data generated from ATAC-seq, along with other genomic approaches, can help uncover chromatin packaging and potential cis-regulatory elements that may be responsible for gene expression. Here, we describe the ATAC-seq approach and give examples from mainly vertebrate embryonic development, where such datasets have identified the highly dynamic nature of chromatin, with differing landscapes between cellular precursors for different lineages

Soil Moisture Active Passive (SMAP) Mission Level 4 Surface and Root Zone Soil Moisture (L4_SM) Product Specification Document

This is the Product Specification Document (PSD) for Level 4 Surface and Root Zone Soil Moisture (L4_SM) data for the Science Data System (SDS) of the Soil Moisture Active Passive (SMAP) project. The L4_SM data product provides estimates of land surface conditions based on the assimilation of SMAP observations into a customized version of the NASA Goddard Earth Observing System, Version 5 (GEOS-5) land data assimilation system (LDAS). This document applies to any standard L4_SM data product generated by the SMAP Project

Soil Moisture Active Passive (SMAP) Mission Level 4 Surface and Root Zone Soil Moisture (L4_SM) Product Specification Document

This is the Product Specification Document (PSD) for Level 4 Surface and Root Zone Soil Moisture (L4_SM) data for the Science Data System (SDS) of the Soil Moisture Active Passive (SMAP) project. The L4_SM data product provides estimates of land surface conditions based on the assimilation of SMAP observations into a customized version of the NASA Goddard Earth Observing System, Version 5 (GEOS-5) land data assimilation system (LDAS). This document applies to any standard L4_SM data product generated by the SMAP Project. The Soil Moisture Active Passive (SMAP) mission will enhance the accuracy and the resolution of space-based measurements of terrestrial soil moisture and freeze-thaw state. SMAP data products will have a noteworthy impact on multiple relevant and current Earth Science endeavors. These include: Understanding of the processes that link the terrestrial water, the energy and the carbon cycles, Estimations of global water and energy fluxes over the land surfaces, Quantification of the net carbon flux in boreal landscapes Forecast skill of both weather and climate, Predictions and monitoring of natural disasters including floods, landslides and droughts, and Predictions of agricultural productivity. To provide these data, the SMAP mission will deploy a satellite observatory in a near polar, sun synchronous orbit. The observatory will house an L-band radiometer that operates at 1.40 GHz and an L-band radar that operates at 1.26 GHz. The instruments will share a rotating reflector antenna with a 6 meter aperture that scans over a 1000 km swath

CP asymmetry for radiative B-meson decay in the supersymmetric standard model

We study a rate asymmetry in the inclusive decay \Bsgamma, assuming the supersymmetric standard model based on N=1 supergravity. A complex coefficient $A$ for scalar-trilinear couplings is the source of CP violation, which is contained in the mass-squared matrices for squarks. The model parameters are nontrivially constrained by experimental results for the branching ratio of the radiative decay and for the electric dipole moments of the neutron and the electron. The decay rate asymmetry is predicted to be much larger than that by the standard model in a wide region of the parameter space compatible with the experiments. Its magnitude can be maximally around 0.1, which will be well accessible at B factories.Comment: 27 pages, Latex, 9 figure

Soil Moisture Active Passive (SMAP) Mission Level 4 Carbon (L4_C) Product Specification Document

This is the Product Specification Document (PSD) for Level 4 Surface and Root Zone Soil Moisture (L4_SM) data for the Science Data System (SDS) of the Soil Moisture Active Passive (SMAP) project. The L4_SM data product provides estimates of land surface conditions based on the assimilation of SMAP observations into a customized version of the NASA Goddard Earth Observing System, Version 5 (GEOS-5) land data assimilation system (LDAS). This document applies to any standard L4_SM data product generated by the SMAP Project

Clinical Results of Complex Subtrochanteric Femoral Fractures with Long Cephalomedullary Hip Nail

Purpose Good results of the cephalomedullary nails have been reported in proximal femoral fractures recently. Based on length of nails and shape of screws fixed in a femoral head for proximal fragment fixation, the proper nail length was in dispute. The purpose of this study was to evaluate the clinical and radiological results of a long cephalomedullary hip nail for the treatment of comminuted subtrochanteric femoral fractures. Materials and Methods Twenty-one consecutive patients with severe subtrochanteric femoral fractures who had undergone intramedullary fixation using long-PFNA II between March 2010 and March 2013 were followed-up for over 12 months. Their mean age was 64.8 years old (range, 43-85 years). Sixteen of 22 cases were high energy trauma. According to Seinsheimer's classification, 5 cases were type IV and 16 cases were type V. For radiological assessment, time to union, change of neck-shaft angle, sliding length, tip-apex distance (TAD) and leg length discrepancy (LLD) were measured. For clinical evaluation, a modified Koval index was investigated. Results: Mean operation time was 96 minutes. An average decrease of neck-shaft angle was 4.5°. The average sliding length of the helical blade was 4.2 mm. Average LLD was 3.0 mm, and TAD was 23.0 mm. Mean modified Koval index score at final follow-up was 4.6 points. All the 21 subtrochanteric fractures healed uneventfully on an average of 24.2 weeks (range, 18-30 weeks). Conclusion: Long cephalomedullary hip nail provides excellent clinical and radiological outcomes in the comminuted subtrochanteric fracture

Science Walden: Exploring the Convergence of Environmental Technologies with Design and Art

Science Walden, which is inspired by two prominent literary works, namely, Walden by Henry David Thoreau (1817-1862) and Walden Two by Burrhus Frederic Skinner (1904-1990), is aimed at establishing a community that embodies humanistic values while embracing scientific advancement to produce renewable energy and water sources. This study attempts to capitalize on feces standard money (FSM) and artistic collaboration between scientists and artists as a means of achieving the forms of life depicted in Walden and Walden Two. On our campus, we designed and built a pavilion that serves as a laboratory where scientific advantages, design, and art are merged. In the pavilion, feces are processed in reactors and facilities for sustainable energy production, and rainwater is harvested and treated for use in daily life. Our application of design and art contributes to easing interaction between the general public and scientists because it visualizes an ambiguous theory and concretizes it into an understandable image.ope

Effects of habitat and livestock on nest productivity of the Asian houbara Chlamydotis macqueenii in Bukhara Province, Uzbekistan

To inform population support measures for the unsustainably hunted Asian houbara Chlamydotis macqueenii (IUCN Vulnerable) we examined potential habitat and land-use effects on nest productivity in the Kyzylkum Desert, Uzbekistan. We monitored 177 nests across different semi-arid shrub assemblages (clay-sand and salinity gradients) and a range of livestock densities (0–80 km-2). Nest success (mean 51.4%, 95% CI 42.4–60.4%) was similar across four years; predation caused 85% of those failures for which the cause was known, and only three nests were trampled by livestock. Nesting begins within a few weeks of arrival when food appears scarce, but later nests were more likely to fail owing to the emergence of a key predator, suggesting foraging conditions on wintering and passage sites may be important for nest productivity. Nest success was similar across three shrub assemblages and was unrelated to landscape rugosity, shrub frequency or livestock density, but was greater with taller mean shrub height (range 13–67 cm) within 50 m. Clutch size (mean = 3.2 eggs) and per-egg hatchability in successful nests (87.5%) did not differ with laying date, shrub assemblage or livestock density. We therefore found no evidence that livestock density reduced nest productivity across the range examined, while differing shrub assemblages appeared to offer similar habitat quality. Asian houbara appear well-adapted to a range of semi-desert habitats and tolerate moderate disturbance by pastoralism. No obvious in situ mitigation measures arise from these findings, leaving regulation and control as the key requirement to render hunting sustainable

Enhancing energy and glucose metabolism by disrupting triglyceride synthesis: Lessons from mice lacking DGAT1

Although the ability to make triglycerides is essential for normal physiology, excess accumulation of triglycerides results in obesity and is associated with insulin resistance. Inhibition of triglyceride synthesis, therefore, may represent a feasible strategy for the treatment of obesity and type 2 diabetes. Acyl CoA:diacylglycerol acyltransferase 1 (DGAT1) is one of two DGAT enzymes that catalyze the final reaction in the known pathways of mammalian triglyceride synthesis. Mice lacking DGAT1 have increased energy expenditure and insulin sensitivity and are protected against diet-induced obesity and glucose intolerance. These metabolic effects of DGAT1 deficiency result in part from the altered secretion of adipocyte-derived factors. Studies of DGAT1-deficient mice have helped to provide insights into the mechanisms by which cellular lipid metabolism modulates systemic carbohydrate and insulin metabolism, and a better understanding of how DGAT1 deficiency enhances energy expenditure and insulin sensitivity may identify additional targets or strategies for the treatment of obesity and type 2 diabetes