Discovery of EST-SSRs in lung cancer: tagged ESTs with SSRs lead to differential amino acid and protein expression patterns in cancerous tissues

Tandem repeats are found in both coding and non-coding sequences of higher organisms. These sequences can be used in cancer genetics and diagnosis to unravel the genetic basis of tumor formation and progression. In this study, a possible relationship between SSR distributions and lung cancer was studied by comparative analysis of EST-SSRs in normal and lung cancerous tissues. While the EST-SSR distribution was similar between tumorous tissues, this distribution was different between normal and tumorous tissues. Trinucleotides tandem repeats were highly different; the number of trinucleotides in ESTs of lung cancer was 3 times higher than normal tissue. Significant negative correlation between normal and cancerous tissue showed that cancerous tissue generates different types of trinucleotides. GGC and CGC were the more frequent expressed trinucleotides in cancerous tissue, but these SSRs were not expressed in normal tissue. Similar to the EST level, the expression pattern of EST-SSRs-derived amino acids was significantly different between normal and cancerous tissues. Arg, Pro, Ser, Gly, and Lys were the most abundant amino acids in cancerous tissues, and Leu, Cys, Phe, and His were significantly more abundant in normal tissues than in cancerous tissues. Next, the putative functions of triplet SSR-containing genes were analyzed. In cancerous tissue, EST-SSRs produce different types of proteins. Chromodomain helicase DNA binding proteins were one of the major protein products of EST-SSRs in the cancerous library, while these proteins were not produced from EST-SSRs in normal tissue. For the first time, the findings of this study confirmed that EST-SSRs in normal lung tissues are different than in unhealthy tissues, and tagged ESTs with SSRs cause remarkable differences in amino acid and protein expression patterns in cancerous tissue. We suggest that EST-SSRs and EST-SSRs differentially expressed in cancerous tissue may be suitable candidate markers for lung cancer diagnosis and prediction.     

Protein attributes contribute to halo-stability, bioinformatics approach

Halophile proteins can tolerate high salt concentrations. Understanding halophilicity features is the first step toward engineering halostable crops. To this end, we examined protein features contributing to the halo-toleration of halophilic organisms. We compared more than 850 features for halophilic and non-halophilic proteins with various screening, clustering, decision tree, and generalized rule induction models to search for patterns that code for halo-toleration. Up to 251 protein attributes selected by various attribute weighting algorithms as important features contribute to halo-stability; from them 14 attributes selected by 90% of models and the count of hydrogen gained the highest value (1.0) in 70% of attribute weighting models, showing the importance of this attribute in feature selection modeling. The other attributes mostly were the frequencies of di-peptides. No changes were found in the numbers of groups when K-Means and TwoStep clustering modeling were performed on datasets with or without feature selection filtering. Although the depths of induced trees were not high, the accuracies of trees were higher than 94% and the frequency of hydrophobic residues pointed as the most important feature to build trees. The performance evaluation of decision tree models had the same values and the best correctness percentage recorded with the Exhaustive CHAID and CHAID models. We did not find any significant difference in the percent of correctness, performance evaluation, and mean correctness of various decision tree models with or without feature selection. For the first time, we analyzed the performance of different screening, clustering, and decision tree algorithms for discriminating halophilic and non-halophilic proteins and the results showed that amino acid composition can be used to discriminate between halo-tolerant and halo-sensitive proteins.     

Performance of Cryptolaemus montrouzieri feeding on Pulvinaria aurantii ovisacs on citrus plants

We studied the performance of the coccinellid Cryptolaemus montrouzieri on citrus plant species infested with orange pulvinaria scale, Pulvinaria aurantii, under controlled conditions in the laboratory. The experimental host plants were blood orange, grapefruit, lemon, pummelo and kumquat. All life history parameters indicated best performance of C. montrouzieri, when reared on P. aurantii ovisacs on the leaves of grapefruit. Pummelo, blood orange, lemon or kumquat were less suitable.     

Growth Performance,Hemato-Immunological Responses,and Digestive Enzyme Activities in Silvery-Black Porgy (<Emphasis Type="Italic">Sparidentex hasta</Emphasis>) Fed Dietary Bovine Lactoferrin

An 8-week study was conducted to evaluate three different diets supplemented with bovine lactoferrin (LF) at 0 (control), 800, and 1200 mg LF kg^?1 diet on somatic growth, hemato-immunological parameters, antioxidant status, and digestive enzyme activities in silvery-black porgy (Sparidentex hasta) juveniles. Fish fed the 800 mg LF kg^?1 diet had higher growth performance and feed utilization parameters than the other groups. Hematological and liver antioxidant parameters were not affected by dietary LF supplementation. Fish fed the 800 mg LF kg^?1 diet had higher plasma lysozyme activity values than the other groups. Total protease activity was higher in fish fed LF-supplemented diets than the control group. Results indicated that diet supplemented with 800 mg kg^?1 for 8 weeks enhanced somatic growth performance, lysozyme activity, and proteolytic digestive enzyme activities in S. hasta, as well as improving feed efficiency parameters like the protein efficiency and feed conversion ratios.     

Constriction of pulmonary artery by peroxide: role of Ca2+ release and PKC

Reactive oxygen species are implicated in pulmonary hypertension and hypoxic pulmonary vasoconstriction. We examined the effects of low concentrations of peroxide on intrapulmonary arteries (IPA). IPAs from Wistar rats were mounted on a myograph for recording tension and estimating intracellular Ca2+ using Fura-PE3. Ca2+ sensitization was examined in alpha-toxin-permeabilized IPAs, and phosphorylation of MYPT-1 and MLC(20) was assayed by Western blot. Peroxide (30 microM) induced a vasoconstriction with transient and sustained components and equivalent elevations of intracellular Ca2+. The transient constriction was strongly suppressed by indomethacin, the TP-receptor antagonist SQ-29584, and the Rho kinase inhibitor Y-27632, whereas sustained constriction was unaffected. Neither vasoconstriction nor elevation of intracellular Ca2+ was affected by removal of extracellular Ca2+, whereas dantrolene suppressed the former and ryanodine abolished the latter. Peroxide-induced constriction of permeabilized IPAs was unaffected by Y-27632 but abolished by PKC inhibitors; these also suppressed constriction in intact IPAs. Peroxide caused translocation of PKCalpha, but had no significant effect on MYPT-1 or MLC(20) phosphorylation. We conclude that in IPAs peroxide causes transient release of vasoconstrictor prostanoids, but sustained constriction is associated with release of Ca2+ from ryanodine-sensitive stores and a PKC-dependent but Rho kinase- and MLC(20)-independent constrictor mechanism.     

Mining expressed sequence tags of rapeseed (Brassica napus L.) to predict the drought responsive regulatory network

Physiology and Molecular Biology of Plants - It is of great significance to understand the regulatory mechanisms by which plants deal with drought stress. Two EST libraries derived from rapeseed...     

Effects of PM2.5 and NO2 on the 8-isoprostane and lung function indices of FVC and FEV1 in students of Ahvaz city,Iran

The aim of this study was to determine the correlation between PM_2.5 and NO₂ pollutants and oxidative stress marker (8-isoprostane) and lung function tests (FVC and FEV₁) in healthy children who were living and studying in three different areas of Ahvaz city including A₁: Naderi site with high traffic, A₂: Alavi Alley site with average traffic, and A₃: Ein 2 site with low traffic (a rural area on the suburb of Ahvaz). 30 students in the 12–13 year-old range were selected from each studied zone (1, 2 and 3 sites) during three months of year. Of each student, one sample was taken every two weeks to measure 8-isoprostane of exhaled breath condensate (EBC). Air pollution data were collected from three air quality monitoring stations. Also, the relationship between air pollution and 8-isoprostane as well as lung function tests were determined using generalized estimating equations (GEE). The mean concentration of PM_2.5 and NO₂ in A₁, A₂ and A₃ areas were 116, 92 and 45 (μg/m³) also 77, 53 and 14 (ppb) respectively. Among all studied students, there was a significant correlation between the increase of mean concentration of PM_2.5 and NO₂ in 1–4 before sampling day, increased 8-isoprostane concentration and decreased FEV₁, while there was no significant correlation between them and decreased FVC. In A₁ site, an increase in IQR (13 μg/m³) PM_2.5 and IQR (6.5 ppb) NO₂ on 1–4 days before sampling was associated with 0.38 unit (95% CI: 0.11, 0.65) and 1.1 unit (95% CI: 0.85, 1.35) increase in 8-isoprostane concentration, also decreased 121 ml and 190 ml FEV₁, respectively. Results showed that the short-term exposure to traffic-related air pollution can decrease the values of lung function indices and increase the oxidative stress. It may adversely affect children’s lungs.