Identification of cis regulatory features in the embryonic zebrafish genome through large-scale profiling of H3K4me1 and H3K4me3 binding sites.

An organism's genome sequence serves as a blueprint for the proteins and regulatory RNAs essential for cellular function. The genome also harbors cis-acting non-coding sequences that control gene expression and are essential to coordinate regulatory programs during embryonic development. However, the genome sequence is largely identical between cell types within a multi-cellular organism indicating that factors such as DNA accessibility and chromatin structure play a crucial role in governing cell-specific gene expression.

Degradation of sulfamonomethoxine with Fe3O4 magnetic nanoparticles as heterogeneous activator of persulfate.

Iron oxide magnetic nanoparticles (Fe(3)O(4) MNPs) can effectively activate persulfate anions (S(2)O(8)(2-)) to produce sulfate free radicals (SO(4)(-)), which are a powerful oxidant with promising applications to degrade organic contaminants. The kinetics of sulfamonomethoxine (SMM) degradation was studied in the system of Fe(3)O(4) MNPs and S(2)O(8)(2-). A complete removal of the added SMM (0.

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system.

FlyFactorSurvey (http://pgfe.umassmed.edu/TFDBS/) is a database of DNA binding specificities for Drosophila transcription factors (TFs) primarily determined using the bacterial one-hybrid system.

Sono-assisted preparation of magnetic magnesium-aluminum layered double hydroxides and their application for removing fluoride.

A simple ultrasound-assisted co-precipitation method in combination with a calcination treatment was developed to prepare magnetic Mg-Al layered double hydroxides composite as an adsorbent material to remove fluoride ions from aqueous solutions. The application of ultrasound in the preparation process promoted the formation of the hydrotalcite-like phase and drastically shortened the time being required for preparation of the crystalline composite. It was found that the ultrasound irradiation assistance decreased the size of the composite particles and increased the specific surface area, being favorable to the improvement of the adsorption capacity.

Visual presentation as a welcome alternative to textual presentation of gene annotation information.

The functions of a gene are traditionally annotated textually using either free text (Gene Reference Into Function or GeneRIF) or controlled vocabularies (e.g., Gene Ontology or Disease Ontology).

Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases.

Zinc finger nucleases (ZFNs) facilitate tailor-made genomic modifications in vivo through the creation of targeted double-stranded breaks. They have been employed to modify the genomes of plants and animals, and cell-based therapies utilizing ZFNs are undergoing clinical trials. However, many ZFNs display dose-dependent toxicity presumably due to the generation of undesired double-stranded breaks at off-target sites.

[Characterization of water-soluble inorganic ions in PM2.5 and PM1.0 in summer in Guangzhou].

PM2.5 and PM1.0 samples were collected simultaneously during July of 2008 in Guangzhou.

Down-regulation of CREB-binding protein expression inhibits thrombin-induced proliferation of endothelial cells: possible relevance to PDGF-B.

Thrombin acts as a potent mitogenic factor for ECs (endothelial cells) by the release of several growth factors, including PDGF-B (platelet-derived growth factor-B). CBP (CREB-binding protein), which functions as a transcriptional coactivator, links the changes in the extracellular stimuli with alterations in gene expression. Therefore, we hypothesized that CBP could mediate thrombin-induced proliferation of ECs via PDGF-B-dependent way.

MicroRNA-23a promotes the growth of gastric adenocarcinoma cell line MGC803 and downregulates interleukin-6 receptor.

MicroRNAs are an evolutionarily conserved class of endogenous noncoding RNAs that modulate gene expression at the post-transcriptional level. Recently, microRNA-23a (miR-23a) has been found to function as a growth-promoting and antiapoptotic factor in hepatocellular carcinoma cells. Our previous study showed that miR-23a was significantly upregulated in gastric adenocarcinoma tissues.

Tumor suppressor A20 protects against cardiac hypertrophy and fibrosis by blocking transforming growth factor-beta-activated kinase 1-dependent signaling.

A20 or tumor necrosis factor-induced protein 3 is a negative regulator of nuclear factor kappaB signaling. A20 has been shown previously to attenuate cardiac hypertrophy in vitro and postmyocardial infarction remodeling in vivo. In the present study, we tested the hypothesis that overexpression of A20 in the murine heart would protect against cardiac hypertrophy in vivo.

A genome-wide RNA interference screen reveals an essential CREB3L2-ATF5-MCL1 survival pathway in malignant glioma with therapeutic implications.

Activating transcription factor-5 (ATF5) is highly expressed in malignant glioma and has a key role in promoting cell survival. Here we perform a genome-wide RNAi screen to identify transcriptional regulators of ATF5. Our results reveal an essential survival pathway in malignant glioma, whereby activation of a RAS-mitogen-activated protein kinase or phosphoinositide-3-kinase signaling cascade leads to induction of the transcription factor cAMP response element-binding protein-3-like-2 (CREB3L2), which directly activates ATF5 expression.

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data.

Background: Chromatin immunoprecipitation (ChIP) followed by high-throughput sequencing (ChIP-seq) or ChIP followed by genome tiling array analysis (ChIP-chip) have become standard technologies for genome-wide identification of DNA-binding protein target sites. A number of algorithms have been developed in parallel that allow identification of binding sites from ChIP-seq or ChIP-chip datasets and subsequent visualization in the University of California Santa Cruz (UCSC) Genome Browser as custom annotation tracks. However, summarizing these tracks can be a daunting task, particularly if there are a large number of binding sites or the binding sites are distributed widely across the genome.

Ultrasensitive fluorometric determination of hydrogen peroxide and glucose by using multiferroic BiFeO(3) nanoparticles as a catalyst.

BiFeO(3) magnetic nanoparticles (BFO MNPs) are used as a catalyst to develop an ultrasensitive method for the determination of H(2)O(2). It is found that BFO MNPs can catalyze the decomposition of H(2)O(2) to produce OH radicals, which in turn oxidize the weakly fluorescent benzoic acid to a strongly fluorescent hydroxylated product with a maximum emission at 405nm. This makes it possible to sensitively quantify traces of H(2)O(2).

Allicin protects against cardiac hypertrophy and fibrosis via attenuating reactive oxygen species-dependent signaling pathways.

Increased oxidative stress has been associated with the pathogenesis of chronic cardiac hypertrophy and heart failure. Since allicin suppresses oxidative stress in vitro and in vivo, we hypothesized that allicin would inhibit cardiac hypertrophy through blocking oxidative stress-dependent signaling. We examined this hypothesis using primary cultured cardiac myocytes and fibroblasts and one well-established animal model of cardiac hypertrophy.

Grape seed proanthocyanidins attenuate vascular smooth muscle cell proliferation via blocking phosphatidylinositol 3-kinase-dependent signaling pathways.

The excess generation of reactive oxygen species (ROS) play important role in the development and progression of diabetes and related vascular complications. Therefore, blocking the production of ROS will be able to improve hyperglycemia-induced vascular dysfunction. The objective of this study was to determine whether a novel IH636 grape seed proanthocyanidins (GSPs) could protect against hyperproliferation of cultured rat vascular smooth muscle cells (VSMCs) induced by high glucose (HG) and determine the related molecular mechanisms.

Efficient removal of organic pollutants with magnetic Nanoscaled BiFeO(3) as a reusable heterogeneous fenton-like catalyst.

BiFeO(3) magnetic nanoparticles (BFO MNPs) were prepared with a sol-gel method and characterized as a catalyst. It was found that BFO MNPs effectively catalyzed the decomposition of H(2)O(2) into *OH radicals, being confirmed with electron spin resonance spin-trapping technique and other radical probing techniques. The strong H(2)O(2)-activating ability of BFO MNPs showed promising applications in the oxidative degradation of organic pollutants.

Breviscapine protects against cardiac hypertrophy through blocking PKC-alpha-dependent signaling.

Breviscapine is a mixture of flavonoid glycosides extracted from the Chinese herbs. Previous studies have shown that breviscapine possesses comprehensive pharmacological functions. However, very little is known about whether breviscapine have protective role on cardiac hypertrophy.

Tetrandrine blocks cardiac hypertrophy by disrupting reactive oxygen species-dependent ERK1/2 signalling.

Background And Purpose: Tetrandrine, a well-known naturally occurring calcium antagonist with anti-inflammatory, antioxidant and anti-fibrogenetic activities, has long been used clinically for treatment of cardiovascular diseases such as hypertension and arrhythmia. However, little is known about the effect of tetrandrine on cardiac hypertrophy. The aims of the present study were to determine whether tetrandrine could attenuate cardiac hypertrophy and to clarify the underlying molecular mechanisms.

Histone acetyltransferase Rtt109 is required for Candida albicans pathogenesis.

Candida albicans is a ubiquitous opportunistic pathogen that is the most prevalent cause of hospital-acquired fungal infections. In mammalian hosts, C. albicans is engulfed by phagocytes that attack the pathogen with DNA-damaging reactive oxygen species (ROS).

LIM and cysteine-rich domains 1 regulates cardiac hypertrophy by targeting calcineurin/nuclear factor of activated T cells signaling.

LIM domain proteins are important regulators in cell growth, cell fate determination, cell differentiation, and remodeling of the cell cytoskeleton. LIM and cysteine-rich domains 1 (Lmcd1) is a novel protein that contain 2 LIM domains with regular spacing in the carboxy-terminal region. However, its roles in cardiac growth remain unknown.

[Progress in Raman spectroscopic measurement of methane hydrate].

Complex thermodynamics and kinetics problems are involved in the methane hydrate formation and decomposition, and these problems are crucial to understanding the mechanisms of hydrate formation and hydrate decomposition. However, it was difficult to accurately obtain such information due to the difficulty of measurement since methane hydrate is only stable under low temperature and high pressure condition, and until recent years, methane hydrate has been measured in situ using Raman spectroscopy. Raman spectroscopy, a non-destructive and non-invasive technique, is used to study vibrational modes of molecules.

Sono-assisted preparation of highly-efficient peroxidase-like Fe(3)O(4) magnetic nanoparticles for catalytic removal of organic pollutants with H(2)O(2).

Fe(3)O(4) magnetic nanoparticles (Fe(3)O(4) MNPs) with much improved peroxidase-like activity were successfully prepared through an advanced reverse co-precipitation method under the assistance of ultrasound irradiation. The characterizations with XRD, BET and SEM indicated that the ultrasound irradiation in the preparation induced the production of Fe(3)O(4) MNPs possessing smaller particle sizes (16.5nm), greater BET surface area (82.

Photochemical removal of aniline in aqueous solutions: switching from photocatalytic degradation to photo-enhanced polymerization recovery.

Organic pollutants may be treated by either a degradation process or a recovery process in the view point of sustainable chemistry. Photocatalytic removal of aniline was investigated in aqueous solutions. It was found that the photocatalytic oxidation of aniline resulted in its degradation or polymerization, depending on its concentration.