Development and application of versatile high density microarrays for genome-wide analysis of Streptomyces coelicolor: characterization of the HspR regulon

Development of high-density microarrays for global analysis of gene expression and transcription factor binding in Streptomyces coelicolor suggests a novel role for HspR in stress adaptation

A systematic review of home-based dietary interventions during radiation therapy for cancer.

Purpose: Our objectives are to assess (1) the acceptability and feasibility of dietary interventions for patients undergoing radiation therapy (RT), and (2) the impact of dietary interventions on patient reported outcomes, toxicities, and survival. Methods: A PICOS/PRISMA/MOOSE selection protocol was used to include articles that evaluate adding dietary interventions to patients receiving RT. Acceptability was defined as (# accepting/# approached); feasibility was (# completing/# approached). Patient-reported outcomes were reported based on questionnaires used in each study and survival was measured from the date of diagnosis until death in each study. Level of evidence was assessed with Center for Evidence-Based Medicine (CEBM) criteria. Results: Sixteen articles were included; among these, 2027 patients were approached regarding the intervention, and 1661 accepted (81.9%); of these, 1543 (92.9%) completed the prescribed diet + RT course. The most common cancers included were gynecological, head and neck, and gastrointestinal. For patients with pelvic cancers, a high fiber diet may improve diarrhea (CEBM level 1b). Enteral nutrition formula, including formulas with proteins such as L-arginine, lipids such as eicosapentaenoic acids, glucids, and ribonucleotides, may help prevent of malnutrition in head and neck cancer patients undergoing RT (level 2b). Vitamin C and β-carotene may reduce of xerostomia in head and neck cancer patients; however, the studies evaluating these vitamins included vitamin E, which increases all-cause mortality (level 2b). No dietary intervention for cancer patients receiving RT has been shown to improve survival. Conclusion: There are limited data to support safe and efficacious use of dietary interventions during RT

Metabolic and evolutionary insights into the closely-related species Streptomyces coelicolor and Streptomyces lividans deduced from high-resolution comparative genomic hybridization

Whilst being closely related to the model actinomycete Streptomyces coelicolor A3(2), S. lividans 66 differs from it in several significant and phenotypically observable ways, including antibiotic production. Previous comparative gene hybridization studies investigating such differences have used low-density (one probe per gene) PCR-based spotted arrays. Here we use new experimentally optimised 104,000 × 60-mer probe arrays to characterize in detail the genomic differences between wild-type S. lividans 66, a derivative industrial strain, TK24, and S. coelicolor M145

Bayesian inference for finite mixtures of generalized linear models with random effects

We present an hierarchical Bayes approach to modeling parameter heterogeneity in generalized linear models. The model assumes that there are relevant subpopulations and that within each subpopulation the individual-level regression coefficients have a multivariate normal distribution. However, class membership is not known a priori, so the heterogeneity in the regression coefficients becomes a finite mixture of normal distributions. This approach combines the flexibility of semiparametric, latent class models that assume common parameters for each sub-population and the parsimony of random effects models that assume normal distributions for the regression parameters. The number of subpopulations is selected to maximize the posterior probability of the model being true. Simulations are presented which document the performance of the methodology for synthetic data with known heterogeneity and number of sub-populations. An application is presented concerning preferences for various aspects of personal computers.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/45757/1/11336_2005_Article_BF02294188.pd

The phosphate stimulon of Bacillus subtilis

EThOS - Electronic Theses Online ServiceGBUnited Kingdo

Anticipatory Life Cycle Analysis of In Vitro Biomass Cultivation for Cultured Meat Production in the United States

Cultured, or in vitro, meat consists of edible biomass grown from animal stem cells in a factory, or carnery. In the coming decades, in vitro biomass cultivation could enable the production of meat without the need to raise livestock. Using an anticipatory life cycle analysis framework, the study described herein examines the environmental implications of this emerging technology and compares the results with published impacts of beef, pork, poultry, and another speculative analysis of cultured biomass. While uncertainty ranges are large, the findings suggest that in vitro biomass cultivation could require smaller quantities of agricultural inputs and land than livestock; however, those benefits could come at the expense of more intensive energy use as biological functions such as digestion and nutrient circulation are replaced by industrial equivalents. From this perspective, large-scale cultivation of in vitro meat and other bioengineered products could represent a new phase of industrialization with inherently complex and challenging trade-offs

Phosphate Starvation Induces the Sporulation Killing Factor of Bacillus subtilis

Bacillus subtilis produces and exports a peptide sporulation killing factor (SkfA) that induces lysis of sibling cells. skfA is part of the skf operon (skfA-H), which is responsible for immunity to SkfA, as well as for production and export of SkfA. Here we report that transcription of skfA is markedly induced when cells of B. subtilis are subjected to phosphate starvation. The role of PhoP in regulation of the skf operon was confirmed by in vitro gel shift assays, which showed that this operon is a new member of the PhoP regulon. A putative stem-loop structure in the skfA-skfB intergenic region is proposed to act as a stabilizer of an skfA-specific transcript

Molecular Diversity via Tetrasubstituted Alkenes Containing a Barbiturate Motif: Synthesis and Biological Activity

The synthesis of a molecularly diverse library of tetrasubstituted alkenes containing a barbiturate motif is described. Base-induced condensation of N1-substituted pyrimidine-2,4,6(1H,3H,5H)-triones with 5-(bis(methylthio)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione gave 3-substituted 5-(methylthio)-2H-pyrano[2,3-d]pyrimidine-2,4,7(1H,3H)-triones (‘pyranopyrimidinones’), regioselectively. A sequence of reactions involving ring-opening of the pyran moiety, displacement of the methylthio group with an amine, re-formation of the pyran ring, and after its final cleavage with an amine, gave tetrasubstituted alkenes (3-amino-3-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)propanamides) with a diversity of substituents. Cleavage of the pyranopyrimidinones with an aniline was facilitated in 2,2,2-trifluoroethanol under microwave irradiation. Compounds were tested against Escherichia coli, Staphylococcus aureus, the yeast Schizosaccharomyces pombe, and the pathogenic fungus Candida albicans. No compounds exhibited activity against E. coli, whilst one compound was weakly active against S. aureus. Three compounds were strongly active against S. pombe, but none was active against C. albicans

Design tools for patient specific and highly controlled melt electrowritten scaffolds

Melt electrowriting (MEW) has grown in popularity in biofabrication research due to its ability to fabricate complex, high-precision networks of fibres. These fibres can mimic the morphology of a natural extracellular matrix, enabling tissue analogues for transplantation or personalised drug screening. To date, MEW has employed two different collector-plate modalities for the fabrication of constructs. Flat collector plates, typical of traditional 3D printing methods, allow for the layer-by-layer fabrication of 2D structures into complex 3D structures. Alternatively, rotating mandrels can be used for the creation of tubular scaffolds. However, unlike other additive manufacturing techniques that can immediately start and stop the extrusion of material during printing, MEW instead requires a continuous flow of polymer. Consequently, conventional g-code control software packages are unsuitable. To overcome this challenge, a suite of customised pattern generation software tools have been developed to enable the design of MEW scaffolds with highly-controlled geometry, including crosshatch, gradient porosity, tubular, and patient-specific configurations. The high level of design control using this approach enables the production of scaffolds with highly adaptable mechanical properties, as well as the potential to influence biological properties for cell attachment and proliferation.</p