pLARmEB: integration of least angle regression with empirical Bayes for multilocus genome-wide association studies.

Multilocus genome-wide association studies (GWAS) have become the state-of-the-art procedure to identify quantitative trait nucleotides (QTNs) associated with complex traits. However, implementation of multilocus model in GWAS is still difficult. In this study, we integrated least angle regression with empirical Bayes to perform multilocus GWAS under polygenic background control. We used an algorithm of model transformation that whitened the covariance matrix of the polygenic matrix K and environmental noise. Markers on one chromosome were included simultaneously in a multilocus model and least angle regression was used to select the most potentially associated single-nucleotide polymorphisms (SNPs), whereas the markers on the other chromosomes were used to calculate kinship matrix as polygenic background control. The selected SNPs in multilocus model were further detected for their association with the trait by empirical Bayes and likelihood ratio test. We herein refer to this method as the pLARmEB (polygenic-background-control-based least angle regression plus empirical Bayes). Results from simulation studies showed that pLARmEB was more powerful in QTN detection and more accurate in QTN effect estimation, had less false positive rate and required less computing time than Bayesian hierarchical generalized linear model, efficient mixed model association (EMMA) and least angle regression plus empirical Bayes. pLARmEB, multilocus random-SNP-effect mixed linear model and fast multilocus random-SNP-effect EMMA methods had almost equal power of QTN detection in simulation experiments. However, only pLARmEB identified 48 previously reported genes for 7 flowering time-related traits in Arabidopsis thaliana.

SCIRR39 promotes neurite extension via RhoA in NGF-induced PC12 cells.

SCIRR39 is an identified upregulated gene in rat primary neuron injury and/or regeneration process with roles largely unexplored. Using real-time quantitative PCR, Western blotting and immunofluorescence, SCIRR39 expression was detected in normal PC12 cells and upregulated in differentiated cells. The results of cell proliferation by Cell Counting Kit and cell cycle by flow cytometry indicated that SCIRR39 inhibited cell proliferation and induced the decrease in S phase. Importantly, immunofluorescent and RhoA pull-down assays showed that SCIRR39 strongly affected the neurite extension of NGF-treated PC12 cells through a RhoA-dependent mechanism, but the truncated mutants of SCIRR39 containing a truncation from 141AA to 211AA or from 397AA to 424AA failed to mock the SCIRR39 effect on neurite extension. Moreover, change of SCIRR39 expression in NGF-treated PC12 cells regulated the expression and phosphorylation of Fyn, a regulator of RhoA activity, but not the expression of ROCK II protein. Finally, immunofluorescence and RhoA pull-down assays revealed that obvious inhibition of neurite extension by SCIRR39 shRNA was reversed by RhoA inhibitor C3-transferase. Our results indicated that SCIRR39 increased the neurite extension in NGF-treated PC12 cells via RhoA, suggesting that SCIRR39 contributes to the regeneration of neuron injury by specifically altering the differentiation program.

Effects of calcium-based sorbents on PCDD/F formation from pentachlorophenol combustion process.

Calcium-based sorbents are widely employed to reduce the acidic gases emission from combustion processes, and also have effects on trace organic pollutants formation and emission. Batch experiments were conducted to investigate the effects of calcium-based sorbents on pentachlorophenol (PCP) forming PCDDs/Fs during high temperature combustion processes. The results indicated that highly chlorinated PCDD/F homologues were the predominant dioxin products from PCP thermo decomposition, and only minor increasing of PCDDs happened when Ca/Cl ratio was lower than 1, while a major jump occurred when Ca/Cl ratio increased from 1 to 2. The CaO addition clearly promoted the production of all chlorinated dibenzo-p-dioxins homologue and 4-7DFs homologue. Comparison of total PCDD/F emission and its I-TEQ for three different calcium-based sorbents addition (CaO, CaCO3, basic fly ash) indicated that CaO and fly ash containing CaO had almost the same promotion effects on PCDDs/Fs originated from PCP, while CaCO3 inhibit PCDD/F formation greatly with inhibition efficiency up to 70%. Such effects may be partly proved by the observed clearly different micro-surface structures of their reaction residues. The mechanism of CaO on condensation and dechlorination reactions for PCP forming PCDDs and acid-base interaction were proposed to speculate the promotion effects of CaO, and the reaction precedence was used to speculate the inhibition effects of CaCO3 on PCDDs/Fs originated from PCP. The results of the present paper might be useful for the industrial application of calcium-based sorbents to control PCDD/F emission.

The efficacy of an albendazole-medicated block in controlling sheep nematodes in Xinjiang province, north-west China.

Medicated feed-blocks containing 2 mg/kg albendazole were fed for 12 days to ewe-lambs naturally infected with nematode worms in north-west China. The cumulative total average intake of albendazole was 15 mg/kg body weight. This treatment was compared with a single oral drench of 15 mg/kg albendazole and with no treatment. Both albendazole treatments were 99% effective in reducing the total strongyle egg counts. The medicated block was 100% effective in reducing the total trichostrongylid worm count, although only 86.4% of the sheep consumed an adequate amount. The single drench was 97% effective. Under the management conditions available to sheep herders in the northern provinces of China, albendazole-medicated feed blocks used at strategic times could effectively control trichostrongylid nematodes.