Deletion of BmoR affects the expression of genes related to thiol/disulfide balance in Bacteroides fragilis

Bacteroides fragilis, an opportunistic pathogen and commensal bacterium in the gut, is one the most aerotolerant species among strict anaerobes. However, the mechanisms that control gene regulation in response to oxidative stress are not completely understood. In this study, we show that the MarR type regulator, BmoR, regulates the expression of genes involved in the homeostasis of intracellular redox state. Transcriptome analysis showed that absence of BmoR leads to altered expression in total of 167 genes. Sixteen of these genes had a 2-fold or greater change in their expression. Most of these genes are related to LPS biosynthesis and carbohydrates metabolism, but there was a signifcant increase in the expression of genes related to the redox balance inside the cell. A pyridine nucleotide-disulfde oxidoreductase located directly upstream of bmoR was shown to be repressed by direct binding of BmoR to the promoter region. The expression of two other genes, coding for a thiosulphate:quinoneoxidoreductase and a thioredoxin, are indirectly afected by bmoR mutation during oxygen exposure. Phenotypic assays showed that BmoR is important to maintain the thiol/disulfde balance in the cell, confrming its relevance to B. fragilis response to oxidative stress

PanGEA: Identification of allele specific gene expression using the 454 technology

<p>Abstract</p> <p>Background</p> <p>Next generation sequencing technologies hold great potential for many biological questions. While mainly used for genomic sequencing, they are also very promising for gene expression profiling. Sequencing of cDNA does not only provide an estimate of the absolute expression level, it can also be used for the identification of allele specific gene expression.</p> <p>Results</p> <p>We developed PanGEA, a tool which enables a fast and user-friendly analysis of allele specific gene expression using the 454 technology. PanGEA allows mapping of 454-ESTs to genes or whole genomes, displaying gene expression profiles, identification of SNPs and the quantification of allele specific gene expression. The intuitive GUI of PanGEA facilitates a flexible and interactive analysis of the data. PanGEA additionally implements a modification of the Smith-Waterman algorithm which deals with incorrect estimates of homopolymer length as occuring in the 454 technology</p> <p>Conclusion</p> <p>To our knowledge, PanGEA is the first tool which facilitates the identification of allele specific gene expression. PanGEA is distributed under the Mozilla Public License and available at: <url>http://www.kofler.or.at/bioinformatics/PanGEA</url></p

Fermentation performance and nutritional assessment of physically processed lentil and green pea flour

BACKGROUND A significant amount of nutrients, including dietary fibers, proteins, minerals, and vitamins are present in legumes, but the presence of anti‐nutritional factors (ANFs) like phytic acid, tannins, and enzyme inhibitors impact the consumption of legume and nutrient availability. In this research, the effect of a physical process (sonication or precooking) and fermentation with Lactobacillus plantarum and Pediococcus acidilactici on ANFs of some legumes was evaluated. RESULTS Total phenolic contents were significantly (p\u3c0.05) reduced for modified and fermented substrates compared to non‐fermented controls. Trypsin inhibitory activity (TIA) was reduced significantly for all substrates except for unsonicated soybean and lentil fermented with L. plantarum and P. acidilactici. When physical processing was done, there was a decrease in TIA for all the substrate. Phytic acid content decreased for physically modified soybean and lentil but not significantly for green pea. Even though there was a decrease in ANFs, there was no significant change in in vitro protein digestibility for all substrates except for unsonicated L. plantarum fermented soybean flour and precooked L. plantarum fermented lentil. Similarly, there was change in amino acid content when physically modified and fermented. CONCLUSION Both modified and unmodified soybean flour, green pea flour, and lentil flour supported the growth of L. plantarum and P. acidilactici. The fermentation of this physically processed legume and pulse flours influenced the non‐nutritive compounds, thereby potentially improving nutritional quality and usage

Application of botryosphaeran as a carbon black adherent on a glassy carbon electrode for the electrochemical determination of cyclobenzaprine

The present work describes the performance of a new voltammetric sensor based on the modification of glassy carbon electrodes (GCE) with carbon black (CB) and botryosphaeran (BOT) (CB-BOT/GCE) for the electroanalytical determination of cyclobenzaprine. BOT is a fungal exocellular (1→3)(1→6)-β-ᴅ-glucan, which was used to improve the adherence of CB onto the surface of GCE. The electrochemical characterisation was performed by electrochemical impedance spectroscopy which showed an improvement in the transfer of electrons on the surface of the sensor developed in relation to the unmodified (bare) GCE. The voltammetric behaviour of cyclobenzaprine was studied using bare GCE, BOT/GCE, CB/GCE, and CB-BOT/GCE. All electrodes presented an oxidation peak (+ 1.0 V) for cyclobenzaprine, while the cyclobenzaprine peak intensity on CB-BOT/GCE was found to be 480% higher than the bare GCE. Through employing square-wave voltammetry, the analytical curve was found to be linear over the concentration range of 2.0 to 20.6 μmol L−1 (in 0.1 mol L−1 NaCl solution) with a detection limit (based on 3-sigma) of 0.63 μmol L−1. The developed electrochemical sensor exhibited excellent sensitivity and selectivity and was successfully applied for the voltammetric determination of cyclobenzaprine in pharmaceutical, biological, and environmental samples for the first time using the CB-BOT/GCE electrochemical sensing platform

A review of exposure assessment methods for epidemiological studies of health effects related to industrially contaminated sites

BACKGROUND: this paper is based upon work from COST Action ICSHNet. Health risks related to living close to industrially contaminated sites (ICSs) are a public concern. Toxicology-based risk assessment of single contaminants is the main approach to assess health risks, but epidemiological studies which investigate the relationships between exposure and health directly in the affected population have contributed important evidence. Limitations in exposure assessment have substantially contributed to uncertainty about associations found in epidemiological studies. OBJECTIVES: to examine exposure assessment methods that have been used in epidemiological studies on ICSs and to provide recommendations for improved exposure assessment in epidemiological studies by comparing exposure assessment methods in epidemiological studies and risk assessments. METHODS: after defining the multi-media framework of exposure related to ICSs, we discussed selected multi-media models applied in Europe. We provided an overview of exposure assessment in 54 epidemiological studies from a systematic review of hazardous waste sites; a systematic review of 41 epidemiological studies on incinerators and 52 additional studies on ICSs and health identified for this review. RESULTS: we identified 10 multi-media models used in Europe primarily for risk assessment. Recent models incorporated estimation of internal biomarker levels. Predictions of the models differ particularly for the routes ‘indoor air inhalation’ and ‘vegetable consumption’. Virtually all of the 54 hazardous waste studies used proximity indicators of exposure, based on municipality or zip code of residence (28 studies) or distance to a contaminated site (25 studies). One study used human biomonitoring. In virtually all epidemiological studies, actual land use was ignored. In the 52 additional studies on contaminated sites, proximity indicators were applied in 39 studies, air pollution dispersion modelling in 6 studies, and human biomonitoring in 9 studies. Exposure assessment in epidemiological studies on incinerators included indicators (presence of source in municipality and distance to the incinerator) and air dispersion modelling. Environmental multi-media modelling methods were not applied in any of the three groups of studies. CONCLUSIONS: recommendations for refined exposure assessment in epidemiological studies included the use of more sophisticated exposure metrics instead of simple proximity indicators where feasible, as distance from a source results in misclassification of exposure as it ignores key determinants of environmental fate and transport, source characteristics, land use, and human consumption behaviour. More validation studies using personal exposure or human biomonitoring are needed to assess misclassification of exposure. Exposure assessment should take more advantage of the detailed multi-media exposure assessment procedures developed for risk assessment. The use of indicators can be substantially improved by linking definition of zones of exposure to existing knowledge of extent of dispersion. Studies should incorporate more often land use and individual behaviour