Co-methylated Genes in Different Adipose Depots of Pig are Associated with Metabolic, Inflammatory and Immune Processes

It is well established that the metabolic risk factors of obesity and its comorbidities are more attributed to adipose tissue distribution rather than total adipose mass. Since emerging evidence suggests that epigenetic regulation plays an important role in the aetiology of obesity, we conducted a genome-wide methylation analysis on eight different adipose depots of three pig breeds living within comparable environments but displaying distinct fat level using methylated DNA immunoprecipitation sequencing. We aimed to investigate the systematic association between anatomical location-specific DNA methylation status of different adipose depots and obesity-related phenotypes. We show here that compared to subcutaneous adipose tissues which primarily modulate metabolic indicators, visceral adipose tissues and intermuscular adipose tissue, which are the metabolic risk factors of obesity, are primarily associated with impaired inflammatory and immune responses. This study presents epigenetic evidence for functionally relevant methylation differences between different adipose depots

TreeFam: a curated database of phylogenetic trees of animal gene families

TreeFam is a database of phylogenetic trees of gene families found in animals. It aims to develop a curated resource that presents the accurate evolutionary history of all animal gene families, as well as reliable ortholog and paralog assignments. Curated families are being added progressively, based on seed alignments and trees in a similar fashion to Pfam. Release 1.1 of TreeFam contains curated trees for 690 families and automatically generated trees for another 11 646 families. These represent over 128 000 genes from nine fully sequenced animal genomes and over 45 000 other animal proteins from UniProt; ∼40–85% of proteins encoded in the fully sequenced animal genomes are included in TreeFam. TreeFam is freely available at and

SilkDB: a knowledgebase for silkworm biology and genomics

The Silkworm Knowledgebase (SilkDB) is a web-based repository for the curation, integration and study of silkworm genetic and genomic data. With the recent accomplishment of a ∼6X draft genome sequence of the domestic silkworm (Bombyx mori), SilkDB provides an integrated representation of the large-scale, genome-wide sequence assembly, cDNAs, clusters of expressed sequence tags (ESTs), transposable elements (TEs), mutants, single nucleotide polymorphisms (SNPs) and functional annotations of genes with assignments to InterPro domains and Gene Ontology (GO) terms. SilkDB also hosts a set of ESTs from Bombyx mandarina, a wild progenitor of B.mori, and a collection of genes from other Lepidoptera. Comparative analysis results between the domestic and wild silkworm, between B.mori and other Lepidoptera, and between B.mori and the two sequenced insects, fruitfly and mosquito, are displayed by using B.mori genome sequence as a reference framework. Designed as a basic platform, SilkDB strives to provide a comprehensive knowledgebase about the silkworm and present the silkworm genome and related information in systematic and graphical ways for the convenience of in-depth comparative studies. SilkDB is publicly accessible at http://silkworm.genomics.org.cn

Whole-genome sequencing of the snub-nosed monkey provides insights into folivory and evolutionary history

Colobines are a unique group of Old World monkeys that principally eat leaves and seeds rather than fruits and insects. We report the sequencing at 146× coverage, de novo assembly and analyses of the genome of a male golden snub-nosed monkey (Rhinopithecus roxellana) and resequencing at 30× coverage of three related species (Rhinopithecus bieti, Rhinopithecus brelichi and Rhinopithecus strykeri). Comparative analyses showed that Asian colobines have an enhanced ability to derive energy from fatty acids and to degrade xenobiotics. We found evidence for functional evolution in the colobine RNASE1 gene, encoding a key secretory RNase that digests the high concentrations of bacterial RNA derived from symbiotic microflora. Demographic reconstructions indicated that the profile of ancient effective population sizes for R. roxellana more closely resembles that of giant panda rather than its congeners. These findings offer new insights into the dietary adaptations and evolutionary history of colobine primates

Hyperoxemia and excess oxygen use in early acute respiratory distress syndrome : Insights from the LUNG SAFE study

Publisher Copyright: © 2020 The Author(s). Copyright: Copyright 2020 Elsevier B.V., All rights reserved.Background: Concerns exist regarding the prevalence and impact of unnecessary oxygen use in patients with acute respiratory distress syndrome (ARDS). We examined this issue in patients with ARDS enrolled in the Large observational study to UNderstand the Global impact of Severe Acute respiratory FailurE (LUNG SAFE) study. Methods: In this secondary analysis of the LUNG SAFE study, we wished to determine the prevalence and the outcomes associated with hyperoxemia on day 1, sustained hyperoxemia, and excessive oxygen use in patients with early ARDS. Patients who fulfilled criteria of ARDS on day 1 and day 2 of acute hypoxemic respiratory failure were categorized based on the presence of hyperoxemia (PaO2 > 100 mmHg) on day 1, sustained (i.e., present on day 1 and day 2) hyperoxemia, or excessive oxygen use (FIO2 ≥ 0.60 during hyperoxemia). Results: Of 2005 patients that met the inclusion criteria, 131 (6.5%) were hypoxemic (PaO2 < 55 mmHg), 607 (30%) had hyperoxemia on day 1, and 250 (12%) had sustained hyperoxemia. Excess FIO2 use occurred in 400 (66%) out of 607 patients with hyperoxemia. Excess FIO2 use decreased from day 1 to day 2 of ARDS, with most hyperoxemic patients on day 2 receiving relatively low FIO2. Multivariate analyses found no independent relationship between day 1 hyperoxemia, sustained hyperoxemia, or excess FIO2 use and adverse clinical outcomes. Mortality was 42% in patients with excess FIO2 use, compared to 39% in a propensity-matched sample of normoxemic (PaO2 55-100 mmHg) patients (P = 0.47). Conclusions: Hyperoxemia and excess oxygen use are both prevalent in early ARDS but are most often non-sustained. No relationship was found between hyperoxemia or excessive oxygen use and patient outcome in this cohort. Trial registration: LUNG-SAFE is registered with ClinicalTrials.gov, NCT02010073publishersversionPeer reviewe

Genome-Wide DNA Methylation Changes between the Superficial and Deep Backfat Tissues of the Pig

Abstract: Adipose tissue is not only a storage organ involved in fuel metabolism, but also an endocrine organ involved in the regulation of insulin sensitivity, thermogenesis, immunity, and inflammation. There are anatomical, cellular, molecular and physiological differences among adipose tissues deposited in different body sites. However, current understanding of the intrinsic differences between the sub-compartments of the subcutaneous adipose tissue remains rudimentary. Here, we analyzed the genome-wide DNA methylation differences between the porcine superficial and deep backfat tissues using methylated DNA immunoprecipitation combined with high-throughput sequencing. We show that the genes with differentially methylated regions in their promoter are mainly involved in the processes of “lipid metabolism ” and “regulation of immune-related cytokines”. Compared with the deep backfat tissue, the promoters of genes related to the ‘positive regulation of cytokine production ’ were significantly hypermethylated in the superficial backfat tissue, which reflects the intrinsic functional and metabolic differencesInt. J. Mol. Sci. 2012, 13 709

Enhanced Transmittance Modulation of SiO2-Doped Crystalline WO3 Films Prepared from a Polyethylene Oxide (PEO) Template

Polyethylene oxide (PEO)-modified silicon dioxide (SiO2)-doped crystalline tungsten trioxide (WO3) films for use as electrochromic layers were prepared on indium tin oxide (ITO) glass by the sol&ndash;gel spin coating technique. The effects of the PEO template and SiO2 on the electrochromic transmittance modulation ability of crystalline WO3 films were investigated. Fourier transform infrared spectroscopy (FT-IR) spectra analysis indicated that PEO was decomposed after annealing at 500 &deg;C for 3 h. X-ray diffraction (XRD) pattern analysis showed that both SiO2 and PEO helped reduce the crystalline grain size of the WO3 films. Atomic force microscope (AFM) images showed that the combined action of SiO2 and PEO was helpful for achieving high surface roughness and a macroporous structure. An electrochromic test indicated that PEO-modified SiO2-doped crystalline WO3 films intercalated more charges (0.0165 C/cm2) than pure WO3 crystalline films (0.0095 C/cm2). The above effects resulted in a good transmittance modulation ability (63.2% at 628 nm) of PEO-modified SiO2-doped crystalline WO3 films, which was higher than that of pure WO3 crystalline films (9.4% at 628 nm)

Effects of Annealing Temperature on Optical Band Gap of Sol-gel Tungsten Trioxide Films

Tungsten trioxide (WO3) is a wide band gap semiconductor material that is used as an important electrochromic layer in electrochromic devices. In this work, the effects of the annealing temperature on the optical band gap of sol-gel WO3 films were investigated. X-ray Diffraction (XRD) showed that WO3 films were amorphous after being annealed at 100 &deg;C, 200 &deg;C and 300 &deg;C, respectively, but became crystallized at 400 &deg;C and 500 &deg;C. An atomic force microscope (AFM) showed that the crystalline WO3 films were rougher than the amorphous WO3 films (annealed at 200 &deg;C and 300 &deg;C). An ultraviolet spectrophotometer showed that the optical band gap of the WO3 films decreased from 3.62 eV to 3.30 eV with the increase in the annealing temperature. When the Li+ was injected into WO3 film in the electrochromic reaction, the optical band gap of the WO3 films decreased. The correlation between the optical band gap and the electrical properties of the WO3 films was found in the electrochromic test by analyzing the change in the response time and the current density. The decrease in the optical band gap demonstrates that the conductivity increases with the corresponding increase in the annealing temperature

All-Sputtering, High-Transparency, Good-Stability Coplanar Top-Gate Thin Film Transistors

In this work, transparent, stable coplanar top-gate thin film transistors (TFTs) with an active layer of neodymium-doped indium oxide and zinc oxide (Nd-IZO) were successfully fabricated on a glass substrate by all sputtering processes. The devices with a post-annealing temperature of 400 &deg;C exhibited good electrical performances with a saturation mobility (&mu;sat) of 4.25 cm2&middot;V&minus;1&middot;S&minus;1, Ion/Ioff ratio about 106, Vth of &minus;0.97 V and SS about 0.34 V/decade. Furthermore, the devices exhibited excellent negative and positive bias stability (NBS, PBS) of only a &Delta;Vth shift of about &minus;0.04 V and 0.05 V after 1 h, respectively. In addition, the devices showed high transparency about 96% over the visible-light region of 400&ndash;700 nm, which indicates a great potential in transparent displays

Zigzag Hollow Cracks of Silver Nanoparticle Film Regulated by Its Drying Micro-environment

Abstract We first verify the critical impact of evaporation on the formation of zigzag hollow cracks by regulating the drying micro-environment of silver nanoparticle film. Uneven evaporation and component segregation contributes to the flows along the surface and inside of droplets. Asymmetric vapor concentration distribution is capable of weakening the surface flow of droplets, thus suppressing the inner compressive stress of nanoparticles and leading to a surface morphology with less cracks. Although defect-free and surface smooth nanoparticle film deposited by a solution-based method remains a big challenge, our work has referential significance to optimize high-quality nanoparticle film with appropriate deposition and curing processes. Moreover, an optimization possibility through the drying micro-environment should be considered in high-end applications due to its enhanced effect on high-resolution patterns