EGPred: prediction of eukaryotic genes using ab initio methods after combining with sequence similarity approaches

EGPred is a Web-based server that combines ab initio methods and similarity searches to predict genes, particularly exon regions, with high accuracy. The EGPred program proceeds in the following steps: (1) an initial BLASTX search of genomic sequence against the RefSeq database is used to identify protein hits with an E-value <1; (2) a second BLASTX search of genomic sequence against the hits from the previous run with relaxed parameters (E-values <10) helps to retrieve all probable coding exon regions; (3) a BLASTN search of genomic sequence against the intron database is then used to detect probable intron regions; (4) the probable intron and exon regions are compared to filter/remove wrong exons; (5) the NNSPLICE program is then used to reassign splicing signal site positions in the remaining probable coding exons; and (6) finally ab initio predictions are combined with exons derived from the fifth step based on the relative strength of start/stop and splice signal sites as obtained from ab initio and similarity search. The combination method increases the exon level performance of five different ab initio programs by 4%-10% when evaluated on the HMR195 data set. Similar improvement is observed when ab initio programs are evaluated on the Burset/Guigo data set. Finally, EGPred is demonstrated on an approximately 95-Mbp fragment of human chromosome 13. The list of predicted genes from this analysis are available in the supplementary material. The EGPred program is computationally intensive due to multiple BLAST runs during each analysis. The EGPred server is available at http://www.imtech.res.in/raghava/egpred/.     

Gender-specific gene expression in post-mortem human brain: localization to sex chromosomes.

Gender differences in brain development and in the prevalence of neuropsychiatric disorders such as depression have been reported. Gender differences in human brain might be related to patterns of gene expression. Microarray technology is one useful method for investigation of gene expression in brain. We investigated gene expression, cell types, and regional expression patterns of differentially expressed sex chromosome genes in brain. We profiled gene expression in male and female dorsolateral prefrontal cortex, anterior cingulate cortex, and cerebellum using the Affymetrix oligonucleotide microarray platform. Differentially expressed genes between males and females on the Y chromosome (DBY, SMCY, UTY, RPS4Y, and USP9Y) and X chromosome (XIST) were confirmed using real-time PCR measurements. In situ hybridization confirmed the differential expression of gender-specific genes and neuronal expression of XIST, RPS4Y, SMCY, and UTY in three brain regions examined. The XIST gene, which silences gene expression on regions of the X chromosome, is expressed in a subset of neurons. Since a subset of neurons express gender-specific genes, neural subpopulations may exhibit a subtle sexual dimorphism at the level of differences in gene regulation and function. The distinctive pattern of neuronal expression of XIST, RPS4Y, SMCY, and UTY and other sex chromosome genes in neuronal subpopulations may possibly contribute to gender differences in prevalence noted for some neuropsychiatric disorders. Studies of the protein expression of these sex-chromosome-linked genes in brain tissue are required to address the functional consequences of the observed gene expression differences.     

Encoded Exposure and Social Norms in Entertainment-Education

Entertainment-education is an effective health communication strategy that combines or embeds educational messages into entertainment programs to bring about social and behavior change. For years, scholars have considered how entertainment-education works. Some contemporary theories posit that entertainment-education does not engender behavior change directly but does so through mediating variables. This study adds to the literature on this topic by exploring the direct relationship between exposure and social norms instead of their relationship through behavior as a mediator. Novel to this study is the use of encoded exposure, a continuous and recognition-based measure of exposure that includes ever watching, recall, involvement, and dose in its operationalization. Using cross-sectional data from Kyunki … Jeena Issi Ka Naam Hai, an entertainment-education program in India, this exploratory analysis indicates a positive and significant relationship between encoded exposure and social norms. How can this finding be applied to future programs? Questions remain, and replication is needed, but if it is not essential to go through behavior in order to change social norms, then implications emerge for the theory and practice of entertainment-education.     

Synthesis and Characterization of Impurities in the Production Process of Lopinavir

Lopinavir is an antiretroviral drug used for the inhibition of HIV protease. Four related substances of lopinavir were observed during the manufacturing process of lopinavir in the laboratory and they were identified. The present work describes the origin, synthesis, characterization, and control of these related substances.     

P2X4 Receptor Regulates Alcohol-Induced Responses in Microglia

Mounting evidence indicates that alcohol-induced neuropathology may result from multicellular responses in which microglia cells play a prominent role. Purinergic receptor signaling plays a key role in regulating microglial function and, more importantly, mediates alcohol-induced effects. Our findings demonstrate that alcohol increases expression of P2X4 receptor (P2X4R), which alters the function of microglia, including calcium mobilization, migration and phagocytosis. Our results show a significant up-regulation of P2X4 gene expression as analyzed by real-time qPCR (***p?p?CX3CL1) by 75 % following 48 h of treatment compared to control (***p?CX3CL1-dependent migration was confirmed to be P2X4 receptor-dependent using the antagonist 5-BDBD, which reversed the effects as compared to alcohol alone (***p?p?p?相似文献