MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Genomics' source. Mon, 06 Feb 2012 09:32:12 +0100 http://www.medworm.com/index.php?rid=5650382&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22293435%26dopt%3DAbstract Authors: Asari M, Omura T, Oka K, Maseda C, Tasaki Y, Shiono H, Matsubara K, Matsuda M, Shimizu K Abstract Discrimination of Alu insertions is a useful tool for geographic ancestry analysis, and is usually performed by Alu element amplification and agarose gel electrophoresis. Here, we have developed a new fluorescence-based method for multiple Alu genotyping in forensic identification. Allele frequencies were determined in 70 Japanese individuals, and we selected 30 polymorphic Alu insertions. Three primers were designed for each Alu locus to discriminate alleles using the 3-6bp differences in amplicon sizes. Furthermore, we classified the amplification primers for the 30 loci into three different sets, and PCR using each set of primers provided 10 loci fragments ranging from 50 t... Genomics journals http://www.medworm.com/rss/comments.php?id=5650382 Thu, 26 Jan 2012 05:00:00 +0100 5650382 http://www.medworm.com/index.php?rid=5650383&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22289416%26dopt%3DAbstract Authors: Cabral RM, Kurban M, Wajid M, Shimomura Y, Petukhova L, Christiano AM Abstract Generalized peeling skin syndrome (PSS) is an autosomal recessive genodermatosis characterized by lifelong, continuous shedding of the upper epidermis. Using whole-genome homozygozity mapping and whole-exome sequencing, we identified a novel homozygous missense mutation (c.229C>T, R77W) within the CHST8 gene, in a large consanguineous family with non-inflammatory PSS type A. CHST8 encodes a Golgi transmembrane N-acetylgalactosamine-4-O-sulfotransferase (GalNAc4-ST1), which we show by immunofluorescence staining to be expressed throughout normal epidermis. A colorimetric assay for total sulfated glycosaminoglycan (GAG) quantification, comparing human keratinocytes (CCD1106 KERTr) expressing wi... Genomics journals http://www.medworm.com/rss/comments.php?id=5650383 Wed, 25 Jan 2012 05:00:00 +0100 5650383 http://www.medworm.com/index.php?rid=5650384&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22281206%26dopt%3DAbstract Authors: Fedick A, Su J, Treff NR Abstract The high prevalence of genetic diseases resulting from gross deletions has highlighted a need for a quick, simple, and reliable method of genotyping these mutations. Here, we developed a novel strategy for applying TaqMan allelic discrimination to accurately genotype 3 different large deletions in a high-throughput manner. Allelic discrimination has previously been used to genotype frame shift and point mutations, and small insertions or deletions six base pairs in length, but not large deletions. The assays designed here recognize a 2502 base pair deletion in the Nebulin (NEB) gene that results in Nemaline Myopathy, a 308,769 base pair deletion in the Gap Junction Protein, beta 6 (GJB6) gene that causes Hearing Loss, and a 6433 base pair ... Genomics journals http://www.medworm.com/rss/comments.php?id=5650384 Tue, 17 Jan 2012 05:00:00 +0100 5650384 http://www.medworm.com/index.php?rid=5650385&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22269447%26dopt%3DAbstract This study provides new insights into the epigenetic systems of LCLs and suggests that more specifically designed experiments are needed to improve our understanding on this topic. PMID: 22269447 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=5650385 Sun, 15 Jan 2012 05:00:00 +0100 5650385 http://www.medworm.com/index.php?rid=5593960&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22240003%26dopt%3DAbstract We present here the de novo assembly and annotation of the transcriptome of Plutella xylostella (diamondback moth (DBM)), a widespread destructive pest of cruciferous plants, using short reads generated by Illumina sequencing from different developmental stages and insecticide-resistant strains. A total of 171,262 non-redundant sequences, denoted as unigenes, were obtained. They represented approximately 100-fold of all DBM mRNA and EST sequences in GenBank thus far. We identified 38,255 unigenes highly similar to the known functional protein-coding genes, most of which were annotated using gene ontology (GO) and orthologous groups of proteins (COG). Global profiling of differentially expressed unigenes revealed enriched GOs and biological pathways that were related to specific development... Genomics journals http://www.medworm.com/rss/comments.php?id=5593960 Thu, 05 Jan 2012 05:00:00 +0100 5593960 http://www.medworm.com/index.php?rid=5593959&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22240004%26dopt%3DAbstract Authors: Qi XH, Xu XW, Lin XJ, Zhang WJ, Chen XH Abstract High-throughput tag-sequencing (Tag-seq) analysis based on the Solexa Genome Analyzer platform was applied to analyze the gene expression profiling of cucumber plant at 5 time points over a 24h period of waterlogging treatment. Approximately 5.8million total clean sequence tags per library were obtained with 143013 distinct clean tag sequences. Approximately 23.69%-29.61% of the distinct clean tags were mapped unambiguously to the unigene database, and 53.78%-60.66% of the distinct clean tags were mapped to the cucumber genome database. Analysis of the differentially expressed genes revealed that most of the genes were down-regulated in the waterlogging stages, and the differentially expressed genes mainly linked to carbon m... Genomics journals http://www.medworm.com/rss/comments.php?id=5593959 Wed, 04 Jan 2012 05:00:00 +0100 5593959 http://www.medworm.com/index.php?rid=5593961&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22234326%26dopt%3DAbstract Authors: Almén MS, Jacobsson JA, Moschonis G, Benedict C, Chrousos GP, Fredriksson R, Schiöth HB Abstract Variants of the FTO gene show strong association with obesity, but the mechanisms behind this association remain unclear. We determined the genome wide DNA methylation profile in blood from 47 female preadolescents. We identified sites associated with the genes KARS, TERF2IP, DEXI, MSI1, STON1 and BCAS3 that had a significant differential methylation level in the carriers of the FTO risk allele (rs9939609). In addition, we identified 20 differentially methylated sites associated with obesity. Our findings suggest that the effect of the FTO obesity risk allele may be mediated through epigenetic changes. Further, these sites might prove to be valuable biomarkers for the underst... Genomics journals http://www.medworm.com/rss/comments.php?id=5593961 Mon, 02 Jan 2012 05:00:00 +0100 5593961 http://www.medworm.com/index.php?rid=5593963&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22227021%26dopt%3DAbstract Authors: Zheng S, Zhao Z Abstract We introduce GenRev, a network-based software package developed to explore the functional relevance of genes generated as an intermediate result from numerous high-throughput technologies. GenRev searches for optimal intermediate nodes (genes) for the connection of input nodes via several algorithms, including the Klein-Ravi algorithm, the limited kWalks algorithm and a heuristic local search algorithm. Gene ranking and graph clustering analyses are integrated into the package. GenRev has the following features. (1) It provides users with great flexibility to define their own networks. (2) Users are allowed to define each gene's importance in a subnetwork search by setting its score. (3) It is standalone and platform independent. (4) It provides an... Genomics journals http://www.medworm.com/rss/comments.php?id=5593963 Thu, 29 Dec 2011 05:00:00 +0100 5593963 http://www.medworm.com/index.php?rid=5593962&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22227022%26dopt%3DAbstract Authors: Mitchell AC, Leak RK, Zigmond MJ, Cameron JL, Mirnics K Abstract Obesity affects over 500million people worldwide, and has far reaching negative health effects. Given that high body mass index (BMI) and insulin resistance are associated with alterations in many regions of brain and that physical activity can decrease obesity, we hypothesized that in Rhesus monkeys (Macaca mulatta) fed a high fat diet and who subsequently received reduced calories BMI would be associated with a unique gene expression signature in motor regions of the brain implicated in neurodegenerative disorders. In the motor cortex with increased BMI we saw the upregulation of genes involved in apoptosis, altered gene expression in metabolic pathways, and the downregulation of pERK1/2, a protein involved... Genomics journals http://www.medworm.com/rss/comments.php?id=5593962 Thu, 29 Dec 2011 05:00:00 +0100 5593962 http://www.medworm.com/index.php?rid=5593964&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22226708%26dopt%3DAbstract In conclusion, SplicingViewer can be widely used for studying alternative splicing easily and efficiently. SplicingViewer can be freely accessed at http://bioinformatics.zj.cn/splicingviewer. PMID: 22226708 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=5593964 Wed, 28 Dec 2011 05:00:00 +0100 5593964 http://www.medworm.com/index.php?rid=5557574&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22206861%26dopt%3DAbstract This study uses genome-wide miRNA profiling to analyze expression in TICs. We connect aberrant miRNA expression and deregulated gene expression in TICs. These findings can contribute to a better understanding of the molecular mechanisms governing TIC development/maintenance and the role that miRNAs have in the fundamental biology of TICs. PMID: 22206861 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=5557574 Tue, 20 Dec 2011 05:00:00 +0100 5557574 http://www.medworm.com/index.php?rid=5543628&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22193333%26dopt%3DAbstract Authors: Philip S, Castro LF, da Fonseca RR, Reis-Henriques MA, Vasconcelos V, Santos MM, Antunes A Abstract Retinoid X receptors (RXR) are transcription factors with important roles in development, reproduction, homeostasis, and cell differentiation. Different types of vertebrate RXRs (a, ß and γ) have arisen from multiple duplication events. The adaptive evolution mechanism that has preserved duplicate RXR paralogs, as well as their role in development and adaptation, is thus far unknown. In this work, we have investigated different aspects of vertebrate RXR evolution. Codon based tests of positive selection identified that RXR was under significant positive selection immediately after the whole genome duplications in vertebrates. Amino acid based rate shift analysis also revea... Genomics journals http://www.medworm.com/rss/comments.php?id=5543628 Wed, 14 Dec 2011 05:00:00 +0100 5543628 http://www.medworm.com/index.php?rid=5523464&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178264%26dopt%3DAbstract In this study, QTL mapping of physiological traits in Medicago truncatula was performed using a set of RILs derived from LR5. Twelve parameters associated with Na(+) and K(+) content in leaves, stems and roots were measured. Broad-sense heritability of these traits was ranged from 0.15 to 0.83 in control and from 0.14 to 0.61 in salt stress. Variation among RILs was dependent on line, treatment and line by treatment effect. We mapped 6 QTLs in control, 2 in salt stress and 5 for sensitivity index. No major QTL was identified indicating that tolerance to salt stress is governed by several genes with low effects. Detected QTL for leaf, stem and root traits did not share the same map locations, suggesting that genes controlling transport of Na(+) and K(+) may be different. The maximum of QTL ... Genomics journals http://www.medworm.com/rss/comments.php?id=5523464 Thu, 08 Dec 2011 05:00:00 +0100 5523464 http://www.medworm.com/index.php?rid=5523463&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178265%26dopt%3DAbstract Authors: Ramaprasad A, Pain A, Ravasi T Abstract Malaria, caused by the protozoan parasite Plasmodium falciparum, affects around 225million people yearly and a huge international effort is directed towards combating this grave threat to world health and economic development. Considerable advances have been made in malarial research triggered by the sequencing of its genome in 2002, followed by several high-throughput studies defining the malarial transcriptome and proteome. A protein-protein interaction (PPI) network seeks to trace the dynamic interactions between proteins, thereby elucidating their local and global functional relationships. Experimentally derived PPI network from high-throughput methods such as yeast two hybrid (Y2H) screens are inherently noisy, but combining the... Genomics journals http://www.medworm.com/rss/comments.php?id=5523463 Thu, 08 Dec 2011 05:00:00 +0100 5523463 http://www.medworm.com/index.php?rid=5523462&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22178800%26dopt%3DAbstract Authors: Tian F, Luo J, Zhang H, Song J Abstract MicroRNAs (miRNAs) are small, non-coding RNAs that regulate gene expression at the post-transcriptional level. Emerging evidence suggests that differential miRNA expression is associated with viral infection and cancer. Marek's disease virus infection induces lymphoma in chickens. However, the host defense response against Marek's disease (MD) progression remains poorly understood. Here, we utilized microarrays to screen miRNAs that were sensitive to Marek's disease virus (MDV) infection. QRT-PCR analysis confirmed the microarray data and revealed expression patterns of some miRNAs in tumor samples. Chicken miRNA gga-miR-15b, which is reduced in infected susceptible chickens and splenic tumors, controls the expression of ATF2 (activa... Genomics journals http://www.medworm.com/rss/comments.php?id=5523462 Wed, 07 Dec 2011 05:00:00 +0100 5523462 http://www.medworm.com/index.php?rid=5486746&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22138042%26dopt%3DAbstract In this study, we proposed two new two-gene classification algorithms which used simple univariate gene selection strategy and constructed simple classification rules based on optimal cut-points for two genes selected. We detected the optimal cut-point with the information entropy principle. We applied the two-gene classification models to eleven cancer gene expression datasets and compared their classification performance to that of some established two-gene classification models like the top-scoring pairs model and the greedy pairs model, as well as standard methods including Diagonal Linear Discriminant Analysis, k-Nearest Neighbor, Support Vector Machine and Random Forest. These comparisons indicated that the performance of our two-gene classifiers was comparable to or better than that... Genomics journals http://www.medworm.com/rss/comments.php?id=5486746 Sun, 27 Nov 2011 05:00:00 +0100 5486746 http://www.medworm.com/index.php?rid=5486747&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22120185%26dopt%3DAbstract Authors: Huang PJ, Lin WC, Chen SC, Lin YH, Sun CH, Lyu PC, Tang P Abstract MicroRNAs (miRNAs) are a class of extensively studied RNAi-associated small RNAs that play a critical role in eukaryotic gene regulation. However, knowledge on the miRNA and its regulation in unicellular eukaryotes is very limited. In order to obtain a better understanding on the origin of miRNA regulation system, we used deep-sequencing technology to investigate the miRNA expression pattern in four deep-branching unicellular flagellates: Giardia lamblia, Trichomonas vaginalis, Tritrichomonas foetus, and Pentatrichomonas hominis. In addition to the known miRNAs that have been described in G. lamblia and T. vaginalis, we identified 14 ancient animal miRNA families and 13 plant-specific families. Bioinformati... Genomics journals http://www.medworm.com/rss/comments.php?id=5486747 Fri, 18 Nov 2011 05:00:00 +0100 5486747 http://www.medworm.com/index.php?rid=5486748&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22100282%26dopt%3DAbstract Authors: Gu JL, Chen SX, Dou TH, Xu MJ, Xu JX, Zhang L, Hu W, Wang SY, Zhou Y Abstract Hox genes are characterized by a highly conserved peptide domain and contribute to antero-posterior axis patterning during embryogenesis. These genes have been widely studied in a variety of animal species due to their central role in evolutionary developmental biology. Based on the published genome assembly and unpublished re-sequencing project data, we present the first genome-wide characterization and comparative genomic analysis of the Hox gene family within Schistosoma japonicum. Eight Hox genes were identified and validated in our investigation. Phylogenetic analysis revealed that these genes are distributed among seven orthology groups of the Hox gene family. Our study further suggested th... Genomics journals http://www.medworm.com/rss/comments.php?id=5486748 Mon, 07 Nov 2011 05:00:00 +0100 5486748 http://www.medworm.com/index.php?rid=5408065&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22079941%26dopt%3DAbstract Authors: Smith AC, Suzuki M, Thompson R, Choufani S, Higgins MJ, Chiu IW, Squire JA, Greally JM, Weksberg R Abstract Beckwith-Wiedemann syndrome (BWS) is an overgrowth syndrome associated with genetic or epigenetic alterations in one of two imprinted domains on chromosome 11p15.5. Rarely, chromosomal translocations or inversions of chromosome 11p15.5 are associated with BWS but the molecular pathophysiology in such cases is not understood. In our series of 3 translocation and 2 inversion patients with BWS, the chromosome 11p15.5 breakpoints map within the centromeric imprinted domain, 2. We hypothesized that either microdeletions/microduplications adjacent to the breakpoints could disrupt genomic sequences important for imprinted gene regulation. An alternate hypothesis was that ep... Genomics journals http://www.medworm.com/rss/comments.php?id=5408065 Thu, 03 Nov 2011 04:00:00 +0100 5408065 http://www.medworm.com/index.php?rid=5408066&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22056789%26dopt%3DAbstract Authors: Lurie-Weinberger MN, Peeri M, Gophna U Abstract Methanobrevibacter smithii is the most abundant archaeon in the human colon. As most of its neighbors are bacterial species, it is expected that lateral gene acquisition from bacteria might have contributed to the evolution and adaptation of this archaeon. We performed a tree-based genome-wide survey of putative lateral gene transfer products in M. smithii, using a phylogenetic pipeline. Over 15% of the coding genes of M. smithii are inferred to be bacterial in origin, based on this analysis. Laterally acquired genes have had the largest contribution to surface functions, and encode glycosyl-transferases and adhesin-like proteins. In addition, several important ABC transporters, especially metal transporters are of bacterial ... Genomics journals http://www.medworm.com/rss/comments.php?id=5408066 Fri, 28 Oct 2011 04:00:00 +0100 5408066 http://www.medworm.com/index.php?rid=5408067&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22050995%26dopt%3DAbstract Authors: Belvedere O, Berri S, Chalkley R, Conway C, Barbone F, Pisa F, Maclennan K, Daly C, Alsop M, Morgan J, Menis J, Tcherveniakov P, Papagiannopoulos K, Rabbitts P, Wood HM Abstract Squamous cell carcinoma of the lung is remarkable for the extent to which the same chromosomal abnormalities are detected in individual tumours. We have used next generation sequencing at low coverage to produce high resolution copy number karyograms of a series of 89 non-small cell lung tumours specifically of the squamous cell subtype. Because this methodology is able to create karyograms from formalin-fixed paraffin-embedded material, we were able to use archival stored samples for which survival data were available and correlate frequently occurring copy number changes with disease outcome. No ... Genomics journals http://www.medworm.com/rss/comments.php?id=5408067 Tue, 25 Oct 2011 04:00:00 +0100 5408067 http://www.medworm.com/index.php?rid=5372784&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22044633%26dopt%3DAbstract Authors: Su J, Shao X, Liu H, Liu S, Qiong W, Zhang Y Abstract DNA methylation changes in repetitive elements (REs) are associated with the regulation of gene transcription, embryonic development, differentiation and carcinogenesis. However, genome-wide analysis of DNA methylation of human REs is lacking. Here, we performed genome-wide methylation analysis of REs in nine repeat types in human embryonic stem cells (H1) and fetal fibroblasts (IMR90), and found that the potential for changes in the DNA methylation of REs was different among the nine repeat types and within different genomic regions. DNA methylation changes in the nine repeat types were related to the GC content and CpG density of the sequence contexts. The differentially methylated REs and targeted genes of different ... Genomics journals http://www.medworm.com/rss/comments.php?id=5372784 Tue, 25 Oct 2011 04:00:00 +0100 5372784 http://www.medworm.com/index.php?rid=5372785&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22036712%26dopt%3DAbstract We report here the identification of three novel EPM2A splice variants with potential to code for five distinct proteins in alternate reading frames. These novel isoforms, when ectopically expressed in cell lines, show distinct subcellular localization, interact with and serve as substrates of malin ubiquitin ligase-the second protein defective in LD. Two phosphatase active isoforms interact to form a heterodimeric complex that is inactive as a phosphatase in vitro, suggesting an antagonistic function for laforin isoforms if expressed endogenously in significant amounts in human tissues. Thus alternative splicing could possibly be one of the mechanisms by which EPM2A may regulate the cellular functions of the proteins it codes for. PMID: 22036712 [PubMed - as supplied by publisher] (So... Genomics journals http://www.medworm.com/rss/comments.php?id=5372785 Wed, 19 Oct 2011 04:00:00 +0100 5372785 http://www.medworm.com/index.php?rid=5372787&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22019378%26dopt%3DAbstract Authors: Taniya T, Tanaka S, Yamaguchi-Kabata Y, Hanaoka H, Yamasaki C, Maekawa H, Barrero RA, Lenhard B, Datta MW, Shimoyama M, Bumgarner R, Chakraborty R, Hopkinson I, Jia L, Hide W, Auffray C, Minoshima S, Imanishi T, Gojobori T Abstract Complex diseases result from contributions of multiple genes that act in concert through pathways. Here we present a method to prioritize novel candidates of disease-susceptibility genes depending on the biological similarities to the known disease-related genes. The extent of disease-susceptibility of a gene is prioritized by analyzing seven features of human genes captured in H-InvDB. Taking rheumatoid arthritis (RA) and prostate cancer (PC) as two examples, we evaluated the efficiency of our method. Highly scored genes obtained included TNFSF... Genomics journals http://www.medworm.com/rss/comments.php?id=5372787 Fri, 14 Oct 2011 04:00:00 +0100 5372787 http://www.medworm.com/index.php?rid=5372789&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22001696%26dopt%3DAbstract We reported a 3-generation family consisting of 18 members, including 5 affected males (the proband, his 2 brothers, his cousin, and his maternal uncle; III1-III4, II8) suffered with CPHD. MRI of the pituitary gland showed hypoplasia of the pituitary gland in affected members. By 19 STR markers and linkage analysis, we found that the disease gene localized between the DXS987 and DXS1226 markers (LOD score=2.408, θ=0). All affected male patients inherited the same haplotype from the female carrier (I4). The proband's mother (II4) and her sister (II3, II6) were obligate female carriers. However, the unaffected males (II(7), II(9)) in the family did not have this haplotype. These observations confirm a new X-linked recessive inherited disease in a Chinese family with CPHD and the pathogenic ... Genomics journals http://www.medworm.com/rss/comments.php?id=5372789 Thu, 06 Oct 2011 04:00:00 +0100 5372789 http://www.medworm.com/index.php?rid=5372788&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22002038%26dopt%3DAbstract Authors: Wang Y, Li X, Hu H Abstract MicroRNAs play pivotal roles in gene regulation. Despite various research efforts on microRNAs, how microRNA target genes are transcriptionally regulated and how the transcriptional regulation of microRNA target genes relates to that of the microRNA genes are not well studied. By investigating the transcriptional regulation of microRNA target genes, we found that different groups of target genes of the same microRNA are co-expressed under different conditions, and these groups rarely overlap with each other for the majority of microRNAs. We also discovered that co-expressed microRNA target genes are often co-regulated, and different groups of target genes of the same microRNA are often regulated differently. In addition, we observed that transcr... Genomics journals http://www.medworm.com/rss/comments.php?id=5372788 Sun, 02 Oct 2011 04:00:00 +0100 5372788 http://www.medworm.com/index.php?rid=5372786&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D22032952%26dopt%3DAbstract Authors: Gamsiz ED, Ouyang Q, Schmidt M, Nagpal S, Morrow EM Abstract Genome-wide characterization of the retinal transcriptome is central to understanding development, physiology and disorders of the visual system. Massively parallel, short-read sequencing of mRNA libraries was used to generate an extensive map of the transcriptome of the adult, murine neural retina. RNA-seq data strongly corroborates prior transcriptome studies by microarray and SAGE. However, several novel features of the retinal transcriptome were discovered. For example, retinal disease genes were discovered to be among the most highly expressed in the transcriptome. We also demonstrate other interesting features of the retinal transcriptome, for example, that the retina appears to employ a very specific and r... Genomics journals http://www.medworm.com/rss/comments.php?id=5372786 Sat, 01 Oct 2011 04:00:00 +0100 5372786 http://www.medworm.com/index.php?rid=5293162&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21600279%26dopt%3DAbstract Authors: Moy C, Aziz MU, Greshock J, Szabo S, McNeil E, Jing J, Conway T, Degenhardt Y, Wooster R, Bachman K Abstract Identification of biomarkers for positive and negative predictors of response to cancer therapeutics can help direct clinical strategies. However, challenges with tissue availability and costs are significant limiting factors for diagnostic assays. To address these challenges, we have customized a high-throughput single nucleotide polymorphism genotyping assay with the objective of simultaneously surveying known somatic mutations and copy number alterations for translational studies in cancer. As constructed, this assay can interrogate 376 known somatic mutations and quantify copy number alterations of genes commonly implicated in tumorigenesis or progression. Valid... Genomics journals http://www.medworm.com/rss/comments.php?id=5293162 Sat, 01 Oct 2011 04:00:00 +0100 5293162 http://www.medworm.com/index.php?rid=5293161&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21971296%26dopt%3DAbstract Authors: Yu T, Bai Y Abstract Analyzing gene expression data at the gene set level greatly improves feature extraction and data interpretation. Currently most efforts in gene set analysis are focused on differential expression analysis - finding gene sets whose genes show first-order relationship with the clinical outcome. However the regulation of the biological system is complex, and much of the change in gene expression dynamics do not manifest in the form of differential expression. At the gene set level, capturing the change in expression dynamics is difficult due to the complexity and heterogeneity of the gene sets. Here we report a systematic approach to detect gene sets that show differential coordination patterns with the rest of the transcriptome, as well as pairs of gene... Genomics journals http://www.medworm.com/rss/comments.php?id=5293161 Sat, 24 Sep 2011 04:00:00 +0100 5293161 http://www.medworm.com/index.php?rid=5272164&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21946387%26dopt%3DAbstract Authors: Coda AB, Sinha AA Abstract Alopecia areata (AA), a non-scarring inflammatory hair loss disorder, is a complex disease determined by genetic and environmental factors that remain largely unknown. Re-analysis of genome-wide microarray data in 9 patient blood and 10 skin samples revealed transcriptional "hot spots" at chromosomes 1q21-q32, 11q12-q14, and 16p13-p13.3 (blood) and 6p21.3, 12q12-q13, and 17q12-q24 (skin) harboring high densities of dysregulated genes. We then integrated AA associated gene expression profiles with previous genome-wide genetic analyses to identify a subset of 112 dysregulated genes that map to putative susceptibility loci. Finally, we analyzed AA patients stratified by defined clinical characteristics, including a history of atopy, autoimmune disea... Genomics journals http://www.medworm.com/rss/comments.php?id=5272164 Sat, 17 Sep 2011 04:00:00 +0100 5272164 http://www.medworm.com/index.php?rid=5237913&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21930198%26dopt%3DAbstract Authors: Li SC, Liao YL, Chan WC, Ho MR, Tsai KW, Hu LY, Lai CH, Hsu CN, Lin WC Abstract Rabbit (Oryctolagus cuniculus) is the only lagomorph animal of which the genome has been sequenced. Establishing a rabbit miRNA resource will benefit subsequent functional genomic studies in mammals. We have generated small RNA sequence reads with SOLiD and Solexa platforms to identify rabbit miRNAs, where we identified 464 pre-miRNAs and 886 mature miRNAs. The brain and heart miRNA libraries were used for further in-depth analysis of isomiR distributions. There are several intriguing findings. First, several rabbit pre-miRNAs form highly conserved clusters. Second, there is a preference in selecting one strand as mature miRNA, resulting in an arm selection preference. Third, we analyzed the is... Genomics journals http://www.medworm.com/rss/comments.php?id=5237913 Sat, 10 Sep 2011 04:00:00 +0100 5237913 http://www.medworm.com/index.php?rid=5213283&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21907785%26dopt%3DAbstract Authors: Trask JS, Garnica WT, Kanthaswamy S, Malhi RS, Smith DG Abstract Although the rhesus macaque (Macaca mulatta) is commonly used for biomedical research and becoming a preferred model for translational medicine, quantification of genome-wide variation has been slow to follow the publication of the genome in 2007. Here we report the properties of 4040 single nucleotide polymorphisms discovered and validated in Chinese and Indian rhesus macaques from captive breeding colonies in the United States. Frequency-matched measures of linkage disequilibrium were much greater in the Indian sample. Although the majority of polymorphisms were shared between the two populations, rare alleles were over twice as common in the Chinese sample. Indian rhesus had higher rates of heterozygosity,... Genomics journals http://www.medworm.com/rss/comments.php?id=5213283 Wed, 31 Aug 2011 04:00:00 +0100 5213283 http://www.medworm.com/index.php?rid=5213282&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21907786%26dopt%3DAbstract Authors: Zhang L, Zheng Y, Jagadeeswaran G, Li Y, Gowdu K, Sunkar R Abstract Sweet Sorghum is largely grown for grain production but also recently emerged as one of the model feedstock plants for biofuel production. In plants, microRNA (miRNA)-guided gene regulation plays a key role in diverse biological processes, thus, their identification in different plant species is essential to understand post-transcriptional gene regulation. To identify miRNAs in Sorghum, we sequenced a small RNA library. Sequence analysis revealed the identity of 29 conserved miRNA families. Importantly, 13 novel miRNAs are identified, seven of which are conserved in closely related monocots. Temporal expression analysis of conserved and novel miRNAs indicated differential expression of several miRNAs. Appr... Genomics journals http://www.medworm.com/rss/comments.php?id=5213282 Wed, 31 Aug 2011 04:00:00 +0100 5213282 http://www.medworm.com/index.php?rid=5213286&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21903159%26dopt%3DAbstract Authors: Hoffmann TJ, Zhan Y, Kvale MN, Hesselson SE, Gollub J, Iribarren C, Lu Y, Mei G, Purdy MM, Quesenberry C, Rowell S, Shapero MH, Smethurst D, Somkin CP, Van den Eeden SK, Walter L, Webster T, Whitmer RA, Finn A, Schaefer C, Kwok PY, Risch N Abstract Four custom Axiom genotyping arrays were designed for a genome-wide association (GWA) study of 100,000 participants from the Kaiser Permanente Research Program on Genes, Environment and Health. The array optimized for individuals of European race/ethnicity was previously described. Here we detail the development of three additional microarrays optimized for individuals of East Asian, African American, and Latino race/ethnicity. For these arrays, we decreased redundancy of high-performing SNPs to increase SNP capacity. The East A... Genomics journals http://www.medworm.com/rss/comments.php?id=5213286 Sun, 28 Aug 2011 04:00:00 +0100 5213286 http://www.medworm.com/index.php?rid=5213285&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21906669%26dopt%3DAbstract In conclusion, we provide an example of horizontal gene transfer of functionally related genes in a pathway to prokaryote from eukaryote. PMID: 21906669 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=5213285 Sun, 28 Aug 2011 04:00:00 +0100 5213285 http://www.medworm.com/index.php?rid=5213284&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21907276%26dopt%3DAbstract Authors: McCord RP, Zhou VW, Yuh T, Bulyk ML Abstract Identifying gene regulatory elements and their target genes in human cells remains a significant challenge. Despite increasing evidence of physical interactions between distant regulatory elements and gene promoters in mammalian cells, many studies consider only promoter-proximal regulatory regions. We identify putative cis-regulatory modules (CRMs) in human skeletal muscle differentiation by combining myogenic TF binding data before and after differentiation with histone modification data in myoblasts. CRMs that are distant (>20kb) from muscle gene promoters are common and are more likely than proximal promoter regions to show differentiation-specific changes in myogenic TF binding. We find that two of these distant CRMs, kn... Genomics journals http://www.medworm.com/rss/comments.php?id=5213284 Tue, 23 Aug 2011 04:00:00 +0100 5213284 http://www.medworm.com/index.php?rid=5146978&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21855625%26dopt%3DAbstract Authors: Williamson JF, McLure CA, Guymer RH, Baird PN, Millman J, Cantsilieris S, Dawkins RL Abstract Age-related macular degeneration (AMD) is the leading cause of blindness in developed countries. It has been proposed that the polymorphism encoding Y402H (T1277C) in the complement factor H gene (CFH) is one of the main determinants of disease. We genotyped the polymorphism at a number of loci in the region encompassing the Regulators of Complement Activation (RCA) on chromosome 1, including T1277C SNP, in 187 patients and 146 controls. Haplotypes have been classified as protective (P) or susceptible (S) with respect to AMD. This included the identification of an S haplotype with a T at 1277. The results show that no single locus should be assumed to be directly responsible for A... Genomics journals http://www.medworm.com/rss/comments.php?id=5146978 Mon, 08 Aug 2011 23:00:00 +0100 5146978 http://www.medworm.com/index.php?rid=5146979&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21851855%26dopt%3DAbstract Authors: Nishida H, Beppu T, Ueda K Abstract The anaerobic thermophilic bacterial genus Dictyoglomus is characterized by the ability to produce useful enzymes such as amylase, mannanase, and xylanase. Despite the significance, the phylogenetic position of Dictyoglomus has not yet been clarified, since it exhibits ambiguous phylogenetic positions in a single gene sequence comparison-based analysis. The number of substitutions at the diverging point of Dictyoglomus is insufficient to show the relationships in a single gene comparison-based analysis. Hence, we studied its evolutionary trait based on whole-genome comparison. Both gene content and orthologous protein sequence comparisons indicated that Dictyoglomus is most closely related to the phylum Thermotogae and it forms a monophy... Genomics journals http://www.medworm.com/rss/comments.php?id=5146979 Sat, 06 Aug 2011 23:00:00 +0100 5146979 http://www.medworm.com/index.php?rid=5132739&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21840390%26dopt%3DAbstract Authors: Xing XB, Li QR, Sun H, Fu X, Zhan F, Huang X, Li J, Chen CL, Shyr Y, Zeng R, Li YX, Xie L Identifying protein-coding genes in eukaryotic genomes remains a challenge in post-genome era due to the complex gene models. We applied a proteogenomics strategy to detect un-annotated protein-coding regions in mouse genome. High-accuracy tandem mass spectrometry (MS/MS) data from diverse mouse samples were generated by LTQ-Orbitrap mass spectrometer in house. Two searchable diagnostic proteomic datasets were constructed, one with all possible encoding exon junctions, and the other with all putative encoding exons, for the discovery of novel exon splicing events and novel uninterrupted protein-coding regions. Altogether 29,586 unique peptides were identified. Aligning backwards to the mo... Genomics journals http://www.medworm.com/rss/comments.php?id=5132739 Wed, 03 Aug 2011 23:00:00 +0100 5132739 http://www.medworm.com/index.php?rid=5132742&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21839161%26dopt%3DAbstract Authors: Xing Y, Zhao X, Cai L Knowledge of the detailed organization of nucleosomes across genomes and the mechanisms of nucleosome positioning is critical for the understanding of gene regulation and expression. In the present work, the bias of 4-mer frequency in nucleosome and linker sequences of the S. cerevisiae genome was analyzed statistically. A novel position-correlation scoring function algorithm based on the bias of 4-mer frequency in linker sequences was presented to distinguish nucleosome vs linker sequences. Five-fold cross-validation demonstrated that the algorithm achieved a good performance with mean area under the receiver operator characteristics curve of 0.981. Next, the algorithm was used to predict nucleosome occupancy throughout the S. cerevisiae genome and relat... Genomics journals http://www.medworm.com/rss/comments.php?id=5132742 Mon, 01 Aug 2011 23:00:00 +0100 5132742 http://www.medworm.com/index.php?rid=5132741&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21839162%26dopt%3DAbstract Authors: Torkamani A, Scott-Van Zeeland AA, Topol EJ, Schork NJ Advances in DNA sequencing technologies have made it possible to rapidly, accurately and affordably sequence entire individual human genomes. As impressive as this ability seems, however, it will not likely to amount to much if one cannot extract meaningful information from individual sequence data. Annotating variations within individual genomes and providing information about their biological or phenotypic impact will thus be crucially important in moving individual sequencing projects forward, especially in the context of the clinical use of sequence information. In this paper we consider the various ways in which one might annotate individual sequence variations and point out limitations in the available methods for do... Genomics journals http://www.medworm.com/rss/comments.php?id=5132741 Mon, 01 Aug 2011 23:00:00 +0100 5132741 http://www.medworm.com/index.php?rid=5132740&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21839163%26dopt%3DAbstract Authors: Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, Fan JB, Shen R We have developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of the human genome. The new high density BeadChip can assay over 480K CpG sites and analyze twelve samples in parallel. The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite sequencing data and input from DNA methylation experts. The well-characterized Infinium® Assay is used for analysis of CpG methylation using bisulfite-converted genomic DNA. We applied this technology to analy... Genomics journals http://www.medworm.com/rss/comments.php?id=5132740 Mon, 01 Aug 2011 23:00:00 +0100 5132740 http://www.medworm.com/index.php?rid=5132743&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21824513%26dopt%3DAbstract Authors: Stano M, Klucar L phiGENOME is a web-based genome browser generating dynamic and interactive graphical representation of phage genomes stored in the phiSITE, database of gene regulation in bacteriophages. phiGENOME is an integral part of the phiSITE web portal (http://www.phisite.org/phigenome) and it was optimised for visualisation of phage genomes with the emphasis on the gene regulatory elements. phiGENOME consists of three components: (i) genome map viewer built using Adobe Flash technology, providing dynamic and interactive graphical display of phage genomes; (ii) sequence browser based on precisely formatted HTML tags, providing detailed exploration of genome features on the sequence level and (iii) regulation illustrator, based on Scalable Vector Graphics (SVG) and desi... Genomics journals http://www.medworm.com/rss/comments.php?id=5132743 Fri, 29 Jul 2011 23:00:00 +0100 5132743 http://www.medworm.com/index.php?rid=5132744&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21821115%26dopt%3DAbstract Authors: Ogoshi K, Hashimoto SI, Nakatani Y, Qu W, Oshima K, Tokunaga K, Sugano S, Hattori M, Morishita S, Matsushima K Global changes in DNA methylation correlate with altered gene expression and genomic instability in cancer. We have developed a methylation-specific digital sequencing (MSDS) method that can assess DNA methylation on a genomic scale. MSDS is a simple, low-cost method that combines the use of methylation-sensitive restriction enzymes with second generation sequencing technology. DNA methylation in two colon cancer cell lines, HT29 and HCT116, was measured using MSDS. When methylation levels were compared between the two cell lines, many differentially methylated regions (DMRs) were identified in CpG island shore regions (located within 2kb of a CpG island), gene body r... Genomics journals http://www.medworm.com/rss/comments.php?id=5132744 Thu, 28 Jul 2011 23:00:00 +0100 5132744 http://www.medworm.com/index.php?rid=5132746&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21803148%26dopt%3DAbstract In this study, stop gain variants were either well expressed in all individuals or were never expressed. Our finding that stop gain variants were generally expressed only when they had an alternate function suggests that most naturally occurring stop gain variants in protein-coding genes are either not transcribed or have their transcripts destroyed. PMID: 21803148 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=5132746 Thu, 21 Jul 2011 23:00:00 +0100 5132746 http://www.medworm.com/index.php?rid=5132745&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21803149%26dopt%3DAbstract In this study, we developed an RE analysis tool, called REMiner, for a chromosome-wide investigation into the occurrence of individual REs and arrangement of clusters of REs, and REMiner's functional features were examined using the human chromosome Y. The algorithm implemented by REMiner focused on unbiased mining of REs in large chromosomes and data interface within a viewer. The data from the chromosome demonstrated that REMiner is an efficient tool in regard to its capacity for a large query size and the availability of a high-resolution viewer, featuring instant retrieval of alignment data and control of magnification and identity ratio. The chromosome-wide survey identified a diverse population of ordered RE arrangements, which may participate in the genome biology. PMID: 2180314... Genomics journals http://www.medworm.com/rss/comments.php?id=5132745 Thu, 21 Jul 2011 23:00:00 +0100 5132745 http://www.medworm.com/index.php?rid=5086084&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21763417%26dopt%3DAbstract In this study, we developed a machine learning approach to predict cancer-causing missense variants. We present a Support Vector Machine (SVM) classifier trained on a set of 3183 cancer-causing variants and an equal number of neutral polymorphisms. The method achieve 93% overall accuracy, a correlation coefficient of 0.86, and area under ROC curve of 0.98. When compared with other previously developed algorithms such as SIFT and CHASM our method results in higher prediction accuracy and correlation coefficient in identifying cancer-causing variants. PMID: 21763417 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=5086084 Wed, 06 Jul 2011 23:00:00 +0100 5086084 http://www.medworm.com/index.php?rid=5086085&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21763416%26dopt%3DAbstract Authors: Castagné R, Zeller T, Rotival M, Szymczak S, Truong V, Schillert A, Trégouët DA, Münzel T, Ziegler A, Cambien F, Blankenberg S, Tiret L In humans, the fraction of X-linked genes with higher expression in females has been estimated to be 5% from microarray studies, a proportion lower than the 25% of genes thought to escape X inactivation. We analyzed 715 X-linked transcripts in circulating monocytes from 1,467 subjects and found an excess of female-biased transcripts on the X compared to autosomes (9.4% vs 5.5%, p<2×10(-5)). Among the genes not previously known to escape inactivation, the most significant one was EFHC2 whose 20% of variability was explained by sex. We also investigated cis expression quantitative trait loci (eQTLs) by analyzing 15,703 X-linked SNPs. The... Genomics journals http://www.medworm.com/rss/comments.php?id=5086085 Tue, 05 Jul 2011 23:00:00 +0100 5086085 http://www.medworm.com/index.php?rid=5037238&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21756994%26dopt%3DAbstract Authors: Ogilvie V, Passmore M, Hyndman L, Jones L, Stevenson B, Wilson A, Davidson H, Kitchen RR, Gray RD, Shah P, Alton EW, Davies JC, Porteous DJ, Boyd AC Respiratory epithelium is the target of therapies, such as gene therapy, for cystic fibrosis (CF) lung disease. To determine the usefulness of the nasal epithelium as a pre-screen for lung-directed therapies, we profiled gene expression in CF and non-CF nasal and bronchial epithelium samples using Illumina HumanRef-8 Expression BeadChips. 863 genes were differentially expressed between CF and non-CF bronchial epithelium but only 15 were differentially expressed between CF and non-CF nasal epithelium (1.5-fold, P≤0.05). The most enriched pathway in CF bronchial epithelium was inflammatory response, whereas in CF nasal epithelium ... Genomics journals http://www.medworm.com/rss/comments.php?id=5037238 Fri, 01 Jul 2011 23:00:00 +0100 5037238 http://www.medworm.com/index.php?rid=5037239&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21741470%26dopt%3DAbstract Authors: Tan YD Receiver operating characteristic (ROC) has been widely used to evaluate statistical methods, but a fatal problem is that ROC cannot evaluate estimation of the false discovery rate (FDR) of a statistical method and hence the area under the curve as a criterion cannot tell us if a statistical method is conservative. To address this issue, we propose an alternative criterion, work efficiency. Work efficiency is defined as the product of the power and degree of conservativeness of a statistical method. We conducted large-scale simulation comparisons among the optimizing discovery procedure (ODP), the Bonferroni (B-) procedure, Local FDR (Localfdr), ranking analysis of the F-statistics (RAF), the Benjamini-Hochberg (BH-) procedure, and significance analysis of microarray da... Genomics journals http://www.medworm.com/rss/comments.php?id=5037239 Wed, 29 Jun 2011 23:00:00 +0100 5037239 http://www.medworm.com/index.php?rid=5037241&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21722724%26dopt%3DAbstract Authors: Kravatskaya GI, Kravatsky YV, Chechetkin VR, Tumanyan VG We analyzed the periodic patterns in E. coli promoters and compared the distributions of the corresponding patterns in promoters and in the complete genome to elucidate their function. Except the three-base periodicity, coincident with that in the coding regions and growing stronger in the region downstream from the transcriptions start (TS), all other salient periodicities are peaked upstream of TS. We found that helical periodicities with the lengths about B-helix pitch ~10.2-10.5bp and A-helix pitch ~10.8-11.1bp coexist in the genomic sequences. We mapped the distributions of stretches with A-, B-, and Z-like DNA periodicities onto E. coli genome. All three periodicities tend to concentrate within non-coding regions w... Genomics journals http://www.medworm.com/rss/comments.php?id=5037241 Tue, 21 Jun 2011 23:00:00 +0100 5037241 http://www.medworm.com/index.php?rid=5037240&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21722725%26dopt%3DAbstract Authors: Pan A, Chanda I, Chakrabarti J The genome/proteome composition of Bdellovibrio bacteriovorus, the predatory microorganism that preys on other Gram-negative bacteria, has been analyzed. The study elucidates that translational selection plays a major role in genome compositional variation with higher intensity compared to other deltaproteobacteria. Other sources of variations having relatively minor contributions are local GC-bias, horizontal gene transfer and strand-specific mutation bias. The study identifies a group of AT-rich genes with distinct codon composition that is presumably acquired by Bdellovibrio recently from Gram-negative prey-bacteria other than deltaproteobacteria. The proteome composition of this species is influenced by various physico-chemical factors, viz, ... Genomics journals http://www.medworm.com/rss/comments.php?id=5037240 Tue, 21 Jun 2011 23:00:00 +0100 5037240 http://www.medworm.com/index.php?rid=4993244&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21704150%26dopt%3DAbstract This study provides evidence that SNPs in miRNA-binding sites may play an important role in increasing risk of cancer. The results also paves way for future studies to validate these results in other well-characterized populations as well as to explore the biological significance of these particular SNPs. PMID: 21704150 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=4993244 Thu, 16 Jun 2011 23:00:00 +0100 4993244 http://www.medworm.com/index.php?rid=4993245&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21693181%26dopt%3DAbstract In this study, we have developed a directed-sequencing strategy to sequence three sea bass chromosomes and compared results with other teleosts. Three BAC DNA pools were created from sea bass BAC clones that mapped to stickleback chromosomes/groups V, XVII and XXI. The pools were sequenced to 17-39x coverage by pyrosequencing. Data assembly was supported by Sanger reads and mate pair data and resulted in superscaffolds of 13.2Mb, 17.5Mb and 13.7Mb respectively. Annotation features of the superscaffolds include 1477 genes. We analyzed size change of exon, intron and intergenic sequence between teleost species and deduced a simple model for the evolution of genome composition in teleost lineage. Combination of second generation sequencing technologies, Sanger sequencing and genome partitioni... Genomics journals http://www.medworm.com/rss/comments.php?id=4993245 Mon, 13 Jun 2011 23:00:00 +0100 4993245 http://www.medworm.com/index.php?rid=4993248&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21683133%26dopt%3DAbstract Authors: Petronella N, Drouin G In humans, the growth hormone/chorionic somatomammotropin gene family is composed of five highly similar genes. We characterized the gene conversions that occurred between the growth hormone genes of 11 primate species. We detected 48 conversions using GENECONV and others were only detected using phylogenetic analyses. Gene conversions were detected in all species analyzed, their average size (±standard deviation) is 197.8±230.4 nucleotides, the size of the conversions is correlated with sequence similarity and converted regions are significantly more GC-rich than non-converted regions. Gene conversions have a stronger homogenizing effect in Hominidae genes than in other primate species. They are also less frequent in conserved gene regions and towards... Genomics journals http://www.medworm.com/rss/comments.php?id=4993248 Sat, 11 Jun 2011 23:00:00 +0100 4993248 http://www.medworm.com/index.php?rid=4993247&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21683780%26dopt%3DAbstract In this study, we isolated promoter CGIs susceptible and resistant to aberrant methylation induction during prostate and breast carcinogenesis. The effect of genome architecture was more evident for promoter CGIs susceptible in both of the two tissues than for promoter CGIs susceptible only in one tissue. Multivariate analysis of promoter CGIs with tissue-nonspecific susceptibility showed that genome architecture, namely a remote location from SINE (OR=5.98; 95% CI=2.33-15.34) and from LINE (OR=2.08; 95% CI=1.03-4.21), was associated with increased susceptibility, independent of epigenetic factors such as the presence of RNA polymerase II (OR=0.09; 95% CI=0.02-0.48) and H3K27me3 (OR=3.28; 95% CI=1.17-9.21). These results showed that methylation susceptibility of promoter CGIs is determined... Genomics journals http://www.medworm.com/rss/comments.php?id=4993247 Sat, 11 Jun 2011 23:00:00 +0100 4993247 http://www.medworm.com/index.php?rid=4993246&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21684327%26dopt%3DAbstract This study provided the data for fine resolution sequence analyses that would yield insight into the molecular mechanisms of notothenioid AFGP gene family evolution driven by Southern Ocean glaciation. PMID: 21684327 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=4993246 Sat, 11 Jun 2011 23:00:00 +0100 4993246 http://www.medworm.com/index.php?rid=4943469&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21672623%26dopt%3DAbstract Authors: Boimel PJ, Cruz C, Segall JE Microarray profiling in breast cancer patients has identified genes correlated with prognosis whose functions are unknown. The purpose of this study was to develop an in vivo assay for functionally screening regulators of tumor progression using a mouse model. Transductant shRNA cell lines were made in the MDA-MB-231 breast cancer line. A pooled population of 25 transductants was injected into the mammary fat pads and tail veins of mice to evaluate tumor growth, and experimental metastasis. The proportions of transductants were evaluated in the tumor and metastases using barcodes specific to each shRNA transductant. We characterized the homeobox 2 transcription factor as a negative regulator, decreasing tumor growth in MDA-MB-231, T47D, and MTLn3 m... Genomics journals http://www.medworm.com/rss/comments.php?id=4943469 Fri, 10 Jun 2011 23:00:00 +0100 4943469 http://www.medworm.com/index.php?rid=4943470&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21672622%26dopt%3DAbstract Authors: Machado JA, Costa AC, Quelhas MD This paper studies the human DNA in the perspective of signal processing. Six wavelets are tested for analyzing the information content of the human DNA. By adopting real Shannon wavelet several fundamental properties of the code are revealed. A quantitative comparison of the chromosomes and visualization through multidimensional and dendograms is developed. PMID: 21672622 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=4943470 Sun, 05 Jun 2011 23:00:00 +0100 4943470 http://www.medworm.com/index.php?rid=4943471&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21651976%26dopt%3DAbstract Authors: Kong Y Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples. Based on a modified Myers's bit-vector dynamic programming algorithm, Btrim can handle indels in adapters and barcodes. It removes low quality regions and trims off adapters at both or either end of the reads. A typical trimming of 30M reads with two sets of adapter pairs can be done in about a minute with a small memory footprint. Btrim is a versatile stand-alone tool that can be used as the first step in virtually all next-generation sequence analysis pipelines. The program is available at http://graphics.med.yale.edu/trim/. PMI... Genomics journals http://www.medworm.com/rss/comments.php?id=4943471 Sun, 29 May 2011 23:00:00 +0100 4943471 http://www.medworm.com/index.php?rid=4943473&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21640814%26dopt%3DAbstract Authors: Heng HH, Liu G, Stevens JB, Bremer SW, Ye KJ, Abdallah BY, Horne SD, Ye CJ While our understanding of gene-based biology has greatly improved, it is clear that the function of the genome and most diseases cannot be fully explained by genes and other regulatory elements. Genes and the genome represent distinct levels of genetic organization with their own coding systems; Genes code parts like protein and RNA, but the genome codes the structure of genetic networks, which are defined by the whole set of genes, chromosomes and their topological interactions within a cell. Accordingly, the genetic code of DNA offers limited understanding of genome functions. In this perspective, we introduce the genome theory which calls for the departure of gene-centric genomic research. To make t... Genomics journals http://www.medworm.com/rss/comments.php?id=4943473 Thu, 26 May 2011 23:00:00 +0100 4943473 http://www.medworm.com/index.php?rid=4943472&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21640815%26dopt%3DAbstract Authors: de Souza Gomes M, Muniyappa MK, Carvalho SG, Guerra-Sá R, Spillane C Mature microRNAs (miRNAs) are small, non-coding regulatory RNAs which can elicit post-transcriptional repression of mRNA levels of target genes. Here, we report the identification of 67 mature and 42 precursor miRNAs in the Schistosoma mansoni parasite. The evolutionarily conserved S. mansoni miRNAs consisted of 26 precursor miRNAs and 35 mature miRNAs, while we identified 16 precursor miRNAs and 32 mature miRNAs that displayed no conservation. These S. mansoni miRNAs are located on seven autosomal chromosomes and a sex (W) chromosome. miRNA expansion through gene duplication was suggested for at least two miRNA families miR-71 and mir-2. miRNA target finding analysis identified 389 predicted mRNA targets fo... Genomics journals http://www.medworm.com/rss/comments.php?id=4943472 Wed, 25 May 2011 23:00:00 +0100 4943472 http://www.medworm.com/index.php?rid=4894078&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21624457%26dopt%3DAbstract Authors: Ritz K, van Schaik BD, Jakobs ME, Aronica E, Tijssen MA, van Kampen AH, Baas F Studying transcriptomes by ultra deep sequencing provides an in-depth picture of transcriptional regulation and it facilitates the detection of rare transcriptional events. Using ultra deep sequencing of amplicons we identified known isoforms and also various new low frequency variants. Most of these variants likely involve the splicing machinery except for two events that we named variations affecting multiple exons, which are mainly deletions affecting parts of adjacent exons and intra-exonic deletions. Both events involve short identical sequences of 1 to 8 nucleotides at the junction and canonical splice sites are missing. They were identified in different genes and species at very low frequenci... Genomics journals http://www.medworm.com/rss/comments.php?id=4894078 Sun, 22 May 2011 23:00:00 +0100 4894078 http://www.medworm.com/index.php?rid=4894079&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21621601%26dopt%3DAbstract Authors: Carr IM, Morgan JE, Diggle CP, Sheridan E, Markham AF, Logan CV, Inglehearn CF, Taylor GR, Bonthron DT Current methods for sequencing clonal populations of DNA molecules yield several gigabases of data per day, typically comprising reads of <100 nt. Such datasets permit widespread genome resequencing and transcriptome analysis or other quantitative tasks. However, this huge capacity can also be harnessed for the resequencing of smaller (gene-sized) target regions, through the simultaneous parallel analysis of multiple subjects, using sample "tagging" or "indexing". These methods promise to have a huge impact on diagnostic mutation analysis and candidate gene testing. Here we describe a software package developed for such studies, offering the ability to resolve pooled sampl... Genomics journals http://www.medworm.com/rss/comments.php?id=4894079 Wed, 18 May 2011 23:00:00 +0100 4894079 http://www.medworm.com/index.php?rid=4894080&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21620950%26dopt%3DAbstract In this study, we determine that acquisition of DNA methylation at the paternal allele of the Gtl2-DMR is initiated after the blastocyst stage and completed by embryonic day 6.5, and that Gtl2 is monoallelically expressed from the maternal allele as early as the blastocyst. Therefore, DNA methylation at the Gtl2-DMR is not a prerequisite for the imprinted expression of Gtl2, which may be involved in the control of proliferation and differentiation of cells during early gestation. We also reveal that a subregion of the IG-DMR exhibits tissue-specific differences in allelic methylation patterns. These results add to the growing body of knowledge elucidating the mechanism whereby parent-of-origin-dependent DNA methylation at the IG-DMR leads to the imprinted expression of the Dlk1-Dio3 cluste... Genomics journals http://www.medworm.com/rss/comments.php?id=4894080 Tue, 17 May 2011 23:00:00 +0100 4894080 http://www.medworm.com/index.php?rid=4894082&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21616136%26dopt%3DAbstract Authors: Bai Y, Meng Y, Huang D, Qi Y, Chen M A substantial number of transcription factor families have been investigated from all kingdoms of life, but a particular class of plant-specific TIFY transcription factors, characterized by a highly conserved TIFY domain, lacks a systemic analysis of its origin and evolutionary relationships among different plant species. After exhaustive genome-wide searches against 14 genomes, TIFY transcription factors were identified and classified into four subfamilies TIFY, PPD, JAZ and ZML according to their different domain architectures. Results show that the TIFY domain of the ZML subfamily possesses a core "TLS[F/Y]XG" motif rather than the "TIFYXG" motif that is dominant in the other three subfamilies. A comprehensive survey of the TIFY family a... Genomics journals http://www.medworm.com/rss/comments.php?id=4894082 Sat, 14 May 2011 23:00:00 +0100 4894082 http://www.medworm.com/index.php?rid=4894081&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21620949%26dopt%3DAbstract Authors: Liu T, Thalamuthu A, Liu JJ, Chen C, Wang Z, Wu R We propose a statistical model for dissecting a multilocus genotypic value into its main (additive and dominant) effects and epistatic effects between different loci in a case-control association study. The model can discern four different kinds of epistasis, additive×additive, additive×dominant, dominant×additive, and dominant×dominant interactions. To test each kind of epistasis, a χ(2) test statistic was computed for a two by two contingency table derived from combined genotypes in both case and control groups. We derived an analytical approach for estimating the asymptotic distribution of the χ(2) test statistic for epistatic tests under the null hypothesis, with the result being consistent with that from Monte Carlo ... Genomics journals http://www.medworm.com/rss/comments.php?id=4894081 Sat, 14 May 2011 23:00:00 +0100 4894081 http://www.medworm.com/index.php?rid=4848975&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21586321%26dopt%3DAbstract Authors: Wang Y, Chen X, Jiang W, Li L, Li W, Yang L, Liao M, Lian B, Lv Y, Wang S, Wang S, Li X MicroRNAs (miRNAs) are non-coding RNAs that play important roles in post-transcriptional regulation. Identification of miRNAs is crucial to understanding their biological mechanism. Recently, machine-learning approaches have been employed to predict miRNA precursors (pre-miRNAs). However, features used are divergent and consequently induce different performance. Thus, feature selection is critical for pre-miRNA prediction. We generated an optimized feature subset including 13 features using a hybrid of genetic algorithm and support vector machine (GA-SVM). Based on SVM, the classification performance of the optimized feature subset is much higher than that of the two feature sets used in mi... Genomics journals http://www.medworm.com/rss/comments.php?id=4848975 Fri, 13 May 2011 23:00:00 +0100 4848975 http://www.medworm.com/index.php?rid=4848977&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21569836%26dopt%3DAbstract Authors: Kalendar R, Lee D, Schulman AH The polymerase chain reaction is fundamental to molecular biology and is the most important practical molecular technique for the research laboratory. We have developed and tested efficient tools for PCR primer and probe design, which also predict oligonucleotide properties based on experimental studies of PCR efficiency. The tools provide comprehensive facilities for designing primers for most PCR applications and their combinations, including standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, as well as a programme to design oligonucleotide sets for long sequence assembly by ligase chain reaction. The in silico PCR primer or probe search ... Genomics journals http://www.medworm.com/rss/comments.php?id=4848977 Mon, 02 May 2011 23:00:00 +0100 4848977 http://www.medworm.com/index.php?rid=4848984&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21565264%26dopt%3DAbstract We describe the development of a next-generation microarray based on the new highly-efficient Affymetrix Axiom genotyping technology that we are using to genotype individuals of European ancestry from the Kaiser Permanente Research Program on Genes, Environment and Health (RPGEH). The array contains 674,517 SNPs, and provides excellent genome-wide as well as gene-based and candidate-SNP coverage. Coverage was calculated using a novel approach based on imputation and cross validation. Preliminary results for the first 80,301 saliva-derived DNA samples from the RPGEH demonstrate very high quality genotypes, with sample success rates above 94% and over 98% of successful samples having SNP call rates exceeding 98%. At steady state, we have produced 462 million genotypes per week for each Axiom... Genomics journals http://www.medworm.com/rss/comments.php?id=4848984 Fri, 29 Apr 2011 23:00:00 +0100 4848984 http://www.medworm.com/index.php?rid=4848983&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21565265%26dopt%3DAbstract Authors: Wang L, Jia P, Wolfinger RD, Chen X, Zhao Z Recent studies have demonstrated that gene set analysis, which tests disease association with genetic variants in a group of functionally related genes, is a promising approach for analyzing and interpreting genome-wide association studies (GWAS) data. These approaches aim to increase power by combining association signals from multiple genes in the same gene set. In addition, gene set analysis can also shed more light on the biological processes underlying complex diseases. However, current approaches for gene set analysis are still in an early stage of development in that analysis results are often prone to sources of bias, including gene set size and gene length, linkage disequilibrium patterns and the presence of overlapping gene... Genomics journals http://www.medworm.com/rss/comments.php?id=4848983 Fri, 29 Apr 2011 23:00:00 +0100 4848983 http://www.medworm.com/index.php?rid=4848976&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21569837%26dopt%3DAbstract Authors: Yao D, Zhang X, Zhao X, Liu C, Wang C, Zhang Z, Zhang C, Wei Q, Wang Q, Yan H, Li F, Su Z High salinity is one of the main factors limiting cotton growth and productivity. The genes that regulate salt stress in TM-1 upland cotton were monitored using microarray and real-time PCR (RT-PCR) with samples taken from roots. Microarray analysis showed that 1503 probe sets were up-regulated and 1490 probe sets were down-regulated in plants exposed for 3h to 100mM NaCl, and RT-PCR analysis validated 42 relevant/related genes. The distribution of enriched gene ontology terms showed such important processes as the response to water stress and pathways of hormone metabolism and signal transduction were induced by the NaCl treatment. Some key regulatory gene families involved in abiotic an... Genomics journals http://www.medworm.com/rss/comments.php?id=4848976 Fri, 29 Apr 2011 23:00:00 +0100 4848976 http://www.medworm.com/index.php?rid=4793923&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21524701%26dopt%3DAbstract Authors: Mondal K, Shetty AC, Patel V, Cutler DJ, Zwick ME We used a RainDance Technologies (RDT) expanded content library to enrich the human X chromosome exome (2.5Mb) from 26 male samples followed by Illumina sequencing. Our multiplex primer library covered 98.05% of the human X chromosome exome in a single tube with 11,845 different PCR amplicons. Illumina sequencing of 24 male samples showed coverage for 97% of the targeted sequences. Sequence from 2 HapMap samples confirmed missing data rates of 2-3% at sites successfully typed by the HapMap project, with an accuracy of at least ~99.5% as compared to reported HapMap genotypes. Our demonstration that a RDT expanded content library can efficiently enrich and enable the routine sequencing of the human X chromosome exome suggests a w... Genomics journals http://www.medworm.com/rss/comments.php?id=4793923 Fri, 15 Apr 2011 23:00:00 +0100 4793923 http://www.medworm.com/index.php?rid=4794053&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21515357%26dopt%3DAbstract Authors: Xiao Y, Xu C, Ping Y, Guan J, Fan H, Li Y, Li X Expression data can reveal subtle transcriptional changes that mediate the clinical phenotype of the disease resulting from interaction between genetic and environmental factors, which offers us a new perspective to prioritize candidate genes. Here, we proposed a novel differential expression pattern (DEP)-based approach integrating numerous disease-specific expression data sets for prioritizing candidate genes. Using breast cancer as a case study, we validated the efficiency of our approach through integrating 12 breast cancer-related expression data sets based on the leave-one-out cross-validation. Particularly, prioritization based on subtype-specific expression data sets could generate significantly higher performance. The pe... Genomics journals http://www.medworm.com/rss/comments.php?id=4794053 Thu, 14 Apr 2011 23:00:00 +0100 4794053 http://www.medworm.com/index.php?rid=4794049&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21515358%26dopt%3DAbstract We describe a novel approach to characterize bacterial composition using deep sequencing of 16S rRNA gene. Our method defines operational taxonomic units based on phylogenetic tree reconstruction and dynamic clustering of sequences using solely sequencing data. These OTUs can be used to identify differences in bacteria abundance between environments. This approach can perform better than previous phylogenetic methods and will significantly improve our understanding of the microfloral role on human diseases by providing a comprehensive analysis of the microbial composition from various bacterial communities. PMID: 21515358 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=4794049 Thu, 14 Apr 2011 23:00:00 +0100 4794049 http://www.medworm.com/index.php?rid=4794018&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21515359%26dopt%3DAbstract Authors: Fox-Walsh K, Davis-Turak J, Zhou Y, Li H, Fu XD RNA-seq technologies are now replacing microarrays for profiling gene expression. Here we describe a robust RNA-seq strategy for multiplex analysis of RNA samples based on deep sequencing. First, an oligo-dT linked to an adaptor sequence is used to prime cDNA synthesis. Upon solid phase selection, second strand synthesis is initiated using a random primer linked to another adaptor sequence. Finally, the library is released from the beads and amplified using a bar-coded primer together with a common primer. This method, referred to as Multiplex Analysis of PolyA-linked Sequences (MAPS), preserves strand information, permits rapid identification of potentially new polyadenylation sites, and profiles gene expression in a highly cost... Genomics journals http://www.medworm.com/rss/comments.php?id=4794018 Thu, 14 Apr 2011 23:00:00 +0100 4794018 http://www.medworm.com/index.php?rid=4742206&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21473906%26dopt%3DAbstract Authors: Wenping H, Yuan Z, Jie S, Lijun Z, Zhezhi W Medicinal Salvia miltiorrhiza is a Chinese herb commonly used for treating cardiovascular diseases and neuroasthenic insomnia. However, little is known at the genetics level about how its compounds are synthesized in that plant. Here, we obtained 56,774 unigenes (average length=467 bases) in its transcriptome by performing Solexa deep sequencing over the entire growing cycle. Unigenes (34,340; 60.49%) were annotated and 2545 unigenes were assigned to specific pathways. Unigenes (1539) were identified as part of five major, secondary-metabolite pathways, covering almost all nodes in the phenylpropanoid and terpenoid pathways. Using Blast search against AGRIS, 1341 unigenes were found homologous to 686 Arabidopsis transcription factor ... Genomics journals http://www.medworm.com/rss/comments.php?id=4742206 Mon, 04 Apr 2011 23:00:00 +0100 4742206 http://www.medworm.com/index.php?rid=4742205&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21473907%26dopt%3DAbstract Authors: Yang X, Zhang H, Li L MicroRNAs (miRNAs) regulate gene expression at the post-transcriptional level in eukaryotes. Exclusive focus on mature miRNA in most expression profiling efforts has prevented effective measurement of the expression of individual miRNA (MIR) genes. Using three sequenced small RNA libraries, we adapted miRDeep, which employs a probabilistic model of miRNA biogenesis, to analyze the miRNA transcriptome in Arabidopsis. We determined that less than 40% annotated MIR genes are expressed in shoot, root or inflorescence. We found that within paralogous families the expression pattern of individual genes correlates with the phylogenetic distance. Combining novel candidates identified in this study, we deduced the maximal number of expressed MIR genes. We further ... Genomics journals http://www.medworm.com/rss/comments.php?id=4742205 Sun, 03 Apr 2011 23:00:00 +0100 4742205 http://www.medworm.com/index.php?rid=4684854&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21466845%26dopt%3DAbstract Authors: Tombácz D, Tóth JS, Boldogkői Z A real-time RT-PCR technique was applied to evaluate the impact of deletion of the virion host shut-off (VHS) gene on the kinetics of pseudorabies virus gene expression. Selective suppression of early gene transcripts by the viral ribonuclease occurs after 4 hours of infection; while VHS protein appears to act non-selectively on the transcripts belonging in different kinetic classes in the first 2 hours of infection. VHS protein disrupts the close correlation between the transcription kinetics of the immediate-early 180 protein and the other pseudorabies virus transcripts. The typical pattern of early gene expression was found to be altered in the VHS gene-deleted virus in that the production rates of their transcripts did not decline from 4 ... Genomics journals http://www.medworm.com/rss/comments.php?id=4684854 Fri, 01 Apr 2011 23:00:00 +0100 4684854 http://www.medworm.com/index.php?rid=4684855&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21457775%26dopt%3DAbstract Authors: Perina D, Korolija M, Roller M, Harcet M, Jeličić B, Mikoč A, Cetković H Equimolecular presence of ribosomal proteins (RPs) in the cell is needed for ribosome assembly and is achieved by synchronized expression of ribosomal protein genes (RPGs) with promoters of similar strengths. Over-represented motifs of RPG promoter regions are identified as targets for specific transcription factors. Unlike RPs, those motifs are not conserved between mammals, drosophila and yeast. We analyzed RPGs proximal promoter regions of three basal metazoans with sequenced genomes: sponge, cnidarian and placozoan and found common features, such as 5'-terminal oligopyrimidine tracts and TATA-boxes. Furthermore, we identified over-represented motifs, some of which displayed the highest similarity ... Genomics journals http://www.medworm.com/rss/comments.php?id=4684855 Mon, 28 Mar 2011 23:00:00 +0100 4684855 http://www.medworm.com/index.php?rid=4684856&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21447378%26dopt%3DAbstract Authors: Papazisi L, Rasko DA, Ratnayake S, Bock GR, Remortel BG, Appalla L, Liu J, Dracheva T, Braisted JC, Shallom S, Jarrahi B, Snesrud E, Ahn S, Sun Q, Rilstone J, Okstad OA, Kolstø AB, Fleischmann RD, Peterson SN Here we report the use of a multi-genome DNA microarray to investigate the genome diversity of Bacillus cereus group members and elucidate the events associated with the emergence of B. anthracis the causative agent of anthrax-a lethal zoonotic disease. We initially performed directed genome sequencing of seven diverse B. cereus strains to identify novel sequences encoded in those genomes. The novel genes identified, combined with those publicly available, allowed the design of a "species" DNA microarray. Comparative genomic hybridization analyses of 41 strains indicates... Genomics journals http://www.medworm.com/rss/comments.php?id=4684856 Sat, 26 Mar 2011 00:00:00 +0100 4684856 http://www.medworm.com/index.php?rid=4684857&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21439368%26dopt%3DAbstract Authors: Conde L, Bracci PM, Halperin E, Skibola CF Non-Hodgkin lymphoma (NHL) is a hematological malignancy of the immune system, and, as with autoimmune and inflammatory diseases (ADs), is influenced by genetic variation in the major histocompatibility complex (MHC). Persons with a history of specific ADs also have increased risk of NHL. As the coexistence of ADs and NHL could be caused by factors common to both diseases, here we examined whether some of the associated genetic signals are shared. Overlapping risk loci for NHL subytpes and several ADs were explored using data from genome-wide association studies. Several common genomic regions and susceptibility loci were identified, suggesting a potential shared genetic background. Two independent MHC regions showed the main overlap,... Genomics journals http://www.medworm.com/rss/comments.php?id=4684857 Wed, 23 Mar 2011 00:00:00 +0100 4684857 http://www.medworm.com/index.php?rid=4627615&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21397683%26dopt%3DAbstract Authors: Pan XY, Tian Y, Huang Y, Shen HB Epistatic miniarray profiling (E-MAP) is a powerful tool for analyzing gene functions and their biological relevance. However, E-MAP data suffers from large proportion of missing values, which often results in misleading and biased analysis results. It is urgent to develop effective missing value estimation methods for E-MAP. Although several independent algorithms can be applied to achieve this goal, their performance varies significantly on different datasets, indicating different algorithms having their own advantages and disadvantages. In this paper, we propose a novel ensemble approach EMDI based on the high-level diversity to impute missing values that consists of two global and four local base estimators. Experimental results on five E-M... Genomics journals http://www.medworm.com/rss/comments.php?id=4627615 Thu, 17 Mar 2011 00:00:00 +0100 4627615 http://www.medworm.com/index.php?rid=4627611&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21419843%26dopt%3DAbstract Authors: Lee E, Kim K, Park T Genome-wide gene expression and genotype data have been integratively analyzed in expression quantitative trait loci (eQTL) studies to elucidate the genetics of gene transcription. Most eQTL analyses have focused on identifying polymorphic genetic variants that influence the expression levels of individual genes, and such analyses may have limitations in explaining gene regulatory pathways that are likely to involve multiple genes and their genetic and/or non-genetic modulators. We have developed a novel two-step method for identifying potential genetic modulators of transcription processes for multiple genes in a biological pathway. We proposed a new weighted window-based peak identification algorithm to improve the detection of genetic modulators for ind... Genomics journals http://www.medworm.com/rss/comments.php?id=4627611 Wed, 16 Mar 2011 00:00:00 +0100 4627611 http://www.medworm.com/index.php?rid=4627613&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21419214%26dopt%3DAbstract Authors: Paik H, Lee E, Park I, Kim J, Lee D Phenotypes of diseases, including prognosis, are likely to have complex etiologies and be derived from interactive mechanisms, including genetic and protein interactions. Many computational methods have been used to predict survival outcomes without explicitly identifying interactive effects, such as the genetic basis for transcriptional variations. We have therefore proposed a classification method based on the interaction between genotype and transcriptional expression features (CORE-F). This method considers the overall 'genetic architecture', referring to genetically based transcriptional alterations that influence prognosis. In comparing the performance of CORE-F with the ensemble tree, the best-performing method predicting patient surv... Genomics journals http://www.medworm.com/rss/comments.php?id=4627613 Tue, 15 Mar 2011 00:00:00 +0100 4627613 http://www.medworm.com/index.php?rid=4627612&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21419215%26dopt%3DAbstract In this study, we used a marsupial-specific EST microarray to identify 47 up-regulated genes during mammary gland involution in the tammar wallaby (Macropus eugenii). These include the pro-apoptotic tumor necrosis factor receptor superfamily 21 (TNFRSF21) gene, whose expression in the mammary gland has not previously been reported. Genes encoding putative novel milk proteins which may protect the mammary gland from infection were also found to be up-regulated, such as amiloride binding protein 1 (ABP1), complement component 1QB (C1QB), complement component 4A (C4A) and colony stimulating factor 2 receptor β (CSF2Rβ). Our results show that the marsupial reproductive strategy was successfully exploited to identify genes and putative novel milk proteins implicated in mammary gland involutio... Genomics journals http://www.medworm.com/rss/comments.php?id=4627612 Tue, 15 Mar 2011 00:00:00 +0100 4627612 http://www.medworm.com/index.php?rid=4627614&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21402142%26dopt%3DAbstract Authors: Qi Y, Sun H, Sun Q, Pan L Microarrays allow researchers to examine the expression of thousands of genes simultaneously. However, identification of genes differentially expressed in microarray experiments is challenging. With an optimal test statistic, we rank genes and estimate a threshold above which genes are considered to be Differentially Expressed Genes(DE). This overcomes the embarrassing short- coming of many statistical methods to determine the cut-off values in ranking analysis. Experiments demonstrate that our method is good performance and avoids the problems with graphical examination and multiple hypotheses testing that affect alternative approaches. Comparing to those well known methods, our method is more sensitive to data sets with small differentially expresse... Genomics journals http://www.medworm.com/rss/comments.php?id=4627614 Fri, 11 Mar 2011 00:00:00 +0100 4627614 http://www.medworm.com/index.php?rid=4566386&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21377523%26dopt%3DAbstract Authors: Reshmi G, Chandra SS, Babu VJ, Babu PS, Santhi WS, Ramachandran S, Lakshmi S, Nair AS, Pillai MR Accurate identification of mature miRNAs is an important requirement for exploring the post-transcriptional regulatory mechanism of organisms. In this work we present a novel computational tool 'Mpred' which first identifies pre-miRNAs and then predicts its mature miRNAs. We first use our method to learn with high accuracy characteristic features of human miRNA precursors from miRbase registry and then apply to sequences from fragile site regions related to cervical cancer in search of novel miRNA genes. The study identified 13 putative miRNA's like sequences and most of them were not related to each other and does not share homology with annotated sequences. Finally, four of the t... Genomics journals http://www.medworm.com/rss/comments.php?id=4566386 Thu, 03 Mar 2011 00:00:00 +0100 4566386 http://www.medworm.com/index.php?rid=4566387&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21376111%26dopt%3DAbstract Authors: Lebron C, Pal P, Brait M, Dasgupta S, Guerrero-Preston R, Looijenga LH, Kowalski J, Netto G, Hoque MO Testicular germ cell tumors (TGCT) represent the most common malignancy among young males. To our knowledge no comprehensive Copy Number Variations (CNVs) studies of TGCT using high-resolution Single Nucleotide Polymorphism (SNP) array have been performed. By a Genome-wide analysis of CNV and loss of heterozygosity (LOH) in 25 primary seminomas, we confirmed several previously reported genomic alterations and discovered eight novel genomic alterations including amplifications and homozygous deletions. Moreover, a comparison of genomic alterations of early and late stage seminoma identified CNVs that correlate with progression, which included deletions in chromosome 4q, 5p, 9q,... Genomics journals http://www.medworm.com/rss/comments.php?id=4566387 Tue, 01 Mar 2011 00:00:00 +0100 4566387 http://www.medworm.com/index.php?rid=4566389&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21371550%26dopt%3DAbstract In this study, selenocystine, a nutritionally available selenoaminoacid, was identified for the first time as a novel agent with anti proliferative activity on human keloids. The 20μM concentration after 48 hours treatment used here was the most effective to reduce keloid fibroblasts growth. We analyzed the gene expression profile of selenocystine treatment response in keloid fibroblasts by the microarray system to characterize the effects of selenocystine on human keloids. The major alterations in keloid fibroblasts following selenocystine exposure included up-regulation of the genes encoding cell death and transcription factors. Prominent down-regulation of genes involved in development, cell adhesion and cytoskeleton, as well as extra cellular matrix genes, usually strongly up-regulate... Genomics journals http://www.medworm.com/rss/comments.php?id=4566389 Mon, 28 Feb 2011 00:00:00 +0100 4566389 http://www.medworm.com/index.php?rid=4566388&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21371551%26dopt%3DAbstract Authors: Baev V, Milev I, Naydenov M, Apostolova E, Minkov G, Minkov I, Yahubyan G Plant microRNAs (miRNAs) are single-stranded 20-22 nt small RNAs (sRNA) that are produced from their own genes. We have developed a de novo genome-wide approach for the computational identification of novel plant miRNAs based on the integration of the complete genome sequence with sRNA libraries. It comprises three modules - the CLUSTERING module identifies genomic regions that have two closely-located unidirectional sRNA clusters, the MIRPLAN module explores the secondary structure of the genomic regions, and the DUPLEX module predicts miRNA/miRNA* duplexes. We applied our approach to the Brachypodium genome and publicly available sRNA libraries and predicted 102 miRNAs. Our results extend the list of k... Genomics journals http://www.medworm.com/rss/comments.php?id=4566388 Mon, 28 Feb 2011 00:00:00 +0100 4566388 http://www.medworm.com/index.php?rid=4566390&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21352905%26dopt%3DAbstract Authors: Lin L, Tang H, Compton RO, Lemke C, Rainville LK, Wang X, Rong J, Rana MK, Paterson AH Genetic mapping studies have suggested that diploid cotton (Gossypium) might be an ancient polyploid. However, further evidence is lacking due to the complexity of the genome and the lack of sequence resources. Here, we used the grape (Vitis vinifera) genome as an out-group in two different approaches to further explore evidence regarding ancient genome duplication (WGD) event(s) in the diploid Gossypium lineage and its (their) effects: a genome-level alignment analysis and a local-level sequence component analysis. Both studies suggest that at least one round of genome duplication occurred in the Gossypium lineage. Also, gene densities in corresponding regions from Gossypium raimondii, V. v... Genomics journals http://www.medworm.com/rss/comments.php?id=4566390 Tue, 22 Feb 2011 00:00:00 +0100 4566390 http://www.medworm.com/index.php?rid=4511636&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21338665%26dopt%3DAbstract Authors: Williamson JF, Steele EJ, Lester S, Kalai O, Millman JA, Wolrige L, Bayard D, Dawkins RL We have identified numerous Ancestral Haplotypes encoding a 14 Mb region of Bota C!9. Three are frequent in Simmental, Angus and Wagyu and have been conserved since common progenitor populations. Others are more relevant to the differences between these 3 breeds including fat content and distribution in muscle. SREBF1 and Growth Hormone, which have been implicated in the production of healthy beef, are included within these haplotypes. However, we conclude that alleles at these 2 loci are less important than other sequences within the haplotypes. Identification of breeds and hybrids is improved by using haplotypes rather than individual alleles. PMID: 21338665 [PubMed - as supplied by ... Genomics journals http://www.medworm.com/rss/comments.php?id=4511636 Fri, 18 Feb 2011 00:00:00 +0100 4511636 http://www.medworm.com/index.php?rid=4511638&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21333733%26dopt%3DAbstract Authors: Qin YF, Fang HM, Tian QN, Bao ZX, Lu P, Zhao JM, Mai J, Zhu ZY, Shu LL, Zhao L, Chen SJ, Liang F, Zhang YZ, Zhang ST Planarians exhibit an extraordinary ability to regenerate lost body parts which is attributed to an abundance of pluripotent somatic stem cells called neoblasts. In this article, we report a transcriptome sequence of a Planaria subspecies Dugesia japonica derived by high-throughput sequencing. In addition, we researched transcriptome changes during different periods of regeneration by using a tag-based digital gene expression (DGE) system. Consequently, 11,913,548 transcriptome sequencing reads were obtained. Finally, these reads were eventually assembled into 37,218 unique unigenes. These assembled unigenes were annotated with various methods. Transcriptome cha... Genomics journals http://www.medworm.com/rss/comments.php?id=4511638 Wed, 16 Feb 2011 00:00:00 +0100 4511638 http://www.medworm.com/index.php?rid=4511637&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21333734%26dopt%3DAbstract Authors: Qian J, Zhang Z, Liang J, Ge Q, Duan X, Ma F, Li F MicroRNA (miRNA) transcription is still not well understood nowadays. To increase the miRNA abundance, we stimulated miRNA transcription with CuSO(4) and knockdown Drosha enzyme using dsRNA in Drosophila S2 cells. The full length transcripts of bantam, miR-276a and miR-277, the 5'-end of miR-8, the 3'-end of miR-2b and miR-10 were obtained. We also conducted a series of miRNA promoter analysis to prove the reliability of RACE results. Luciferase-reporter assays proved that both bantam and miR-276a promoters successfully drove the expressions of downstream luciferase genes. The promoter activities were impaired by introducing one or multiple mutations at predicted transcription factor binding sites. Chromatin immunoprecipitatio... Genomics journals http://www.medworm.com/rss/comments.php?id=4511637 Wed, 16 Feb 2011 00:00:00 +0100 4511637 http://www.medworm.com/index.php?rid=4511639&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21324351%26dopt%3DAbstract Authors: Zhang SH, Wang L It has been reported that there is a majority triplet profile among genomes, which was considered as a reflection of general mechanisms of genome evolution (Albrecht-Buehler, 2007). However, there are actually, according to our further analysis and at least among prokaryotic genomes, two common triplet profiles: one is from low-GC content genomes; the other is from high-GC content genomes. Both common profiles would be direct reflections of GC content variations and strand symmetry of genomic sequences. PMID: 21324351 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=4511639 Sat, 12 Feb 2011 00:00:00 +0100 4511639 http://www.medworm.com/index.php?rid=4511641&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21316444%26dopt%3DAbstract In this study, we develop a general parametric AFT model for identifying survival trait loci, in which the flexible generalized F distribution, including many commonly used distributions as special cases, is specified as the baseline survival distribution. EM algorithm for maximum likelihood estimation of model parameters is given. Simulations are conducted to validate the flexibility and the utility of the proposed mapping procedure. In analyzing survival time following hyperoxic acute lung injury (HALI) of mice in an F(2) mating population, the generalized F distribution performed best among the six competing survival distributions and detected four QTLs controlling differential HALI survival. PMID: 21316444 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=4511641 Thu, 10 Feb 2011 00:00:00 +0100 4511641 http://www.medworm.com/index.php?rid=4511640&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21316445%26dopt%3DAbstract We describe here the use of one-step cloning for the fast and efficient generation of deletion vectors that are produced in a one-step reaction by inserting two PCR products into an organism-specific, generic acceptor system. This worked efficiently for all 16 tested constructs directed against genes in the amoeba Dictyostelium discoideum. Saving cost and time, the used protocol represents a significant advancement in the generation of such plasmids compared to the conventionally applied restriction enzyme/ligation approach. Using appropriate selection markers, similar systems could also be useful in other organisms, where genes can be knocked out by homologous recombination. PMID: 21316445 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=4511640 Thu, 10 Feb 2011 00:00:00 +0100 4511640 http://www.medworm.com/index.php?rid=4454000&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21295131%26dopt%3DAbstract Authors: Wang X, Laurie JD, Liu T, Wentz J, Liu XS The profiling of small RNAs by high throughput sequencing (smRNA-Seq) has revealed the complexity of the RNA world. Here, we describe a computational scheme for dissecting the plant smRNAome by integrating smRNA-Seq datasets in Arabidopsis thaliana. Our analytical approach first defines ab initio the genomic loci that produce smRNAs as basic units, then utilizes principal component analysis (PCA) to predict novel miRNAs. Secondary structure prediction of candidates' putative precursors discovered a group of long hairpin double-stranded RNAs (lh-dsRNAs) formed by inverted duplications of decayed coding genes. These gene remnants produce miRNA-like small RNAs which are predominantly 21-and 22-nt long, dependent of DCL1 but independent of... Genomics journals http://www.medworm.com/rss/comments.php?id=4454000 Tue, 01 Feb 2011 00:00:00 +0100 4454000 http://www.medworm.com/index.php?rid=4454001&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21281709%26dopt%3DAbstract Authors: Podder S, Ghosh TC Functional redundancy by gene duplication appears to be a common phenomenon in biological system and hence understanding its underlying mechanism deserves much attention. Here, we investigated the differences between functional compensation of monogenic and polygenic disease genes which are unexplored till date. We found that the competence of functional buffering varies in the order of non-disease genes>monogenic disease genes>polygenic disease genes. This fact has been explained by the sequence identity, expression profile similarity, interaction partners and cellular locations between duplicated pairs. Moreover, we observed an inverse relationship between backup capacity and the non-synonymous substitution rate of disease and non-disease genes while... Genomics journals http://www.medworm.com/rss/comments.php?id=4454001 Mon, 31 Jan 2011 00:00:00 +0100 4454001 http://www.medworm.com/index.php?rid=4454002&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21266193%26dopt%3DAbstract Authors: Shin SC, Lee KM, Kang YM, Kim K, Lim SA, Yang KH, Kim CS, Kim JY, Nam SY, Jin YW, Kim HS AKR/J mice carrying leukemia viral inserts develop thymic lymphoma. Recently, we demonstrated that the incidence of thymic lymphoma was decreased when these mice were raised in a low-dose-rate γ-irradiation facility. In contrast, mice irradiated at a high-dose rate developed severe thymic lymphoma and died much earlier. To understand the genetic changes occurred by low- versus high-dose-rate γ-irradiation whole genome microarray was performed. Both groups of mice demonstrated up-regulation of Ifng, Igbp1, and IL7 in their thymuses, however, mice exposed to high-dose-rate γ-irradiation exhibited marked down-regulation of Sp3, Il15, Traf6, IL2ra, Pik3r1, and Hells. In contrast, low-dose-r... Genomics journals http://www.medworm.com/rss/comments.php?id=4454002 Sun, 23 Jan 2011 00:00:00 +0100 4454002 http://www.medworm.com/index.php?rid=4454003&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21256207%26dopt%3DAbstract Authors: Clark LA, Tsai KL, Starr AN, Nowend KL, Murphy KE Harlequin is a pigmentary trait of the domestic dog that is controlled by two autosomal loci: the melanosomal gene, SILV, and a modifier gene, harlequin (H), previously localized to chromosome 9. Heterozygosity for both retrotransposon insertion in SILV and mutation in H causes a pattern of black patches on a white background. Homozygosity for H is embryonic lethal. Fine mapping of the harlequin locus revealed a 25kb interval wherein all harlequin Great Danes are heterozygous for a common haplotype. This region contains one gene, PSMB7, which encodes the β2 catalytic subunit of the proteasome. Sequence analysis identified a coding variant in exon 2 that segregates with harlequin patterning. The substitution predicts the replac... Genomics journals http://www.medworm.com/rss/comments.php?id=4454003 Thu, 20 Jan 2011 00:00:00 +0100 4454003 http://www.medworm.com/index.php?rid=4388454&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21241792%26dopt%3DAbstract We present the complete genomic sequence of a lytic bacteriophage ϕAB1 which can infect many clinical isolates of multidrug-resistant Acinetobacter baumannii. The recently isolated bacteriophage displays morphology resembling Podoviridae family. The ϕAB1 genome is a linear double-stranded DNA of 41,526 bp containing 46 possible open reading frames (ORFs). The majority of the predicted structural proteins were identified as part of the phage particle by mass spectrometry analysis. According to the virion morphology, overall genomic structure, and the phylogenetic tree of RNA polymerase, we propose that ϕAB1 is a new member of the ϕKMV-like phages. Additionally, we identified four ORFs encoding putative HNH endonucleases, one of which is presumed to integrate and create a genes-in-pieces... Genomics journals http://www.medworm.com/rss/comments.php?id=4388454 Fri, 14 Jan 2011 00:00:00 +0100 4388454 http://www.medworm.com/index.php?rid=4388455&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21223998%26dopt%3DAbstract Authors: McIver LJ, Fondon JW, Skinner MA, Garner HR We performed an analysis of global microsatellite variation on the two kindreds sequenced at high depth (~20×-60×) in the 1000 Genomes Project pilot studies because alterations in these highly mutable repetitive sequences have been linked with many phenotypes and disease risks. The standard alignment technique performs poorly in microsatellite regions as a consequence of low effective coverage (~1×-5×) resulting in 79% of the informative loci exhibiting non-Mendelian inheritance patterns. We used a more stringent approach in computing robust allelotypes resulting in 94.4% of the 1095 informative repeats conforming to traditional inheritance. The high-confidence allelotypes were analyzed to obtain an estimate of the minimum polymo... Genomics journals http://www.medworm.com/rss/comments.php?id=4388455 Sun, 09 Jan 2011 00:00:00 +0100 4388455 http://www.medworm.com/index.php?rid=4388456&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21211562%26dopt%3DAbstract Authors: Chen YA, Choufani S, Ferreira JC, Grafodatskaya D, Butcher DT, Weksberg R The Illumina Infinium HumanMethylation27 BeadChip (Illumina 27k) microarray is a high-throughput platform capable of interrogating the human DNA methylome. In a search for autosomal sex-specific DNA methylation using this microarray, we discovered autosomal CpG loci showing significant methylation differences between the sexes. However, we found that the majority of these probes cross-reacted with sequences from sex chromosomes. Moreover, we determined that 6-10% of the microarray probes are non-specific and map to highly homologous genomic sequences. Using probes targeting different CpGs that are exact duplicates of each other, we investigated the precision of these repeat measurements and concluded tha... Genomics journals http://www.medworm.com/rss/comments.php?id=4388456 Tue, 04 Jan 2011 00:00:00 +0100 4388456 http://www.medworm.com/index.php?rid=4388459&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21195161%26dopt%3DAbstract In this study, we have used high throughput screens and developed a comparative genomic approach, termed Functionome mapping, to discover conserved responses to UVC-damage. Functionome mapping uses gene ontology (GO) information to link proteins with similar biological functions from different organisms, and we have used it to compare 303, 311 and 288 UVC-toxicity modulating proteins from Escherichia coli, Schizosaccharomyces pombe and Saccharomyces cerevisiae, respectively. We have demonstrated that all three organisms use DNA repair, translation and aerobic respiration associated processes to modulate the toxicity of UVC, with these last two categories highlighting the importance of ribosomal proteins and electron transport machinery. Our study has demonstrated that comparative genomic a... Genomics journals http://www.medworm.com/rss/comments.php?id=4388459 Thu, 30 Dec 2010 00:00:00 +0100 4388459 http://www.medworm.com/index.php?rid=4388458&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21195162%26dopt%3DAbstract Authors: Chung H, McClure MC Microsatellite (MS) markers in the SLA-1 region were characterized via sequencing analysis with BAC clones generated from the National Institute of Health miniature pigs (MIPs). A total of 16 BAC clones were sequenced producing 15,228 shotgun reads, corresponding to 11.2 X sequencing coverage, that were used to construct a contig of 12.18Mb in length. MS markers were compared with previously deposited GenBank sequences to verify the existence of 423 potential MS candidate markers in the SLA-1 region. Evaluation of these polymorphisms confirmed 59 markers in MIPs, and the combined data including sequences from GenBank revealed 155 polymorphic MS markers. MS markers identified from this analysis can be used to provide an alternative method to direct typing fo... Genomics journals http://www.medworm.com/rss/comments.php?id=4388458 Thu, 30 Dec 2010 00:00:00 +0100 4388458 http://www.medworm.com/index.php?rid=4388457&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21195163%26dopt%3DAbstract Authors: Chen YF, Tung CL, Chang Y, Hsiao WC, Su LJ, Sun HS EBV infects more than 90% of the human population and persists in most individuals as a latent infection where the viral genome is silenced by host-driven methylation. The lytic cycle is initiated when the viral protein Zta binds to methylated BRLF1 and BRRF1 promoters. Although studies reveal the role of Zta and methylation changes in the viral genome upon EBV infection to reactivation, whether Zta plays any role in alteration of methylation in the host genome remains unknown. Using an inducible model, we demonstrate that global DNA methylation, based on whole-genome 5-methylcytosine content, and regional DNA methylation in repetitive elements, imprinting genes and the X chromosome, remains unchanged in response to Zta expres... Genomics journals http://www.medworm.com/rss/comments.php?id=4388457 Thu, 30 Dec 2010 00:00:00 +0100 4388457 http://www.medworm.com/index.php?rid=4297473&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21147216%26dopt%3DAbstract Authors: Yukawa Y, Dieci G, Alzapiedi M, Hiraga A, Hirai K, Yamamoto Y, Sugiura M The transcription start site (TSS) is useful to predict gene and to understand transcription initiation. Although vast data on mRNA TSSs are available, little is known about tRNA genes because of rapid processing. Using a tobacco in vitro transcription system under conditions of impaired 5' end processing, TSSs were determined for 64 Arabidopsis tRNA genes. This analysis revealed multiple TSSs distributed in a region from 10 to 2bp upstream of the mature tRNA coding sequence (-10 to -2). We also analyzed 31 Saccharomyces cerevisiae tRNA genes that showed a smaller number but a broader distribution (-13 to -1) of TSSs. In both cases, transcription was initiated preferentially at adenosine, and a common 'TC... Genomics journals http://www.medworm.com/rss/comments.php?id=4297473 Mon, 13 Dec 2010 00:00:00 +0100 4297473 http://www.medworm.com/index.php?rid=4297472&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21156202%26dopt%3DAbstract Authors: Singh S, Li SS Phthalates are widely used as plasticizers to soften and increase the flexibility in polyvinyl chloride plastics, but they can leach into the surrounding environment. There is sufficient evidence in rodents that phthalate exposure causes developmental and reproductive toxicity. The curated interactions between 16 phthalates and genes/proteins were obtained from Comparative Toxicogenomics Database (CTD), and a total of 445 interactions between the five most frequently curated phthalates (DEHP/MEHP and DBP/BBP/MBP) and 249 unique genes/proteins were found. The GeneOntology, pathways and networks of these 249 unique genes/proteins were fully analyzed. The pathways and networks of top 34 genes/proteins were found to be very similar to those of the 249 unique genes/p... Genomics journals http://www.medworm.com/rss/comments.php?id=4297472 Mon, 13 Dec 2010 00:00:00 +0100 4297472 http://www.medworm.com/index.php?rid=4297471&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21156203%26dopt%3DAbstract Authors: Li W, He C, Freudenberg J We introduce a piecewise linear regression called "hockey stick regression" to model the relationship between genetic and physical lengths of chromosomes in a genome. This piecewise linear regression is an extension of the two-parameter linear regression we proposed earlier [W. Li and J. Freudenberg, Two-parameter characterization of chromosome-scale recombination rate, Genome Res., 19 (2009) 2300-2307]. We use this, as well as the one-piece regression with a fixed y-intercept, to compare the two competing hypotheses concerning the minimum number of required chiasmata for meiosis: minimum one chiasma per chromosome (PC) and per chromosome arm (PA). Using statistical model selection and testing, we show that for human genome data, one-piece PC (PC1) is... Genomics journals http://www.medworm.com/rss/comments.php?id=4297471 Mon, 13 Dec 2010 00:00:00 +0100 4297471 http://www.medworm.com/index.php?rid=4297470&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21159321%26dopt%3DAbstract Authors: Koo DH, Hong CP, Batley J, Chung YS, Edwards D, Bang JW, Hur Y, Lim YP Centromeric, subtelomeric, and telomeric repetitive DNAs were characterized in Brassica species and the related Raphanus sativus and Arabidopsis thaliana. In general, rapid divergence of the repeats was found. The centromeric tandem satellite repeats were differentially distributed in the species studied, suggesting that centromeric repeats have diverged during the evolution of the A/C and B genome lineages. Sequence analysis of centromeric repeats suggested rapid evolution. Pericentromere-associated retrotransposons were identified and showed divergence during the evolution of the lineages as centromeric repeats. A novel subtelomeric tandem repeat from B. nigra was found to be conserved across the diploid ... Genomics journals http://www.medworm.com/rss/comments.php?id=4297470 Mon, 13 Dec 2010 00:00:00 +0100 4297470 http://www.medworm.com/index.php?rid=4243215&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21126569%26dopt%3DAbstract Authors: Xiong Y, Wang M, Fang K, Xing Q, Feng G, Shen L, He L, Qin S While many studies have been focused on CYP2C9*2 and *3，there was a lack of large full gene sequencing on CYP2C9, and this study was designed to fill this gap. We used direct sequencing to systematically screen genetic polymorphisms of the CYP2C9 gene including the 5' -flanking region (2kb), all exons and their adjoining intron regions and the 3' UTR in 400 unrelated healthy Chinese Han volunteers. A total of 27 different CYP2C9 polymorphisms were identified, 3 of which were novel, including one in intron 6, a synonymous variant (1137T>C, Tyr379Tyr), and a deletion mutation in the 3'UTR (1739-1740ATdel), which potentially influences the stability of CYP2C9 mRNA. We identified CYP2C9*1, *2, *3, *8, *11, and *31, ... Genomics journals http://www.medworm.com/rss/comments.php?id=4243215 Mon, 29 Nov 2010 00:00:00 +0100 4243215 http://www.medworm.com/index.php?rid=4243214&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21126570%26dopt%3DAbstract Authors: Brault LS, Cooper CA, Famula TR, Murray JD, Penedo MC Equine Cerebellar Abiotrophy (CA) is a neurological disease found in Arabian horses. CA is characterized by post-natal degeneration of the Purkinje cells of the cerebellum. Signs of CA include ataxia, head tremors, and a lack of balance equilibrium. We have discovered linkage of the CA phenotype to a microsatellite marker on ECA2 and identified a region of conserved homozygosity spanning approximately 142 Kb. Complete sequencing of the four genes in this region identified one SNP found only in Arabian horses, located in exon 4 of TOE1 and approximately 1200 base pairs upstream of MUTYH, adjacent to a possible binding site for the transcription factor GATA2. qPCR analysis of cDNA from the cerebella of affected and unaffected... Genomics journals http://www.medworm.com/rss/comments.php?id=4243214 Mon, 29 Nov 2010 00:00:00 +0100 4243214 http://www.medworm.com/index.php?rid=4211690&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21112384%26dopt%3DAbstract In this study, the authors focused on the biologically realistic promoter prediction of plant genomes. By analyzing the correlative conservation, GC-compositional bias and specific structural patterns of TATA and TATA-less promoters in PlantPromDB, a hybrid multi-feature approach based on support vector machine (SVM) for predicting the two types of promoters was developed by integrating local word content, GC-Skew and DNA geometric flexibility. Compared with the TSSP-TCM program on the same test dataset, the better prediction results were obtained. Especially for the TATA-less promoter, the accuracy is 10% higher than the result of TSSP-TCM program. The good performance for the hybrid promoters and the experimental data also indicate that our method has the ability for locating the promote... Genomics journals http://www.medworm.com/rss/comments.php?id=4211690 Thu, 25 Nov 2010 00:00:00 +0100 4211690 http://www.medworm.com/index.php?rid=4211695&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21111805%26dopt%3DAbstract In this study, we showed that using HH interaction analysis is possible to assist researchers in gaining more insight into identifying genetic risk factors for complex diseases. PMID: 21111805 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=4211695 Wed, 24 Nov 2010 00:00:00 +0100 4211695 http://www.medworm.com/index.php?rid=4211702&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21111040%26dopt%3DAbstract Authors: Fontanesi L, Beretti F, Martelli PL, Colombo M, Dall'olio S, Occidente M, Portolano B, Casadio R, Matassino D, Russo V We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Sarda, Massese, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9kb, respectively. A comparative analysis between the identified sheep CNVRs and those repor... Genomics journals http://www.medworm.com/rss/comments.php?id=4211702 Tue, 23 Nov 2010 00:00:00 +0100 4211702 http://www.medworm.com/index.php?rid=4163614&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21059387%26dopt%3DAbstract Authors: Lee BY, Cho S, Shin DH, Kim H Copy number variation (CNV) is an attractive emerging approach to study the association with various diseases. We performed a CNV-based genome-wide association study of pulmonary function measures (FEV(1), FVC and FEV(1)/FVC) in KARE cohorts. Affymetrix Genome-wide human SNP array 5.0 was used to measure genome wide variation and CNV segmentation was performed using Golden Helix SVS 7.0. Single and multivariate regressions were used for the association study using the R statistical package and The Dabatase for Annotation, Visualization and Integrated (DAVID v6.7b) tool for the functional annotation. We identified significantly associated 1260 CNVs with pulmonary function measures of FEV(1) and FVC. Functional gene classification and annotation ana... Genomics journals http://www.medworm.com/rss/comments.php?id=4163614 Fri, 05 Nov 2010 00:00:00 +0100 4163614 http://www.medworm.com/index.php?rid=4134566&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21044881%26dopt%3DAbstract Authors: Ortiz-Estevez M, De Las Rivas J, Fontanillo C, Rubio A DNA copy number aberrations (CNAs) are genetic alterations common in cancer cells. Their transcriptional consequences are still poorly understood. Based on the fact that DNA copy number (CN) is highly correlated with the genomic position, we have applied a segmentation algorithm to gene expression (GE) to explore its relation with CN. We have found a strong correlation between segmented CN (sCN) and segmented GE (sGE), corroborating that CNAs have clear effects on genome-wide expression. We have found out that most of the recurrent regions of sGE are common to those obtained from sCN analysis. Results for two cancer datasets confirm the known targets of aberrations and provide new candidates to study. The suggested methodo... Genomics journals http://www.medworm.com/rss/comments.php?id=4134566 Thu, 28 Oct 2010 00:00:00 +0100 4134566 http://www.medworm.com/index.php?rid=4134568&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21035537%26dopt%3DAbstract Authors: Müller K, Krohn K, Eszlinger M, Ludgate M, Führer D Thyroid autonomy is a frequent cause of thyrotoxicosis in regions with iodine deficiency. Epidemiological data suggest that iodide may influence the course of pre-existing thyroid autonomy. Making use of FRTL-5 cells stably expressing a constitutively activating TSH receptor mutation as an in-vitro model of thyroid autonomy, we investigated the impact of iodide on proliferation, function and changes in global gene expression. We demonstrate that iodine inhibits growth in TSHR WT and L629F mutant FRTL-5 cells and downregulates e.g. protocadherin cluster (pcdha1-13) and thyroid responsive element (thrsp). In addition functional genes e.g. iodotyrosine deiodinase (iyd) and oncogen junB are upregulated, while sodium-iodide-symp... Genomics journals http://www.medworm.com/rss/comments.php?id=4134568 Wed, 27 Oct 2010 00:00:00 +0100 4134568 http://www.medworm.com/index.php?rid=4134567&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D21035538%26dopt%3DAbstract Authors: Uluisik I, Kaya A, Unlu ES, Avsar K, Karakaya HC, Yalcin T, Koc A Boron is an essential micronutrient for plants and it is either necessary or beneficial for animals. Studies identified only few genes related to boron metabolism thus far and details of how boron is imported into cells and used in cell metabolism are largely unknown. In order to identify genes that play role in boron metabolism, we screened the entire set of yeast haploid deletion mutants and identified 6 mutants that were resistant to toxic levels of boron, and 21 mutants that were highly sensitive to boron treatment. Furthermore, we performed a proteomic approach to identify additional proteins that are significantly up-regulated by boron treatment. Our results revealed many genes and pathways related to boro... Genomics journals http://www.medworm.com/rss/comments.php?id=4134567 Wed, 27 Oct 2010 00:00:00 +0100 4134567 http://www.medworm.com/index.php?rid=4120919&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20977933%26dopt%3DAbstract Authors: Schanen BC, Li X MicroRNAs (miRNAs) are members of a growing family of non-coding transcripts, 21-23 nucleotides long, which regulate a diverse collection of biological processes and various diseases by RNA-mediated gene-silencing mechanisms. While currently many studies focus on defining the regulatory functions of miRNAs, few are directed towards how miRNA genes are themselves transcriptionally regulated. Recent studies of miRNA transcription have elucidated RNA polymerase II as the major polymerase of miRNAs, however, little is known of the structural features of miRNA promoters, especially those of mammalian miRNAs. Here, we review the current literature regarding features conserved among miRNA promoters useful for their detection and the current novel methodologies availa... Genomics journals http://www.medworm.com/rss/comments.php?id=4120919 Sat, 23 Oct 2010 00:00:00 +0100 4120919 http://www.medworm.com/index.php?rid=4120920&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20974243%26dopt%3DAbstract Authors: Rossi S, Tsirigos A, Amoroso A, Mascellani N, Rigoutsos I, Calin GA, Volinia S A large number of loci for genetic diseases have been mapped on the human genome and a group of hereditary diseases among them have thus far proven unsuccessful to identify. It is conceivable that such "unclonable" diseases are not linked to abnormalities of protein coding genes (PCGs), but of non-coding RNAs (ncRNAs). We developed a novel approach termed OMiR, (OMIM and miRNAs) to test whether microRNAs (miRNAs) exhibit any associations with mapped genetic diseases not yet associated with a PCG. We found that "orphan" genetic disease loci were proximal to miRNA loci more frequently than to loci for which the responsible protein coding gene is known, thus suggesting that miRNAs might be the elusive ... Genomics journals http://www.medworm.com/rss/comments.php?id=4120920 Fri, 22 Oct 2010 00:00:00 +0100 4120920 http://www.medworm.com/index.php?rid=4087330&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20951196%26dopt%3DAbstract Authors: Narendra V, Lytkin NI, Aliferis CF, Statnikov A De-novo reverse-engineering of genome-scale regulatory networks is an increasingly important objective for biological and translational research. While many methods have been recently developed for this task, their absolute and relative performance remains poorly understood. The present study conducts a rigorous performance assessment of 32 computational methods/variants for de-novo reverse-engineering of genome-scale regulatory networks by benchmarking these methods in 15 high-quality datasets and gold-standards of experimentally verified mechanistic knowledge. The results of this study show that some methods need to be substantially improved upon, while others should be used routinely. Our results also demonstrate that several ... Genomics journals http://www.medworm.com/rss/comments.php?id=4087330 Tue, 12 Oct 2010 23:00:00 +0100 4087330 http://www.medworm.com/index.php?rid=4087329&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20951197%26dopt%3DAbstract Authors: Selles B, Jacquot JP, Rouhier N Protein disulfide isomerases (PDIs) are eukaryotic oxidoreductases essential for oxidative protein folding. Their diversity in photosynthetic organisms was assessed by analyzing 24 sequenced genomes belonging to algal, lycophyte, bryophyte and angiosperm phyla. This phylogenetic analysis led to an updated classification into 9 classes (PDI-A to -F, -L, -M, -S) which differed by the number of Trx domains and the presence of additional domains (D, COPII, J and ARMET). From an evolutionary perspective, the distribution and protein architecture of PDIs differ considerably between algae and terrestrial plants, 5 PDI classes are common whereas 1 is specific to terrestrial plants and 3 to algae. Some algal PDI-Fs possess selenocysteine residues. The PD... Genomics journals http://www.medworm.com/rss/comments.php?id=4087329 Tue, 12 Oct 2010 23:00:00 +0100 4087329 http://www.medworm.com/index.php?rid=4087328&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20951198%26dopt%3DAbstract Authors: Castagnone-Sereno P, Deleury E, Danchin EG, Perfus-Barbeoch L, Abad P Proteases perform essential physiological functions in all living organisms. In parasitic helminths, they are of particular importance for tissue penetration, digestion of host tissues for nutrition, and evasion of host immune responses. The recent availability of the genome sequence of the nematode Meloidogyne incognita has allowed the analysis of the protease repertoire of this major crop pathogen. The M. incognita degradome consists of at least 334 proteases that are distributed into 43 families of the five known catalytic classes. Expression profiling identified protease genes with differential trancript level between eggs and infective juveniles. Comparing the M. incognita degradome with those of five o... Genomics journals http://www.medworm.com/rss/comments.php?id=4087328 Tue, 12 Oct 2010 23:00:00 +0100 4087328 http://www.medworm.com/index.php?rid=4057362&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20934504%26dopt%3DAbstract Authors: Colak D, Al-Dhalaan H, Nester M, Albakheet A, Al-Younes B, Al-Hassnan Z, Al-Dosari M, Chedrawi A, Al-Owain M, Abudheim N, Al-Alwan L, Al-Odaib A, Ozand P, Inan MS, Kaya N Rett syndrome (RTT) is an X-linked neurodevelopmental disorder characterized by derangements in nervous system especially in cognition and behavior. The present study aims to understand the molecular underpinnings of two subtypes of RTT, classic RTT and Rett-like, and to elucidate common pathways giving rise to common RTT phenotype using genomic and transcriptomic approaches. Mutation screening on selected nuclear genes revealed only MECP2 mutations in a subset of classic RTT patients. MLPA assays and mtDNA screenings were all negative. Genome-wide copy number analysis indicated a novel duplication on X chrom... Genomics journals http://www.medworm.com/rss/comments.php?id=4057362 Wed, 06 Oct 2010 23:00:00 +0100 4057362 http://www.medworm.com/index.php?rid=4037383&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20923700%26dopt%3DAbstract Authors: Owczarek-Lipska M, Plattet P, Zipperle L, Drögemüller C, Posthaus H, Dolf G, Braunschweig MH Cardiomyopathies are severe degenerative disorders of the myocardium that lead to heart failure. During the last three decades bovine dilated cardiomyopathy (BDCMP) was observed worldwide in cattle of Holstein-Friesian origin. In the Swiss cattle population BDCMP affects Fleckvieh and Red Holstein breeds. The heart of affected animals is enlarged due to dilation of both ventricles. Clinical signs are caused by systolic dysfunction and affected individuals die as a result of severe heart insufficiency. BDCMP follows an autosomal recessive pattern of inheritance and the disease-causing locus was mapped to bovine chromosome 18 (BTA18). In the present study we describe the successful ide... Genomics journals http://www.medworm.com/rss/comments.php?id=4037383 Fri, 01 Oct 2010 23:00:00 +0100 4037383 http://www.medworm.com/index.php?rid=4037384&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20888900%26dopt%3DAbstract Authors: Tan YD Development of statistical methods has become very necessary for large-scale correlation analysis in the current "omic" data. We propose ranking analysis of correlation coefficients (RAC) based on transforming correlation matrix into correlation vector and conducting a "locally ranking" strategy that significantly reduces computational complexity and load. RAC gives estimation of null correlation distribution and an estimator of false discovery rate (FDR) for finding gene-pairs of being correlated in expressions obtained by comparison between the ranked observed correlation coefficients and the ranked estimated ones at a given threshold level. The simulated and real data show that the estimated null correlation distribution is the exact same with the true one and the FD... Genomics journals http://www.medworm.com/rss/comments.php?id=4037384 Wed, 29 Sep 2010 23:00:00 +0100 4037384 http://www.medworm.com/index.php?rid=4037385&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20887780%26dopt%3DAbstract Authors: Goldstein O, Kukekova AV, Aguirre GD, Acland GM Fine mapping followed by candidate gene analysis of erd - a canine hereditary retinal degeneration characterized by aberrant photoreceptor development - established that the disease cosegregates with a SINE insertion in exon 4 of the canine STK38L/NDR2 gene. The mutation removes exon 4 from STK38L transcripts and is predicted to remove much of the N-terminus from the translated protein, including binding sites for S100B and Mob Proteins, part of the protein kinase domain, and a Thr-75 residue critical for autophosphorylation. Although known to have roles in neuronal cell function, the STK38L pathway has not previously been implicated in normal or abnormal photoreceptor development. Loss of STK38L function in erd provides novel po... Genomics journals http://www.medworm.com/rss/comments.php?id=4037385 Mon, 27 Sep 2010 23:00:00 +0100 4037385 http://www.medworm.com/index.php?rid=4024068&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20858542%26dopt%3DAbstract Authors: Severyn CJ, Rotwein P Repulsive guidance molecule c (RGMc) plays a critical role in iron metabolism. Inactivating mutations cause juvenile hemochromatosis, a severe iron overload disorder. Understanding mechanisms controlling RGMc biosynthesis has been hampered by minimal information about the RGMc gene. Here we define the structure, examine the evolution, and establish mechanisms of regulation of the mouse RGMc gene. RGMc is a 4-exon gene that undergoes alternative RNA splicing to yield 3 mRNAs with 5' different untranslated regions. Gene transcription is induced during myoblast differentiation, producing all 3 mRNAs. We identify 3 critical promoter elements responsible for transcriptional activation in skeletal muscle, comprising paired E-boxes, a putative Stat and/or Ets el... Genomics journals http://www.medworm.com/rss/comments.php?id=4024068 Sat, 18 Sep 2010 23:00:00 +0100 4024068 http://www.medworm.com/index.php?rid=3960655&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20828606%26dopt%3DAbstract Authors: Wang QQ, Liu F, Chen XS, Ma XJ, Zeng HQ, Yang ZM Cotton fibre as a single-celled trichome is a biological model system for studying cell differentiation and elongation. However, the complexity of its gene expression and regulatory mechanism allows only marginal progress. Here, we report the high-throughput tag-sequencing (Tag-seq) analysis using Solexa Genome Analyzer platform on transcriptome of -2~1 (fibre initiation, stage I) and 2~8 (fibre elongation, stage II) days post anthesis (DPA) cotton (Gossypium hirsutum) ovules (wildtype: WT, Xuzhou 142 and its mutant: fuzzless/lintless or flM, in the same background). To this end, we sequenced 3.5 to 3.8 million tags representing 0.7 to 1.0 million unique transcripts for each library (WT1, WT2, M1 and M2). After removal of low qu... Genomics journals http://www.medworm.com/rss/comments.php?id=3960655 Sun, 05 Sep 2010 23:00:00 +0100 3960655 http://www.medworm.com/index.php?rid=3960656&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20826206%26dopt%3DAbstract Authors: Su CH, Shih CH, Chang TH, Tsai HK In budding yeast, approximately a quarter of adjacent genes are divergently transcribed (divergent gene pairs). Whether genes in a divergent pair share the same regulatory system is still unknown. By examining transcription factor (TF) knockout experiments, we found that most TF knockout only altered the expression of one gene in a divergent pair. This prompted us to conduct a comprehensive analysis in silico to estimate how many divergent pairs are regulated by common sets of TFs (cis-regulatory modules, CRMs) using TF binding sites and expression data. Analyses of ten expression datasets show that only a limited number of divergent gene pairs share CRMs in any single dataset. However, around half of divergent pairs do share a regulatory syst... Genomics journals http://www.medworm.com/rss/comments.php?id=3960656 Thu, 02 Sep 2010 23:00:00 +0100 3960656 http://www.medworm.com/index.php?rid=3960658&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20800674%26dopt%3DAbstract Authors: Yu Y, Ping J, Chen H, Jiao L, Zheng S, Han ZG, Hao P, Huang J The human liver plays a vital role in meeting the body's metabolic needs and maintaining homeostasis. To address the molecular mechanisms of liver function, we integrated multiple gene expression datasets from microarray, MPSS, SAGE and EST platforms to generate a transcriptome atlas of the normal human liver. Our results show that 17396 genes are expressed in the human liver. 238 genes were identified as liver enrichment genes, involved in the functions of immune response and metabolic processes, from the MPSS and EST datasets. A comparative analysis of liver transcriptomes was performed in humans, mice and rats with microarray datasets shows that the expression profile of homologous genes remains significantly dif... Genomics journals http://www.medworm.com/rss/comments.php?id=3960658 Wed, 25 Aug 2010 23:00:00 +0100 3960658 http://www.medworm.com/index.php?rid=3960657&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20801210%26dopt%3DAbstract Authors: Bulla GA, Luong Q, Shrestha S, Reeb S, Hickman S Silencing of tissue-specific gene expression in mammalian somatic cell hybrids is a well-documented epigenetic phenomenon which is both profound (involving a large number of genes) and enigmatic. . Our aim was to utilize whole-genome microarray analyses to determine the true extent of gene silencing on a genomic level. By comparing gene expression profiles of hepatoma x fibroblast cell hybrids with those of parental cells, we have identified over 300 liver-enriched genes that are repressed at least 5-fold in the cell hybrids, the majority of which are repressed at least 10-fold. Also, we identify nearly 200 fibroblast-enriched genes that are repressed at least 5-fold. Silenced hepatic genes include several that encode transcript... Genomics journals http://www.medworm.com/rss/comments.php?id=3960657 Wed, 25 Aug 2010 23:00:00 +0100 3960657 http://www.medworm.com/index.php?rid=3908478&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20736060%26dopt%3DAbstract Authors: Watanabe Y, Numata K, Murata S, Osada Y, Saito R, Nakaoka H, Yamamoto N, Watanabe K, Kato H, Abe K, Kiyosawa H The functionality of sense-antisense transcripts (SATs), although widespread throughout the mammalian genome, is largely unknown. Here, we analyzed the SATs expression and its associated promoter DNA methylation status by surveying 12 tissues of mice to gain insights into the relationship between expression and DNA methylation of SATs. We have found that sense and antisense expression positively correlate in most tissues. However, in some SATs with tissue-specific expression, the expression level of a transcript from a CpG island-bearing promoter is low when the promoter DNA methylation is present. In these circumstances, the expression level of its opposite strand tr... Genomics journals http://www.medworm.com/rss/comments.php?id=3908478 Fri, 20 Aug 2010 23:00:00 +0100 3908478 http://www.medworm.com/index.php?rid=3908479&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20732410%26dopt%3DAbstract We report the results of a chemogenomic profiling aimed to explore the mode of action of a quinolic analogue of the p300 histone acetyltransferase (HAT) inhibitor anacardic acid, named MC1626. This compound reduced histone H3 acetylation in a dose-dependent manner and the HATs Gcn5 and Rtt109, which specifically target H3 lysines, were the only ones that caused chemical-genetic synthetic sickness with MC1626 when mutated. Deletion of specific Gcn5 (e.g., Ada1) and Rtt109 (e.g., Asf1) multiprotein complex components also enhanced MC1626 sensitivity. In addition to N-terminal H3 lysines, MC1626 inhibits H3-K56 acetylation, a histone modification that, in yeast, is exclusively supported by Rtt109 and indirectly influences DNA integrity. Several DNA repair mutants were found to be sensitive to... Genomics journals http://www.medworm.com/rss/comments.php?id=3908479 Thu, 19 Aug 2010 23:00:00 +0100 3908479 http://www.medworm.com/index.php?rid=3908480&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20728532%26dopt%3DAbstract In this study, we conducted genome-wide alternative splicing analyses focusing on new internal exon birth derived from TEs in human, mouse, and zebrafish genomes. We identified two different exon sets, TE-spliced exons and non-TE-spliced exons. The proportion of TE-spliced exons was nearly twice as high as the proportion of non-TE-spliced exons in the coding sequence (CDS) region. Detailed analysis of various families of TEs in three different species of TE-spliced exons revealed a different pattern in zebrafish. In our analysis, we could identify the functional role of TE insertions in the vertebrate genome affecting mRNA splicing machinery. Their effects can be directly linked to the shift from constitutive to alternative splicing during primate evolution. Our results indicate that TEs h... Genomics journals http://www.medworm.com/rss/comments.php?id=3908480 Wed, 18 Aug 2010 23:00:00 +0100 3908480 http://www.medworm.com/index.php?rid=3881217&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20709168%26dopt%3DAbstract We present examples of the use of our web application and we compare results of our computations with the results obtained by using other existing tools for searches for exact tandem repeats. PMID: 20709168 [PubMed - as supplied by publisher] (Source: Genomics) Genomics journals http://www.medworm.com/rss/comments.php?id=3881217 Wed, 11 Aug 2010 23:00:00 +0100 3881217 http://www.medworm.com/index.php?rid=3881218&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20691777%26dopt%3DAbstract Authors: Heruth DP, Hawkins T, Logsdon DP, Gibson MI, Sokolovsky IV, Nsumu NN, Major SL, Fegley B, Woods GM, Lewing KB, Neville KA, Cornetta K, Peterson KR, White RA KLF1 regulates definitive erythropoiesis of red blood cells by facilitating transcription through high affinity binding to CACCC elements within its erythroid specific target genes including those encoding erythrocyte membrane skeleton (EMS) proteins. Deficiencies of EMS proteins in humans lead to the hemolytic anemia Hereditary Spherocytosis (HS) which includes a subpopulation with no known genetic defect. Here we report that a mutation, E339D, in the second zinc finger domain of KLF1 is responsible for HS in the mouse model Nan. The causative nature of this mutation was verified with an allelic test cross between Nan/+ a... Genomics journals http://www.medworm.com/rss/comments.php?id=3881218 Wed, 04 Aug 2010 23:00:00 +0100 3881218 http://www.medworm.com/index.php?rid=3832332&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20688151%26dopt%3DAbstract We report here an oligonucleotide tiling microarray designed to specifically target 518 single nucleotide polymorphisms (SNPs) between the two sequenced rice (Oryza sativa) subspecies indica and japonica. The tiling array included all 25-mer probes interrogating each SNP by placing the polymorphic site at all 25 possible positions within the probe. Through hybridization to a titration series in which the japonica- and indica-derived cDNA templates were mixed with altering proportions, a regression model was used to screen for diagnostic probe sets for each SNP. Our result indicates that 284 (55%) SNPs have at least one diagnostic probe pair suitable for distinguishing and quantifying the relative abundance of allele-specific transcripts. As a proof-of-concept, we analyzed allele-specific e... Genomics journals http://www.medworm.com/rss/comments.php?id=3832332 Sun, 01 Aug 2010 23:00:00 +0100 3832332 http://www.medworm.com/index.php?rid=3832331&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20688152%26dopt%3DAbstract Authors: Cui P, Lin Q, Ding F, Xin C, Gong W, Zhang L, Geng J, Zhang B, Yu X, Yang J, Hu S, Yu J To compare the two RNA-sequencing protocols, ribo-minus RNA-sequencing (rmRNA-seq) and polyA-selected RNA-sequencing (mRNA-seq), we acquired transcriptomic data-52 and 32 million alignable reads of 35 bases in length-from the mouse cerebrum, respectively. We found that a higher proportion, 44% and 25%, of the uniquely alignable rmRNA-seq reads, is in intergenic and intronic regions, respectively, as compared to 23% and 15% from the mRNA-seq dataset. Further analysis made an additional discovery of transcripts of protein-coding genes (such as histone, heg1, and dux), ncRNAs, snoRNAs, snRNAs, and novel ncRNAs as well as repeat elements in rmRNA-seq dataset. This result suggests that rmRNA-seq... Genomics journals http://www.medworm.com/rss/comments.php?id=3832331 Sun, 01 Aug 2010 23:00:00 +0100 3832331 http://www.medworm.com/index.php?rid=3817867&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20650312%26dopt%3DAbstract We examined the influence of genes in this region on T2D and BMI in two European American case-control populations. SNPs were genotyped in 300 diabetic patients and 310 controls. A subset of 72 SNPs were further genotyped in 470 cases and 442 controls. All genes examined showed evidence of association with T2D in the initial sample (additive P-value [P(a)]=0.00090-0.045). SNPs near PREX1 were also associated in the second case-control population (P(a)=0.017-0.042). The combined analysis resulted in the same SNPs, among others, associated with T2D (P(a)=0.0013-0.041). Stratification analysis by T2D status showed that association with BMI was observed solely in cases (P(a)=0.0018-0.041). Mediation testing revealed that 30-40% of the effects of these SNPs on T2D were significantly mediated by... Genomics journals http://www.medworm.com/rss/comments.php?id=3817867 Wed, 28 Jul 2010 23:00:00 +0100 3817867 http://www.medworm.com/index.php?rid=3817866&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20654709%26dopt%3DAbstract Authors: Papazisi L, Ratnayake S, Remortel BG, Bock GR, Liang W, Saeed AI, Liu J, Fleischmann RD, Kilian M, Peterson SN Here we report the use of a multi-genome DNA microarray to elucidate the genomic events associated with the emergence of the clonal variants of Haemophilus influenzae biogroup aegyptius causing Brazilian Purpuric Fever (BPF), an important pediatric disease with a high mortality rate. We performed directed genome sequencing of strain HK1212 unique loci to construct a species DNA microarray. Comparative genome hybridization using this microarray enabled us to determine and compare gene complements, and infer reliable phylogenomic relationships among members of the species. The higher genomic variability observed in the genomes of BPF-related strains (clones) and their c... Genomics journals http://www.medworm.com/rss/comments.php?id=3817866 Wed, 28 Jul 2010 23:00:00 +0100 3817866 http://www.medworm.com/index.php?rid=3817865&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20659549%26dopt%3DAbstract Authors: Guyon R, Senger F, Rakotomanga M, Sadequi N, Volckaert FA, Hitte C, Galibert F The selective breeding of fish for aquaculture purposes requires the understanding of the genetic basis of traits such as growth, behaviour, resistance to pathogens and sex determinism. Access to well-developed genomic resources is a prerequisite to improve the knowledge of these traits. Having this aim in mind, a radiation hybrid (RH) panel of European sea bass (Dicentrarchus labrax) was constructed from splenocytes irradiated at 3000rad, allowing the construction of a 1581 marker RH map. A total of 1440 gene markers providing ~4400 anchors with the genomes of three-spined stickleback, medaka, pufferfish and zebrafish, helped establish synteny relationships with these model species. The identificat... Genomics journals http://www.medworm.com/rss/comments.php?id=3817865 Fri, 23 Jul 2010 23:00:00 +0100 3817865 http://www.medworm.com/index.php?rid=3817868&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20647041%26dopt%3DAbstract Authors: Phillips JC, Lembcke L, Chamberlin T Spontaneous tumors in dogs share many of the same features of their human orthologues including clinical behavior, response to treatment, and molecular defects. It is therefore natural to consider the use of dogs and their spontaneous malignancies in the study of complex disease such as cancer. Scottish Deerhounds are a giant breed of dogs that exhibit a high incidence of bone cancer. Our previous work suggested that osteosarcoma within this breed could be explained by the presence of a major gene of dominant effect. Herein, we use a whole genome mapping approach to evaluate a four-generation pedigree of Scottish Deerhounds for linkage of their osteosarcoma phenotype. Using this approach we found evidence of linkage (Z(max)=5.766) between t... Genomics journals http://www.medworm.com/rss/comments.php?id=3817868 Sat, 17 Jul 2010 23:00:00 +0100 3817868 http://www.medworm.com/index.php?rid=3773372&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20643205%26dopt%3DAbstract Authors: Xing J, Watkins WS, Shlien A, Walker E, Huff CD, Witherspoon DJ, Zhang Y, Simonson TS, Weiss RB, Schiffman JD, Malkin D, Woodward SR, Jorde LB High-throughput genotyping data are useful for making inferences about human evolutionary history. However, the populations sampled to date are unevenly distributed, and some areas (e.g., South and Central Asia) have rarely been sampled in large-scale studies. To assess human genetic variation more evenly, we sampled 296 individuals from 13 worldwide populations that are not covered by previous studies. By combining these samples with a data set from our laboratory and the HapMap II samples, we assembled a final dataset of ~250,000 SNPs in 850 individuals from 40 populations. With more uniform sampling, the estimate of global genetic di... Genomics journals http://www.medworm.com/rss/comments.php?id=3773372 Thu, 15 Jul 2010 23:00:00 +0100 3773372 http://www.medworm.com/index.php?rid=3764086&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20633636%26dopt%3DAbstract Authors: Ahrazem O, Trapero A, Gómez MD, Rubio-Moraga A, Gómez-Gómez L The plastoglobule-targeted enzyme carotenoid cleavage dioxygenase (CCD4) mediates the formation of volatile C(13) ketones, such as beta-ionone, by cleaving the C(9)-C(10) and C(9')-C(10') double bonds of cyclic carotenoids. Here, we report the isolation and analysis of CCD4 genomic DNA regions in Crocus sativus. Different CCD4 alleles have been identified: CsCCD4a which is found with and without an intron and CsCCD4b that showed the presence of a unique intron. The presence of different CCD4 alleles was also observed in other Crocus species. Furthermore, comparison of the locations of CCD4 introns within the coding region with CCD4 genes from other plant species suggests that independent gain/losses have oc... Genomics journals http://www.medworm.com/rss/comments.php?id=3764086 Sun, 11 Jul 2010 23:00:00 +0100 3764086 http://www.medworm.com/index.php?rid=3764087&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20620207%26dopt%3DAbstract Authors: Muthusamy V, Bosenberg M, Wajapeyee N Epigenetic changes refer to heritable changes that may modulate gene expression without affecting DNA sequence. DNA methylation is one such heritable epigenetic change, which is causally associated with the transcription regulation of many genes in mammalian genome. Altered DNA methylation has been implicated in a wide variety of human diseases including cancer. Understanding the regulation of DNA methylation is likely to improve the ability to diagnose and treat these diseases. With the advent of high-throughput RNA interference (RNAi) screens, answering epigenetic questions on a genomic scale is now possible. Two recent genome-wide RNAi screens have addressed the regulation of DNA methylation in cancer, leading to the identification of t... Genomics journals http://www.medworm.com/rss/comments.php?id=3764087 Tue, 06 Jul 2010 23:00:00 +0100 3764087 http://www.medworm.com/index.php?rid=3730760&cid=s_35587_50_f&fid=35587&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D20603211%26dopt%3DAbstract Authors: Crainey JL, Hurst J, Wilson MD, Hall A, Post RJ A Bacterial Artificial Chromosome (BAC) library was made from wild-caught Simulium squamosum, which is an important vector of human onchocerciasis. The library is composed of 12,288 BACs, with an average insert size of 128kb, and is expected to contain approximately 1.54 GB of cloned DNA. Random BAC-end sequencing generated over 95 kb of DNA sequence data from which putative S. squamosum gene sequences and novel repetitive DNA families were identified, including DNA transposons, retrotransposons and simple sequence repeats (SSRs). The sequence survey also provided evidence of DNA of microbial origin, and dissection of sample blackflies indicated that that some of those used to prepare the library were likely to be parasitized by ... Genomics journals http://www.medworm.com/rss/comments.php?id=3730760 Thu, 01 Jul 2010 23:00:00 +0100 3730760