H-bonding in liquid N-methylformamide as studied by X-ray scattering

A structural investigation of liquid N-methylformamide, C(2)H(5)NO, was performed at room temperature and atmospheric pressure using X-ray scattering. Experimental data are analysed to yield the molecular structure factor and the distinct pair correlation function. The more dominant form (cis or trans) is considered and the H-bonding parameters are deduced. In order to describe the local arrangement in the liquid, different models are examined.     

Urease-encoding genes in ammonia-oxidizing bacteria

Many but not all ammonia-oxidizing bacteria (AOB) produce urease (urea amidohydrolase, EC 3.5.1.5) and are capable of using urea for chemolithotrophic growth. We sequenced the urease operons from two AOB, the beta-proteobacterium Nitrosospira sp. strain NpAV and the gamma-proteobacterium Nitrosococcus oceani. In both organisms, all seven urease genes were contiguous: the three structural urease genes ureABC were preceded and succeeded by the accessory genes ureD and ureEFG, respectively. Green fluorescent protein reporter gene fusions revealed that the ure genes were under control of a single operon promoter upstream of the ureD gene in Nitrosococcus oceani. Southern analyses revealed two copies of ureC in the Nitrosospira sp. strain NpAV genome, while a single copy of the ure operon was detected in the genome of Nitrosococcus oceani. The ureC gene encodes the alpha subunit protein containing the active site and conserved nickel binding ligands; these conserved regions were suitable primer targets for obtaining further ureC sequences from additional AOB. In order to develop molecular tools for detecting the ureolytic ecotype of AOB, ureC genes were sequenced from several beta-proteobacterial AOB. Pairwise identity values ranged from 80 to 90% for the UreC peptides of AOB within a subdivision. UreC sequences deduced from AOB urease genes and available UreC sequences in the public databases were used to construct alignments and make phylogenetic inferences. The UreC proteins from beta-proteobacterial AOB formed a distinct monophyletic group. Unexpectedly, the peptides from AOB did not group most closely with the UreC proteins from other beta-proteobacteria. Instead, it appears that urease in beta-proteobacterial autotrophic ammonia oxidizers is the product of divergent evolution in the common ancestor of gamma- and beta-proteobacteria that was initiated before their divergence during speciation. Sequence motifs conserved for the proteobacteria and variable regions possibly discriminatory for ureC from beta-proteobacterial AOB were identified for future use in environmental analysis of ureolytic AOB. These gene sequences are the first publicly available for ure genes from autotrophic AOB.     

First synthesis of double headed 1,3,4-oxadiazino[6,5-b]indole acyclo C-nucleosides

Condensation of 1,3-dihydro-2,3-dioxo-2H-indoles (la-c) with galactaric acid bis hydrazide (2) gave the corresponding galactaric acid bis[2-(1,2-dihydro-2-oxo-3H-indol-3-ylidene)hydrazides] (3a-c). Acetylation of the latter compounds with acetic anhydride in the presence of pyridine at ambient temperature gave the 2,3,4,5-tetra-O-acetylgalactaric acid bis[2-(1,2-dihydro-2-oxo-1-substituted-3H-indol-3-ylidene)hydrazides] (4b-d). Heterocyclization of the tetra-O-acetates 4b-d by heating with thionyl chloride afforded the double headed acyclo C-nucleosides: 1,2,3,4-tetra-O-acetyl- 1,4-bis[9-substituted-1,3,4-oxadiazino[6,5-b]indol-2-yl-1-ium]-galacto-tetritol dichlorides (5b-d). Structures of the prepared compounds were elucidated from their spectral properties.     

Essential oil of Daucus glaber Forssk

The composition of the essential oil of the fruits, leaves and stems of Daucus glaber Forssk has been studied by GC/MS. It was found that, the essential oil of the fruits consists of monoterpene hydrocarbons (limonene and sylvestrene are the majors) and phenylpropanoids (elemicin is the major). Sylvestrene has never been reported before in the essential oil of any Daucus species. The study of the essential oil of the leaves revealed the presence of monoterpene hydrocarbons; limonene and gamma-terpinene are the majors and a small amount of sylvestrene. The essential oil of stems consists of monoterpene hydrocarbons (gamma-terpinene is the major), terpene alcohols (mainly 4-terpineol) and phenylpropanoids (myristicin and elemicin are the majors). It is interesting that, the essential oil of the fruits is free from any oxygenated terpenes while that of the stems is free from limonene and sylvestrene which are present in the essential oil of the fruits and leaves in fairly large amounts The essential oil of the fruits, leaves and stems shows broad antimicrobial activities against both gram positive and gram negative bacteria. In addition, the volatile oil of the stem, particularly, show activities against Candida albicans (yeast). Also, the prepared oils have variable cytotoxic activities with LC50 21.52, 36.01 and 42.34 microg/ml, respectively.     

Bms1p, a G-domain-containing protein, associates with Rcl1p and is required for 18S rRNA biogenesis in yeast

Maturation of 18S rRNA and biogenesis of the 40S ribosomes in yeast requires a large number of trans-acting factors, including the U3 small nucleolar ribonucleoprotein (U3 snoRNP), and the recently characterized cyclase-like protein Rcl1p. U3 snoRNP is a key particle orchestrating early 35S rRNA cleavage events. A unique property of Rcl1p is that it specifically associates with U3 snoRNP, but this association appears to occur only at the level of nascent ribosomes and not with the U3 monoparticle. Here we report the characterization of Bms1p, a protein that associates with Rcl1p in multiple structures, including a specific complex sedimenting at around 10S. Like Rcl1p, Bms1p is an essential, evolutionarily conserved, nucleolar protein, and its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits. The N-terminal domain of Bms1p has structural features found in regulatory GTPases and we demonstrate that mutations of amino acids implicated in GTP/GDP binding affect Bms1p activity in vivo. The results indicate that Bms1p may act as a molecular switch during maturation of the 40S ribosomal subunit in the nucleolus.     

Induction of indolamine 2,3-dioxygenase in primary human macrophages by human immunodeficiency virus type 1 is strain dependent

Increased kynurenine pathway metabolism has been implicated in the etiology of AIDS dementia complex (ADC). The rate-limiting enzyme for this pathway is indolamine 2,3-dioxygenase (IDO). We tested the efficacy of different strains of human immunodeficiency virus type 1 (HIV1-BaL, HIV1-JRFL, and HIV1-631) to induce IDO in cultured human monocyte-derived macrophages (MDM). A significant increase in both IDO protein and kynurenine synthesis was observed after 48 h in MDM infected with the brain-derived HIV-1 isolates, laboratory-adapted (LA) HIV1-JRFL, and primary isolate HIV1-631. In contrast, almost no kynurenine production or IDO protein was evident in MDM infected with the highly replicating macrophage-tropic LA strain HIV1-BaL. The induction of IDO and kynurenine synthesis by HIV1-JRFL and HIV1-631 declined to baseline levels by day 8 postinfection. Abundant HIV-1 replication did not reduce the ability of exogenous gamma interferon (IFN-gamma) to induce IDO and kynurenine synthesis in HIV-infected MDM. The addition of anti-IFN-gamma antibody to MDM infected with HIV1-JRFL resulted in an absence of detectable IDO protein after 48 h and a decrease of 64% +/- 1% in supernatant kynurenine concentration. Together, these results indicate that only selected strains of HIV-1 are capable of inducing IDO synthesis and subsequent kynurenine metabolism in MDM. The induction of IDO, while apparently independent of replication capacity, appears to be mediated by a transient production of IFN-gamma in MDM responding to the initial infection with selected strains of HIV-1.     

Low-cost culture medium for the production of proteases by <Emphasis Type="Italic">Bacillus mojavensis</Emphasis> SA and their potential use for the preparation of antioxidant protein hydrolysate from meat sausage by-products

The present study aims to maximize proteases production by Bacillus mojavensis SA strain and their use to produce bioactive protein hydrolysates from a meat by-product. The production of SA bacteria proteases was maximized using a culture medium based on wheat bran, which offer an advantage in minimizing the production cost and enhancing the enzyme activity by using agro-industrial wastes. The composition of media and cultural conditions for optimal proteases production by B. mojavensis SA strain were investigated. A successful and significant improvement of the alkaline proteases production (four folds) by the SA strain was achieved using the medium composed of (g/l): wheat bran, 50.0; KH₂PO₄, 0.5; K₂HPO₄, 0.5; CaCl₂, 2.0; pH 6.0, where the growth conditions were monitored at 37 °C with an agitation speed of 200 rpm. Interestingly, the enzyme preparation of B. mojavensis was applied for the preparation of protein hydrolysates from a meat by-product. Hydrolysis was carried out for 180 min at pH 12.0. The resulting hydrolysate displayed an important antioxidant activity as evaluated by the radical scavenging capacity, the reducing power, and the β-carotene bleaching inhibition. The present study showed the high proteases’ producing level by B. mojavensis SA strain in a low-cost fermentation medium (wheat bran) and their potential use in the production of bioactive protein hydrolysate from meat by-products.     

Simeprevir oxidative degradation product: Molecular modeling,in silico toxicity and resolution by synchronous spectrofluorimetry

In this article, one of the potential degradation products of the novel antiviral drug simeprevir was isolated and characterized by means of infrared (IR) and mass spectrometry. Moreover, comparative molecular docking, ADMET (absorption, distribution, metabolism, excretion – toxicity) and insilico toxicity prediction studies were applied to evaluate the activity of simeprevir and its degradation product. Furthermore,a simple, accurate and selective second derivative synchronous spectrofluorimetric method was developed for the determination of simeprevir in the presence of its oxidative degradation product.The synchronous fluorescence spectra of both compounds were measured in ethanol at pH 2.0 usingΔλ of 140 nm and the peak amplitude of the second derivative spectra were measured at 442 nm. The method was rectilinear over the concentration range of 0.2 to 2.0 μg/ml and validated according to the ICH (International Conference on Harmonization) guidelines. Moreover, the method was statistically compared to the reverse‐phase high‐performance liquid chromatography (RP‐HPLC) method and good results were obtained.     

Novel <Emphasis Type="Italic">Collophorina</Emphasis> and <Emphasis Type="Italic">Coniochaeta</Emphasis> species from <Emphasis Type="Italic">Euphorbia polycaulis</Emphasis>, an endemic plant in Iran

During a study on the biodiversity of yeasts and yeast-like ascomycetes from wild plants in Iran, four strains of yeast-like filamentous fungi were isolated from a healthy plant of Euphorbia polycaulis in the Qom Province, Iran (IR. of). All four strains formed small hyaline one-celled conidia from integrated conidiogenous cells directly on hyphae and sometimes on discrete phialides, as well as by microcyclic conidiation. Two strains additionally produced conidia in conidiomata that open by rupture. The internal transcribed spacer (ITS) sequences suggested the placement of these strains in the genera Collophorina (Leotiomycetes) and Coniochaeta (Sordariomycetes), respectively. Blast search results on NCBI GenBank and phylogenetic analyses of ITS, the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the translation elongation factor 1α (EF-1α) sequences, and the nuclear large subunit ribosomal gene (LSU), partial actin (ACT), and β-tubulin (TUB) sequences, respectively, revealed the isolates to belong to three new species, that are described here as Collophorina euphorbiae, Coniochaeta iranica, and C. euphorbiae. All three species are characterised by morphological, physiological, and molecular data.     

Priming of Nicotiana benthamiana antioxidant defences using brown seaweed extracts

Extracts from the brown seaweeds Cystoseira myriophylloides, Laminaria digitata and Fucus spiralis were evaluated as plant defence inducers against the wild fire disease of Nicotiana benthamiana. Seeds’ imbibition in aqueous seaweed extracts (SE) results in plants with reduced disease severity. In addition, bacterial populations were significantly reduced in these plants when compared to those germinated in sterile distilled water. They primed N. benthamiana for H₂O₂ accumulation and for enhanced activity of several antioxidant enzymes including catalase, ascorbate peroxidase, guaiacol peroxidase and polyphenol oxidase. These results revealed that soaking of seeds in SE before sowing allows N. benthamiana to reduce pathogen attack and can be easily applied in practice.