Differential binding and co-binding pattern of FOXA1 and FOXA3 and their relation to H3K4me3 in HepG2 cells revealed by ChIP-seq

Background  

The forkhead box/winged helix family members FOXA1, FOXA2, and FOXA3 are of high importance in development and specification of the hepatic linage and the continued expression of liver-specific genes.     

A new perspective on the use of plant secondary metabolites to inhibit methanogenesis in the rumen

Recently, greenhouse gas emissions have been of great concern globally. Ruminant livestock due to production of methane during normal fermentation in the rumen contributes substantially to the greenhouse effects. During the recent decade, a paradigm shift has been initiated whether plant secondary metabolites (PSM) could be exploited as natural safe feed additives alternative to chemical additives to inhibit enteric methanogenesis. More than 200,000 defined structures of PSM have been known. Some plants or their extracts with high concentrations of bioactive PSM such as saponins, tannins, essential oils, organosulphur compounds, flavonoids and many other metabolites appear to have potential to inhibit methane production in the rumen. The possible mechanisms and effects of many PSM on rumen methanogenesis are not clearly understood. Saponins may decrease methanogenesis through the inhibition of rumen protozoa and in turn may suppress the numbers and activity of methanogens. Although the direct effect of saponins on methanogens has not been demonstrated, saponins might inhibit methanogens at high doses. Tannins may inhibit the methanogenesis directly and also via inhibition of protozoal growth. Essential oils, organosulphur compounds and flavonoids appear to have direct effects against methanogens, and a reduction of protozoa associated methanogenesis probably plays a minor role for these metabolites. The chemical structure and molecular weight of the PSM and chemical composition of diets dependent upon the different feeding regimes may influence the effects of PSM on methane production. Although PSM may negatively affect nutrient utilization, there is evidence that methanogenesis could be suppressed without adversely affecting rumen fermentation, which could be exploited to mitigate methane emission in ruminants.     

Synthesis of chitosan–polycaprolactone blend for control delivery of ofloxacin drug

In the present research work chitosan has been blended with different amounts of polycaprolactone (PCL) (80:20, 75:25, 60:40 and 50:50) for using them for control delivery of ofloxacin. The blends were characterized by Fourier transmission infra red spectroscopy (FTIR), UV–visible spectroscopy (UV), scanning electron microscopy (SEM), X-ray diffraction (XRD) analysis. From the FTIR spectra the various groups present in chitosan and PCL blend were monitored. The homogeneity, morphology and crystallinity of the blends were ascertained from SEM and XRD data, respectively. The swelling studies have been measured at different drug loading. The kinetics of the drug delivery system has been systematically studied. Drug release kinetics was analyzed by plotting the cumulative release data vs. time by fitting to an exponential equation which indicated the non-Fickian type of kinetics. The drug release was investigated at different pH medium and it was found that the drug release depends upon the pH medium as well as the nature of matrix.     

Luminescent metalloreceptors with pendant macrocyclic ionophore: Synthesis, characterization, electrochemistry and ion-binding study

Metalloreceptors containing ruthenium(II) bipyridine unit as fluorophore and pendant macrocyclic units as ionophore have been synthesized and their luminescence and electrochemical properties have been investigated. Ion-binding study of these fluoroionophore with the anions F⁻, Cl⁻, Br⁻, I⁻, , , , , CH₃COO⁻, and and cations Na⁺, K⁺, Mg²⁺, Ca²⁺, Zn²⁺, Ba²⁺, Sr²⁺ Cd²⁺, Hg²⁺, Pb²⁺ and Cu²⁺, monitored by luminescence and ¹H NMR spectral changes, reveal strong interactions of and F⁻ for 2 and 3 and of Cu²⁺ only for 3. Luminescence titrations for 2 and 3 have been carried out to determine binding constants (K_s), and the calculated values are in the range 2.85 × 10² to 4.48 × 10⁴ M⁻¹. The ¹H NMR spectral changes for 2 and 3 with the addition of increasing concentration of F⁻ and exhibit substantial low-field shift of the CONH proton indicating its involvement in complex formation with the anions. The adduct of 2 and 3 have been isolated and characterized by ¹H and ³¹P NMR, mass and IR spectroscopy. The results are discussed in light of selectivity, structures of the anion bound complexes and their luminescence property.     

Effects of management regime and plant species on the enzyme activity and genetic structure of N-fixing, denitrifying and nitrifying bacterial communities in grassland soils

Management by combined grazing and mowing events is commonly used in grasslands, which influences the activity and composition of soil bacterial communities. Whether observed effects are mediated by management-induced disturbances, or indirectly by changes in the identity of major plant species, is still unknown. To address this issue, we quantified substrate-induced respiration (SIR), and the nitrification, denitrification and free-living N(2)-fixation enzyme activities below grass tufts of three major plant species (Holcus lanatus, Arrhenatherum elatius and Dactylis glomerata) in extensively or intensively managed grasslands. The genetic structures of eubacterial, ammonia oxidizing, nitrate reducing, and free-living N(2)-fixing communities were also characterized by ribosomal intergenic spacer analysis, and denaturing gradient gel electrophoresis (DGGE) or restriction fragment length polymorphism (RFLP) targeting group-specific genes. SIR was not influenced by management and plant species, whereas denitrification enzyme activity was influenced only by plant species, and management-plant species interactions were observed for fixation and nitrification enzyme activities. Changes in nitrification enzyme activity were likely largely explained by the observed changes in ammonium concentration, whereas N availability was not a major factor explaining changes in denitrification and fixation enzyme activities. The structures of eubacterial and free-living N(2)-fixing communities were essentially controlled by management, whereas the diversity of nitrate reducers and ammonia oxidizers depended on both management and plant species. For each functional group, changes in enzyme activity were not correlated or were weakly correlated to overall changes in genetic structure, but around 60% of activity variance was correlated to changes in five RFLP or DGGE bands. Although our conclusions should be tested for other ecosystems and seasons, these results show that predicting microbial changes induced by management in grasslands requires consideration of management-plant species interactions.     

Inorganic phosphate nanorods are a novel fluorescent label in cell biology

We report the first use of inorganic fluorescent lanthanide (europium and terbium) ortho phosphate [LnPO₄·H₂O, Ln = Eu and Tb] nanorods as a novel fluorescent label in cell biology. These nanorods, synthesized by the microwave technique, retain their fluorescent properties after internalization into human umbilical vein endothelial cells (HUVEC), 786-O cells, or renal carcinoma cells (RCC). The cellular internalization of these nanorods and their fluorescence properties were characterized by fluorescence spectroscopy (FS), differential interference contrast (DIC) microscopy, confocal microscopy, and transmission electron microscopy (TEM). At concentrations up to 50 μg/ml, the use of [³H]-thymidine incorporation assays, apoptosis assays (TUNEL), and trypan blue exclusion illustrated the non-toxic nature of these nanorods, a major advantage over traditional organic dyes     

Cationic DMPC/DMTAP lipid bilayers: molecular dynamics study

Cationic lipid membranes are known to form compact complexes with DNA and to be effective as gene delivery agents both in vitro and in vivo. Here we employ molecular dynamics simulations for a detailed atomistic study of lipid bilayers consisting of a mixture of cationic dimyristoyltrimethylammonium propane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC). Our main objective is to examine how the composition of the DMPC/DMTAP bilayers affects their structural and electrostatic properties in the liquid-crystalline phase. By varying the mole fraction of DMTAP, we have found that the area per lipid has a pronounced nonmonotonic dependence on the DMTAP concentration, with a minimum around the point of equimolar DMPC/DMTAP mixture. We show that this behavior has an electrostatic origin and is driven by the interplay between positively charged TAP headgroups and the zwitterionic phosphatidylcholine (PC) heads. This interplay leads to considerable reorientation of PC headgroups for an increasing DMTAP concentration, and gives rise to major changes in the electrostatic properties of the lipid bilayer, including a significant increase of total dipole potential across the bilayer and prominent changes in the ordering of water in the vicinity of the membrane. Moreover, chloride counterions are bound mostly to PC nitrogens implying stronger screening of PC heads by Cl ions compared to TAP headgroups. The implications of these findings are briefly discussed.     

Acute p38 MAPK activation decreases force development in ventricular myocytes

Evidence suggests that p38 mitogen-activated protein kinase (MAPK) activation influences cardiac function on an acute basis. The characterization and mechanisms by which this occurs were investigated in the present study. Adult rat ventricular myocytes treated with 1 mM arsenite for 30 min had a 16-fold increase in p38 MAPK phosphorylation that was attenuated by SB-203580 (a p38 MAPK inhibitor). Extracellular signal-regulated protein kinase (ERK) and c-Jun NH2-terminal kinase (JNK) were also minimally activated, but this activation was not sensitive to SB-203580. In addition, arsenite caused a p38 MAPK-independent translocation/activation of protein phosphatase 2a (PP2a) and decrease in phosphorylation of myosin light chain 2 (LC2). Arsenite-p38 MAPK activation led to translocation of heat shock protein 27 but not alpha B-crystallin to the myofilaments. Using isolated cardiomyocytes, we determined that arsenite reduces isometric tension without a change in Ca2+ sensitivity of tension via p38 MAPK and lowers myofibrillar actomyosin Mg2+-ATPase activity in a p38 MAPK-independent manner. Thus arsenite induces a p38 MAPK-independent change in PP2a and LC2 that may account for the arsenite-dependent decrease in ATPase and a p38 MAPK-dependent modification of the myofilaments that decreases myocardial force development.