Proteomic analysis of the rat ovary following chronic low-dose exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)

2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a ubiquitously distributed endocrine-disrupting chemical and reproductive toxicant. In order to elucidate low-dose TCDD-mediated effects on reproductive or endocrine functions, female Sprague-Dawley rats were orally administered various concentrations (20, 50, or 125 ng/kg once weekly) TCDD for 29 wk. A proteomic analysis of the ovaries by two-dimensional gel electrophoresis and matrix-assisted laser desorption/ionization (MALDI) tandem mass spectrometry showed distinct changes in the levels of several proteins that are relevant markers of TCDD toxicity. Serum estradiol (E2) levels of TCDD-treated animals were markedly lower than control. There were no significant differences in bone mineral density (BMD) of femurs. The body weight of the 125-ng/kg TCDD group was significantly decreased relative to control and there was also a significant reduction in absolute and relative ovarian weights. Expressions of selenium binding protein 2, glutathione S-transferase mu type 3, Lrpap1 protein, NADPH, and peptidylprolyl isomerase D were upregulated, while prohibitin and N-ethylmaleimide-sensitive factor expression levels were downregulated. Data provide further insight into the mechanisms by which TCDD disrupts ovarian function by indicating which differential protein expressions following low-dose TCDD exposure

The effect of deuteration on organic magnetoresistance

NOTICE: this is the author’s version of a work that was accepted for publication in Synthetic Metals. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in SYNTHETIC METALS, 161, 7-8, (2011) DOI 10.1016/j.synthmet.2010.11.04

A distinct influenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia

Introduction Diagnosis of severe influenza pneumonia remains challenging because of a lack of correlation between the presence of influenza virus and clinical status. We conducted gene-expression profiling in the whole blood of critically ill patients to identify a gene signature that would allow clinicians to distinguish influenza infection from other causes of severe respiratory failure, such as bacterial pneumonia, and noninfective systemic inflammatory response syndrome. Methods Whole-blood samples were collected from critically ill individuals and assayed on Illumina HT-12 gene-expression beadarrays. Differentially expressed genes were determined by linear mixed-model analysis and overrepresented biological pathways determined by using GeneGo MetaCore. Results The gene-expression profile of H1N1 influenza A pneumonia was distinctly different from those of bacterial pneumonia and systemic inflammatory response syndrome. The influenza gene-expression profile is characterized by upregulation of genes from cell-cycle regulation, apoptosis, and DNA-damage-response pathways. In contrast, no distinctive gene-expression signature was found in patients with bacterial pneumonia or systemic inflammatory response syndrome. The gene-expression profile of influenza infection persisted through 5 days of follow-up. Furthermore, in patients with primary H1N1 influenza A infection in whom bacterial co-infection subsequently developed, the influenza gene-expression signature remained unaltered, despite the presence of a superimposed bacterial infection. Conclusions The whole-blood expression-profiling data indicate that the host response to influenza pneumonia is distinctly different from that caused by bacterial pathogens. This information may speed the identification of the cause of infection in patients presenting with severe respiratory failure, allowing appropriate patient care to be undertaken more rapidly

Prospects for dedicated energy crop production and attitudes towards agricultural straw use: the case of livestock farmers

Second generation biofuels utilising agricultural by-products (e.g. straw), or dedicated energy crops (DECs) produced on ‘marginal’ land, have been called for. A structured telephone survey of 263 livestock farmers, predominantly located in the west or ‘marginal’ upland areas of England captured data on attitudes towards straw use and DECs. Combined with farm physical and business data, the survey results show that 7.2% and 6.3% of farmers would respectively consider growing SRC and miscanthus, producing respective maximum potential English crop areas of 54,603 ha and 43,859 ha. If higher market prices for straw occurred, most livestock farmers would continue to buy straw. Reasons for not being willing to consider growing DECs include concerns over land quality, committing land for a long time period, lack of appropriate machinery, profitability, and time to financial return; a range of moral, land quality, production conflict and lack of crop knowledge factors were also cited. Results demonstrate limited potential for the production of DECs on livestock farms in England. Changes in policy support to address farmer concerns with respect to DECs will be required to incentivise farmers to increase energy crop production. Policy support for DEC production must be cognisant of farm-level economic, tenancy and personal objectives

Northern European trees show a progressively diminishing response to increasing atmospheric carbon dioxide concentrations

In order to predict accurately how elevated atmospheric CO2 concentrations will affect the global carbon cycle, it is necessary to know how trees respond to increasing CO2 concentrations. In this paper we examine the response over the period AD 1895 – 1994 of three tree species growing across northern Europe to increases in atmospheric CO2 concentrations using parameters derived from stable carbon isotope ratios of trunk cellulose. Using the isotope data we calculate values of intrinsic water-use efficiency (IWUE) and intercellular CO2 concentrations in the leaf (ci). Our results show that trees have responded to higher levels of atmospheric CO2 by increasing IWUE whilst generally maintaining constant ci values. However, the IWUE of most of the trees in this study has not continued to rise in line with increasing atmospheric CO2. This behaviour has implications for estimations of future terrestrial carbon storage

Nonlinear wave transmission and pressure on the fixed truncated breakwater using NURBS numerical wave tank

Fully nonlinear wave interaction with a fixed breakwater is investigated in a numerical wave tank (NWT). The potential theory and high-order boundary element method are used to solve the boundary value problem. Time domain simulation by a mixed Eulerian-Lagrangian (MEL) formulation and high-order boundary integral method based on non uniform rational B-spline (NURBS) formulation is employed to solve the equations. At each time step, Laplace equation is solved in Eulerian frame and fully non-linear free-surface conditions are updated in Lagrangian manner through material node approach and fourth order Runge-Kutta time integration scheme. Incident wave is fed by specifying the normal flux of appropriate wave potential on the fixed inflow boundary. To ensure the open water condition and to reduce the reflected wave energy into the computational domain, two damping zones are provided on both ends of the numerical wave tank. The convergence and stability of the presented numerical procedure are examined and compared with the analytical solutions. Wave reflection and transmission of nonlinear waves with different steepness are investigated. Also, the calculation of wave load on the breakwater is evaluated by first and second order time derivatives of the potential

The Complete Chloroplast Genome Sequence of Date Palm (Phoenix dactylifera L.)

BACKGROUND: Date palm (Phoenix dactylifera L.), a member of Arecaceae family, is one of the three major economically important woody palms--the two other palms being oil palm and coconut tree--and its fruit is a staple food among Middle East and North African nations, as well as many other tropical and subtropical regions. Here we report a complete sequence of the data palm chloroplast (cp) genome based on pyrosequencing. METHODOLOGY/PRINCIPAL FINDINGS: After extracting 369,022 cp sequencing reads from our whole-genome-shotgun data, we put together an assembly and validated it with intensive PCR-based verification, coupled with PCR product sequencing. The date palm cp genome is 158,462 bp in length and has a typical quadripartite structure of the large (LSC, 86,198 bp) and small single-copy (SSC, 17,712 bp) regions separated by a pair of inverted repeats (IRs, 27,276 bp). Similar to what has been found among most angiosperms, the date palm cp genome harbors 112 unique genes and 19 duplicated fragments in the IR regions. The junctions between LSC/IRs and SSC/IRs show different features of sequence expansion in evolution. We identified 78 SNPs as major intravarietal polymorphisms within the population of a specific cp genome, most of which were located in genes with vital functions. Based on RNA-sequencing data, we also found 18 polycistronic transcription units and three highly expression-biased genes--atpF, trnA-UGC, and rrn23. CONCLUSIONS: Unlike most monocots, date palm has a typical cp genome similar to that of tobacco--with little rearrangement and gene loss or gain. High-throughput sequencing technology facilitates the identification of intravarietal variations in cp genomes among different cultivars. Moreover, transcriptomic analysis of cp genes provides clues for uncovering regulatory mechanisms of transcription and translation in chloroplasts

Ammonia reduction by trees (ART). Summary report

The aim of Ammonia Reduction by Trees (ART) project was to provide new scientific evidence on tree planting for reducing the impact of ammonia emissions from farming to inform better advice, guidance and incentives for farmers on ammonia mitigation through treebelt planting