eQTL Viewer: visualizing how sequence variation affects genome-wide transcription

Background  

Expression Quantitative Trait Locus (eQTL) mapping methods have been used to identify the genetic basis of gene expression variations. To map eQTL, thousands of expression profiles are related with sequence polymorphisms across the genome through their correlated variations. These eQTL distribute in many chromosomal regions, each of which can include many genes. The large number of mapping results produced makes it difficult to consider simultaneously the relationships between multiple genomic regions and multiple expressional profiles. There is a need for informative bioinformatics tools to assist the visualization and interpretation of these mapping results.     

Mapping phosphoproteins in <Emphasis Type="Italic">Mycoplasma genitalium</Emphasis> and <Emphasis Type="Italic">Mycoplasma pneumoniae</Emphasis>

Background  

Little is known regarding the extent or targets of phosphorylation in mycoplasmas, yet in many other bacterial species phosphorylation is known to play an important role in signaling and regulation of cellular processes. To determine the prevalence of phosphorylation in mycoplasmas, we examined the CHAPS-soluble protein fractions of Mycoplasma genitalium and Mycoplasma pneumoniae by two-dimensional gel electrophoresis (2-DE), using a combination of Pro-Q Diamond phosphoprotein stain and ³³P labeling. Protein spots that were positive for phosphorylation were identified by peptide mass fingerprinting using MALDI-TOF-TOF mass spectrometry.     

A genetically explicit model of speciation by sensory drive within a continuous population in aquatic environments

Background  

The sensory drive hypothesis predicts that divergent sensory adaptation in different habitats may lead to premating isolation upon secondary contact of populations. Speciation by sensory drive has traditionally been treated as a special case of speciation as a byproduct of adaptation to divergent environments in geographically isolated populations. However, if habitats are heterogeneous, local adaptation in the sensory systems may cause the emergence of reproductively isolated species from a single unstructured population. In polychromatic fishes, visual sensitivity might become adapted to local ambient light regimes and the sensitivity might influence female preferences for male nuptial color. In this paper, we investigate the possibility of speciation by sensory drive as a byproduct of divergent visual adaptation within a single initially unstructured population. We use models based on explicit genetic mechanisms for color vision and nuptial coloration.     

Fatal inanition in reindeer (<Emphasis Type="Italic">Rangifer tarandus tarandus</Emphasis>): Pathological findings in completely emaciated carcasses

Background  

In a project to determine the causes of winter mortality in reindeer in Finnmark County, northern Norway, the most frequent diagnosis turned out to be complete emaciation, despite several of the reindeer having been given silage for up to 4 weeks before they died. The present paper describes autopsy results and other findings in these animals.     

Involvement of Lysophosphatidic Acid,Sphingosine 1-Phosphate and Ceramide 1-Phosphate in the Metabolization of Phosphatidic Acid by Lipid Phosphate Phosphatases in Bovine Rod Outer Segments

The aim of the present research was to evaluate the generation of [2-3H]diacylglycerol ([2-3H]DAG) from [2-3H]-Phosphatidic acid ([2-3H]PA) by lipid phosphate phosphatases (LPPs) at different concentrations of lysophosphatidic acid (LPA), sphingosine 1-phosphate (S1P), and ceramide 1-phosphate (C1P) in purified ROS obtained from dark-adapted retinas (DROS) or light-adapted retinas (BLROS) as well as in ROS membrane preparations depleted of soluble and peripheral proteins. Western blot analysis revealed the presence of LPP3 exclusively in all membrane preparations. Immunoblots of entire ROS and depleted ROS did not show dark-light differences in LPP3 levels. LPPs activities were diminished by 53% in BLROS with respect to DROS. The major competitive effect on PA hydrolysis was exerted by LPA and S1P in DROS and by C1P in BLROS. LPPs activities in depleted ROS were similar to the activity observed in entire DROS and BLROS, respectively. LPA, S1P and C1P competed at different extent in depleted DROS and BLROS. Sphingosine and ceramide inhibited LPPs activities in entire and depleted DROS. Ceramide also inhibited LPPs activities in entire and in depleted BLROS. Our findings are indicative of a different degree of competition between PA and LPA, S1P and C1P by LPPs depending on the illumination state of the retina.     

Trace Element Status of Chronic Renal Patients Undergoing Hemodialysis

The purpose of this study was to examine the status of trace elements (Cu, Zn, and Fe) and minerals (Mg, K, Na, and Cl) and the level of biochemical parameters (urea, creatinine, total protein, albumin, and glucose) in hemodialysis (HD) patients. This study included 30 HD patients (25 men and 5 women) aged 52.12 +/- 3.13 years and 30 healthy subjects (23 men and 7 women) aged 51.64 +/- 2.22 years. This study investigated the status of trace elements and minerals in HD patients. It was found that the total HD patients (before and after dialysis) had statistically lower Zn and albumin in the after-dialysis group K and Cl levels and higher Mg, creatinine, and urea in the before-dialysis group K and in the after-dialysis group glucose levels than those of the controls. It was determined that the results might be helpful in monitoring patients with renal failure in terms of insufficiency or excess of trace elements and minerals. There was positive correlation for Mg-K (r = 0.64; p = 0.001), creatinine-urea (r = 0.59; p = 0.001), K-urea (r = 0.56; p = 0.001), K-creatinine (r = 0.52; p = 0.003), Mg-creatinine (r = 0.47; p = 0.008), Zn-albumin (r = 0.40; p = 0.028), and Zn-creatinine (r = 0.40; p = 0.031) in the before-dialysis session. There was also positive correlation for creatinine-urea (r = 0.56; p = 0.001), K-urea (r = 0.39; p = 0.035), and Mg-creatinine (r = 0.38; p = 0.041) in the after-analysis session. As a result of the analysis of regression between serum levels of albumin and zinc in total HD patients, the use of the level of albumin might be a suitable choice in determining zinc deficiency resulting from the decrease in the level of zinc in parallel to that of albumin. The results also suggest that the relationship between creatinine and K, Mg, and Zn could be ascribed to the loss of renal function.