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.     

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.     

Persistence and prevention of aluminium- and paraquat-induced adaptive response to methyl mercuric chloride in plant cells in vivo

Induction and persistence of adaptive response by aluminium (Al), 1 or 10 microM, and paraquat (PQ), 5 or 10 microM, against genotoxicity of methyl mercuric chloride (MMCl), 1.26 microM, a standard environmental genotoxin, was investigated in root meristem cells of Allium cepa. Subsequently, three metabolic inhibitors, namely, 3-aminobezamide (3-AB, 10 or 100 microM), an inhibitor of poly(ADP-ribose) polymerase (PARP) implicated in DNA repair and/or apoptosis, cycloheximide (CH, 0.1 or 1 microM), an inhibitor of protein synthesis, and buthionine sulfoximine (BSO, 100 microM or 1mM), an inhibitor of glutathione synthesis were tested for their ability to prevent the adaptive response induced by conditioning doses of Al, 10 or 100 microM; and PQ, 5 or 100 microM, against MMCl-challenge, 1.26 or 100 microM, in root meristems of A. cepa or embryonic shoots of Hordeum vulgare, respectively. The findings demonstrated that once triggered, the Al- or PQ-adaptive response to MMCl could persist for at least 48h in root meristems of A. cepa. Furthermore, the adaptive response could effectively be prevented by 3-AB, to a lesser degree by CH, and the least by BSO, suggesting primarily the involvement of PARP and implicating DNA repair in the underlying mechanisms of adaptive response in plant cells in vivo.     

Survival of cold-stressed Campylobacter jejuni on ground chicken and chicken skin during frozen storage

Campylobacter jejuni is prevalent in poultry, but the effect of combined refrigerated and frozen storage on its survival, conditions relevant to poultry processing and storage, has not been evaluated. Therefore, the effects of refrigeration at 4 degrees C, freezing at -20 degrees C, and a combination of refrigeration and freezing on the survival of C. jejuni in ground chicken and on chicken skin were examined. Samples were enumerated using tryptic soy agar containing sheep's blood and modified cefoperazone charcoal deoxycholate agar. Refrigerated storage alone for 3 to 7 days produced a reduction in cell counts of 0.34 to 0.81 log10 CFU/g in ground chicken and a reduction in cell counts of 0.31 to 0.63 log10 CFU/g on chicken skin. Declines were comparable for each sample type using either plating medium. Frozen storage, alone and with prerefrigeration, produced a reduction in cell counts of 0.56 to 1.57 log10 CFU/g in ground chicken and a reduction in cell counts of 1.38 to 3.39 log10 CFU/g on chicken skin over a 2-week period. The recovery of C. jejuni following freezing was similar on both plating media. The survival following frozen storage was greater in ground chicken than on chicken skin with or without prerefrigeration. Cell counts after freezing were lower on chicken skin samples that had been prerefrigerated for 7 days than in those that had been prerefrigerated for 0, 1, or 3 days. This was not observed for ground chicken samples, possibly due to their composition. C. jejuni survived storage at 4 and -20 degrees C with either sample type. This study indicates that, individually or in combination, refrigeration and freezing are not a substitute for safe handling and proper cooking of poultry.