Defining the chromatin signature of inducible genes in T cells

BACKGROUND Specific chromatin characteristics, especially the modification status of the core histone proteins, are associated with active and inactive genes. There is growing evidence that genes that respond to environmental or developmental signals may possess distinct chromatin marks. Using a T cell model and both genome-wide and gene-focused approaches, we examined the chromatin characteristics of genes that respond to T cell activation. RESULTS To facilitate comparison of genes with similar basal expression levels, we used expression-profiling data to bin genes according to their basal expression levels. We found that inducible genes in the lower basal expression bins, especially rapidly induced primary response genes, were more likely than their non-responsive counterparts to display the histone modifications of active genes, have RNA polymerase II (Pol II) at their promoters and show evidence of ongoing basal elongation. There was little or no evidence for the presence of active chromatin marks in the absence of promoter Pol II on these inducible genes. In addition, we identified a subgroup of genes with active promoter chromatin marks and promoter Pol II but no evidence of elongation. Following T cell activation, we find little evidence for a major shift in the active chromatin signature around inducible gene promoters but many genes recruit more Pol II and show increased evidence of elongation. CONCLUSIONS These results suggest that the majority of inducible genes are primed for activation by having an active chromatin signature and promoter Pol II with or without ongoing elongation

Engineering a highly active thermophilic β-glucosidase to enhance its pH stability and saccharification performance

BACKGROUND: β-Glucosidase is an important member of the biomass-degrading enzyme system, and plays vital roles in enzymatic saccharification for biofuels production. Candidates with high activity and great stability over high temperature and varied pHs are always preferred in industrial practice. To achieve cost-effective biomass conversion, exploring natural enzymes, developing high level expression systems and engineering superior mutants are effective approaches commonly used. RESULTS: A newly identified β-glucosidase of GH3, Bgl3A, from Talaromyces leycettanus JCM12802, was overexpressed in yeast strain Pichia pastoris GS115, yielding a crude enzyme activity of 6000 U/ml in a 3 L fermentation tank. The purified enzyme exhibited outstanding enzymatic properties, including favorable temperature and pH optima (75 °C and pH 4.5), good thermostability (maintaining stable at 60 °C), and high catalytic performance (with a specific activity and catalytic efficiency of 905 U/mg and 9096/s/mM on pNPG, respectively). However, the narrow stability of Bgl3A at pH 4.0–5.0 would limit its industrial applications. Further site-directed mutagenesis indicated the role of excessive O-glycosylation in pH liability. By removing the potential O-glycosylation sites, two mutants showed improved pH stability over a broader pH range (3.0–10.0). Besides, with better stability under pH 5.0 and 50 °C compared with wild type Bgl3A, saccharification efficiency of mutant M1 was improved substantially cooperating with cellulase Celluclast 1.5L. And mutant M1 reached approximately equivalent saccharification performance to commercial β-glucosidase Novozyme 188 with identical β-glucosidase activity, suggesting its great prospect in biofuels production. CONCLUSIONS: In this study, we overexpressed a novel β-glucosidase Bgl3A with high specific activity and high catalytic efficiency in P. pastoris. We further proved the negative effect of excessive O-glycosylation on the pH stability of Bgl3A, and enhanced the pH stability by reducing the O-glycosylation. And the enhanced mutants showed much better application prospect with substantially improved saccharification efficiency on cellulosic materials. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13068-016-0560-8) contains supplementary material, which is available to authorized users

Female Employment and Gender Gaps in China

This open access book investigates female employment and the gender gap in the labor market and households during China’s economic transition period. It provides the reader with academic evidence for understanding the mechanism of female labor force participation, the determinants of the gender gap in the labor market, and the impact of policy transformation on women’s wages and employment in China from an economics perspective. The main content of this book includes three parts―women’s family responsibilities and women’s labor supply (child care, parent care, and women’s employment), the gender gap in the labor market and society (gender gaps in wages, Communist Party membership, and participation in social activity), and the impacts of policy transformation on women’s wages and employment (the social security system and the educational expansion policy on women’s wages and employment) in China. This book provides academic evidence about these issues based on economics theories and econometric analysis methods using many kinds of long-term Chinese national survey data. This book is highly recommended to readers who are interested in up-to-date and in-depth empirical studies of the gender gap and women’s employment in China during the economic transition period. This book is of interest to various groups such as readers who are interested in the Chinese economy, policymakers, and scholars with econometric analysis backgrounds

Female Employment and Gender Gaps in China

This open access book investigates female employment and the gender gap in the labor market and households during China’s economic transition period. It provides the reader with academic evidence for understanding the mechanism of female labor force participation, the determinants of the gender gap in the labor market, and the impact of policy transformation on women’s wages and employment in China from an economics perspective. The main content of this book includes three parts―women’s family responsibilities and women’s labor supply (child care, parent care, and women’s employment), the gender gap in the labor market and society (gender gaps in wages, Communist Party membership, and participation in social activity), and the impacts of policy transformation on women’s wages and employment (the social security system and the educational expansion policy on women’s wages and employment) in China. This book provides academic evidence about these issues based on economics theories and econometric analysis methods using many kinds of long-term Chinese national survey data. This book is highly recommended to readers who are interested in up-to-date and in-depth empirical studies of the gender gap and women’s employment in China during the economic transition period. This book is of interest to various groups such as readers who are interested in the Chinese economy, policymakers, and scholars with econometric analysis backgrounds

A characterization on (g,f)(g,f)-parity orientations

Let $G$ be a graph and $g,f:V(G)\to2^N$ be two set functions such that $g(v)\le f(v)$ and $g(v)\equiv f(v)\pmod 2$ for every $v\in V(G)$. An orientation $O$ of $G$ is called a $(g,f)$-parity orientation if $g(v)\le d^+_O(v)\le f(v)$ and $g(v)\equiv d^+_O(v)\pmod 2$ for every $v\in V(G)$. In this paper, we give a Tutte-type characterization for a graph to have a $(g,f)$-parity orientation

A characterization on orientations of graphs avoiding given lists on out-degrees

Let $G$ be a graph and $F:V(G)\to2^N$ be a set function. The graph $G$ is said to be \emph{F-avoiding} if there exists an orientation $O$ of $G$ such that $d^+_O(v)\notin F(v)$ for every $v\in V(G)$, where $d^+_O(v)$ denotes the out-degree of $v$ in the directed graph $G$ with respect to $O$. In this paper, we give a Tutte-type good characterization to decide the $F$-avoiding problem when for every $v\in V(G)$, $|F(v)|\leq \frac{1}{2}(d_G(v)+1)$ and $F(v)$ contains no two consecutive integers. Our proof also gives a simple polynomial algorithm to find a desired orientation. As a corollary, we prove the following result: if for every $v\in V(G)$, $|F(v)|\leq \frac{1}{2}(d_G(v)+1)$ and $F(v)$ contains no two consecutive integers, then $G$ is $F$-avoiding. This partly answers a problem proposed by Akbari et. al.(2020

Intersubband Transitions in Lead Halide Perovskite-Based Quantum Wells for Mid-Infrared Detectors

Due to their excellent optical and electrical properties as well as versatile growth and fabrication processes, lead halide perovskites have been widely considered as promising candidates for green energy and opto-electronic related applications. Here, we investigate their potential applications at infrared wavelengths by modeling the intersubband transitions in lead halide perovskite-based quantum well systems. Both single-well and double-well structures are studied and their energy levels as well as the corresponding wavefunctions and intersubband transition energies are calculated by solving the one-dimensional Schr\"odinger equations. By adjusting the quantum well and barrier thicknesses, we are able to tune the intersubband transition energies to cover a broad range of infrared wavelengths. We also find that the lead-halide perovskite-based quantum wells possess high absorption coefficients, which are beneficial for their potential applications in infrared photodetectors. The widely tunable transition energies and high absorption coefficients of the perovskite-based quantum well systems, combined with their unique material and electrical properties, may enable an alternative material system for the development of infrared photodetectors.Comment: 24 pages, 5 figure

Evidence for Two Modes of Synergistic Induction of Apoptosis by Mapatumumab and Oxaliplatin in Combination with Hyperthermia in Human Colon Cancer Cells

Colorectal cancer is the third leading cause of cancer-related mortality in the world-- the main cause of death from colorectal cancer is hepatic metastases, which can be treated with isolated hepatic perfusion (IHP). Searching for the most clinically relevant approaches for treating colorectal metastatic disease by isolated hepatic perfusion (IHP), we developed the application of oxaliplatin concomitantly with hyperthermia and humanized death receptor 4 (DR4) antibody mapatumumab (Mapa), and investigated the molecular mechanisms of this multimodality treatment in human colon cancer cell lines CX-1 and HCT116 as well as human colon cancer stem cells Tu-12, Tu-21 and Tu-22. We showed here, in this study, that the synergistic effect of the multimodality treatment-induced apoptosis was caspase dependent and activated death signaling via both the extrinsic apoptotic pathway and the intrinsic pathway. Death signaling was activated by c-Jun N-terminal kinase (JNK) signaling which led to Bcl-xL phosphorylation at serine 62, decreasing the anti-apoptotic activity of Bcl-xL, which contributed to the intrinsic pathway. The downregulation of cellular FLICE inhibitory protein long isoform (c-FLIPL) in the extrinsic pathway was accomplished through ubiquitination at lysine residue (K) 195 and protein synthesis inhibition. Overexpression of c-FLIPL mutant (K195R) and Bcl-xL mutant (S62A) completely abrogated the synergistic effect. The successful outcome of this study supports the application of multimodality strategy to patients with colorectal hepatic metastases who fail to respond to standard chemoradiotherapy that predominantly targets the mitochondrial apoptotic pathway. © 2013 Song et al

The Relationship of Ultra-Low Permeability Sandstone Aspect Ratio With Porosity, Permeability

The ultra-low permeability sandstone reservoir has large aspect ratio which significantly influences the multi-phase percolation characteristic. The ratio could be accurately measured by rate-controlled mercury porosimetry, but the testing technology is expensive, time-consuming and core-contaminating. There is not a simple effective method to describe the aspect ratio. The pores of the ultra-low permeability sandstone are mainly connected by the very long narrow throats, which could be advantageously simulated by the compound capillary bundles model. The analytical expressions of porosity and permeability about major pore structure parameters are established based on the model for the tight porous media. After solving the two expressions, the relationship between aspect ratio and parameter combination of porosity, permeability is obtained for the ultra-low permeable sandstone. Then the relation is fitted in this article using many previous published rate-controlled mercury data on compact sandstone and the relevance is strong, which proves that aspect ratio of tight rock is able to be calculated with its porosity and permeability.Key words: Ultra-low permeability sandstone; Aspect ratio; Pore; Throat; Porosity; Permeabilit