The gut microbes in inflammatory bowel disease: Future novel target option for pharmacotherapy.

Gut microbes constitute the main microbiota in the human body, which can regulate biological processes such as immunity, cell proliferation, and differentiation, hence playing a specific function in intestinal diseases. In recent years, gut microbes have become a research hotspot in the pharmaceutical field. Because of their enormous number, diversity, and functional complexity, gut microbes have essential functions in the development of many digestive diseases.

Differential Coexpression Network Analysis for Gene Expression Data.

Gene expression profiling by microarray has been used to uncover molecular variations in many areas. The traditional analysis method to gene expression profiling just focuses on the individual genes, and the interactions among genes are ignored, while genes play their roles not by isolations but by interactions with each other. Consequently, gene-to-gene coexpression analysis emerged as a powerful approach to solve the above problems.

Identification of Transcriptional Modules and Key Genes in Chickens Infected with Serovar Pullorum Using Integrated Coexpression Analyses.

Pullorum is one of the leading causes of mortality in poultry. Understanding the molecular response in chickens in response to the infection by is important in revealing the mechanisms of pathogenesis and disease progress. There have been studies on identifying genes associated with infection by differential expression analysis, but the relationships among regulated genes have not been investigated.

Electrochemistry-mass spectrometry for mechanism study of oxygen reduction at water/oil interface.

Electrochemistry methods have been widely employed in the development of renewable energy, and involved in various processes, e.g. water splitting and oxygen reduction.

A 41-gene signature derived from breast cancer stem cells as a predictor of survival.

Purpose: The aim of this study was to evaluate the ability of a 41-gene signature derived from breast cancer stem cells (BCSCs) to estimate the risk of metastasis and survival in breast cancer patients.

Methods: The centroid expression of the 41-gene signature derived from BCSCs was applied as the threshold to classify patients into two separate groups--patients with high expression (high-EL) of the prognostic signature and patients with low expression (low-EL). The predictive ability of the 41-gene signature was evaluated by Cox regression model and was compared against other popular tests, such as Oncotype and MammaPrint.

DCGL v2.0: an R package for unveiling differential regulation from differential co-expression.

Motivation: Differential co-expression analysis (DCEA) has emerged in recent years as a novel, systematic investigation into gene expression data. While most DCEA studies or tools focus on the co-expression relationships among genes, some are developing a potentially more promising research domain, differential regulation analysis (DRA). In our previously proposed R package DCGL v1.

Systems perspectives on erythromycin biosynthesis by comparative genomic and transcriptomic analyses of S. erythraea E3 and NRRL23338 strains.

Background: S. erythraea is a Gram-positive filamentous bacterium used for the industrial-scale production of erythromycin A which is of high clinical importance. In this work, we sequenced the whole genome of a high-producing strain (E3) obtained by random mutagenesis and screening from the wild-type strain NRRL23338, and examined time-series expression profiles of both E3 and NRRL23338.

Low-cost industrially available molybdenum boride and carbide as "platinum-like" catalysts for the hydrogen evolution reaction in biphasic liquid systems.

Rarely reported low-cost molybdenum boride and carbide microparticles, both of which are available in abundant quantities due to their widespread use in industry, adsorb at aqueous acid-1,2-dichloroethane interfaces and efficiently catalyse the hydrogen evolution reaction in the presence of the organic electron donor - decamethylferrocene. Kinetic studies monitoring biphasic reactions by UV/vis spectroscopy, and further evidence provided by gas chromatography, highlight (a) their superior rates of catalysis relative to other industrially significant transition metal carbides and silicides, as well as a main group refractory compound, and (b) their highly comparable rates of catalysis to Pt microparticles of similar dimensions. Insight into the catalytic processes occurring for each adsorbed microparticle was obtained by voltammetry at the liquid-liquid interface.

A new thermostable β-glucosidase mined from Dictyoglomus thermophilum: properties and performance in octyl glucoside synthesis at high temperatures.

A new β-glucosidase (DtGH) representing 40% identity with an apple seed glycosidase (ASG) was cloned from Dictyoglomus thermophilum. DtGH showed extremely high thermostability in aqueous solution, with half-lives of 533, 44, and 5 h measured at 70, 80 and 90 °C, respectively. Therefore it was used for direct glycosylation of n-octanol at 70 °C instead of 50 °C as usually.

Link-based quantitative methods to identify differentially coexpressed genes and gene pairs.

Background: Differential coexpression analysis (DCEA) is increasingly used for investigating the global transcriptional mechanisms underlying phenotypic changes. Current DCEA methods mostly adopt a gene connectivity-based strategy to estimate differential coexpression, which is characterized by comparing the numbers of gene neighbors in different coexpression networks. Although it simplifies the calculation, this strategy mixes up the identities of different coexpression neighbors of a gene, and fails to differentiate significant differential coexpression changes from those trivial ones.

Periodic mesoporous organosilicas with controlled pore symmetries for peptides enrichment.

Periodic mesoporous organosilicas (PMOs) with controlled structures have been synthesized by using cetyltrimethylammonium bromide (CTAB) and sodium perfluorooctanoate (PFONa) as co-templates, 1,2-bis (triethoxysilyl)ethane (BTEE) as an organosilica precursor. By increasing the weight ratio of PFONa/CTAB, a structure transformation from a cubic (Pm-3n) to a two-dimensional hexagonal (p6m) mesostructure and then to multilamellar vesicles can be observed. The cubic and hexagonal samples have similar particle size (200-750 nm), pore size (2.

Nanomaterial-assisted laser desorption ionization for mass spectrometry-based biomedical analysis.

Nanomaterials have been widely used to assist laser desorption ionization of biomolecules for mass spectrometry analysis. Compared with classical matrix-assisted laser desorption ionization, strategies based on nanomaterial-assisted ionization generate a clean background, which is of great benefit for the qualitative and quantitative analysis of small biomolecules, such as therapeutic and diagnostic molecules. As label-free platforms, they have successfully been used for high-throughput enzyme activity/inhibition monitoring and also for tissue imaging to map in situ the distribution of peptides, metabolites and drugs.

Analyses of copy number variation of GK rat reveal new putative type 2 diabetes susceptibility loci.

Large efforts have been taken to search for genes responsible for type 2 diabetes (T2D), but have resulted in only about 20 in humans due to its complexity and heterogeneity. The GK rat, a spontanous T2D model, offers us a superior opportunity to search for more diabetic genes. Utilizing array comparative genome hybridization (aCGH) technology, we identifed 137 non-redundant copy number variation (CNV) regions from the GK rats when using normal Wistar rats as control.

DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data.

Summary: Gene coexpression analysis was developed to explore gene interconnection at the expression level from a systems perspective, and differential coexpression analysis (DCEA), which examines the change in gene expression correlation between two conditions, was accordingly designed as a complementary technique to traditional differential expression analysis (DEA). Since there is a shortage of DCEA tools, we implemented in an R package 'DCGL' five DCEA methods for identification of differentially coexpressed genes and differentially coexpressed links, including three currently popular methods and two novel algorithms described in a companion paper. DCGL can serve as an easy-to-use tool to facilitate differential coexpression analyses.

Electrochemical aspects of electrospray and laser desorption/ionization for mass spectrometry.

Soft-ionization methods, namely electrospray ionization and laser desorption/ionization, are widely used to transfer large molecules as intact gas-phase ions either from a solution or from a solid substrate. During both processes, in-source electrochemical and photoelectrochemical reactions occur. These electrode reactions, which take place at interfaces, play important roles in influencing the ionization products, but they have received little attention.

Electrochemical reactions and ionization processes.

Electrochemical or photo-electrochemical reactions in both electrospray ionization and laser desorption ionization are discussed stressing the role of the electrode reaction in influencing the ionization process. In particular, upon application of a high voltage during electrospray ionization, the emitter includes a working electrode, where redox reactions are observed, such as electro-generation of benzoquinone and metal ions. In contrast, the target plate in laser-induced desorption ionization also acts as a photo-electrode, especially when modified with a mesoporous semiconductor.

Recent advances in proteolysis and peptide/protein separation by chromatographic strategies.

This review gives a broad glance on the progress of recent advances on proteolysis and peptide/protein separation by chromatographic strategies in the past ten years, covering the main research in these areas especially in China. The reviewed research focused on enzymatic micro-reactors and peptide separation in bottom-up approaches, and protein and peptide separation in top-down approaches. The new enzymatic micro-reactor is able to accelerate proteolytic reaction rate from conventionally a couple of hours to a few seconds, and the multiple dimensional chromatographic-separation with various models or arrays could sufficiently separate the proteomic mixture.

Time-resolved transcriptome analysis of Bacillus subtilis responding to valine, glutamate, and glutamine.

Microorganisms can restructure their transcriptional output to adapt to environmental conditions by sensing endogenous metabolite pools. In this paper, an Agilent customized microarray representing 4,106 genes was used to study temporal transcript profiles of Bacillus subtilis in response to valine, glutamate and glutamine pulses over 24 h. A total of 673, 835, and 1135 amino-acid-regulated genes were identified having significantly changed expression at one or more time points in response to valine, glutamate, and glutamine, respectively, including genes involved in cell wall, cellular import, metabolism of amino-acids and nucleotides, transcriptional regulation, flagellar motility, chemotaxis, phage proteins, sporulation, and many genes of unknown function.