The Residue Threonine 82 of DevR (DosR) Is Essential for DevR Activation and Function in Mycobacterium tuberculosis Despite Its Atypical Location

The DevR (DosR) response regulator initiates the bacterial adaptive response to a variety of signals, including hypoxia in in vitro models of dormancy. Its receiver domain works as a phosphorylation-mediated switch to activate the DNA binding property of its output domain. Receiver domains are characterized by the presence of several highly conserved residues, and these sequence features correlate with structure and hence function. In response regulators, interaction of phosphorylated aspartic acid at the active site with the conserved threonine is believed to be crucial for phosphorylation-mediated conformational change. DevR contains all the conserved residues, but the structure of its receiver domain in the unphosphorylated protein is strikingly different, and key threonine (T82), tyrosine (Y101), and lysine (K104) residues are placed uncharacteristically far from the D54 phosphorylation site. In view of the atypical location of T82 in DevR, the present study aimed to examine the importance of this residue in the activation mechanism. Mycobacterium tuberculosis expressing a DevR T82A mutant protein is defective in autoregulation and supports hypoxic induction of the DevR regulon only very weakly. These defects are ascribed to slow and partial phosphorylation and the failure of T82A mutant protein to bind cooperatively with DNA. Our results indicate that the T82 residue is crucial in implementing conformational changes in DevR that are essential for cooperative binding and for subsequent gene activation. We propose that the function of the T82 residue in the activation mechanism of DevR is conserved in spite of the unusual architecture of its receiver domain.     

Characterization of the Nit6803 nitrilase homolog from the cyanotroph Pseudomonas fluorescens NCIMB 11764

We report the purification and characterization of a nitrilase (E.C. 3.5.5.1) (Nit11764) essential for the assimilation of cyanide as the sole nitrogen source by the cyanotroph, Pseudomonas fluorescens NCIMB 11764. Nit11764, is a member of a family of homologous proteins (nitrile_sll0784) for which the genes typically reside in a conserved seven-gene cluster known as Nit1C. The physical properties and substrate specificity of Nit11764 resemble those of Nit6803, the current reference protein for the family, and the only true nitrilase that has been crystallized. The substrate binding pocket of the two enzymes places the substrate in direct proximity to the active site nucleophile (C160) and conserved catalytic triad (Glu44, Lys126). The two enzymes exhibit a similar substrate profile, however, for Nit11764, cinnamonitrile, was found to be an even better substrate than fumaronitrile the best substrate previously identified for Nit6803. A higher affinity for cinnamonitrile (Km 1.27 mM) compared to fumaronitrile (Km 8.57 mM) is consistent with docking studies predicting a more favorable interaction with hydrophobic residues lining the binding pocket. By comparison, 3,4-dimethoxycinnamonitrile was a poorer substrate the substituted methoxyl groups apparently hindering entry into the binding pocket. in situ ¹H NMR studies revealed that only one of the two nitrile substituents in the dinitrile, fumaronitrile, was attacked yielding trans-3-cyanoacrylate (plus ammonia) as a product. The essentiality of Nit11764 for cyanotrophy remains uncertain given that cyanide itself is a poor substrate and the catalytic efficiencies for even the best of nitrile substrates (~5 × 10³ M^?1 s^?1) is less than stellar.     

A novel herbal product based on Piper betle and Sphaeranthus indicus essential oils: Toxicity,repellent activity and impact on detoxifying enzymes GST and CYP450 of Aedes aegypti Liston (Diptera: Culicidae)

Fresh leaves of Piper betle Linn. (Piperales: Piperaceae) and Sphaeranthus indicus Linn. (Asterales: Asteraceae), commonly known as betel leaves and East Indian globe thistle, respectively, were harvested and steam distilled for the extraction of P. betle and S. indicus crude volatile oils (Pb-CVO and Si-CVO, respectively). LC₅₀ calculated on 3^rd instar larvae of dengue mosquito Aedes aegypti Linn. (Diptera: Culicidae) was 42.17?ppm for PbSi-CVO (i.e., herbal formulation based on the EOs of P. betle and S. indicus). The larval and pupal duration were significantly longer post-treatment with 100?ppm of PbSi-CVO, if compared to control. We observed that PbSi-CVO significantly altered the detoxifying enzymes GST and CYP450 compared to the expression of control. Sub-lethal concentrations of PbSi-CVO showed strong repellent properties against dengue mosquitoes, without adverse reactions on the volunteers experiencing the repellent assays. Lastly, the adulticidal activity of PbSi-CVO was studied. Overall, our study outlined that this herbal product represents a promising candidate for the development of botanical based adulticidal agents.     

Nonlinear optoacoustic readings from diffusive media at near‐infrared wavelengths

Optoacoustic (photoacoustic) imaging assumes that the detected signal varies linearly with laser energy. However, nonlinear intensity responses as a function of light fluence have been suggested in optoacoustic microscopy, that is, within the first millimeter of tissue. In this study, we explore the presence of nonlinearity deeper in tissue (~4 mm), as it relates to optoacoustic mesoscopy, and investigate the fluence required to delineate a switch from linear to nonlinear behavior. Optoacoustic signal nonlinearity is studied for different materials, different wavelengths and as a function of changes in the scattering and absorption coefficient of the medium imaged. We observe fluence thresholds in the mJ/cm² range and preliminary find that different materials may exhibit different nonlinearity patterns. We discuss the implications of nonlinearity in relation to image accuracy and quantification in optoacoustic tomography.      

Protective effects of 6-ureido/thioureido-2,4,5-trimethylpyridin-3-ols against 4-hydroxynonenal-induced cell death in adult retinal pigment epithelial-19 cells

Dysfunction or progressive degeneration of retinal pigment epithelium (RPE) contributes in the initial pathogenesis of age-related macular degeneration (AMD) causing irreversible vision loss, which makes RPE the prime target of the disease. The present study aimed to identify compounds to protect 4-hydroxynonenal (4-HNE)-induced RPE cell death by inhibiting NADPH oxidase 4 (NOX4) activity, not just as free radical scavengers, using ARPE-19, a human adult retinal pigment epithelial cell line, as a RPE representative. Novel thirty-two 6-ureido/thioureido-2,4,5-trimethylpyridin-3-ol derivatives 17 were synthesized and tested. We found that there was a strong correlation between level of protective effect of compounds 17 against 4-HNE-induced APRE-19 cell death and that of inhibitory activity against 4-HNE-induced superoxide production, and that most of the compounds 17 showed minimal DPPH radical scavenging activity. Compound 17–28 showed the best protective activity against 4-HNE-induced superoxide production (79.5% inhibition) and cell death (85.1% recovery) at 10?μM concentration, which was better than that of VAS2870, a NOX2/4 inhibitor. In addition, compound 17–28 blocked 4-HNE-induced apoptosis of ARPE-19 cells in a concentration-dependent manner. The results indicate that compound 17–28 may be a lead compound to develop AMD therapeutics.     

Radiosynthesis and in vivo evaluation of [11C]MOV as a PET imaging agent for COX-2

Radiosynthesis and in vivo evaluation of [¹¹C]4-[5-(4-methylphenyl)-3-(trifluoromethyl)-1H-pyrazol-1-yl]benzenesulfonamide (methoxy analogue of valdecoxib, [¹¹C]MOV), a COX-2 inhibitor, was conducted in rat and baboon. Synthesis of the reference standard MOV (3), and its desmethyl precursor 2 for radiolabeling were performed using 1,2-diphenylethan-1-one as the starting material in five steps with 15% overall yield. Radiosynthesis of [¹¹C]MOV was accomplished in 40?±?10% yield and?>99% radiochemical purity by reacting the precursor 2 in dimethyl formamide (DMF) with [¹¹C]CH₃I followed by removal of the dimethoxytrityl (DMT) protective group using trifluroacetic acid. PET studies in anesthetized baboon showed very low uptake and homogeneous distribution of [¹¹C]MOV in brain. The radioligand underwent rapid metabolism in baboon plasma. MicroPET studies in male Sprague Dawley rats revealed [¹¹C]MOV binding in lower thorax. The tracer binding in rats was partially blocked in heart and duodenum by the administration of 1?mg/kg oral dose of COX-2 inhibitor valdecoxib.     

Sources of Biomass Feedstock Variability and the Potential Impact on Biofuels Production

Terrestrial lignocellulosic biomass has the potential to be a carbon neutral and domestic source of fuels and chemicals. However, the innate variability of biomass resources, such as herbaceous and woody materials, and the inconsistency within a single resource due to disparate growth and harvesting conditions, presents challenges for downstream processes which often require materials that are physically and chemically consistent. Intrinsic biomass characteristics, including moisture content, carbohydrate and ash compositions, bulk density, and particle size/shape distributions are highly variable and can impact the economics of transforming biomass into value-added products. For instance, ash content increases by an order of magnitude between woody and herbaceous feedstocks (from ～0.5 to 5 %, respectively) while lignin content drops by a factor of two (from ～30 to 15 %, respectively). This increase in ash and reduction in lignin leads to biofuel conversion consequences, such as reduced pyrolysis oil yields for herbaceous products as compared to woody material. In this review, the sources of variability for key biomass characteristics are presented for multiple types of biomass. Additionally, this review investigates the major impacts of the variability in biomass composition on four conversion processes: fermentation, hydrothermal liquefaction, pyrolysis, and direct combustion. Finally, future research processes aimed at reducing the detrimental impacts of biomass variability on conversion to fuels and chemicals are proposed.© 2015 Battelle Energy Alliance, LLC, contract manager for Idaho National Laboratory.     

Identification of peptide hormones of the amphipathic helix class using the helical hydrophobic moment algorithm

Eisenberg's helical hydrophobic moment (less than mu H greater than) algorithm was applied to the analysis of the primary structure of amphipathic alpha-helical peptide hormones and an optimal method for identifying other peptides of this class determined. We quantitate and compare known amphipathic helical peptide hormones with a second group of peptides with proven nonamphipathic properties and determine the best method of distinguishing between them. The respective means of the maximum 11 residue less than mu H greater than for the amphipathic helical and control peptides were 0.46 (+/-/-0.07) and 0.33 (0.07) (P + 0.004). To better reflect the amphipathic potential of the entire peptide, the percent of 11 residue segments in each peptide above a particular less than mu H greater than was plotted vs less than mu H greater than. The resulting curves are referred to as HM-C. The mean HM-C (of the two groups) was highly significantly different such that the HM-C method was superior to others in its ability to distinguish amphipathic from nonamphipathic peptides. Several potential new members of this structural class were identified using this approach. Molecular modeling of a portion of one of these, prolactin inhibitory factor, reveals a strongly amphipathic alpha helix at residues 4-21. This computer-based method may enable rapid identification of peptides of the amphipathic alpha-helix class.     

An alternative route for infecting armadillos with Mycobacterium leprae

A nine-banded armadillo was inoculated with Mycobacterium leprae in both hind footpads. The animals were usually inoculated intravenously, or intradermally in the abdominal skin. Profuse multiplication of the bacilli occurred at the injection sites after more than two years. Eventually bacteraemia developed, and large numbers of the organisms were found in skin biopsies and in lymph nodes. There was limited dissemination of the bacteria into the spleen and the liver, and peripheral nerve invasion by the bacilli was also detected. M. leprae remained viable in the liver tissue, kept frozen at -80 degrees C for three years. This experimental system would be useful in testing the effects of certain immunological and chemotherapeutic agents against M. leprae by injecting them directly at the infection site.