Regulation of stress-associated scaffold proteins JIP1 and JIP3 on the c-Jun NH2-terminal kinase in ischemia-reperfusion

Ischemia-reperfusion (IR)-induced cell apoptosis involves the activation of c-Jun NH2-terminal kinase (JNK). The activation of JNK requires the presence of scaffold proteins called JNK-interacting proteins (JIP), which bind several members of a signaling cascade for proper signaling specificity. In this study, the expression of scaffold proteins JIP1 and JIP3 and their roles in the regulation of JNK activity were investigated in simulated IR in a cell model (H9c2). JIP1 protein expression was significantly decreased, whereas JIP3 protein expression was increased in IR H9c2 cells. Adenovirus-induced overexpression of JIP1 reduced IR-induced JNK activity and apoptosis. Conversely, overexpression of JIP3 increased JNK activity and apoptosis following IR. Depletion of endogenous JIP1 by siRNA treatment increased the IR-induced JNK activity, whereas siRNA-mediated depletion of endogenous JIP3 inhibited JNK activity. These results suggest that JIP1 and JIP3 play important roles in the activation of JNK during simulated IR challenge in H9c2 cells.     

Glucose transport in developing Ehrlich ascites tumor cells: parallel changes in the rate of glucose uptake and cytochalasin B binding activity during tumor development and methotrexate treatment

The ability of Ehrlich ascites tumor cells to take up glucose increased progressively during the course of tumor development. Simultaneously as the rate of uptake rose, the density of a class of glucose-reversible binding sites for cytochalasin B on the cell surface also increased. In its stereospecificity requirement toward competing sugars and in its sensitivity to phloretin and diethylstilbestrol, this class of binding sites resembled the putative glucose carriers identified in various other cell systems and may represent the glucose transporter in Ehrlich ascites cells. Work with methotrexate (MTX) substantiated this view. Methotrexate arrested tumor growth, inhibited glucose uptake, and reduced the number of cytochalasin B binding sites. In both MTX-treated and untreated cells, the magnitude of changes in number of cytochalasin B binding sites closely paralleled and sufficiently accounted for the magnitude of changes in glucose uptake. Qualitative changes in the turnover and affinity for substrate of the putative glucose carrier need not be invoked.     

Comparison of Methanotrophic Community and Methane Oxidation between Rhizospheric and Non-Rhizospheric Soils

Using particulate methane monooxygenase (pMMO) encoding gene, pmoA-based terminal-restrict fragment length polymorphism (T-RFLP), the methanotrophic communities between rhizospheric soils (RSs) and non-rhizospheric soil (NRSs) of landfill cover (LC), riparian wetland (RW) and rice paddy (RP) were compared before and after pre-incubation of 90 days. The ultimate potential of methane oxidation rate (UPMOR) and gene copy number of pmoA were evaluated in the soil samples after pre-incubation. Compared to the methanotrophic community in the soil samples before pre-incubation, type II methanotrophs, the Methylocystis-Methylosinus group, was mostly increased after pre-incubation, regardless of the soil type. The UPMOR (11.82 ± 0.27 μmol-CH₄· g^?1 _soil-DW·h^?1) in the LC-RS was significantly higher than that (9.57 ± 0.14 μmol-CH₄· g^?1 _soil-DW·h^?1) in the LC-NRS. However, no significant difference was found between RSs and NRSs in the RW (15.28 ± 0.91 and 13.23 ± 0.69 μmol-CH₄· g^?1 _soil-DW·h^?1, respectively) and RP (13.81 ± 1.04 and 12.81 ± 2.40 μmol-CH₄· g^?1 _soil-DW·h^?1, respectively) soils. There was no significantly difference in the gene copy numbers of pmoA in the RSs compared with those in the NRSs at all of the sampling sites. This study provides basic metagenomic information about both rhizospheric and non-rhizospheric methanotrophs, which will be helpful in developing a better strategy of biological methane removal from both natural and anthropogenic major methane sources.     

The landscape of DNA repeat elements in human heart failure

DNA methylation is a chemical modification of cytosine bases that is pivotal for gene regulation, cellular specification and cancer development. Here, we describe an R package, methylKit, that rapidly analyzes genome-wide cytosine epigenetic profiles from high-throughput methylation and hydroxymethylation sequencing experiments. methylKit includes functions for clustering, sample quality visualization, differential methylation analysis and annotation features, thus automating and simplifying many of the steps for discerning statistically significant bases or regions of DNA methylation. Finally, we demonstrate methylKit on breast cancer data, in which we find statistically significant regions of differential methylation and stratify tumor subtypes. methylKit is available at http://code.google.com/p/methylkit.     

Quantitative and temporal proteome analysis of butyrate-treated colorectal cancer cells

Colorectal cancer is one of the most common cancers in developed countries, and its incidence is negatively associated with high dietary fiber intake. Butyrate, a short-chain fatty acid fermentation by-product of fiber induces cell maturation with the promotion of growth arrest, differentiation, and/or apoptosis of cancer cells. The stimulation of cell maturation by butyrate in colonic cancer cells follows a temporal progression from the early phase of growth arrest to the activation of apoptotic cascades. Previously we performed two-dimensional DIGE to identify differentially expressed proteins induced by 24-h butyrate treatment of HCT-116 colorectal cancer cells. Herein we used quantitative proteomics approaches using iTRAQ (isobaric tags for relative and absolute quantitation), a stable isotope labeling methodology that enables multiplexing of four samples, for a temporal study of HCT-116 cells treated with butyrate. In addition, cleavable ICAT, which selectively tags cysteine-containing proteins, was also used, and the results complemented those obtained from the iTRAQ strategy. Selected protein targets were validated by real time PCR and Western blotting. A model is proposed to illustrate our findings from this temporal analysis of the butyrate-responsive proteome that uncovered several integrated cellular processes and pathways involved in growth arrest, apoptosis, and metastasis. These signature clusters of butyrate-regulated pathways are potential targets for novel chemopreventive and therapeutic drugs for treatment of colorectal cancer.     

Solution‐Processed Ternary Oxides as Carrier Transport/Injection Layers in Optoelectronics

With the remarkable progress in solution‐processed optoelectronics, high performance is required of the carrier transport/injection layer. Ternary oxides containing a variety of crystal structures, and adjustable composition that results in tunable optical and electrical properties, are one of the promising class of candidates to fulfill the requirements of carrier transport/injection layers for high‐performance and stable optoelectronic devices. Solution‐processed ternary oxides have seen considerable progress in recent decades, due to their advantages in the quest to design low‐cost, high‐performance, large‐scale, and stable optoelectronic devices. Herein, the recent advances of solution‐processed ternary oxides are reviewed. The first section consists of a brief introduction to the topic. In the following section, the fundamentals of the effect of tuning ternary oxide composition are summarized. Section three briefly reviews the synthesis approaches for preparing ternary oxides. Section four discusses the recent progress of solution‐processed ternary oxide as carrier transport/injection layer in optoelectronic devices (such as organic solar cells, perovskite solar cells, organic light emitting diodes, etc.). In this section, the impact of controlling ternary oxide composition on device performance and stability is highlighted. Finally, a brief summary and an outlook are given.