A Role for FACT in RNA Polymerase II Promoter-Proximal Pausing.

FACT (facilitates chromatin transcription) is an evolutionarily conserved histone chaperone that was initially identified as an activity capable of promoting RNA polymerase II (Pol II) transcription through nucleosomes in vitro. In this report, we describe a global analysis of FACT function in Pol II transcription in Drosophila. We present evidence that loss of FACT has a dramatic impact on Pol II elongation-coupled processes including histone H3 lysine 4 (H3K4) and H3K36 methylation, consistent with a role for FACT in coordinating histone modification and chromatin architecture during Pol II transcription.

Co-fermentation of the main sugar types from a beechwood organosolv hydrolysate by several strains of results in effective lactic acid production.

is an interesting facultative anaerobic microorganism for biotechnological production of lactic acid that arouses interest. To determine the efficiency of biotechnological production of lactic acid from lignocellulosic feedstock hydrolysates, five strains were grown in lignocellulose organosolv hydrolysate from ethanol/water-pulped beechwood. Parameter estimation based on a Monod-type model was used to derive the basic key parameters for a performance evaluation of the batch process.

Selective binding of choline by a phosphate-coordination-based triple helicate featuring an aromatic box.

In nature, proteins have evolved sophisticated cavities tailored for capturing target guests selectively among competitors of similar size, shape, and charge. The fundamental principles guiding the molecular recognition, such as self-assembly and complementarity, have inspired the development of biomimetic receptors. In the current work, we report a self-assembled triple anion helicate (host 2) featuring a cavity resembling that of the choline-binding protein ChoX, as revealed by crystal and density functional theory (DFT)-optimized structures, which binds choline in a unique dual-site-binding mode.

Cytonuclear Epistasis Controls the Density of Symbiont in Nongonadal Tissues of Mosquito .

, a bacterial symbiont infecting arthropods and nematodes, is vertically transmitted through the female germline and manipulates its host's reproduction to favor infected females. also infects somatic tissues where it can cause nonreproductive phenotypes in its host, including resistance to viral pathogens. -mediated phenotypes are strongly associated with the density of in host tissues.

A brief dataset on the model-based evaluation of the growth performance of Bacillus coagulans and l-lactic acid production in a lignin-supplemented medium.

The data presented in this article are related to the research article entitled "Model-based characterization of growth performance and l-lactic acid production with high optical purity by thermophilic in a lignin-supplemented mixed substrate medium (R. Glaser and J. Venus, 2016) [1]".

Model-based characterisation of growth performance and l-lactic acid production with high optical purity by thermophilic Bacillus coagulans in a lignin-supplemented mixed substrate medium.

Three Bacillus coagulans strains were characterised in terms of their ability to grow in lignin-containing fermentation media and to consume the lignocellulose-related sugars glucose, xylose, and arabinose. An optical-density high-throughput screening was used for precharacterisation by means of different mathematical models for comparison (Logistic, Gompertz, Baranyi, Richards & Stannard, and Schnute). The growth response was characterised by the maximum growth rate and lag time.

Unraveling the Structure-Affinity Relationship between Cucurbit[n]urils (n = 7, 8) and Cationic Diamondoids.

We report the measurement of the binding constants (K) for cucurbit[n]uril (n = 7, 8) toward four series of guests based on 2,6-disubstituted adamantanes, 4,9-disubstituted diamantanes, 1,6-disubstituted diamantanes, and 1-substituted adamantane ammonium ions by direct and competitive H NMR spectroscopy. Compared to the affinity of CB[7]·Diam(NMe), the adamantane diammonium ion complexes (e.g.

A Nexus between Theory and Experiment: Non-Empirical Quantum Mechanical Computational Methodology Applied to Cucurbit[n]uril⋅Guest Binding Interactions.

A training set of eleven X-ray structures determined for biomimetic complexes between cucurbit[n]uril (CB[7 or 8]) hosts and adamantane-/diamantane ammonium/aminium guests were studied with DFT-D3 quantum mechanical computational methods to afford ΔG binding energies. A novel feature of this work is that the fidelity of the BLYP-D3/def2-TZVPP choice of DFT functional was proven by comparison with more accurate methods. For the first time, the CB[n]⋅guest complex binding energy subcomponents [for example, ΔE , ΔE , ΔG , binding entropy (-TΔS), and induced fit E , E ] were calculated.

Enzyme-based lignocellulose hydrolyzation - Brief data survey for cellulase performance characterization on behalf of the Sauter mean diameter of raw material particles.

The data presented here supports the informational background of enzyme-based lignocellulose hydrolyzation, cellulase characterization, and sugar yield prediction for the work "Enzyme-based lignocellulose hydrolyzation - Sauter mean diameter of raw materials as a basis for cellulase performance characterization and yield prediction" by Glaser [1]. Glucose yields from the enzymatic hydrolysis of the raw materials were shown as a function of cellulase enzyme loading as well as of particle size with different solid loading. The data for the proposed methods of the determination of enzyme activity in inhomogeneous samples of lignocellulosic raw materials are presented.

Enzyme-based lignocellulose hydrolyzation--Sauter mean diameter of raw materials as a basis for cellulase performance characterization and yield prediction.

The characterization of cellulase performance for industrial-scale processes holds special challenges. A huge gap exists between the enzyme characterization in a laboratory and large-scale process performances. Common cellulase mixtures from Novozymes and enzymes provided by Moscow State University were used to hydrolyze wheat straw, grass, pine wood, and aspen wood.

Influence of hydrophobic residues on the binding of CB[7] toward diammonium ions of common ammonium···ammonium distance.

We report the binding constants of CB[7] toward a series of naphthalene diammonium and 4,4'-dipiperidinium derivatives and compare the results with those obtained previously for CB[7]·3b by (1)H NMR and X-ray crystallography. The nature of binding in the host·guest complexes was investigated using quantum mechanical tools.

Screening of strains in lignin supplemented minimal medium with high throughput turbidity measurements.

The aim of this study was to extend the options for screening and characterization of microorganism through kinetic growth parameters. In order to obtain data, automated turbidimetric measurements were accomplished to observe the response of strains of . For the characterization, it was decided to examine the influence of varying concentrations of lignin with respect to bacterial growth.

Somatic Wolbachia (Rickettsiales: Rickettsiaceae) levels in Culex quinquefasciatus and Culex pipiens (Diptera: Culicidae) and resistance to West Nile virus infection.

The endosymbiotic bacteria Wolbachia pipientis Hertig infects a wide variety of insect species and can increase viral resistance in its host. Wolbachia naturally infects Culex quinquefasciatus Say and Culex pipiens L. mosquitoes, both vectors of West Nile virus (WNV).

Kinase-mediated changes in nucleosome conformation trigger chromatin decondensation via poly(ADP-ribosyl)ation.

Dynamically controlled posttranslational modifications of nucleosomal histones alter chromatin condensation to regulate transcriptional activation. We report that a nuclear tandem kinase, JIL-1, controls gene expression by activating poly(ADP-ribose) polymerase-1 (PARP-1). JIL-1 phosphorylates the C terminus of the H2Av histone variant, which stimulates PARP-1 enzymatic activity in the surrounding chromatin, leading to further modification of histones and chromatin loosening.

Cucurbit[7]uril⋅guest pair with an attomolar dissociation constant.

Host⋅guest complexes between cucurbit[7] (CB[7]) or CB[8] and diamantane diammonium ion guests 3 or 6 were studied by (1) H NMR spectroscopy and X-ray crystallography. (1) H NMR competition experiments revealed that CB[7]⋅6 is among the tightest monovalent non-covalent complexes ever reported in water with Ka =7.2×10(17)  M(-1) in pure D2 O and 1.

Solution- and solid-state conformations of C(α)-alkyl analogues of methylphenidate (Ritalin) salts: avoidance of gauche(+)gauche(-) interactions.

Alkyl analogues of methylphenidate (Ritalin) salts are slow onset, long duration dopamine reuptake inhibitors with a potential use as a cocaine abuse pharmacotherapy. X-ray crystallographic studies and nuclear magnetic resonance (NMR) investigations strongly suggest that avoidance of sterically unfavorable gauche(-)gauche(+) orientations effectively influences both the C(α)-alkyl side chain conformation and the formation of a predominant rotamer about the CH-CH bond ligating piperidine and C(Ar)R moieties. The favored CH-CH rotamer in D(2)O and in CD(2)Cl(2) of the pharmacologically interesting i-Bu and CH(2)-cyc-Pnt (RS,RS)-salts has the same antiperiplanar arrangement that was found in the crystal structures, although there clearly is a fast equilibrium involving smaller amounts of synclinal partners.

The native Wolbachia endosymbionts of Drosophila melanogaster and Culex quinquefasciatus increase host resistance to West Nile virus infection.

Background: The bacterial endosymbiont Wolbachia pipientis has been shown to increase host resistance to viral infection in native Drosophila hosts and in the normally Wolbachia-free heterologous host Aedes aegypti when infected by Wolbachia from Drosophila melanogaster or Aedes albopictus. Wolbachia infection has not yet been demonstrated to increase viral resistance in a native Wolbachia-mosquito host system.

Methodology/principal Findings: In this study, we investigated Wolbachia-induced resistance to West Nile virus (WNV; Flaviviridae) by measuring infection susceptibility in Wolbachia-infected and Wolbachia-free D.

Isolation and characterization of poly- and oligosaccharides from the red microalga Porphyridium sp.

The current study forms part of an ongoing research effort focusing on the elucidation of the chemical structure of the sulfated extracellular polysaccharide of the red microalga Porphyridium sp. (UTEX 637). We report here on the chemical structure of a fraction separated from an acidic crude extract of the polysaccharide, as investigated by methylation analysis, carboxyl reduction-methylation analysis, desulfation-methylation analysis, partial acid hydrolysis, Smith degradation, together with 1D and 2D (1)H and (13)C NMR spectroscopy.

The Drosophila protein palmitoylome: characterizing palmitoyl-thioesterases and DHHC palmitoyl-transferases.

Palmitoylation is the post-translational addition of a palmitate moiety to a cysteine residue through a covalent thioester bond. The addition and removal of this modification is controlled by both palmitoyl acyl-transferases and thioesterases. Using bioinformatic analysis, we identified 22 DHHC family palmitoyl acyl-transferase homologs in the Drosophila genome.

West Nile virus infection of Drosophila melanogaster induces a protective RNAi response.

To determine if West Nile virus (WNV) infection of insect cells induces a protective RNAi response, Drosophila melanogaster S2 and Aedes albopictus C6/36 cells were infected with WNV, and the production of WNV-homologous small RNAs was assayed as an indicator of RNAi induction. A distinct population of approximately 25 nt WNV-homologous small RNAs was detected in infected S2 cells but not C6/36 cells. RNAi knockdown of Argonaute 2 in S2 cells resulted in slightly increased susceptibility to WNV infection, suggesting that some WNV-homologous small RNAs produced in infected S2 cells are functional small interfering RNAs.

Nucleosome organization in the Drosophila genome.

Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly Drosophila melanogaster and compare it to that from the yeast Saccharomyces cerevisiae.

Chiral recognition via helical sense and phase in a crystalline supramolecular array of intermeshed triple-helices.

Hexatertiary butyl-substituted D(3)-symmetrical cage ligands composed of octahedral bidentate complexes of Ni(II) or Cu(II) ligated on either side to triskelion arrangements of three salicyl rings bound to a central nitrogen hub atom exhibit triple-helical conformations. Maximization of intermolecular aromatic-aromatic interactions between these complexes promote extended tongue and groove interleaving and affords a supramolecular array of diastereomeric intermeshed C(3)-symmetrical triple-helices perpetuating sideways throughout alternating enantiomeric layer stacks in the entire P-3 space group crystal lattice. Chiral recognition within these supramolecular ensembles is based upon the principles of helical sense and phase.

The novel FluoroChrome ImmunoAssay -- (FCIA). The role of molecular environment upon molecular structure exemplified by constriction of a flourescence-photochrome flanked by two proteins.

A rapid, sensitive, and quantitative novel immunoassay [FluoroChrome ImmunoAssay, FCIA] technique was developed which auspiciously combines both the high sensitivity of fluorescence measurements with the high specificity of an antibody. As opposed to existing immunoassays, FCIA is performed without separation of antibody-bound haptens from those that are free, and utilizes fluorescence measurements from widely available standard commercial fluorimeters. FCIA is based on the hypothesis that an appropriately designed stilbene-antigen analogue probe will suffer considerable steric hindrance to trans-cis photoisomerization when bound within the combined constraints of both an antibody binding site and a second globular protein.

Performance testing of NIOSH Method 5524/ASTM Method D-7049-04, for determination of metalworking fluids.

A performance test of NIOSH Method 5524/ASTM Method D-7049-04 for analysis of metalworking fluids (MWF) was conducted. These methods involve determination of the total and extractable weights of MWF samples; extractions are performed using a ternary blend of toluene:dichloromethane:methanol and a binary blend of methanol:water. Six laboratories participated in this study.

Palmitoyl-protein thioesterase 1 deficiency in Drosophila melanogaster causes accumulation of abnormal storage material and reduced life span.

Human neuronal ceroid lipofuscinoses (NCLs) are a group of genetic neurodegenerative diseases characterized by progressive death of neurons in the central nervous system (CNS) and accumulation of abnormal lysosomal storage material. Infantile NCL (INCL), the most severe form of NCL, is caused by mutations in the Ppt1 gene, which encodes the lysosomal enzyme palmitoyl-protein thioesterase 1 (Ppt1). We generated mutations in the Ppt1 ortholog of Drosophila melanogaster to characterize phenotypes caused by Ppt1 deficiency in flies.