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 'BMC Genomics - Latest articles' source. Thu, 09 Feb 2012 09:43:28 +0100 http://www.medworm.com/index.php?rid=5672470&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F62 Conclusions: Taken together, our data suggest a robust cellular response that is likely regulated both at the transcriptional and post-transcriptional level in response to hypoxia by the human pathogenic mold A. fumigatus. As with other pathogenic fungi, the induction of glycolysis and transcriptional down-regulation of the TCA cycle and oxidative phosphorylation appear to major components of the hypoxia response in this pathogenic mold. In addition, a significant induction of the transcripts involved in ergosterol biosynthesis is consistent with previous observations in the pathogenic yeasts Candida albicans and Cryptococcus neoformans indicating conservation of this response to hypoxia in pathogenic fungi. Because ergosterol biosynthesis enzymes also require iron as a co-factor, the incr... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5672470 Mon, 06 Feb 2012 05:00:00 +0100 5672470 http://www.medworm.com/index.php?rid=5663352&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F60 Conclusions: In summary, the MTDB enables the exploration and comparative analysis of putative transporters in M. truncatula. A user-friendly web interface and regular updates make MTDB valuable to researchers in related fields. The MTDB is freely available now to all users at http://bioinformatics.cau.edu.cn/MtTransporter/. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5663352 Mon, 06 Feb 2012 05:00:00 +0100 5663352 http://www.medworm.com/index.php?rid=5663351&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F61 Conclusions: The novel strategy of first genotyping and then phenotyping a tagging population as proposed here is, in particular, applicable for long-lived, difficult to transform plant species. We could demonstrate the power of the ATDs transposon approach and the simplicity to induce ATDs transposition in vitro. Since a transposon is able to pass chromosomal boundaries, only very few primary transposon-carrying transgenic lines are required for the establishment of large transposon tagging populations. In contrast to T-DNA-based activation tagging, which is plagued by a lack of transformation efficiency and its time consuming nature, this for the first time, makes it feasible one day to tag (similarly to Arabidopsis) every gene within a perennial plant genome. (Source: BMC Genomics - Lat... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5663351 Mon, 06 Feb 2012 05:00:00 +0100 5663351 http://www.medworm.com/index.php?rid=5663353&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F58 Conclusions: Our findings confirm that the SOS response of the Vibrionaceae is strongly linked with pathogenicity and suggest that the characterization of the newly identified members of this regulon could provide key insights into the pathogenesis of Vibrio. The persistent location of key SOS genes in the large chromosome across several bacterial groups confirms that the SOS response plays an essential role in these organisms and sheds light into the mechanisms of evolution of global transcriptional networks involved in adaptability and rapid response to environmental changes, suggesting that small chromosomes may act as evolutionary test beds for the rewiring of transcriptional networks. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5663353 Fri, 03 Feb 2012 05:00:00 +0100 5663353 http://www.medworm.com/index.php?rid=5654734&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F55 Conclusions: Oikopleura has the smallest number of CYP genes among sequenced animal genomes and lacks the AhR signaling pathway. However it appears to have basic xenobiotic inducible biotransformation genes such as a conserved genotoxic stress response gene set. Our genome survey and expression study does not support a role of AhR signaling pathway in the chemical defense of metazoans prior to the emergence of vertebrates. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654734 Thu, 02 Feb 2012 05:00:00 +0100 5654734 http://www.medworm.com/index.php?rid=5654733&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F56 Conclusions: Our results have direct implications for resource allocation and further sequencing projects. It can be extrapolated that the number of newly identified genes still significantly increases with increasing number of new sequenced genomes. Furthermore, genome analysis of multiple phototrophic strains allows us to obtain a detailed picture of metabolic diversity that can serve as a starting point for biotechnological applications and automated metabolic reconstructions. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654733 Thu, 02 Feb 2012 05:00:00 +0100 5654733 http://www.medworm.com/index.php?rid=5654732&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F57 Conclusion: This study provides insight into the lignocellulose-degradation mechanisms by filamentous fungi and allows for the identification of a number of enzymes that are potentially useful to further improve the industrial lignocellulose bioconversion process. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654732 Thu, 02 Feb 2012 05:00:00 +0100 5654732 http://www.medworm.com/index.php?rid=5654738&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F51 Conclusion: These results document an important role for LRH-1 in hepatic metabolism through acting predominantly at proximal promoter sites and working in concert with additional nuclear receptors that bind to neighboring sites (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654738 Wed, 01 Feb 2012 05:00:00 +0100 5654738 http://www.medworm.com/index.php?rid=5654737&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F52 Drosophila melanogaster fruit flies raised in a zero-gravity environment created by a superconducting magnet show substantial changes in the expression of many essential genes, suggesting that extended weightlessness during space flight could also potentially have negative effects on cellular processes. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654737 Wed, 01 Feb 2012 05:00:00 +0100 5654737 http://www.medworm.com/index.php?rid=5654736&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F53 Conclusions: D. mojavensis chromosomal inversions were generated by multiple mechanisms, an observation that does not provide support for increased mutation rate as explanation for rapid chromosomal evolution. On the other hand, we have found a number of alterations of genes at the breakpoints with putative adaptive consequences that directly point to natural selection as the cause of D. mojavensis rapid chromosomal evolution. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654736 Wed, 01 Feb 2012 05:00:00 +0100 5654736 http://www.medworm.com/index.php?rid=5654735&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F54 Conclusions: Pathways analysis, using gene and protein expression data from two cell culture models, confirmed specific human HCC phenotypes with regard to CYPs and kinases, and revealed a zonation-related pattern of expression. Ubiquitin-mediated regulation mechanism gives plausible explanations of our findings. Altogether, our results suggest that strategies aimed at inhibiting activated kinases and signaling pathways may lead to enhanced metabolism-mediated drug resistance of treated tumors. If that were the case, mitigating inhibition or targeting inactive forms of kinases would be an alternative. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654735 Wed, 01 Feb 2012 05:00:00 +0100 5654735 http://www.medworm.com/index.php?rid=5654740&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F49 Conclusions: This study provides an understanding of the early defense signaling in rice cells. Components of the calcium and lipid signaling as well as MAPK cascade were modulated, by signals from surface receptors and cytosolic R-proteins, to arouse jasmonic acid and ethylene signaling and suppress auxin signaling through various transcription factors. Abscisic acid modulation was also evident through the expression regulation of transcription factors involved with its functions. Moreover adjustments in expression levels of components of primary as well as secondary metabolism, protein trafficking and turnout were apparent, highlighting the complexity of defense response. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654740 Tue, 31 Jan 2012 05:00:00 +0100 5654740 http://www.medworm.com/index.php?rid=5654739&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F50 Background: The liver X receptors (LXRs) are oxysterol sensing nuclear receptors with multiple effects on metabolism and immune cells. However, the complete genome-wide cistrome of LXR in cells of human origin has not yet been provided. Results: We performed ChIP-seq in phorbol myristate acetate-differentiated THP-1 cells (macrophage-type) after stimulation with the potent synthetic LXR ligand T0901317 (T09). Microarray gene expression analysis was performed in the same cellular model. We identified 1357 genome-wide LXR locations (FDR (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654739 Tue, 31 Jan 2012 05:00:00 +0100 5654739 http://www.medworm.com/index.php?rid=5654741&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F48 Conclusion: We show that the combination of whole genome association and selection signature mapping based on the same SNPs increases the power to detect loci influencing complex traits. The locus specific permutation based integrated haplotype score provides a formal test of significance in selection signature mapping. Importantly it does not rely on knowledge of ancestral and derived allele states.KEY WORDS selection signature, whole genome association, cattle, complex trait (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5654741 Mon, 30 Jan 2012 05:00:00 +0100 5654741 http://www.medworm.com/index.php?rid=5642450&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F47 Conclusions: Our results demonstrate that, with a suitable assembly methodology, WGP builds more robust physical maps than the SNaPshot technology in wheat and that WGP can be adapted to any genome. Moreover, WGP tag integration in sequence assemblies improves low quality assembly. However, to achieve a high quality draft sequence assembly, a sequencing depth of 25x paired-end reads is required, at which point WGP tag integration does not provide additional scaffolding value. Finally, we suggest that WGP tags can support the efficient sequencing of BAC pools by enabling reliable assignment of sequence scaffolds to their BAC of origin, a feature that is of great interest when using BAC pooling strategies to reduce the cost of sequencing large genomes. (Source: BMC Genomics - Latest articles... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5642450 Mon, 30 Jan 2012 05:00:00 +0100 5642450 http://www.medworm.com/index.php?rid=5633822&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F46 Conclusions: From all the obtained genes, 114 genes were up-regulated and 133 were down-regulated. Based on the NCBI GenBank and Gene Ontology databases, most of these genes are involved in relevant cell functions such as metabolism, transport, translation, signal transduction and cell cycle. After quantitative PCR analysis, the observed underexpression of the selected genes could underlie the previously reported OA-induced cytoskeleton disruption, neurotransmission alterations and in vivo neurotoxic effects. The basal expression levels obtained at 48 h suggested that surviving cells were able to recover from OA-caused gene expression alterations. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5633822 Fri, 27 Jan 2012 05:00:00 +0100 5633822 http://www.medworm.com/index.php?rid=5633826&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F42 Conclusion: T-quantile normalization applied separately on the channels and Tukey's biweight scaling outperform other methods in terms of the conservation of enriched and un-enriched signal separation, as well as in identification of genomic regions known to be enriched. T-quantile normalization is preferable as it additionally improves comparability between microarrays. In contrast, popular normalization approaches like quantile, LOWESS, Peng's method and VSN normalization alter the data distributions of regulation microarrays to such an extent that using these approaches will impact the reliability of the downstream analysis substantially. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5633826 Wed, 25 Jan 2012 05:00:00 +0100 5633826 http://www.medworm.com/index.php?rid=5633825&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F43 Conclusions: By employing PBS approach in NGS, large-scale multiplexed pooled samples could be practically analyzed in parallel so that high-throughput sequencing economically meets the requirements of samples which are low sequencing throughput demand. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5633825 Wed, 25 Jan 2012 05:00:00 +0100 5633825 http://www.medworm.com/index.php?rid=5633824&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F44 Conclusion: miRdSNP provides a comprehensive data source of dSNPs and robust tools for exploring their distance from miRNA target sites on the 3'UTRs of human genes. miRdSNP enables researchers to further explore the molecular mechanism of gene dysregulation for dSNPs at posttranscriptional level. miRdSNP is freely available on the web at http://mirdsnp.ccr.buffalo.edu. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5633824 Wed, 25 Jan 2012 05:00:00 +0100 5633824 http://www.medworm.com/index.php?rid=5633823&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F45 Conclusions: This is the first study to describe the comprehensive bovine milk transcriptome in Holstein cows. The results revealed that 69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk somatic cells. Most of the genes were ubiquitously expressed in all three stages of lactation. However, a fraction of the milk transcriptome has genes devoted to specific functions unique to the lactation stage. This indicates the ability of milk somatic cells to adapt to different molecular functions according to the biological need of the animal. This study provides a valuable insight into the biology of lactation in the cow, as well as many avenues for future research on the bovine lactome. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5633823 Wed, 25 Jan 2012 05:00:00 +0100 5633823 http://www.medworm.com/index.php?rid=5633829&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F39 Conclusion: Our studies have established conserved groups of nearly 800 protein clusters present in all haloarchaea, with a subset of 55 which are predicted to be accessory proteins that may be critical or essential for success in an extreme environment. These studies support core and signature genes and proteins as valuable concepts for understanding phylogenetic and phenotypic characteristics of coherent groups of organisms. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5633829 Tue, 24 Jan 2012 05:00:00 +0100 5633829 http://www.medworm.com/index.php?rid=5633828&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F40 Conclusions: These results suggest that RNase 8 may diverge considerably from typical RNase A family ribonucleases and may likewise exhibit unique function. This finding prompts a reconsideration of what we have previously termed functional pseudogenes, as RNase 8 may be responding to constraints that promote significant functional divergence from the canonical structure and enzymatic activity characteristic of the RNase A family. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5633828 Tue, 24 Jan 2012 05:00:00 +0100 5633828 http://www.medworm.com/index.php?rid=5633827&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F41 Conclusions: The miRNAome from artichoke, including novel miRNAs, was unveiled, providing useful information on the expression in different organs and conditions. New target genes were identified. We suggest that the generation of secondary short-interfering RNAs from miR393 target can be a general rule in the plant kingdom. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5633827 Tue, 24 Jan 2012 05:00:00 +0100 5633827 http://www.medworm.com/index.php?rid=5623739&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F37 Conclusions: We hypothesize that Spot 42 plays a key role in the central metabolism, in part by regulating the pyruvat dehydrogenase enzyme complex via pirin. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5623739 Tue, 24 Jan 2012 05:00:00 +0100 5623739 http://www.medworm.com/index.php?rid=5623738&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F38 Conclusions: Comparative genomic analyses across 12 Staphylococcus species provide hypotheses about lineages in which human adaptation has taken place and contributions of horizontal transfer in pathogenesis. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5623738 Tue, 24 Jan 2012 05:00:00 +0100 5623738 http://www.medworm.com/index.php?rid=5615702&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F36 Conclusions: The propagation of metabolic changes across the network of metabolism demonstrates that modification of the Delta9 desaturases places C.elegans into a catabolic state compared with wildtype controls. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5615702 Fri, 20 Jan 2012 05:00:00 +0100 5615702 http://www.medworm.com/index.php?rid=5615706&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F32 Conclusions: Implementation of a validated pipeline for NGS data acquisition and analysis provides highly reproducible results that are stable and predictable for molecular epidemiological applications. When draft genomes are collected at 15X-20X coverage and passed through a quality filter as part of a data analysis pipeline, including sub-passaged replicates defined by a few SNPs, they can be accurately placed in a phylogenetic context. This reproducibility applies to all levels within and between serovars of Salmonella suggesting that investigators using these methods can have confidence in their conclusions. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5615706 Thu, 19 Jan 2012 05:00:00 +0100 5615706 http://www.medworm.com/index.php?rid=5615705&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F33 Conclusions: Overall, these findings reveal the complexity of gene expression changes during liver development and maturation, and provide a foundation to predict responses to chemical and drug exposure as a function of early life-stages. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5615705 Thu, 19 Jan 2012 05:00:00 +0100 5615705 http://www.medworm.com/index.php?rid=5615704&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F34 Conclusion: The problems of ascertainment bias and missing information due to genotyping errors are widely recognized as limiting factors in genetic studies. We have conducted the first formal analysis of the effect of novel variants on genotyping arrays, and we have shown that these variants account for a large portion of miscalled and uncalled genotypes. Genetic studies will benefit from substantial improvements in the accuracy of their results by incorporating VINOs in their analyses. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5615704 Thu, 19 Jan 2012 05:00:00 +0100 5615704 http://www.medworm.com/index.php?rid=5615703&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F35 Conclusions The IntegromeDB search engine allows scanning data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. To perfect the resource design and usability, we welcome and encourage the community feedback. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5615703 Thu, 19 Jan 2012 05:00:00 +0100 5615703 http://www.medworm.com/index.php?rid=5615709&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F29 Conclusions: Our results show that centromeric repeat arrays on T. brucei chromosomes are more similar in size to those of higher eukaryotes than previously suspected. This information provides a firmer framework for investigating aspects of chromosome segregation and will allow epigenetic features associated with the process to be more accurately mapped. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5615709 Wed, 18 Jan 2012 05:00:00 +0100 5615709 http://www.medworm.com/index.php?rid=5615708&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F30 Conclusions: Microarray analysis revealed that the target of JTX might be the transcription machinery regulating the steady-state level of genes involved in the ISGF3-IRF7 cascade, whose effect is bi-directional in a strain- and microbiota-dependent manner. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5615708 Wed, 18 Jan 2012 05:00:00 +0100 5615708 http://www.medworm.com/index.php?rid=5615707&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F31 Conclusions: The cDNA sequences reported here expand existing feline genomic resources by providing high-quality sequences annotated with comparative genomic information providing functional, clinical, nutritional and orthologous gene information. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5615707 Wed, 18 Jan 2012 05:00:00 +0100 5615707 http://www.medworm.com/index.php?rid=5602648&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F28 Conclusions: The reduction of globin transcripts in whole blood samples constitutes a reproducible and reliable method that can enrich data obtained from next generation sequencing-based expression profiling. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5602648 Wed, 18 Jan 2012 05:00:00 +0100 5602648 http://www.medworm.com/index.php?rid=5602649&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F24 Conclusions: Our estimates of LD, although in good agreement with previous reports, are more comprehensive and based on a larger panel of markers. Our estimates also confirmed earlier findings reporting higher LD in pigs than in American Holstein cattle, especially at increasing marker distances (>1 Mb). High average LD (r2>0.4) between adjacent SNP found in this study is an important precursor for the implementation of marker assisted selection within a livestock species.Results of this study are relevant to the US purebred pig industry and critical for the design of programs of whole genome marker assisted evaluation and selection. In addition, results indicate that a more cost efficient implementation of marker assisted selection using low density panels with genotype imputation, would ... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5602649 Tue, 17 Jan 2012 05:00:00 +0100 5602649 http://www.medworm.com/index.php?rid=5602650&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F23 Conclusions: The provided protocol for RT-qPCR arrays enables straight-forward microRNA expression analysis. It is fully automatable, compliant with the MIQE guidelines and can be completed in only 1 day. The application of these arrays revealed microRNAs that may mediate monocyte host defence mechanisms by regulating the TGF-beta signalling upon Salmonella infection. The introduced arrays are furthermore suited for customised quantification of any class of small non-coding RNAs as exemplified by snRNAs and thus provide a versatile tool for ubiquitous applications. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5602650 Mon, 16 Jan 2012 05:00:00 +0100 5602650 http://www.medworm.com/index.php?rid=5590914&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F19 Conclusions: Mass sequence data of Chinese bayberry was obtained and the expression profiles were examined during fruit ripening. The UniGenes were annotated, providing a platform for functional genomic research with this species. Using pathway mapping and expression profiles, the molecular mechanisms for changes in fruit color and taste during ripening were examined. This provides a reference for the study of complicated metabolism in non-model perennial species. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590914 Fri, 13 Jan 2012 05:00:00 +0100 5590914 http://www.medworm.com/index.php?rid=5590913&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F20 Conclusions: The SBP marker technology described here allowed the development of molecular markers for targeted genomic regions of Arabidopsis. It should facilitate isolation of co-dominant molecular markers for targeted genomic regions of any animal or plant species, whose genomic sequences have been assembled. This technology will particularly facilitate the development of high density molecular marker maps, essential for cloning genes based on their genetic map positions and identifying tightly linked molecular markers for selecting desirable genotypes in animal and plant breeding experiments. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590913 Fri, 13 Jan 2012 05:00:00 +0100 5590913 http://www.medworm.com/index.php?rid=5590912&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F21 Conclusions: This paper describes the generation and characterisation of full-length cDNA sequences from E. tenella second generation merozoites and provides new insights into the E. tenella transcriptome. The data generated will be useful for the development and validation of diagnostic and control strategies for coccidiosis and will be of value in annotation of the E. tenella genome sequence. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590912 Fri, 13 Jan 2012 05:00:00 +0100 5590912 http://www.medworm.com/index.php?rid=5590911&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F22 Conclusions: Despite the small sample size, a total of 25 haplotypes and three single markers were identified including genomic regions not previously reported. The haplotypes that were analysed showed large effects on trait level. However, little overlap of QTL between breeds was observed. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590911 Fri, 13 Jan 2012 05:00:00 +0100 5590911 http://www.medworm.com/index.php?rid=5590916&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F17 Conclusion: LPS-primed MEC are fitter to repel pathogens and better protected against misguided attacks of the immune response. Attenuated is the exuberant expression of factors potentially promoting immunopathological processes. MEC therefore recapitulate many aspects of ET known so far from professional immune cells. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590916 Thu, 12 Jan 2012 05:00:00 +0100 5590916 http://www.medworm.com/index.php?rid=5590915&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F18 Conclusions: This approach, which leverages the advantages of RNA-seq approaches, enabled rapid generation of gene-linked SNP and haplotype markers. The general approach presented in this study can be easily applied to other non-model eukaryotes irrespective of the ploidy level to identify gene-linked polymorphisms that are expected to facilitate efficient Gene Assisted Breeding (GAB), genotyping and population genetics studies. The identified SNP haplotypes reveal some of the allelic differences in the two sweet cherry cultivars analyzed. The identification of these SNP and haplotype markers is expected to significantly improve the genomic resources for sweet cherry and facilitate efficient GAB in this non-model crop. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590915 Thu, 12 Jan 2012 05:00:00 +0100 5590915 http://www.medworm.com/index.php?rid=5590917&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F16 Conclusions: The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post-natal growth and development and subsequent lactogenesis and fertility. We have identified a large number of variants segregating at significantly different frequencies between cattle groups divergent for calving interval plausibly harbouring causative variants contributing to heritable variation. To our knowledge, this is the first report describing sequencing of targeted genomic regions in any livestock species using groups wi... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590917 Wed, 11 Jan 2012 05:00:00 +0100 5590917 http://www.medworm.com/index.php?rid=5590920&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F13 Conclusions: A set of 622 SNP markers providing consistent results was selected. Of the markers mined from Clementine, 80.5% were successfully transferred to the whole Citrus gene pool. Despite the ascertainment biases in relation to the Clementine origin, the SNP data confirm the important stratification of the gene pools around C. maxima, C. medica and C. reticulata as well as previous hypothesis on the origin of secondary species. The implemented SNP marker set will be very useful for comparative genetic mapping in Citrus and genetic association in C. reticulata. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590920 Tue, 10 Jan 2012 05:00:00 +0100 5590920 http://www.medworm.com/index.php?rid=5590919&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F14 Conclusions: Draft microbial genomes contain many ORF fragments. Where these correspond to the same gene they have particular potential to confound comparative gene content analyses. Given our findings, and the rapid increase in the number of microbial draft quality genomes, we suggest that accounting for gene fragmentation and its associated biases is important when designing comparative genomic projects. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590919 Tue, 10 Jan 2012 05:00:00 +0100 5590919 http://www.medworm.com/index.php?rid=5590918&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F15 Conclusions: Through comprehensive transcriptome analysis, we not only identified 29 novel gene families potentially involved in the biosynthesis of cardiac glycosides but also characterized a large number of mlncRNAs. Our results suggest the importance of mlncRNAs in secondary metabolism and stress response in D. purpurea. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5590918 Tue, 10 Jan 2012 05:00:00 +0100 5590918 http://www.medworm.com/index.php?rid=5575520&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F7 Conclusions: A combination of high throughput sequencing and molecular biology approaches was used to explore the involvement of miRNAs during fruit ripening. Several miRNAs showed differential expression profiles during fruit ripening, and a number of miRNAs were influenced by ethylene treatment. The results suggest the importance of miRNAs in fruit ripening and ethylene response. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5575520 Mon, 09 Jan 2012 05:00:00 +0100 5575520 http://www.medworm.com/index.php?rid=5567116&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F6 Conclusions: We developed significant molecular resources for C. lectularius putatively involved in metabolic resistance as well as those participating in other modes of insecticide resistance. RNA-Seq profiles of PR strains combined with tissue-specific profiles and molecular docking revealed multi-level insecticide resistance in C. lectularius. Future research that is targeted towards RNA interference (RNAi) on the identified metabolic targets such as cytochrome P450s and cuticular proteins could lay the foundation for a better understanding of the genetic basis of insecticide resistance in C. lectularius. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5567116 Fri, 06 Jan 2012 05:00:00 +0100 5567116 http://www.medworm.com/index.php?rid=5567118&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F4 Conclusions: This in-depth comparative analysis of nematode miRNAs reveals the high level of divergence across species and identifies novel sequences potentially involved in development. Expression of novel miRNAs may reflect adaptations to different environments and lifestyles. Our findings provide a detailed foundation for further study of the evolution and function of miRNAs within nematodes and for identifying potential targets for intervention. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5567118 Wed, 04 Jan 2012 05:00:00 +0100 5567118 http://www.medworm.com/index.php?rid=5567117&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F5 Conclusions: Initial errors are accumulated throughout the evolutionary analysis, generating artificially high rates of event predictions and leading to substantial uncertainty in the conclusions. This study emphasizes the urgent need for error detection and quality control strategies in order to efficiently extract knowledge from the new genome data. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5567117 Wed, 04 Jan 2012 05:00:00 +0100 5567117 http://www.medworm.com/index.php?rid=5567121&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F1 Conclusion: We have developed a robust and optimized Next-Generation sequencing library amplification method suitable for extremely AT-rich genomes. The new amplification conditions significantly reduce bias and retain the complexity of either extremes of base composition. This development will greatly benefit sequencing clinical samples that often require amplification due low mass of DNA starting material. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5567121 Tue, 03 Jan 2012 05:00:00 +0100 5567121 http://www.medworm.com/index.php?rid=5567120&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F2 Conclusion: A recently described yeast inverse one-hybrid screening allowed us to identify new Hh/Gli target genes, functionally important in different contexts of vertebrate embryonic development. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5567120 Tue, 03 Jan 2012 05:00:00 +0100 5567120 http://www.medworm.com/index.php?rid=5567119&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F13%2F3 Conclusion: The RAD tag sequencing approach is a cost-effective and rapid method to develop SNP markers in a highly heterozygous species. Our approach permitted to generate a large and robust SNP datasets by the adoption of optimized filtering criteria. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5567119 Tue, 03 Jan 2012 05:00:00 +0100 5567119 http://www.medworm.com/index.php?rid=5556135&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F637 Conclusions: These findings evoke an evolutionary scenario in which many CNEs evolved early in the vertebrate lineage to co-ordinate Hox-dependent gene-regulatory interactions that pattern the vertebrate head. In a broader context, our evolutionary analyses reveal that CNEs are composed of tightly linked transcription-factor binding-sites (TFBSs), which can be systematically identified through phylogenetic footprinting approaches. By placing a large number of ancient vertebrate CNEs into a developmental context, our findings promise to have a significant impact on efforts toward de-coding gene-regulatory elements that underlie vertebrate development, and will facilitate building general models of regulatory element evolution. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5556135 Fri, 30 Dec 2011 05:00:00 +0100 5556135 http://www.medworm.com/index.php?rid=5556134&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F638 Conclusions: We propose two explanations, the mutational pressure hypothesis, and the adaptive hypothesis. The mutational pressure hypothesis is that different co-factors bind to RNA pol II at different phases of transcription, producing different mutational regimes. The adaptive hypothesis is that cytidine triphosphate deficiency may lead to C-avoidance at the 3' ends of transcripts to control the flow of RNA pol II molecules and reduce their frequency of collisions. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5556134 Fri, 30 Dec 2011 05:00:00 +0100 5556134 http://www.medworm.com/index.php?rid=5556133&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F639 Conclusions: Our work demonstrates how FISH, which is assembly independent, can be efficiently used to solve assembly problems frequently encountered using the shotgun approach. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5556133 Fri, 30 Dec 2011 05:00:00 +0100 5556133 http://www.medworm.com/index.php?rid=5556138&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F634 Conclusions: Transcriptional profiling of thyroid hormone disrupted animals coupled with a novel bioinformatics search revealed new thyroid response elements associated with genes previously unknown to be responsive to thyroid hormone. The work provides insight into thyroid response element sequence motif characteristics. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5556138 Thu, 29 Dec 2011 05:00:00 +0100 5556138 http://www.medworm.com/index.php?rid=5556137&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F635 Conclusion: We provide an improved methodology for measuring gene expression changes in evolutionary diverged species using RNA Seq, where experimental artifacts can mimic evolutionary effects. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5556137 Thu, 29 Dec 2011 05:00:00 +0100 5556137 http://www.medworm.com/index.php?rid=5556136&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F636 Conclusion: A machine learning multivariate feature tool has been implemented in parallel and locally installable form, for plant miRNA target identification. The performance was assessed and compared through comprehensive testing and benchmarking, suggesting a reliable performance and gross usability for transcriptome wide plant miRNA target identification. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5556136 Thu, 29 Dec 2011 05:00:00 +0100 5556136 http://www.medworm.com/index.php?rid=5541614&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F631 Conclusion: Cluster thinning has a profound effect on several important cellular processes and metabolic pathways including carbohydrate metabolism and the synthesis and transport of secondary products. The integrated agronomic, biochemical and transcriptomic data revealed that the positive impact of cluster thinning on final berry composition reflects a much more complex outcome than simply enhancing the normal ripening process. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5541614 Fri, 23 Dec 2011 05:00:00 +0100 5541614 http://www.medworm.com/index.php?rid=5541613&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F632 Conclusions: Our investigation suggests that GC content is a predictor of AAR content in the protein coding sequence under certain conditions. Although angiosperm AARs lack conservation and 3D structure, a fraction of the proteins that contain AARs may be functionally important and are under extensive regulation in plant cells. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5541613 Fri, 23 Dec 2011 05:00:00 +0100 5541613 http://www.medworm.com/index.php?rid=5531301&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F627 Conclusion: These data suggest that H2BK123ub1 facilitates cross talk between chromatin and pre-mRNA splicing by modulating the distribution of intronic and exonic histone modifications. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531301 Thu, 22 Dec 2011 05:00:00 +0100 5531301 http://www.medworm.com/index.php?rid=5531300&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F628 Conclusion: We provide the first detailed annotation of the C. parapsilosis genome, based on gene predictions and transcriptional analysis. We identified a number of novel ORFs and other transcribed regions, and detected transcripts from approximately 90% of the annotated protein coding genes. We found that the transcription factor Upc2 role has a conserved role as a major regulator of the hypoxic response in C. parapsilosis and C. albicans. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531300 Thu, 22 Dec 2011 05:00:00 +0100 5531300 http://www.medworm.com/index.php?rid=5531299&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F629 Conclusions: A hybrid sequencing strategy using low sequencing depth of 454 and high sequencing depth of Illumina provided the good quality assembly with high N50 value and relatively low cost. A combination of Newbler, Velvet, and MIRA can be used to assemble the 454 sequence reads and the Illumina reads effectively. The assembled sequence can serve as a resource for comparative genome analysis. Additional long reads using the third generation sequencing platforms are needed to sequence through repetitive genome regions that should further enhance the sequence assembly. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531299 Thu, 22 Dec 2011 05:00:00 +0100 5531299 http://www.medworm.com/index.php?rid=5531298&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F630 Conclusions: Endothelial adaptation to mild-moderate hypothermia down-regulates anabolic processes and increases the reducing capacity of cells to enhance their resistance to oxidation and injury associated with 0 degrees C storage and rewarming. Inducing these characteristics in a clinical setting could potentially limit the damaging effects of energy insufficiency due to ischemia and prevent the disruption of integrated metabolism at low temperatures. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531298 Thu, 22 Dec 2011 05:00:00 +0100 5531298 http://www.medworm.com/index.php?rid=5531302&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F626 Conclusion: We have generated and characterized a reference transcriptome for rainbow trout that represents multiple tissues responding to multiple stressors common to aquaculture production environments. This resource compliments existing public transcriptome data and will facilitate approaches aiming to evaluate gene expression associated with stress in this species. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531302 Wed, 21 Dec 2011 05:00:00 +0100 5531302 http://www.medworm.com/index.php?rid=5531307&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F621 Conclusion: In this study, we report 14 new species and 8 new higher taxa that were not previously known to harbor DIRS1-like retrotransposons. Now reported in 61 species, these elements appear widely distributed among eukaryotes, even if they remain undetected in streptophytes and mammals. Especially in unikonts, a broad range of taxa from Cnidaria to Sauropsida harbors such elements. Both the distribution and the similarities between the DIRS1-like element phylogeny and conventional phylogenies of the host species suggest that DIRS1-like retrotransposons emerged early during the radiation of eukaryotes. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531307 Tue, 20 Dec 2011 05:00:00 +0100 5531307 http://www.medworm.com/index.php?rid=5531306&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F622 Conclusions: Although millions of SNPs have been identified, only a small subset needs to be genotyped in order to accurately predict ancestry with a minimal error rate in a cost-effective manner. In this article, we compared various methods for selecting ancestry informative SNPs using simulations as well as SNP genotype data from samples of admixed populations and showed that the In measure estimates ancestry proportion (in an admixed population) with lower bias and mean square error. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531306 Tue, 20 Dec 2011 05:00:00 +0100 5531306 http://www.medworm.com/index.php?rid=5531305&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F623 Conclusions: Detailed analyses of immune and olfaction gene expression across phenotypes demonstrated how transcriptomic analyses can inform our understanding of processes central to the biology of B. terrestris and the social Hymenoptera in general. For example, examination of immunity-related genes identified high conservation of important immunity pathway components across individual specimens from the life cycle stages while olfactory-related genes exhibited differential expression with a wider repertoire of gene expression within adults, especially sexuals, in comparison to immature stages. As there is an absence of replication across the samples, the results of this study are preliminary but provide a number of candidate genes which may be related to distinct phenotypic stage express... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531305 Tue, 20 Dec 2011 05:00:00 +0100 5531305 http://www.medworm.com/index.php?rid=5531304&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F624 Conclusions: Our data demonstrate the power of bioinformatic analyses for the identification of biologically relevant sequence motifs. LTSM and the here found LTSM-binding proteins NonO and SFPQ were discovered through a synergistic combination of bioinformatic and biochemical methods and are regulators of the expression of a set of genes of the translational apparatus in a distance-dependent manner. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531304 Tue, 20 Dec 2011 05:00:00 +0100 5531304 http://www.medworm.com/index.php?rid=5531303&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F625 Conclusions: This systems biology approach coupling proteome and transcriptome measurements provides a comprehensive view of viral gene expression that could not have been attained using each methodology independently. Detection of viral proteins in combination with viral transcripts is a potentially powerful method for establishing virus-disease relationships. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5531303 Tue, 20 Dec 2011 05:00:00 +0100 5531303 http://www.medworm.com/index.php?rid=5519567&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F611 Conclusions: This study demonstrates that genome-wide transcriptional profiling of PBL can distinguish active M. bovis-infected animals from control non-infected animals. Furthermore, the results obtained support previous investigations demonstrating that mycobacterial infection is associated with host transcriptional suppression. These data support the use of transcriptomic technologies to enable the identification of robust, reliable transcriptional markers of active M. bovis infection. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5519567 Mon, 19 Dec 2011 05:00:00 +0100 5519567 http://www.medworm.com/index.php?rid=5519566&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F612 Conclusions: Our results contribute to understanding the role of Simulium saliva in transmission of Onchocerca volvulus and evolution of salivary proteins in black flies. It also consists of a platform for mining novel anti-hemostatic compounds, vaccine candidates against filariasis, and immuno-epidemiologic markers of vector exposure. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5519566 Mon, 19 Dec 2011 05:00:00 +0100 5519566 http://www.medworm.com/index.php?rid=5519565&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F613 Conclusions: The heterotrimeric G-protein pathway is crucial for the interconnection of nutrient signaling and light response of T. reesei, with the class I phosducin-like protein PhLP1, GNB1 and GNG1 acting as important nodes, which influence light responsiveness, glycoside hydrolase gene transcription and sexual development. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5519565 Mon, 19 Dec 2011 05:00:00 +0100 5519565 http://www.medworm.com/index.php?rid=5519564&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F614 Conclusions: Our work demonstrates that training on organism-specific data results in an improvement that extends to related species. PhosTryp is freely available at http://phostryp.bio.uniroma2.it (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5519564 Mon, 19 Dec 2011 05:00:00 +0100 5519564 http://www.medworm.com/index.php?rid=5519563&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F615 Conclusion: The map presented here represents a valuable resource for addressing important questions of interest to evolution (the process of re-diploidization), aquaculture and salmonid life history biology and not least as a resource to aid the assembly of the forthcoming Atlantic salmon reference genome sequence. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5519563 Mon, 19 Dec 2011 05:00:00 +0100 5519563 http://www.medworm.com/index.php?rid=5519568&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F609 Conclusions: Three putative autonomous elements were identified, which encoded an intact Rep motif and a DNA helicase domain, suggesting that autonomous helitrons may exist in modern maize. The results indicate that gene fragments captured during the transposition of many helitrons happen in a stepwise way, with multiple gene fragments within one helitron resulting from several sequential transpositions. In addition, we have proposed a potential mechanism regarding how helitrons with multiple termini are generated. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5519568 Sat, 17 Dec 2011 05:00:00 +0100 5519568 http://www.medworm.com/index.php?rid=5510716&cid=s_34030_50_f&fid=34030&url=%24%7Bitem.link%7D Conclusions: Pest resistance was associated with individual candidate genes as well as with trans-regulatory hotspots along the spruce genome. Our results showed that specific genes within the phenylpropanoid pathway have been duplicated and diversified in the conifer in a process fundamentally different from short-lived angiosperm species. These findings add to the information about the role of the phenylpropanoid pathway in the evolution of plant defense mechanisms against insect pests and provide substantial potential for the functional characterization of several not yet resolved alternative pathways in plant defenses. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5510716 Fri, 16 Dec 2011 05:00:00 +0100 5510716 http://www.medworm.com/index.php?rid=5510718&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F606 Conclusions: Ae. aegypti has a large piRNA complement that maps to transposons but primarily gene sequences, including many viral-derived sequences. This, together with the more uniform distribution of piRNA clusters throughout its genome suggests that some aspects of the piRNA system differ between Ae. aegypti and D. melanogaster. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5510718 Thu, 15 Dec 2011 05:00:00 +0100 5510718 http://www.medworm.com/index.php?rid=5510717&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F607 Conclusions: This study has revealed strong genetic structure in the gene expression program within ovine longissimus lumborum muscle. The balance between muscle protein synthesis, at the levels of both transcription and translation control, and protein catabolism mediated by regulated proteolysis is likely to be the primary determinant of the genetic merit for the muscling trait in this sheep population. There is also evidence that high genetic merit for muscling is associated with a fibre type shift toward fast glycolytic fibres. This study provides insight into mechanisms, presumably subject to strong artificial selection, that underpin enhanced muscling in sheep populations. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5510717 Thu, 15 Dec 2011 05:00:00 +0100 5510717 http://www.medworm.com/index.php?rid=5510720&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F604 Conclusions: Recognizing the role of subfunctionalization as a dosage-imbalance buffer in gene duplication events enabled us to reconcile its mechanistic nonadaptive origin with its adaptive role as an enabler of the evolution of genetic redundancy. This constructive role was established in this paper by proving the following assertion: If subfunctionalization is indeed adaptive, its effect on paralog segregation should scale with the dosage sensitivity of the duplicated genes. Thus, subfunctionalization becomes adaptive in response to the selection forces arising from the fitness bottleneck imposed by gene duplication. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5510720 Wed, 14 Dec 2011 05:00:00 +0100 5510720 http://www.medworm.com/index.php?rid=5510719&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F605 Conclusions: Our results suggest that the cold-stress response of mRNA expression may be governed mainly through regulatory modes other than miRNA-mediated regulation. MiRNAs in animal brains might act more as developmental regulators than thermal adaptability regulators. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5510719 Wed, 14 Dec 2011 05:00:00 +0100 5510719 http://www.medworm.com/index.php?rid=5499911&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F601 Conclusion: Experimental results establish the principle that dynamic chromatin remodeling data can be used in lieu of gene expression data to discover binding motifs and their transcription factor binding sites. Our approach can be applied using only dynamic nucleosome positioning data, independent from any knowledge of gene function or expression. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5499911 Tue, 13 Dec 2011 05:00:00 +0100 5499911 http://www.medworm.com/index.php?rid=5499910&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F602 Conclusions: Novel temporal patterns of gene expression have been uncovered, suggesting a unique,coordinated and highly complex mechanism underlying the muscle wasting associated withAQM in ICU patients and providing new target genes and avenues for intervention studies. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5499910 Tue, 13 Dec 2011 05:00:00 +0100 5499910 http://www.medworm.com/index.php?rid=5499909&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F603 Conclusions: The Gene Wiki is a rapidly growing corpus of text focused on human gene function. Here, we demonstrate that the Gene Wiki can be a powerful resource for generating ontology-based gene annotations. These annotations can be used immediately to improve workflows for building curated gene annotation databases and knowledge-based statistical analyses. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5499909 Tue, 13 Dec 2011 05:00:00 +0100 5499909 http://www.medworm.com/index.php?rid=5499913&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F598 Conclusions: Combining this read length with sequencing in the 5' to 3' direction would allow a read length of over twenty bases on a single tag. Implementing mate-paired tags and this SBL variation could enable >95% coverage of the genome. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5499913 Mon, 12 Dec 2011 05:00:00 +0100 5499913 http://www.medworm.com/index.php?rid=5499912&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F599 Conclusions: Our findings suggest that a combination of factors contribute to duplicate gene persistence following whole genome duplication, but that the total expression level and evenness of expression across tissues and through development before duplication are most important. We speculate that these parameters are useful predictors of duplicate gene longevity after whole genome duplication in other taxa. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5499912 Mon, 12 Dec 2011 05:00:00 +0100 5499912 http://www.medworm.com/index.php?rid=5491465&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F597 Conclusions: In the present study, we employed a liquid hybridisation capture system to enrich for exon regions and then combined with bisulfite sequencing to examine the methylation statuses for the first time. This technique is highly sensitive and flexible and can be applied to identify differentially methylated regions (DMRs) at specific genomic locations of interest, such as within regulatory elements or promoters. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5491465 Thu, 08 Dec 2011 05:00:00 +0100 5491465 http://www.medworm.com/index.php?rid=5481684&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F595 Background: Wolbachia are endosymbiotic bacteria that are frequently found in arthropods and nematodes. These maternally inherited bacteria manipulate host reproduction by several mechanisms including cytoplasmic incompatibility (CI). CI is the most common phenotype induced by Wolbachia and results in the developmental arrest of embryos derived from crosses between Wolbachia-infected males and uninfected females. Although the molecular mechanisms of CI are currently unknown, several studies suggest that host sperm is modified by Wolbachia during spermatogenesis. Results: We compared the gene expression of Drosophila melanogaster larval testes with and without the wMel strain of Wolbachia to identify candidate genes that could be involved in the interaction between Wolbachia and the insect ... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5481684 Tue, 06 Dec 2011 05:00:00 +0100 5481684 http://www.medworm.com/index.php?rid=5481683&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F596 Conclusions: Genome-wide investigation of GPCRs in two platyhelminth genomes reveals an extensive and complex receptor signaling repertoire with many unique features. This work provides important sequence and functional leads for understanding basic flatworm receptor biology, and sheds light on a lucrative set of anthelmintic drug targets. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5481683 Tue, 06 Dec 2011 05:00:00 +0100 5481683 http://www.medworm.com/index.php?rid=5481686&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F593 Conclusion: The evolving role for CTCF in ER biology is complex, but is likely to be multifunctional and possibly influenced by the specific genomic locus. Our data suggest a positive, pro-transcriptional role for CTCF in ER-mediated gene expression in breast cancer cells. CTCF not only provides boundaries for accessible and 'protected' transcriptional blocks, but may also influence the actual binding of ER to the chromatin, thereby modulating the estrogen-mediated gene expression changes observed in breast cancer cells. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5481686 Mon, 05 Dec 2011 05:00:00 +0100 5481686 http://www.medworm.com/index.php?rid=5481685&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F594 Conclusions: The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5481685 Mon, 05 Dec 2011 05:00:00 +0100 5481685 http://www.medworm.com/index.php?rid=5472849&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F591 Conclusion: In this study we report the identification of a causal mutation for infertility caused by spermatogenic arrest at an early meiotic phase. Our results highlight the role of TEX14 specifically in spermatogenesis and the importance of specific genomic remodeling events as causes for inherited defects. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5472849 Fri, 02 Dec 2011 05:00:00 +0100 5472849 http://www.medworm.com/index.php?rid=5472848&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F592 Conclusions: We provided a network-based analysis to detect dysfunctional modules and disease genes of CHD by modeling the information transmission from source disease genes to targets of differentially expressed genes. Our method resulted in 12 modules from the constructed CHD subnetwork. We further identified and prioritized candidate disease genes of CHD from these dysfunctional modules. In conclusion, module analysis not only revealed several important findings with regard to the underlying molecular mechanisms of CHD, but also suggested the distinct network properties of causal disease genes which lead to identification of candidate CHD genes. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5472848 Fri, 02 Dec 2011 05:00:00 +0100 5472848 http://www.medworm.com/index.php?rid=5463706&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F590 Conclusion: Our findings demonstrate that a significant number of genes are still absent from the incomplete human reference genome, highlighting the importance of further refining the human reference genome and curating those missing genes. Our study also shows the importance of de novo transcriptome assembly. The comparative approach between reference genome and other related human genomes based on the transcriptome provide an alternative way to refine the human reference genome. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5463706 Fri, 02 Dec 2011 03:28:10 +0100 5463706 http://www.medworm.com/index.php?rid=5463708&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F588 Conclusions: The majority of Ds-related sequences in maize correspond to Dsl elements that do not transpose in the presence of Ac. Unlike actively transposing elements, many Dsl elements are inserted in repetitive DNA, where they probably become methylated and begin to decay. The filler DNA present in most elements is occasionally captured from genes, a rare feature in transposons of the hAT superfamily to which Ds belongs. Maize inbreds of different origin are highly polymorphic in their DNA transposon makeup. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5463708 Thu, 01 Dec 2011 05:00:00 +0100 5463708 http://www.medworm.com/index.php?rid=5463707&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F589 Conclusions: The magnitude of systematic processing noise in a microarray experiment is variable across probes and experiments, however it is generally the case that procedures earlier in the sample-preparation workflow are liable to introduce the most noise. Careful experimental design is important to protect against noise, detailed meta-data should always be provided, and diagnostic procedures should be routinely performed prior to downstream analyses for the detection of bias in microarray studies. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5463707 Thu, 01 Dec 2011 05:00:00 +0100 5463707 http://www.medworm.com/index.php?rid=5463709&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F587 Conclusion: It is necessary to continue to sequence cDNA from different developmental stages, particularly those of non-erythrocytic stages. The presence of antisense transcripts in some gametocyte and ookinete genes suggests that these antisense RNA may play an important role in gene expression regulation and parasite development. Future gene expression studies should make use of directional cDNA libraries. Antisense transcripts may partly explain the observed discrepancy between levels of mRNA and protein expression. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5463709 Wed, 30 Nov 2011 05:00:00 +0100 5463709 http://www.medworm.com/index.php?rid=5463711&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F585 Conclusions: P. damicornis now joins the handful of coral species for which extensive transcriptomic data are publicly available. Through PocilloporaBase (www.PocilloporaBase.org), one can obtain assembled contigs and raw reads and query the data according to a wide assortment of attributes including taxonomic origin, PFAM motif, KEGG pathway, and GO annotation. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5463711 Tue, 29 Nov 2011 05:00:00 +0100 5463711 http://www.medworm.com/index.php?rid=5463710&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F586 Conclusions: These findings suggest that although the full complement of the major RNA degradation mechanisms were present - and likely functional - early in eukaryotic evolution, the composition and function of the complexes is more variable than previously appreciated. We suggest that the missing components of the exosome complex provide an explanation for the stable abundance of sterile RNA species in Giardia. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5463710 Tue, 29 Nov 2011 05:00:00 +0100 5463710 http://www.medworm.com/index.php?rid=5453127&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F583 Conclusion: Transcriptional induction of DNA damage response is an essential feature of the bactericidal effect of trimethoprim. Either the observation of the transcriptional response or DNA damage itself, or both, is made possible by thymine starvation when other folate-dependent metabolites are not limited. The effect of DNA damage by the drug takes place prior to its bactericidal effect, at the beginning of the lag stage of the treatment. Mutations in the deoxyribose nucleotide salvage pathway can affect duration of the lag as well as the rate of killing. This information can be used to postulate certain mechanistic differences between direct thymine starvation in thymidylate synthase deficient mutants and thymine starvation by anti-folate inhibitors. (Source: BMC Genomics - Latest arti... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5453127 Mon, 28 Nov 2011 05:00:00 +0100 5453127 http://www.medworm.com/index.php?rid=5453126&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F584 Conclusions: The genome information and phenotypic data obtained in vitro and in a chicken infection model provided little evidence of fixed adaptation to a specific host. Instead, the dominant C. jejuni ST-21 appeared to be characterized by phenotypic flexibility and high genetic microdiversity, revealing properties of a generalist. High genetic flexibility might allow generalist variants of C. jejuni to reversibly express diverse fitness factors in changing environments. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5453126 Mon, 28 Nov 2011 05:00:00 +0100 5453126 http://www.medworm.com/index.php?rid=5446420&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F579 Conclusions: To demonstrate the capabilities of the new microarray, we analyzed transcript levels for cultures grown under nitrogen as well as sulfate limitation, and compared the results with recently published microarray and RNA-seq data. We could thereby confirm previous results derived from data on nutrient-starvation induced gene expression of a group of genes related to protein transport and adaptation of the metabolism as well as genes related to efficient light harvesting, light energy distribution and photosynthetic electron transport. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5446420 Fri, 25 Nov 2011 05:00:00 +0100 5446420 http://www.medworm.com/index.php?rid=5446419&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F580 Conclusions: There is a difference between viral and cellular CpG underrepresentation. There is a significant correlation between viral observed and expected CpG numbers. There are lack of correlation between PCS from several genomic region pairs, especially those involving LCR and E6. L2 and L1 ORF behavior is opposite to that of oncogenes E6 and E7. The first pair possesses relatively low numbers of CpG sites clustered in CGIs while the oncogenes possess a relatively high number of CpG sites not associated to CGIs. In all HPVs, E2/E4 is the only region with at least one CGI and shows a higher content of CpG sites in every HPV type with an identified E4. The mucosal HR-HPVs show either the shortest CGI size, followed by the mucosal LR-HPVs and lastly by the cutaneous viral subgroup, and a... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5446419 Fri, 25 Nov 2011 05:00:00 +0100 5446419 http://www.medworm.com/index.php?rid=5446418&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F581 Conclusions: The amphipod P. hawaiensis has higher transcript complexity than known insect transcriptomes, and trans-splicing does not appear to be a major contributor to this complexity. We discuss the importance of a reliable comparative genomic framework within which to consider findings from new crustacean models such as D. pulex and P. hawaiensis, as well as the need for development of further substantial crustacean genomic resources. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5446418 Fri, 25 Nov 2011 05:00:00 +0100 5446418 http://www.medworm.com/index.php?rid=5446417&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F582 Conclusions: our work provides novel insights into epigenetic gene regulation by native lipoproteins. Furthermore, we provide an example of DNMT1 acting as a de novo DNA methyltransferase independently of canonical de novo enzymes, and show proof of principle that de novo DNA methylation can occur independently of a functional Dicer/micro-RNA pathway in mammals. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5446417 Fri, 25 Nov 2011 05:00:00 +0100 5446417 http://www.medworm.com/index.php?rid=5446422&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F576 Conclusions: Extensive diversity was observed in the number and content of the T6SS loci among the Pantoea and Erwinia species. Genomic islands could be observed within some of T6SS loci, which are associated with the hcp and vgrG proteins and carry putative effector domain proteins. We propose new hypotheses concerning a role for these islands in the acquisition of T6SS effectors and the development of novel evolved VgrG and Hcp proteins. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5446422 Thu, 24 Nov 2011 05:00:00 +0100 5446422 http://www.medworm.com/index.php?rid=5446421&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F577 Conclusions: The genome of Thermus scotoductus SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to Thermus thermophilus. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of Thermus scotoductus illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5446421 Thu, 24 Nov 2011 05:00:00 +0100 5446421 http://www.medworm.com/index.php?rid=5446425&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F571 Conclusions: The global gene expression profiles provide insight into the cellular mechanisms that regulate the unique characteristics observed in immortal DF-1 CEF cells. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5446425 Wed, 23 Nov 2011 05:00:00 +0100 5446425 http://www.medworm.com/index.php?rid=5446424&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F574 Conclusions: The establishment of a MAPK "road map" based on the most advanced mosquito genome annotation can accelerate our understanding of host-pathogen interactions and broader physiology of An. gambiae and other mosquito species. Further, future efforts to develop predictive models of anopheline cell signaling responses, based on iterative construction and refinement of data-based and literature-based knowledge of the MAP kinase cascades and other networked pathways will facilitate identification of the "master signaling regulators" in biomedically important mosquito species. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5446424 Wed, 23 Nov 2011 05:00:00 +0100 5446424 http://www.medworm.com/index.php?rid=5446423&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F575 Conclusions: This study represents the first transcriptional profiling approach investigating the effects of different concentrations of gossypol in a lepidopteran species. H. armigera's transcriptional response to gossypol feeding is tissue- and dose-dependent and involves diverse detoxifying mechanisms not only to alleviate direct effects of gossypol but also indirect damage such as pH disturbance and oxygen radical formation. Genes discovered through this transcriptional approach may be additional candidates for understanding gossypol detoxification and coping with gossypol-induced stress. In a generalist herbivore that has evolved transcriptionally-regulated responses to a variety of different plant compounds, hormesis may be due to a lower induction threshold of growth-promoting, stre... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5446423 Wed, 23 Nov 2011 05:00:00 +0100 5446423 http://www.medworm.com/index.php?rid=5436177&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F569 Conclusion: The eight scaffolds contained about 215- 225 Mb of peach genomic sequences with one SNP/ ~40,000 bases. All sequences from Roche 454 and Illumina/Solexa have been submitted to NCBI for public use in the Short Read Archive database. SNPs have been deposited in the NCBI SNP database. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5436177 Tue, 22 Nov 2011 05:00:00 +0100 5436177 http://www.medworm.com/index.php?rid=5436179&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F567 Conclusion: Our results demonstrate that stratifying genetic population by molecular phenotypes followed by QTL analysis on various subtypes can lead to identification of novel and interacting QTL. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5436179 Mon, 21 Nov 2011 05:00:00 +0100 5436179 http://www.medworm.com/index.php?rid=5436178&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F568 Conclusions: Our study provides an abundance of linked markers spanning all chromosomes. Many of these markers are also found in multiple populations of T. californicus, and in two other species in the genus. The genomic resource we have developed will enable mapping throughout the geographical range of this species and in closely related species. This linkage map will facilitate genome sequencing, mapping and assembly in an ecologically and taxonomically interesting group for which genomic resources are currently under development. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5436178 Mon, 21 Nov 2011 05:00:00 +0100 5436178 http://www.medworm.com/index.php?rid=5426995&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F566 Conclusions: Our observations suggest strikingly similar organization of interband chromatin in polytene chromosomes and in chromosomes from cell lines thereby reflecting the existence of a basic principle of interphase chromosome organization. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5426995 Fri, 18 Nov 2011 05:00:00 +0100 5426995 http://www.medworm.com/index.php?rid=5415627&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F564 Conclusions: AluScan, implemented with just a small number of H-type and T-type inter-Alu PCR primers, provides an effective capture of a diversity of genome-wide sequences for analysis. The method, by enabling an examination of gene-enriched regions containing exons, introns, and intergenic sequences with modest capture and sequencing costs, computation workload and DNA sample requirement is particularly well suited for accelerating the discovery of somatic mutations, as well as analysis of disease-predisposing germline polymorphisms, by making possible the comparative genome-wide scanning of DNA sequences from large human cohorts. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5415627 Thu, 17 Nov 2011 05:00:00 +0100 5415627 http://www.medworm.com/index.php?rid=5415626&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F565 Conclusions: The NOD/SCID xenograft mouse model provides a reproducible experimental system in which to investigate clinically-relevant mechanisms of drug-induced gene regulation in ALL; the 8 hour timepoint provides the highest number of significantly differentially expressed genes; time-matched controls are redundant and excellent recovery scores can be obtained with 3 replicates. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5415626 Thu, 17 Nov 2011 05:00:00 +0100 5415626 http://www.medworm.com/index.php?rid=5415629&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F562 Conclusion: Radiation hybrids are a useful tool for high resolution mapping of cis and trans loci capable of affecting gene expression due to copy number change. Analysis of two independent radiation hybrid panels show agreement in their findings and may serve as a discovery source for novel regulatory loci in noncoding regions of the genome. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5415629 Wed, 16 Nov 2011 05:00:00 +0100 5415629 http://www.medworm.com/index.php?rid=5415628&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F563 Conclusions: Finding latent factors using GLFD brings extra insight into the mechanisms of the disease/drug response. The R code of the method is available at http://userwww.service.emory.edu/~tyu8/GLFD. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5415628 Wed, 16 Nov 2011 05:00:00 +0100 5415628 http://www.medworm.com/index.php?rid=5415632&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F559 Conclusions: Substantial genetic differences exist between the Black Angus and Holstein animals sequenced in this work and the Hereford reference sequence, and some of this variation is predicted to affect evolutionarily conserved amino acids or gene copy number. The deeply annotated SNPs and CNVs identified in this resequencing study can serve as useful genetic tools, and as candidates in searches for phenotype-altering DNA differences. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5415632 Tue, 15 Nov 2011 05:00:00 +0100 5415632 http://www.medworm.com/index.php?rid=5415631&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F560 Conclusions: Our findings suggest that HNF4alpha, in addition to regulating gene expression via high affinity binding sites, may also modulate transcription via low affinity sites in Alu repeats. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5415631 Tue, 15 Nov 2011 05:00:00 +0100 5415631 http://www.medworm.com/index.php?rid=5415630&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F561 Conclusions: Our rigorous approach provides a template for the analysis of the regulation of large gene families and demonstrates some of the difficulties and pitfalls of such analyses. Although currently available bioinformatics methods cannot detect all transcriptional regulatory elements, our thorough analysis of OR promoters shows that in the case of this gene family, experimental approaches have probably already identified all the binding factors common to large fractions of OR promoters. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5415630 Tue, 15 Nov 2011 05:00:00 +0100 5415630 http://www.medworm.com/index.php?rid=5415634&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F557 Conclusions: Our results provide high resolution mapping of diverse classes of genomic variation in an individual bovine genome and demonstrate that structural variation surpasses sequence variation as the main component of genomic variability. Better accuracy of SNP detection was achieved with little loss of sensitivity when algorithms that implemented mapping quality were used. IBD regions were found to be instrumental for calculating resequencing SNP accuracy, while SNP detection within CNVs tended to be less reliable. CNV discovery was affected dramatically by platform resolution and coverage biases. The combined data for this study showed that at a moderate level of sequencing coverage, an ensemble of platforms and tools can be applied together to maximize the accurate detection of se... BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5415634 Mon, 14 Nov 2011 05:00:00 +0100 5415634 http://www.medworm.com/index.php?rid=5415633&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F558 Conclusions: The MetJ regulon is present and functional in five orders of gammaproteobacteria: Enterobacteriales, Pasteurellales, Vibrionales, Aeromonadales and Alteromonadales. New regulatory activity for MetJ was identified in the genomic data and verified experimentally. This strategy should be applicable for the elucidation of regulatory pathways in other systems by using the extensive sequencing data currently being generated. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5415633 Mon, 14 Nov 2011 05:00:00 +0100 5415633 http://www.medworm.com/index.php?rid=5404031&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F556 Conclusion: This study provided abundant ESTs that could contribute greatly to disclosing novel genes in marine fish. Furthermore, the alterations of predicted gene expression patterns reflected possible responses of these fish to the virus infection. Taken together, our data not only provided new information for identification of novel genes from marine vertebrates, but also shed new light on the understanding of defense mechanisms of marine fish to viral pathogens. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5404031 Sat, 12 Nov 2011 05:00:00 +0100 5404031 http://www.medworm.com/index.php?rid=5404033&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F553 Conclusions: The BAC library for bald cypress is the first to be generated for a conifer species outside of the family Pinaceae. The Taxodium BAC library was shown to be useful in gene isolation and genome characterization and should be an important tool in gymnosperm comparative genomics, physical mapping, genome sequencing, and gene/polymorphism discovery. The single/low-copy (SL) component of bald cypress is 4.6 times the size of the Arabidopsis genome. As suggested for other gymnosperms, the large amount of SL DNA in Taxodium is likely the result of divergence among ancient repeat copies and gene/pseudogene duplication. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5404033 Fri, 11 Nov 2011 05:00:00 +0100 5404033 http://www.medworm.com/index.php?rid=5404032&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F554 A new genetic nomenclature for the anole lizard genus, which contains important emerging model species, offers a standardized gene vocabulary and also presents a template for similar initiatives in other research communities. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5404032 Fri, 11 Nov 2011 05:00:00 +0100 5404032 http://www.medworm.com/index.php?rid=5394521&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F551 Conclusions: The sympathetic neuron model is one of the best studied models of neuronal apoptosis. Overall, our microarray data gives a comprehensive overview of, and provides new information about, signalling pathways and transcription factors that are regulated by NGF withdrawal. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5394521 Tue, 08 Nov 2011 05:00:00 +0100 5394521 http://www.medworm.com/index.php?rid=5394520&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F552 Conclusions: RNA-seq is a powerful tool to gain insight into complex transcriptomes. In addition to uncovering many unnanotated genes, our study allowed us to determine that a considerable fraction is made up of long non-coding transcripts and transposable elements. Their biological roles remain to be determined in future studies. In terms of differences in expression between Large White and Iberian pigs, these were largest for genes involved in spermatogenesis and lipid metabolism, which is consistent with phenotypic extreme differences in prolificacy and fat deposition between these two breeds. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5394520 Tue, 08 Nov 2011 05:00:00 +0100 5394520 http://www.medworm.com/index.php?rid=5394522&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F550 Conclusions: Results indicate that Giardia intestinalis and Trichomonas vaginalis, like their distant multicellular relatives, contain a rich infrastructure of RNA-based processing. From here we can investigate the evolution of RNA processing networks in eukaryotes. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5394522 Sun, 06 Nov 2011 04:00:00 +0100 5394522 http://www.medworm.com/index.php?rid=5394524&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F548 Conclusion: Genetic analysis of transcription levels revealed dependence among molecular phenotypes as being affected by variation at the same loci. We observed the genetic variation of molecular phenotypes in a specific situation of cellular stress thus contributing to a better description of muscle physiologic response. In turn, this suggests that large amounts of genetic variation, mediated through transcriptional networks, can drive transient cell response phenotypes and contribute to organismal adaptative potential. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5394524 Fri, 04 Nov 2011 04:00:00 +0100 5394524 http://www.medworm.com/index.php?rid=5394523&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F549 Conclusions: We found that HMGA1 induces inflammatory pathways early in lymphoid tumorigenesis and pathways involved in stem cells, cell cycle progression, and cancer in established tumors. HMGA1 also dyregulates genes and pathways involved in stem cells, cellular development and hematopoiesis at both early and late stages of tumorigenesis. These results provide insight into HMGA1 function during tumor development and point to cellular pathways that could serve as therapeutic targets in lymphoid and other human cancers with aberrant HMGA1 expression. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5394523 Fri, 04 Nov 2011 04:00:00 +0100 5394523 http://www.medworm.com/index.php?rid=5372229&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F543 Conclusions: Our results demonstrate that conclusions based only on databases with automatically annotated ncRNAs can be erroneous. Special investigations aimed to distinguish true RNA genes from their pseudogenes should be done. Zhu and coworkers, as well as most other groups studying vertebrate snoRNAs, give new names to newly described homologs of human snoRNAs, which significantly complicates comparison between different species. It seems necessary to develop a uniform nomenclature for homologs of human snoRNAs in other vertebrates, e.g., human gene names prefixed with several-letter code denoting the vertebrate species. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372229 Thu, 03 Nov 2011 04:00:00 +0100 5372229 http://www.medworm.com/index.php?rid=5372228&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F544 Conclusions: In this study we introduce a general framework to accurately predict the level of RNAPII recruitment, elongation, stalling and mRNA expression from chromatin signals. The versatility of the method also makes it ideally suited to investigate other genomic data. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372228 Thu, 03 Nov 2011 04:00:00 +0100 5372228 http://www.medworm.com/index.php?rid=5372227&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F545 Conclusions: The genome sequence of C. variabile provides detailed insights into the distinct metabolic features of this bacterium, implying a strong adaption to the iron-depleted cheese surface habitat. By combining in silico data obtained from the genome annotation with previous experimental knowledge, occasional observations on genes that are involved in the complex metabolic capacity of C. variabile were integrated into a global view on the lifestyle of this species. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372227 Thu, 03 Nov 2011 04:00:00 +0100 5372227 http://www.medworm.com/index.php?rid=5372226&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F546 Conclusions: With the miRNA expression library we provide a versatile tool for the systematic elucidation of miRNA function. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372226 Thu, 03 Nov 2011 04:00:00 +0100 5372226 http://www.medworm.com/index.php?rid=5372225&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F547 Conclusions: Our mining approach demonstrates that one can capitalize on genome-wide expression profiling to capture dynamic properties of a complex network. To the best of our knowledge, this is the first attempt in applying mining approaches to explore gene switches on a genome-scale, and the identification of TACSTD2 demonstrates that single cell-level bistability can be predicted from microarray data. Experimental confirmation of the computational results suggest TACSTD2 could be a potential biomarker and attractive candidate for drug therapy against both ER+ and ER- subtypes of breast cancer, including the triple negative subtype. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372225 Thu, 03 Nov 2011 04:00:00 +0100 5372225 http://www.medworm.com/index.php?rid=5372234&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F537 Conclusion: The reported common carp physical map is the first physical map of the common carp genome. It should be a valuable genome resource facilitating whole genome sequence assembly and characterization of position-based genes important for aquaculture traits. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372234 Wed, 02 Nov 2011 04:00:00 +0100 5372234 http://www.medworm.com/index.php?rid=5372233&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F538 Conclusions: For the most productive genotype, the ability to express a broader set of genes in response to water availability appears to be a key characteristic in the maintenance of biomass growth during the dry season. Its strategy may involve a decrease of photosynthetic activity during the dry season associated with resources reallocation through major changes in the expression of primary metabolism associated genes. Further efforts will be needed to assess the adaptive nature of the genes highlighted in this study. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372233 Wed, 02 Nov 2011 04:00:00 +0100 5372233 http://www.medworm.com/index.php?rid=5372232&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F539 Conclusions: A collection of high-quality ESTs for B. chinense obtained by 454 pyrosequencing is provided here for the first time. These data should aid further research on the functional genomics of B. chinense and other Bupleurum species. The candidate genes for enzymes involved in saikosaponin biosynthesis, especially the P450s and UGTs, that were revealed provide a substantial foundation for follow-up research on the metabolism and regulation of the saikosaponins. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372232 Wed, 02 Nov 2011 04:00:00 +0100 5372232 http://www.medworm.com/index.php?rid=5372231&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F540 Conclusions: We conclude that RNA-Seq greatly improves the accuracy of prediction of protein-coding genes in the reassembled cucumber genome. The comparison between the two gene sets also suggests that it is feasible to use RNA-Seq reads to annotate newly sequenced or less-studied genomes. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372231 Wed, 02 Nov 2011 04:00:00 +0100 5372231 http://www.medworm.com/index.php?rid=5372230&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F542 Conclusions: This study identifies numerous gene exchanges between intracellular Legionellales and Chlamydiales bacteria, which could preferentially occur within common inclusions in their amoebal hosts. Therefore it contributes to improve our knowledge on the intra-amoebal gene properties associated to their specific lifestyle. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5372230 Wed, 02 Nov 2011 04:00:00 +0100 5372230 http://www.medworm.com/index.php?rid=5353723&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F525 Conclusions: A number of soybean genes were differentially expressed between the low-N-tolerant and low-N-sensitive varieties under N-limited conditions. Some of these genes may be candidates for improving NUE. These findings will help to provide a detailed understanding of NUE mechanisms, and also provide a basis for breeding soybean varieties that are tolerant to low-N conditions. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5353723 Wed, 26 Oct 2011 04:00:00 +0100 5353723 http://www.medworm.com/index.php?rid=5353725&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F523 Conclusions: There is significant genomic diversity among different strains in S. suis, and the gain and loss of large amount of genes are involved in shaping their genomes. This is indicated by (i) pairwise gene content comparisons between every pair of these strains, (ii) the open pan-genome of this species, (iii) the observed indels, invertions and rearrangements in the collinearity analysis. Phylogenetic relationships may be associated with serotype, as serotype 2 strains are closely related and distinct from other serotypes like 1, 3, 7 and 9, but more strains need to be sequenced to confirm this. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5353725 Tue, 25 Oct 2011 04:00:00 +0100 5353725 http://www.medworm.com/index.php?rid=5353724&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F524 Conclusion: This study identified a set of genes whose expression is altered by DEHP exposure in mammalian embryo cells. This is the first study that elucidates the genomic changes of DEHP involved in the organization of the cytoskeleton. The latter genes may be candidates as biomarkers predictive of early events in the multistep carcinogenic process. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5353724 Tue, 25 Oct 2011 04:00:00 +0100 5353724 http://www.medworm.com/index.php?rid=5342151&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F522 Conclusions: Overall, the combined gene expression, compositional and biochemical studies demonstrated a large panel of metabolic and physiological effects induced by total substitution of both FM and FO in the diets of European sea bass and revealed physiological characteristics associated with the two half-sibfamilies. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5342151 Sun, 23 Oct 2011 04:00:00 +0100 5342151 http://www.medworm.com/index.php?rid=5342152&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F521 Conclusions: : The NLL BAC library and BAC-end sequences are powerful resources for genetic and genomic research on lupin. These resources will provide a robust platform for future high-resolution mapping, map-based cloning, comparative genomics and assembly of whole-genome sequencing data for this species. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5342152 Fri, 21 Oct 2011 04:00:00 +0100 5342152 http://www.medworm.com/index.php?rid=5342158&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F515 Conclusions: Our results revealed a list of combinatorial genomic features that are significantly associated with gene expression in ES cells, suggesting potential cofactors of the ChIP-seq TFs for gene regulation. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5342158 Thu, 20 Oct 2011 04:00:00 +0100 5342158 http://www.medworm.com/index.php?rid=5342157&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F516 Conclusions: We demonstrated that the amount of mRNA is precisely reflected by the phased phosphorylation of Ser2 and Ser5. In particular, even the most "pausing" genes, for which only Ser5 is phosphorylated, were detectable at a certain level of mRNA. Our analysis indicated that the complexity of quantitative regulation of mRNA levels could be classified into three categories according to the phosphorylation state of RNAPII. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5342157 Thu, 20 Oct 2011 04:00:00 +0100 5342157 http://www.medworm.com/index.php?rid=5342156&cid=s_34030_50_f&fid=34030&url=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2164%2F12%2F517 Conclusions: We aimed at providing the scientific community with the most exhaustive overview on the human NumtSome, a resource whose aim is to support different research applications ranging from studies concerning human structural variation, diversity, and disease, as well as the detection of false heteroplasmic mtDNA variants. Upon implementation of the NumtS tracks, the application of the BLAT program on the UCSC genome browser has now become an additional tool to check for heteroplasmic artefacts, supported by data available through the NumtS tracks. (Source: BMC Genomics - Latest articles) BMC Genomics - Latest articles journals http://www.medworm.com/rss/comments.php?id=5342156 Thu, 20 Oct 2011 04:00:00 +0100 5342156