Database on Demand – An online tool for the custom generation of FASTA‐formatted sequence databases

In mass spectrometry‐based proteomics, most conventional search engines match spectral data to sequence databases. These search databases thus play a crucial role in the identification process. While search engines can derive peptides in silico from protein sequences, this is usually limited to standard digestion algorithms. Customized search databases that provide detailed control over the search space can vastly outperform such standard strategies, especially in gel‐free proteomics experiments. Here we present Database on Demand, an easy‐to‐use web tool that can quickly produce a wide variety of customized search databases.     

<Emphasis Type="Italic">Leptospira</Emphasis> seroprevalence and associations between seropositivity,clinical disease and host factors in horses

Background  

A cross-sectional study was carried out to determine the seroprevalence of different serovars of Leptospira spp. and their association with clinical disease and host factors in Swedish horses.     

Adenosine activation of a nuclear pool of protein kinase C in rat splenocytes

The stimulatory effects of adenosine analogues on a nuclear pool of protein kinase C (PKC) were examined using isolated rat splenocyte nuclei. Nuclear receptors met pharmacological criteria of A1 adenosine receptors including a potency profile in which cyclopentyladenosine (CPA), a selective A1 agonist, was more potent than 2-phenylaminoadenosine (2PAA), a selective A2 agonist. The selective A1 receptor agonist N6-1-(phenyl-2R-propyl) adenosine (R-PIA) activated PKC whereas the S diastereomer did not. The adenosine-induced PKC response could be attenuated using a monoclonal antibody to PKC, an A1 receptor antagonist, three known PKC inhibitors and pertussis toxin (PTX). The results suggest that adenosine may exert immunomodulatory effects through the activation of nuclear PKC.     

Modification of deoxyribose-phosphate residues by extracts of ataxia telangiectasia cells

The release of DNA 5'-terminal deoxyribose-phosphate residues from enzymatically incised apurinic/apyrimidinic sites by human cell extracts has been under investigation. During the course of these studies, we observed that ataxia telangiectasia cell extracts modify deoxyribose-phosphate (dRp) residues by converting them to an altered form, dRp-X, which shows altered chromatographic properties on HPLC analysis. The chemical nature of the adduct is as yet unknown, but dRp-X is stable to both heat and acid. The modification requires an enzymatic activity and a low-molecular weight co-factor. Extracts of normal cells contain a dialyzable inhibitor that suppresses the reaction occurring with ataxia telangiectasia cell extracts. Formation of dRp-X has been observed in 7 out of 7 ataxia telangiectasia lymphoblastoid lines which represent at least 3 genetic complementation groups. Similar modification of dRp did not occur with extracts of cells of normal origin, nor those representing Fanconi's anaemia, xeroderma pigmentosum, Bloom's syndrome, Werner's syndrome or Friedreich's ataxia.     

Influence of dietary selenium on the mutagenic activity of perfusate and bile from rat liver, perfused with 1,1-dimethylhydrazine

The mutagenic effect of 1,1-dimethylhydrazine (UDMH) was studied in the liver perfusion/cell culture system. Male Wistar rats, fed a selenium-deficient diet with or without selenium supplementation in the drinking water, were used as liver donors. UDMH caused an increased mutation frequency in Chinese hamster V79 cells exposed in the perfusate. The effect was statistically significant with both selenium-deficient and selenium-supplemented livers. With selenium-deficient livers, a significant mutagenic effect was also obtained when V79 cells were treated with bile collected after the administration of UDMH. Bile flow and bile acid excretion were not affected by UDMH treatment of selenium-deficient or selenium-supplemented livers. There was a tendency towards reduced C-oxygenation of N,N-dimethylaniline in microsomes from selenium-deficient livers perfused with UDMH. The lactate/pyruvate ratio in the perfusate was increased by UDMH, the effect being more pronounced with selenium-deficient than selenium-supplemented livers.     

An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development

Background  

Accuracy in quantitative real-time RT-PCR is dependent on high quality RNA, consistent cDNA synthesis, and validated stable reference genes for data normalization. Reference genes used for normalization impact the results generated from expression studies and, hence, should be evaluated prior to use across samples and treatments. Few statistically validated reference genes have been reported in grapevine. Moreover, success in isolating high quality RNA from grapevine tissues is typically limiting due to low pH, and high polyphenolic and polysaccharide contents.     

An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development

Background  

The response regulators represent the elements of bacterial two-component system and have been characterized from dicot plants like Arabidopsis but little information is available on the monocots, including the cereal crops. The aim of this study was to characterize type-A response regulator genes from rice, and to investigate their expression in various organs as well as in response to different hormones, including cytokinin, and environmental stimuli.     

The chemosensory basis for behavioral divergence involved in sympatric host shifts. I. Characterizing olfactory receptor neuron classes responding to key host volatiles

The recent shift of Rhagoletis pomonella from its native host hawthorn to introduced, domestic apple has been implicated as an example of sympatric speciation. Recent studies suggest that host volatile preference might play a fundamental role in host shifts and subsequent speciation in this group. Single sensillum electrophysiology was used to test a proposed hypothesis that differences in R. pomonella olfactory preference are due to changes in the number or odor specificity of olfactory receptor neurons. Individuals were analyzed from apple, hawthorn, and flowering dogwood-origin populations, as well as from the blueberry maggot, Rhagoletis mendax Curran (an outgroup). Eleven compounds were selected as biologically relevant stimuli from previous electroantennographic/behavioral studies of the three R. pomonella populations to host fruit volatiles. Cluster analysis of 99 neuron responses showed that cells from all tested populations could be grouped into the same five classes, ranging from those responding to one or two volatiles to those responding to several host volatiles. Topographical mapping also indicated that antennal neuron locations did not differ by class or fly taxa. Our results do not support the hypothesis that differences in host preference among Rhagoletis populations are a result of alterations in the number or class of receptor neurons responding to host volatiles.