N-aralkylated Derivatives Of 1-aminobenzotriazole: Isozyme-selective Mechanism-based Inhibitors Of Guinea Pig Cytochrome P-450

1-Aminobenzotriazole (ABT) and its N-benzyl (BBT), N-{dollar}\alpha{dollar}-methylbenzyl ({dollar}\alpha{dollar}MB), and N-{dollar}\alpha{dollar}-ethylbenzyl ({dollar}\alpha{dollar}EB) derivatives were compared for their potency and isozyme-selectivity for mechanism-based inactivation of guinea pig hepatic and pulmonary cytochrome P450 (P450) in vitro, through the use of isozyme selective substrates for the guinea pig orthologs of rabbit P450 2B4, 1A1, and 4B1 (P450 2Bx, 1A1, 4Bx, respectively). {dollar}\alpha{dollar}MB, {dollar}\alpha{dollar}EB, and to a lesser extent, BBT, selectively inactivated P450 2Bx in pulmonary microsomes from untreated or {dollar}\beta{dollar}-naphthoflavone ({dollar}\beta{dollar}NF)-induced, and hepatic microsomes from phenobarbital (PB)-induced, guinea pigs. P450 loss caused by ABT paralleled the inhibition of enzyme activity in hepatic and pulmonary microsomes; however, P450 loss caused by BBT, {dollar}\alpha{dollar}MB or {dollar}\alpha{dollar}EB was never greater than 45% even when monooxygenase activity was inhibited by virtually 100%. BBT, {dollar}\alpha{dollar}MB and {dollar}\alpha{dollar}EB were more potent inhibitors of P450 activity in hepatic and pulmonary microsomes from untreated compared to induced guinea pigs.;The NADPH-dependent metabolism, and covalent binding to protein, of ({dollar}\sp{lcub}14{rcub}{dollar}C) ABT,N-benzyl-1-amino- ({dollar}\sp{lcub}14{rcub}{dollar}C) 2,3-benzotriazole( ({dollar}\sp{lcub}14{rcub}{dollar}C) 2,3-BBT), and N- ({dollar}\sp{lcub}14{rcub}{dollar}C) 7-benzyl-1-aminobenzotriazole ( ({dollar}\sp{lcub}14{rcub}{dollar}C) 7-BBT), were examined in guinea pig hepatic or pulmonary microsomes. Hepatic microsomes from {dollar}\beta{dollar}NF (vs PB) treated guinea pigs metabolized ({dollar}\sp{lcub}14{rcub}{dollar}C) ABT, ({dollar}\sp{lcub}14{rcub}{dollar}C) 2,3-BBT or ({dollar}\sp{lcub}14{rcub}{dollar}C) 7-BBT more extensively and to more products. NADPH-dependent covalent binding to microsomal protein of ({dollar}\sp{lcub}14{rcub}{dollar}C) 2,3-BBT or ({dollar}\sp{lcub}14{rcub}{dollar}C) 7-BBT was greater than that of ({dollar}\sp{lcub}14{rcub}{dollar}C) ABT in hepatic microsomes, especially those from PB-induced animals, and the covalently modified proteins co-migrated with P450 2Bx on Western blots. Covalent binding per nmol P450 in pulmonary microsomes was 3- to 4-fold higher with ({dollar}\sp{lcub}14{rcub}{dollar}C) 2,3-BBT than with ({dollar}\sp{lcub}14{rcub}{dollar}C) 7-BBT or ({dollar}\sp{lcub}14{rcub}{dollar}C) ABT.; ({dollar}\sp{lcub}14{rcub}{dollar}C) BBT, at a dose which effectively inhibited pulmonary P450 2Bx, was rapidly metabolized and excreted by guinea pigs following i.v. administration, with 75% of the radiolabel excreted in the urine within 12 hr. By 48 hr, {dollar}\u3c{dollar}1% of the radiolabel was present in liver, lungs, or kidneys of these animals.;In summary, BBT, {dollar}\alpha{dollar}MB, and {dollar}\alpha{dollar}EB are potent isozyme selective (P450 2Bx) inhibitors of guinea pig hepatic and pulmonary microsomal P450. BBT is metabolized in vitro to at least two reactive species capable of covalent modification of protein, and is rapidly ({dollar}\u3c{dollar}12 hr) metabolized and excreted in vivo

Secrets for sale? Innovation and the nature of knowledge in an early industrial district: the potteries, 1750-1851

This article investigates innovation and knowledge circulation in the North Staffordshire Potteries during the eighteenth and early nineteenth centuries. It evaluates new empirical evidence of formal and informal patterns of knowledge creation and dissemination in order to highlight tensions between forms of open knowledge sharing and the private appropriation of returns to innovative activity. By presenting new patent data it shows that formal protection was not a widespread strategy in the industry. It uses patent specifications to determine what types of knowledge were, and could be, patented in the district, and by whom. A range of sources are used to demonstrate evidence of innovation and knowledge appropriation outside of the patent system. The article identifies distinct types of knowledge in the industry and shows how differences in these led to a range of strategies being employed by potters, with the role of secrecy highlighted as a particularly prevalent and effective strategy

Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes

<p>Abstract</p> <p>Background</p> <p>New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, <it>Caenorhabditis elegans, Drosophila melanogaster, Mus musculus </it>and <it>Saccharomyces cerevisiae</it>, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset.</p> <p>Results</p> <p>Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from <it>Ancylostoma caninum </it>and <it>Haemonchus contortus </it>- two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools.</p> <p>Conclusions</p> <p>The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.</p

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

© 2016 Rinke et al. High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100-1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics

Host-linked soil viral ecology along a permafrost thaw gradient

Climate change threatens to release abundant carbon that is sequestered at high latitudes, but the constraints on microbial metabolisms that mediate the release of methane and carbon dioxide are poorly understood1,2,3,4,5,6,7. The role of viruses, which are known to affect microbial dynamics, metabolism and biogeochemistry in the oceans8,9,10, remains largely unexplored in soil. Here, we aimed to investigate how viruses influence microbial ecology and carbon metabolism in peatland soils along a permafrost thaw gradient in Sweden. We recovered 1,907 viral populations (genomes and large genome fragments) from 197 bulk soil and size-fractionated metagenomes, 58% of which were detected in metatranscriptomes and presumed to be active. In silico predictions linked 35% of the viruses to microbial host populations, highlighting likely viral predators of key carbon-cycling microorganisms, including methanogens and methanotrophs. Lineage-specific virus/host ratios varied, suggesting that viral infection dynamics may differentially impact microbial responses to a changing climate. Virus-encoded glycoside hydrolases, including an endomannanase with confirmed functional activity, indicated that viruses influence complex carbon degradation and that viral abundances were significant predictors of methane dynamics. These findings suggest that viruses may impact ecosystem function in climate-critical, terrestrial habitats and identify multiple potential viral contributions to soil carbon cycling

Progression of C-reactive protein from birth through preadolescence varies by mode of delivery

INTRODUCTION: Delivery via caesarean section (C-section) has been associated with an increased risk of childhood chronic diseases such as obesity and asthma, which may be due to underlying systemic inflammation. However, the impact of specific C-section types may be differential, as emergency C-sections typically involve partial labor and/or membrane rupture. Our objectives were to determine if mode of delivery associates with longitudinal profiles of high sensitivity CRP (hs-CRP) -a marker of systemic inflammation-from birth through preadolescence, and to examine if CRP mediates the association between mode of delivery and preadolescent body mass index (BMI). METHODS: Data from the WHEALS birth cohort (N = 1,258) were analyzed; 564 of the 1,258 children in the cohort had data available for analysis. Longitudinal plasma samples (birth through 10-years of age) from 564 children from were assayed for hs-CRP levels. Maternal medical records were abstracted to obtain mode of delivery. Growth mixture models (GMMs) were used to determine classes of hs-CRP trajectories. Poisson regression with robust error variance was used to calculate risk ratios (RRs). RESULTS: Two hs-CRP trajectory classes were identified: class 1 (76% of children) was characterized by low hs-CRP, while class 2 (24% of children) was characterized by high and steadily increasing hs-CRP. In multivariable models, children delivered via planned C-section had 1.15 times higher risk of being in hs-CRP class 2, compared to vaginal deliveries (p = 0.028), while no association was found for unplanned C-section deliveries [RR (95% CI) = 0.96 (0.84, 1.09); p = 0.49]. Further, the effect of planned C-section on BMI z-score at age 10 was significantly mediated by hs-CRP class (percent mediated = 43.4%). CONCLUSIONS: These findings suggest potentially beneficial effects of experiencing partial or full labor, leading to a lower trajectory of systemic inflammation throughout childhood and decreased BMI during preadolescence. These findings may have implications for chronic disease development later in life

Highlights from the Student Council Symposium 2011 at the International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology

The Student Council (SC) of the International Society for Computational Biology (ISCB) organized their annual symposium in conjunction with the Intelligent Systems for Molecular Biology (ISMB) conference