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 'Comparative and Functional Genomics' source. Sat, 20 Mar 2010 15:46:58 +0100 http://www.medworm.com/index.php?rid=3321332&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F782924.html A survey of a complete gene synteny comparison has been carried out between twenty fully sequenced strains from the genus Escherichia with the aim of finding yet uncharacterised genes implicated in the metabolism of uropathogenic strains of E. coli (UPEC). Several sets of adjacent colinear genes have been identified which are present in all four UPEC included in this study (CFT073, F11, UTI89, and 536), annotated with putative metabolic functions, but are not found in any other strains considered. An operon closely homologous to that encoding the L-sorbose degradation pathway in Klebsiella pneumoniae has been identified in E. coli CFT073; this operon is present in all of the UPEC considered, but only in 7 of the other 16 strains. The operon's function has been confirmed by cloning the ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3321332 Tue, 02 Mar 2010 17:07:04 +0100 3321332 http://www.medworm.com/index.php?rid=3297500&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F505701.html Glyphosate has been shown to act as an inhibitor of an aromatic amino acid biosynthetic pathway, while other pathways that may be affected by glyphosate are not known. Cross species hybridizations can provide a tool for elucidating biological pathways conserved among organisms. Comparative genome analyses have indicated a high level of colinearity among grass species and Festuca, on which we focus here, and showed rearrangements common to the Pooideae family. Based on sequence conservation among grass species, we selected the Affymetrix GeneChip Wheat Genome Array as a tool for the analysis of expression profiles of three Festuca (fescue) species with distinctly different tolerances to varying levels of glyphosate. Differences in transcript expression were recorded upon foliar glyphosate a... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3297500 Tue, 23 Feb 2010 16:17:35 +0100 3297500 http://www.medworm.com/index.php?rid=3261799&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F302620.html In this study, we compared 4,219 Pst expression sequence tags (ESTs) to the genomic sequence of P. graminis f. sp. tritici (Pgt), the wheat stem rust fungus, using BLAST searches. The percentages of homologous genes varied greatly among different Pst libraries with 54.51%, 51.21%, and 13.61% for the urediniospore, germinated urediniospore, and haustorial libraries, respectively, with an average of 33.92%. The 1,432 Pst genes with significant homology with Pgt sequences were grouped into physical groups corresponding to 237 Pgt supercontigs. The physical relationship was demonstrated by 12 pairs (57%), out of 21 selected Pst gene pairs, through PCR screening of a Pst BAC library. The results indicate that the Pgt genome sequence is useful in constructing Pst physical map... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3261799 Thu, 11 Feb 2010 15:54:30 +0100 3261799 http://www.medworm.com/index.php?rid=3261798&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F354649.html In this study, complete inventories of putative functional ABC systems of five Brucella species have been compiled and compared. ABC systems of Brucella melitensis 16M, Brucella abortus 9-941, Brucella canis RM6/66, Brucella suis 1330, and Brucella ovis 63/290 were identified and aligned. High numbers of ABC systems, particularly nutrient importers, were found in all Brucella species. However, differences in the total numbers of ABC systems were identified (B. melitensis, 79; B. suis, 72; B. abortus 64; B. canis, 74; B. ovis, 59) as well as specific differences in the functional ABC systems of the Brucella species. Since B. ovis is not known to cause human brucellosis, functional ABC systems absent in the B. ovis genome may represent virulence factors in human brucellosis. (Source: Compara... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3261798 Thu, 11 Feb 2010 15:54:30 +0100 3261798 http://www.medworm.com/index.php?rid=3224651&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F761512.html Gene conversion is an important biological process that involves the transfer of genetic (sequence) information from one gene to another. This can have a variety of effects on an organism, both short-term and long-term and both positive and detrimental. In an effort to better understand this process, we searched through over 3,000 abstracts that contain research on gene conversions, tagging the important data and performing an analysis on what we extract. Through this we established trends that give a better insight into gene conversion research and genetic research in general. Our results show the importance of the process and the importance of continuing gene conversion research. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3224651 Sun, 31 Jan 2010 15:48:27 +0100 3224651 http://www.medworm.com/index.php?rid=3215426&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F659301.html Over ninety percent of the value of cotton comes from its fiber; however, the genetic mechanisms governing fiber development are poorly understood. Due to their biochemical and morphological diversity in fiber cells cotton fiber mutants have been useful in examining fiber development; therefore, using the Ligon Lintless (Li-1) mutant, a monogenic dominant cotton mutant with very short fibers, we employed the high throughput approaches of microarray technology and real time PCR to gain insights into what genes were critical during the secondary cell wall synthesis stage. Comparative transcriptome analysis of the normal TM-1 genotype and the near isogenic Li-1 revealed that over 100 transcripts were differentially expressed at least 2-fold during secondary wall biogenesis, although the genet... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3215426 Thu, 28 Jan 2010 16:24:16 +0100 3215426 http://www.medworm.com/index.php?rid=3211130&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F245927.html We analyzed inheritance of DNA methylation in reciprocal F1 hybrids (subsp. japonica cv. Nipponbare × subsp. indica cv. Kasalath) of rice (Oryza sativa L.) using restriction landmark genome scanning (RLGS), and detected differing RLGS spots between the parents and reciprocal F1 hybrids. MspI/HpaII restriction sites in the DNA from these different spots were suspected to be heterozygously methylated in the Nipponbare parent. These spots segregated in F1 plants, but did not segregate in selfed progeny of Nipponbare, showing non-Mendelian inheritance of the methylation status. As a result of RT-PCR and sequencing, a specific allele of the gene nearest to the methylated sites was expressed in reciprocal F1 plants, showing evidence of biased allelic expression. These results show the app... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3211130 Wed, 27 Jan 2010 15:47:36 +0100 3211130 http://www.medworm.com/index.php?rid=3188077&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F914762.html We employed Murine GeneChips to delineate the global transcriptional profiles of the livers, lungs, and spleens in a mouse pneumonic plague infection model with wild-type (WT) Y. pestis CO92 and its Braun lipoprotein (Δlpp) mutant with reduced virulence. These organs showed differential transcriptional responses to infection with WT Y. pestis, but the overall host functional processes affected were similar across all three tissues. Gene expression alterations were found in inflammation, cytokine signaling, and apoptotic cell death-associated genes. Comparison of WT and Δlpp mutant-infected mice indicated significant overlap in lipopolysaccharide- (LPS-) associated gene expression, but the absence of Lpp perturbed host cell signaling at critical regulatory junctions resulting ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3188077 Wed, 20 Jan 2010 16:14:19 +0100 3188077 http://www.medworm.com/index.php?rid=3091748&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F875901.html Genomewide analyses of distances between orthologous gene pairs from the ascidian species Ciona intestinalis and Ciona savignyi were compared with those of vertebrates. Combining this data with a detailed and careful use of vertebrate fossil records, we estimated the time of divergence between the two ascidians nearly 180 My. This estimation was obtained after correcting for the different substitution rates found comparing several groups of chordates; indeed we determine here that on average Ciona species evolve 50% faster than vertebrates. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3091748 Wed, 16 Dec 2009 15:34:38 +0100 3091748 http://www.medworm.com/index.php?rid=3018394&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F212345.html Conclusions. IL-8 appears to be associated with cachexia from patients with low-third gastric cancer. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=3018394 Mon, 23 Nov 2009 15:28:52 +0100 3018394 http://www.medworm.com/index.php?rid=2950037&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F983636.html This report provides definite evidence of true orthology between these defensins and reveals molecular diversity of a mammalian specific domain responsible for their antimicrobial activity. Specifically, this analysis demonstrates that eleven amino acid residues of the antimicrobial domain have been mutated by positive selection to confer protein niche specialization. These data support the notion that natural selection acts as evolutionary force driving the proliferation and diversification of defensins and introduce a novel strategy for the design of more effective antibiotics. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2950037 Mon, 02 Nov 2009 15:55:04 +0100 2950037 http://www.medworm.com/index.php?rid=2915198&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F406421.html The objective is to comparatively analyze mutations specifically those that caused the frameshift and nonsense mutations and to assess their scale and potential impacts on human-chimpanzee divergence. Genomewide analysis of human and chimpanzee exons with ExonVar identified a number of species-specific, exon-disrupting mutations in chimpanzees but much fewer in humans. Many were found on genes involved in important biological processes such as T cell lineage development, the pathogenesis of inflammatory diseases, and antigen induced cell death. A “less-is-more” model was previously established to illustrate the role of the gene inactivation and disruptions during human evolution. Here this analysis suggested a different model where the chimpanzee-specific exon-disrupting mutati... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2915198 Thu, 22 Oct 2009 14:44:38 +0100 2915198 http://www.medworm.com/index.php?rid=2911274&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F836172.html Mycobacterium tuberculosis mtFabD is an essential malonyl-CoA:AcpM transacylase and is important for vital protein-protein interactions within type 2 fatty acid synthase FASII. mtFabD contacts KasA, KasB, FabH, InhA, and possibly also HadAB, HadBC, and FabG1/MabA. Disruption of mtFabD's interactions during FASII has been proposed for drug development. Here, the gene for a mitochondrially targeted mtFabD was ectopically expressed in Saccharomyces cerevisiae mct1Δ mutant cells lacking the corresponding mitochondrial malonyl-CoA transferase Mct1p, allowing the mutants to recover their abilities to respire on glycerol and synthesize lipoic acid. Hence, mtFabD could physiologically function in an environment lacking holo-AcpM or other native interaction partners. (Source: Comparative... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2911274 Wed, 21 Oct 2009 14:49:28 +0100 2911274 http://www.medworm.com/index.php?rid=2882332&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F947490.html The Drosophila E(spl)m4 gene contains some highly conserved motifs (such as the Brd box, GY box, K box, and CAAC motif) in its 3′ untranslated region (3′UTR). It was shown to be a microRNA target gene in Drosophila and to play an important role in the regulation of neurogenesis. We identified a homologue of the E(spl)m4 gene from Bombyx mori called BmEm4 and examined the expression patterns of BmEm4 mRNA and protein. There was a lack of correlation in the expression of the mRNA and protein between the different developmental stages, which raises the possibility of posttranscriptional regulation of the BmEm4 mRNA. Consistent with this idea is the finding that the 3′ UTR contains two putative binding sites for microRNAs. Moreover, given that the expression is the highest... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2882332 Mon, 12 Oct 2009 14:31:22 +0100 2882332 http://www.medworm.com/index.php?rid=2868096&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F380719.html Sequencing of over 40 fungal and oomycete genomes has been completed. The next major challenge in modern fungal/oomycete biology is now to translate this plethora of genome sequence information into biological functions. Reverse genetics has emerged as a seminal tool for functional genomics investigations. Techniques utilized for reverse genetics like targeted gene disruption/replacement, gene silencing, insertional mutagenesis, and targeting induced local lesions in genomes will contribute greatly to the understanding of gene function of fungal and oomycete pathogens. This paper provides an overview on high-throughput reverse genetics approaches to decode fungal/oomycete genomes. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2868096 Wed, 07 Oct 2009 16:00:20 +0100 2868096 http://www.medworm.com/index.php?rid=2838245&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F365637.html Protein Kinase-Like Non-kinases (PKLNKs), which are closely related to protein kinases, lack the crucial catalytic aspartate in the catalytic loop, and hence cannot function as protein kinase, have been analysed. Using various sensitive sequence analysis methods, we have recognized 82 PKLNKs from four higher eukaryotic organisms, namely, Homo sapiens, Mus musculus, Rattus norvegicus, and Drosophila melanogaster. On the basis of their domain combination and function, PKLNKs have been classified mainly into four categories: (1) Ligand binding PKLNKs, (2) PKLNKs with extracellular protein-protein interaction domain, (3) PKLNKs involved in dimerization, and (4) PKLNKs with cytoplasmic protein-protein interaction module. While members of the first two classes of PKLNKs have transmembrane domain... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2838245 Mon, 28 Sep 2009 17:58:44 +0100 2838245 http://www.medworm.com/index.php?rid=2711177&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F201325.html Conclusion. The implemented option for the determination of minimal altered regions (MARs) from a series of tumor samples is a step forward in the identification of new tumor suppressor genes or oncogenes. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2711177 Wed, 19 Aug 2009 11:19:22 +0100 2711177 http://www.medworm.com/index.php?rid=2600471&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F705034.html The objectives of this study were to characterize tick gene expression profile in Ixodes scapularis ticks and cultured ISE6 cells in response to infection with A. phagocypthilum and to compare tick gene expression responses in A. phagocytophilum- and A. marginale-infected tick cells by microarray and real-time RT-PCR analyses. The results of these studies demonstrated modulation of tick gene expression by A. phagocytophilum and provided evidence of different gene expression responses in tick cells infected with A. phagocytophilum and A. marginale. These differences in Anaplasma-tick interactions may reflect differences in pathogen life cycle in the tick cells. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2600471 Wed, 15 Jul 2009 11:47:26 +0100 2600471 http://www.medworm.com/index.php?rid=2592846&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F905894.html Functional modification of transcription regulators may lead to developmental changes and phenotypical differences between species. In this work, we study the influence of alternative splicing on transcription factors in human and mouse. Our results show that the impact of alternative splicing on transcription factors is similar in both species, meaning that the ways to increase variability should also be similar. However, when looking at the expression patterns of transcription factors, we observe that they tend to diverge regardless of the role of alternative splicing. Finally, we hypothesise that transcription regulation of alternatively spliced transcription factors could play an important role in the phenotypical differences between species, without discarding other phenomena or funct... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2592846 Sun, 12 Jul 2009 11:49:14 +0100 2592846 http://www.medworm.com/index.php?rid=2568180&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F820381.html Nudix enzymes are a superfamily with a conserved common reaction mechanism that provides the capacity for the hydrolysis of a broad spectrum of metabolites. We used hidden Markov models based on Nudix sequences from the PFAM and PROSITE databases to identify Nudix hydrolases encoded by the Arabidopsis genome. 25 Nudix hydrolases were identified and classified into 11 individual families by pairwise sequence alignments. Intron phases were strikingly conserved in each family. Phylogenetic analysis showed that all multimember families formed monophyletic clusters. Conserved familial sequence motifs were identified with the MEME motif analysis algorithm. One motif (motif 4) was found in three diverse families. All proteins containing motif 4 demonstrated a degree of preference for substrates c... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2568180 Sun, 05 Jul 2009 11:46:03 +0100 2568180 http://www.medworm.com/index.php?rid=2555166&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2000%2F124868.abs.html This review explores the UK CropNet site. The project is aimed at aiding the comparative mapping of cereal and other crop genomes. The site provides software tools for use by those working on genome mapping, and access to an array of databases that will be of interest to all members of the plant genomics research community, using several ACeDB interfaces. All screen views from the website are reproduced with the kind permission of Dr Sean May, Director, Nottingham Arabidopsis Stock Centre (NASC). (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2555166 Tue, 30 Jun 2009 16:16:06 +0100 2555166 http://www.medworm.com/index.php?rid=2555165&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2000%2F107461.abs.html The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60–80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, co... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2555165 Tue, 30 Jun 2009 16:16:06 +0100 2555165 http://www.medworm.com/index.php?rid=2500510&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F416040.html The eukaryotic F-box protein family is characterized by an F-box motif that has been shown to be critical for the controlled degradation of regulatory proteins. We identified a gene encoding an F-box protein from a cDNA library of silkworm pupae, which has an ORF of 1821 bp, encoding a predicted 606 amino acids. Bioinformatic analysis on the amino acid sequence shows that BmFBXO21 has a low degree of similarity to proteins from other species, and may be related to the regulation of cell-cycle progression. We have detected the expression pattern of BmFBXO21 mRNA and protein and performed immunohistochemistry at three different levels. Expression was highest in the spinning stage, and in the tissues of head, epidermis, and genital organs. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2500510 Thu, 25 Jun 2009 08:38:22 +0100 2500510 http://www.medworm.com/index.php?rid=2467202&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2002%2F259617.abs.html Research on biological data integration has traditionally focused on the development of systems for the maintenance and interconnection of databases. In the next few years, public and private biotechnology organisations will expand their actions to promote the creation of a post-genome semantic web. It has commonly been accepted that artificial intelligence and data mining techniques may support the interpretation of huge amounts of integrated data. But at the same time, these research disciplines are contributing to the creation of content markup languages and sophisticated programs able to exploit the constraints and preferences of user domains. This paper discusses a number of issues on intelligent systems for the integration of bioinformatic resources. (Source: Comparative and Function... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467202 Wed, 10 Jun 2009 00:58:25 +0100 2467202 http://www.medworm.com/index.php?rid=2467201&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2004%2F259179.abs.html The MicroCore toolkit is a suite of analysis programs for microarray and proteomics data that is open source and programmed exclusively in Java. MicroCore provides a flexible and extensible environment for the interpretation of functional genomics data through visualization. The first version of the application (downloadable from the MicroCore website: http://www.ucl.ac.uk/oncology/MicroCore/microcore.htm), implements two programs—PIMs (protein interaction maps) and MicroExpress—and is soon to be followed by an extended version which will also feature a fuzzy k-means clustering application and a Java-based R plug-in for microarray analysis. PIMs and MicroExpress provide a simple yet powerful way of graphically relating large quantities of expression data from multiple experime... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467201 Wed, 10 Jun 2009 00:58:25 +0100 2467201 http://www.medworm.com/index.php?rid=2467200&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2003%2F257839.abs.html (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467200 Wed, 10 Jun 2009 00:58:25 +0100 2467200 http://www.medworm.com/index.php?rid=2467199&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F049356.abs.html By combining crystallographic information with protein-interaction data obtained through traditional experimental means, this paper determines the most appropriate method for generating protein-interaction networks that incorporate data derived from protein complexes. We propose that a combined method should be considered; in which complexes composed of five chains or less are decomposed using the matrix model, whereas the spoke model is used to derive pairwise interactions for those with six chains or more. The results presented here should improve the accuracy and relevance of studies investigating the topology of protein-interaction networks. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467199 Wed, 10 Jun 2009 00:58:25 +0100 2467199 http://www.medworm.com/index.php?rid=2467198&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F043070.abs.html It has been suggested that there are special evolutionary forces that act on sex chromosomes. Hemizygosity of the X chromosome in male mammals has led to selection for male-advantage genes, and against genes posing extreme risks of tumor development. A similar bias against cancer genes should also apply to the Z chromosome that is present as a single copy in female birds. Using comparative database analysis, we found that there was no significant underrepresentation of cancer genes on the chicken Z, nor on the Z-orthologous regions of human chromosomes 5 and 9. This result does not support the hypothesis that genes involved in cancer are selected against on the sex chromosomes. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467198 Wed, 10 Jun 2009 00:58:25 +0100 2467198 http://www.medworm.com/index.php?rid=2467197&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F058721.abs.html Previous studies in the yeast Saccharomyces cerevisiae have shown that genes encoding subunits of macromolecular complexes have similar evolutionary rates (K) and expression levels (E). Besides, it is known that the expression of a gene is a strong predictor of its rate of evolution (i.e., E and K are correlated). Here we show that intracomplex variation of subunit expression correlates with intracomplex variation of their evolutionary rates (using two different measures of dispersion). However, a similar trend was observed for randomized complexes. Therefore, using a mathematical transformation, we created new variables capturing intracomplex variation of both E and K. The values of these new compound variables were smaller for real complexes than for randomized ones. This shows that prot... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467197 Wed, 10 Jun 2009 00:58:25 +0100 2467197 http://www.medworm.com/index.php?rid=2467196&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F047161.abs.html We have identified four repeats and ten domains that are novel in proteins encoded by the Bacillus anthracis str. Ames proteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residue YEFF domain, (4) 109-amino-acid-residue IMxxH domain, (5) 103-amino-acid-residue VxxT domain, (6) 84-amino-acid-residue ExW domain, (7) 104-amino-acid-residue NTGFIG do... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467196 Wed, 10 Jun 2009 00:58:25 +0100 2467196 http://www.medworm.com/index.php?rid=2467195&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F090578.abs.html Conclusions. The SCS normalisation results using 16 macroarray data sets from a Bacillus subtilis experiment confirm that the method is capable of reducing undesirable experimental variation whilst retaining important biological information. The ease and speed of implementation mean that this method can be easily adapted to other multicondition time/strain series single colour array data. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467195 Wed, 10 Jun 2009 00:58:25 +0100 2467195 http://www.medworm.com/index.php?rid=2467194&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F047304.abs.html This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) specification (v1.1), consens... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467194 Wed, 10 Jun 2009 00:58:25 +0100 2467194 http://www.medworm.com/index.php?rid=2467193&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F025751.abs.html To elucidate the evolution of cyanobacterial envelopes and the relation between gene content and environmental adaptation, cell envelope structures and components of unicellular and filamentous cyanobacteria were analyzed in comparative genomics. Hundreds of envelope biogenesis genes were divided into 5 major groups and annotated according to their conserved domains and phylogenetic profiles. Compared to unicellular species, the gene numbers of filamentous cyanobacteria expanded due to genome enlargement effect, but only few gene families amplified disproportionately, such as those encoding waaG and glycosyl transferase 2. Comparison of envelope genes among various species suggested that the significant variance of certain cyanobacterial envelope biogenesis genes should be the response to ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467193 Wed, 10 Jun 2009 00:58:25 +0100 2467193 http://www.medworm.com/index.php?rid=2467192&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F021676.abs.html Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare) proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns wi... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467192 Wed, 10 Jun 2009 00:58:25 +0100 2467192 http://www.medworm.com/index.php?rid=2467191&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F089596.abs.html Two-dimensional gel-electrophoresis (2-DE) images show the expression levels of several hundreds of proteins where each protein is represented as a blob-shaped spot of grey level values. The spot detection, that is, the segmentation process has to be efficient as it is the first step in the gel processing. Such extraction of information is a very complex task. In this paper, we propose a novel spot detector that is basically a morphology-based method with the use of a seeded region growing as a central paradigm and which relies on the spot correlation information. The method is tested on our synthetic as well as on real gels with human samples from SWISS-2DPAGE (two-dimensional polyacrylamide gel electrophoresis) database. A comparison of results is done with a method called pixel value co... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467191 Wed, 10 Jun 2009 00:58:25 +0100 2467191 http://www.medworm.com/index.php?rid=2467190&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F060964.abs.html Tandemly arrayed genes (TAGs) account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members and their expression similarity. There is also a weak negative correlation between chromosomal proximity of TAG members and their expression similarity. We did not detect any significant relationship b... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467190 Wed, 10 Jun 2009 00:58:25 +0100 2467190 http://www.medworm.com/index.php?rid=2467189&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F035604.abs.html The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467189 Wed, 10 Jun 2009 00:58:25 +0100 2467189 http://www.medworm.com/index.php?rid=2467188&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2007%2F057513.abs.html Nasopharyngeal carcinoma (NPC) is a rare malignancy in most parts of the world, but is one of the most common cancers in Southeast Asia. Both genetic and environmental factors contribute to the tumorigenesis of NPC, most notably the consumption of certain salted food items and Epstein-Barr virus infection. This review will focus on the current progress of the genetic analysis of NPC (genetic susceptibilities and somatic alterations). We will review the current advances in genomic technologies and their shaping of the future direction of NPC research. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467188 Wed, 10 Jun 2009 00:58:25 +0100 2467188 http://www.medworm.com/index.php?rid=2467187&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F451930.html We have identified two genomic islands, that is, BCEGI-1 and BCEGI-2, in the genome of Bacillus cereus ATCC 10987, based on comparative analysis with Bacillus cereus ATCC 14579. Furthermore, by using the cumulative GC profile and performing homology searches between the two genomes, the integration sites of the two genomic islands were determined at single-nucleotide resolution. BCEGI-1 is integrated between 159705 bp and 198000 bp, whereas BCEGI-2 is integrated between the end of ORF BCE4594 and the start of the intergenic sequence immediately following BCE4626, that is, from 4256803 bp to 4285534 bp. BCEGI-1 harbors two bacterial Tn7 transposons, which have two sets of genes encoding TnsA, B, C, and... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467187 Wed, 10 Jun 2009 00:58:25 +0100 2467187 http://www.medworm.com/index.php?rid=2467186&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F254836.html To identify key regulators of subminimum inhibitory concentration (sub-MIC) antibiotic response in the Pasteurella multocida proteome, we applied systems approaches. Using 2D-LC-ESI-MS2, we achieved 53% proteome coverage. To study the differential protein expression in response to sub-MIC antibiotics in the context of protein interaction networks, we inferred P. multocida Pm70 protein interaction network from orthologous proteins. We then overlaid the differential protein expression data onto the P. multocida protein interaction network to study the bacterial response. We identified proteins that could enhance antimicrobial activity. Overall compensatory response to antibiotics was characterized by altered expression of proteins involved in purine metabolism, stress response, and cell ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467186 Wed, 10 Jun 2009 00:58:25 +0100 2467186 http://www.medworm.com/index.php?rid=2467185&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F565631.html There has been much interest in CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, because they are considered gene markers and involved in gene regulation. To date, there has been no genome-wide analysis of CGIs in the fish genome. We first evaluated the performance of three popular CGI identification algorithms in four fish genomes (tetraodon, stickleback, medaka, and zebrafish). Our results suggest that Takai and Jones' (2002) algorithm is most suitable for comparative analysis of CGIs in the fish genome. Then, we performed a systematic analysis of CGIs in the four fish genomes using Takai and Jones' algorithm, compared to other vertebrate genomes. We found that both the number of CGIs and the CGI density vary greatly among these genomes. Remarkably, each fish... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467185 Wed, 10 Jun 2009 00:58:25 +0100 2467185 http://www.medworm.com/index.php?rid=2467184&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F609684.html We report on the clinical, cytogenetic, and molecular findings in a boy with autism carrying a de novo translocation t(7;16)(p22.1;p11.2). The chromosome 16 breakpoint disrupts the paralogous SLC6A8 gene also called SLC6A10 or CT2. Predicted translation of exons and RT-PCR analysis reveal specific expression of the creatine transporter paralogous in testis and brain. Several studies reported on the role of X-linked creatine transporter mutations in individuals with mental retardation, with or without autism. The existence of disruption in SLC6A8 paralogous gene associated with idiopathic autism suggests that this gene may be involved in the autistic phenotype in our patient. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467184 Wed, 10 Jun 2009 00:58:25 +0100 2467184 http://www.medworm.com/index.php?rid=2467183&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F571023.html RNA methylation, which is a form of posttranscriptional modification, is catalyzed by S-adenosyl-L-methionone-dependent RNA methyltransterases (RNA MTases). We have identified a novel silkworm gene, BmRNAMTase, containing a 369-bp open reading frame that encodes a putative protein containing 122 amino acid residues and having a molecular weight of 13.88 kd. We expressed a recombinant His-tagged BmRNAMTase in E. coli BL21 (DE3), purified the fusion protein by metal-chelation affinity chromatography, and injected a New Zealand rabbit with the purified protein to generate anti-BmRNAMTase polyclonal antibodies. Immunohistochemistry revealed that BmRNAMTase is abundant in the cytoplasm of Bm5 cells. In addition, using RNA interference to reduce the intracellular activity and content of BmRNAMTa... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467183 Wed, 10 Jun 2009 00:58:25 +0100 2467183 http://www.medworm.com/index.php?rid=2467182&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F623145.html Orientia tsutsugamushi, the causative agent of scrub typhus, is an obligate intracellular bacterium that belongs to the order of Rickettsiales. Recently, we have reported that O. tsutsugamushi has a unique genomic structure, consisting of highly repetitive sequences, and suggested that it may provide valuable insight into the evolution of intracellular bacteria. Here, we have used genomic information to construct the major metabolic pathways of O. tsutsugamushi and performed a comparative analysis of the metabolic genes and pathways of O. tsutsugamushi with other members of the Rickettsiales order. While O. tsutsugamushi has the ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467182 Wed, 10 Jun 2009 00:58:25 +0100 2467182 http://www.medworm.com/index.php?rid=2467181&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F879023.html Cryptosporidium parvum and C. hominis are related protozoan pathogens which infect the intestinal epithelium of humans and other vertebrates. To explore the evolution of these parasites, and identify genes under positive selection, we performed a pairwise whole-genome comparison between all orthologous protein coding genes in C. parvum and C. hominis. Genome-wide calculation of the ratio of nonsynonymous versus synonymous nucleotide substitutions (dN/dS) was performed to detect the impact of positive and purifying selection. Of 2465 pairs of orthologous genes, a total of 27 (1.1%) showed a high ratio of nonsynonymous substitutions, consistent with positive selection. A majority of these genes were annotated as hypothetical proteins. In addition, proteins with transmembrane and signal p... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467181 Wed, 10 Jun 2009 00:58:25 +0100 2467181 http://www.medworm.com/index.php?rid=2467180&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F634283.html Cohesin is a protein complex that regulates sister chromatid cohesin during cell division. Malfunction in chromatid cohesin results in chromosome missegregation and aneuploidy. Here, we report that mutations of MCD1 and PDS5, two major components of cohesin in budding yeast, cause apoptotic cell death, which is characterized by externalization of phosphatidylserine at cytoplasmic membrane, chromatin condensation and fragmentation, and ROS production. Microarray analysis suggests that the cell death caused by mutation of MCD1 or PDS5 is due to the internal stress response, contrasting to the environmental or external stress response induced by external stimuli, such as hydrogen peroxide. A common feature shared by the internal stress response and external stress response is the response to ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467180 Wed, 10 Jun 2009 00:58:25 +0100 2467180 http://www.medworm.com/index.php?rid=2467179&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F545269.html Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94%) have parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tan... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467179 Wed, 10 Jun 2009 00:58:25 +0100 2467179 http://www.medworm.com/index.php?rid=2467178&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2008%2F284508.html Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of other cyanobacteria, indicating different phylogenetic histories of the two genera from other cyanobacteria isolated from freshwater, soil, or symbiont. Strain Gloeobacter... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467178 Wed, 10 Jun 2009 00:58:25 +0100 2467178 http://www.medworm.com/index.php?rid=2467177&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F549387.html In the present study, a positive training set of 30 known human imprinted gene coding regions are compared with a set of 72 randomly sampled human nonimprinted gene coding regions (negative training set) to identify genomic features common to human imprinted genes. The most important feature of the present work is its ability to use multivariate analysis to look at variation, at coding region DNA level, among imprinted and non-imprinted genes. There is a force affecting genomic parameters that appears through the use of the appropriate multivariate methods (principle components analysis (PCA) and quadratic discriminant analysis (QDA) to analyse quantitative genomic data. We show that variables, such as CG content, [bp]% CpG islands, [bp]% Large Tandem Repeats, and [bp]% Simple ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467177 Wed, 10 Jun 2009 00:58:25 +0100 2467177 http://www.medworm.com/index.php?rid=2467176&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F950171.html Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in part to the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467176 Wed, 10 Jun 2009 00:58:25 +0100 2467176 http://www.medworm.com/index.php?rid=2467175&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F379317.html In this study, I analyzed 62 and 48 subunits of the histone-modifying protein complexes of Saccharomyces cerevisiae and Schizosaccharomyces pombe, respectively. The evolutionary conservation levels of the 110 subunits were measured. The measurements revealed that the conservation levels of the catalytic subunits are significantly higher than those of the associated subunits of the histone acetyltransferase and deacetylase complexes; however, the conservation level of the catalytic subunits is similar to that of the associated subunits of the histone methyltransferase complexes. Thus, in the fungal histone acetylation and deacetylation systems, the catalytic subunits of histone-modifying protein complexes are conserved and the associated subunits are evolutionary lineage-specific. In contra... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467175 Wed, 10 Jun 2009 00:58:25 +0100 2467175 http://www.medworm.com/index.php?rid=2467174&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F510270.html In this study, we employed evolutionary genomic approaches to investigate the impact of recombination on the core genome of Rickettsia. Phylogenetic network and phylogenetic compatibility matrix analyses are clearly consistent with the hypothesis that recombination has occurred frequently during Rickettsia evolution. 28% of Rickettsia core genes (194 out of 690) are found to present the evidence of recombination under four independent statistical methods. Further functional classification shows that these recombination events occur across all functional categories, with a significant overrepresentation in the cell wall/membrane/envelope biogenesis, which may provide a molecular basis for the parasite adaptation to host immunity. This evolutionary genomic analysis provides insight into ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467174 Wed, 10 Jun 2009 00:58:25 +0100 2467174 http://www.medworm.com/index.php?rid=2467173&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2Fjournals%2Fcfg%2F2009%2F837514.html Head and neck/oral cancer (HNOC) is a devastating disease. Despite advances in diagnosis and treatment, mortality rates have not improved significantly over the past three decades. Improvement in patient survival requires a better understanding of the disease progression so that HNOC can be detected early in the disease process and targeted therapeutic interventions can be deployed. Accumulating evidence suggests that microRNAs play important roles in many human cancers. They are pivotal regulators of diverse cellular processes including proliferation, differentiation, apoptosis, survival, motility, and morphogenesis. MicroRNA expression patterns may become powerful biomarkers for diagnosis and prognosis of HNOC. In addition, microRNA therapy could be a novel strategy for HNOC prevention a... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2467173 Wed, 10 Jun 2009 00:58:25 +0100 2467173 http://www.medworm.com/index.php?rid=2454470&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F837514 Head and neck/oral cancer (HNOC) is a devastating disease. Despite advances in diagnosis and treatment, mortality rates have not improved significantly over the past three decades. Improvement in patient survival requires a better understanding of the disease progression so that HNOC can be detected early in the disease process and targeted therapeutic interventions can be deployed. Accumulating evidence suggests that microRNAs play important roles in many human cancers. They are pivotal regulators of diverse cellular processes including proliferation, differentiation, apoptosis, survival, motility, and morphogenesis. MicroRNA expression patterns may become powerful biomarkers for diagnosis and prognosis of HNOC. In addition, microRNA therapy could be a novel strategy for HNOC prevention a... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2454470 Fri, 05 Jun 2009 19:50:29 +0100 2454470 http://www.medworm.com/index.php?rid=2435767&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F510270 In this study, we employed evolutionary genomic approaches to investigate the impact of recombination on the core genome of Rickettsia. Phylogenetic network and phylogenetic compatibility matrix analyses are clearly consistent with the hypothesis that recombination has occurred frequently during Rickettsia evolution. 28% of Rickettsia core genes (194 out of 690) are found to present the evidence of recombination under four independent statistical methods. Further functional classification shows that these recombination events occur across all functional categories, with a significant overrepresentation in the cell wall/membrane/envelope biogenesis, which may provide a molecular basis for the parasite adaptation to host immunity. This evolutionary genomic analysis provides insight into ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2435767 Wed, 27 May 2009 05:51:45 +0100 2435767 http://www.medworm.com/index.php?rid=2421713&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F379317 In this study, I analyzed 62 and 48 subunits of the histone-modifying protein complexes of Saccharomyces cerevisiae and Schizosaccharomyces pombe, respectively. The evolutionary conservation levels of the 110 subunits were measured. The measurements revealed that the conservation levels of the catalytic subunits are significantly higher than those of the associated subunits of the histone acetyltransferase and deacetylase complexes; however, the conservation level of the catalytic subunits is similar to that of the associated subunits of the histone methyltransferase complexes. Thus, in the fungal histone acetylation and deacetylation systems, the catalytic subunits of histone-modifying protein complexes are conserved and the associated subunits are evolutionary lineage-specific. In contra... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2421713 Wed, 20 May 2009 03:35:21 +0100 2421713 http://www.medworm.com/index.php?rid=2362984&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F950171 Until recently microarray experiments often involved relatively few arrays with only a single representation of each gene on each array. A complete genome microarray with multiple spots per gene (spread out spatially across the array) was developed in order to compare the gene expression of a marine cyanobacterium and a knockout mutant strain in a defined artificial seawater medium. Statistical methods were developed for analysis in the special situation of this case study where there is gene replication within an array and where relatively few arrays are used, which can be the case with current array technology. Due in part to the replication within an array, it was possible to detect very small changes in the levels of expression between the wild type and mutant strains. One interesting ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2362984 Fri, 24 Apr 2009 17:47:52 +0100 2362984 http://www.medworm.com/index.php?rid=2320878&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2009%2F549387 In the present study, a positive training set of 30 known human imprinted gene coding regions are compared with a set of 72 randomly sampled human nonimprinted gene coding regions (negative training set) to identify genomic features common to human imprinted genes. The most important feature of the present work is its ability to use multivariate analysis to look at variation, at coding region DNA level, among imprinted and non-imprinted genes. There is a force affecting genomic parameters that appears through the use of the appropriate multivariate methods (principle components analysis (PCA) and quadratic discriminant analysis (QDA) to analyse quantitative genomic data. We show that variables, such as CG content, [bp]% CpG islands, [bp]% Large Tandem Repeats, and [bp]% Simple ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2320878 Fri, 10 Apr 2009 23:11:29 +0100 2320878 http://www.medworm.com/index.php?rid=2007268&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F284508 Fatty acid desaturases are enzymes that introduce double bonds into the hydrocarbon chains of fatty acids. The fatty acid desaturases from 37 cyanobacterial genomes were identified and classified based upon their conserved histidine-rich motifs and phylogenetic analysis, which help to determine the amounts and distributions of desaturases in cyanobacterial species. The filamentous or N2-fixing cyanobacteria usually possess more types of fatty acid desaturases than that of unicellular species. The pathway of acyl-lipid desaturation for unicellular marine cyanobacteria Synechococcus and Prochlorococcus differs from that of other cyanobacteria, indicating different phylogenetic histories of the two genera from other cyanobacteria isolated from freshwater, soil, or symbiont. Strain Gloeobacter... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=2007268 Wed, 03 Dec 2008 15:16:59 +0100 2007268 http://www.medworm.com/index.php?rid=1811662&cid=s_37045_50_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F545269 Tandemly arrayed genes (TAGs) are duplicated genes that are linked as neighbors on a chromosome, many of which have important physiological and biochemical functions. Here we performed a survey of these genes in 11 available vertebrate genomes. TAGs account for an average of about 14% of all genes in these vertebrate genomes, and about 25% of all duplications. The majority of TAGs (72–94%) have parallel transcription orientation (i.e., they are encoded on the same strand) in contrast to the genome, which has about 50% of its genes in parallel transcription orientation. The majority of tandem arrays have only two members. In all species, the proportion of genes that belong to TAGs tends to be higher in large gene families than in small ones; together with our recent finding that tan... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1811662 Sun, 21 Sep 2008 14:33:12 +0100 1811662 http://www.medworm.com/index.php?rid=1718069&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%28200012%2917%3A4%253C283%3A%3AAID-YEA52%253E3.0.CO%253B2-F The analysis of genomics data needs to become as automated as its generation. Here we present a novel data-mining approach to predicting protein functional class from sequence. This method is based on a combination of inductive logic programming clustering and rule learning. We demonstrate the effectiveness of this approach on the M. tuberculosis and E. coli genomes, and identify biologically interpretable rules which predict protein functional class from information only available from the sequence. These rules predict 65% of the ORFs with no assigned function in M. tuberculosis and 24% of those in E. coli, with an estimated accuracy of 60–80% (depending on the level of functional assignment). The rules are founded on a combination of detection of remote homology, co... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1718069 Wed, 20 Aug 2008 15:12:38 +0100 1718069 http://www.medworm.com/index.php?rid=1718068&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%28200012%2917%3A4%253C272%3A%3AAID-YEA48%253E3.0.CO%253B2-2 The Mycobacterium tuberculosis complex is associated with a remarkably low level of structural gene polymorphism. As part of a search for alternative forms of genetic variation that may act as a source of biological diversity in M. tuberculosis, we have identified a region of the genome that is highly variable amongst a panel of unrelated clinical isolates. Fifteen of 24 isolates examined contained one or more copies of the M. tuberculosis-specific IS6110 insertion element within this 20 kb variable region. In nine of the isolates, including the laboratory-passaged strain H37Rv, genomic deletions were identified, resulting in loss of between two and 13 genes. In each case, deletions were associated with the presence of a copy of the IS6110 element. Absence of flanking tri- or tetra-nucleot... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1718068 Wed, 20 Aug 2008 15:12:38 +0100 1718068 http://www.medworm.com/index.php?rid=1718067&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000630%2917%3A2%253C154%3A%3AAID-YEA18%253E3.0.CO%253B2-Z (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1718067 Wed, 20 Aug 2008 15:12:38 +0100 1718067 http://www.medworm.com/index.php?rid=1718066&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000630%2917%3A2%253C146%3A%3AAID-YEA24%253E3.0.CO%253B2-A (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1718066 Wed, 20 Aug 2008 15:12:38 +0100 1718066 http://www.medworm.com/index.php?rid=1710416&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000930%2917%3A3%253C218%3A%3AAID-YEA37%253E3.0.CO%253B2-X A recent flurry of publications and media attention has revived interest in the question of how many genes exist in the human genome. Here, I review the estimates and use genomic sequence data from human chromosomes 21 and 22 to establish my own prediction. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1710416 Sun, 17 Aug 2008 14:42:57 +0100 1710416 http://www.medworm.com/index.php?rid=1710415&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000930%2917%3A3%253C211%3A%3AAID-YEA26%253E3.0.CO%253B2-7 Increasingly mRNA expression patterns established using a variety of molecular technologies such as cDNA microarrays, SAGE and cDNA display are being used to identify potential regulatory genes and as a means of providing valuable insights into the biological status of the starting sample. Until recently, the application of these techniques has been limited to mRNA isolated from millions or, at very best, several thousand cells thereby restricting the study of small samples and complex tissues. To overcome this limitation a variety of amplification approaches have been developed which are capable of broadly evaluating mRNA expression patterns in single cells. This review will describe approaches that have been employed to examine global gene expression patterns either in small numbers of c... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1710415 Sun, 17 Aug 2008 14:42:57 +0100 1710415 http://www.medworm.com/index.php?rid=1710414&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000930%2917%3A3%253C201%3A%3AAID-YEA30%253E3.0.CO%253B2-R We have developed a sensitive quantitative RT–PCR procedure suitable for the analysis of small samples, including single cells, and have used it to measure levels of potassium channel mRNAs in a panel of human tissues and small numbers of cells grown in culture. The method involves an initial global amplification of cDNA derived from all added polyadenylated mRNA followed by quantitative RT–PCR of individual genes using specific primers. In order to facilitate rapid and accurate processing of samples, we have adapted the approach to allow use of TaqMan™ real-time quantitative PCR. We demonstrate that the approach represents a major improvement over existing conventional and real-time quantitative PCR approaches, since it can be applied to samples equivalent to a single... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1710414 Sun, 17 Aug 2008 14:42:57 +0100 1710414 http://www.medworm.com/index.php?rid=1710413&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000930%2917%3A3%253C188%3A%3AAID-YEA27%253E3.0.CO%253B2-E The role of peroxisomal processes in the maintenance of neurons has not been thoroughly investigated. We propose using Caenorhabditis elegans as a model organism for studying the molecular basis underlying neurodegeneration in certain human peroxisomal disorders, e.g. Zellweger syndrome, since the nematode neural network is well characterized and relatively simple in function. Here we have identified C. elegans PEX-5 (C34C6.6) representing the receptor for peroxisomal targeting signal type 1 (PTS1), defective in patients with such disorders. PEX-5 interacted strongly in a two-hybrid assay with Gal4p–SKL, and a screen using PEX-5 identified interaction partners that were predominantly terminated with PTS1 or its variants. A list of C. elegans proteins with similarities to well-charac... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1710413 Sun, 17 Aug 2008 14:42:57 +0100 1710413 http://www.medworm.com/index.php?rid=1710412&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000930%2917%3A3%253C170%3A%3AAID-YEA25%253E3.0.CO%253B2-V We propose a scheme for the origin of mitochondria based on phylogenetic reconstructions with more than 400 yeast nuclear genes that encode mitochondrial proteins. Half of the yeast mitochondrial proteins have no discernable bacterial homologues, while one-tenth are unequivocally of α-proteobacterial origin. These data suggest that the majority of genes encoding yeast mitochondrial proteins are descendants of two different genomic lineages that have evolved in different modes. First, the ancestral free-living α-proteobacterium evolved into an endosymbiont of an anaerobic host. Most of the ancestral bacterial genes were lost, but a small fraction of genes supporting bioenergetic and translational processes were retained and eventually transferred to what became the host nuclear ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1710412 Sun, 17 Aug 2008 14:42:57 +0100 1710412 http://www.medworm.com/index.php?rid=1710411&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000930%2917%3A3%253C235%3A%3AAID-YEA36%253E3.0.CO%253B2-X (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1710411 Sun, 17 Aug 2008 14:42:57 +0100 1710411 http://www.medworm.com/index.php?rid=1686932&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000630%2917%3A2%253C134%3A%3AAID-YEA19%253E3.3.CO%253B2-T (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1686932 Thu, 07 Aug 2008 14:58:49 +0100 1686932 http://www.medworm.com/index.php?rid=1686931&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000630%2917%3A2%253C124%3A%3AAID-YEA23%253E3.0.CO%253B2-L (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1686931 Thu, 07 Aug 2008 14:58:49 +0100 1686931 http://www.medworm.com/index.php?rid=1686930&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000630%2917%3A2%253C111%3A%3AAID-YEA17%253E3.0.CO%253B2-G On direct comparison of minimal sets of ordered clones from bacterial artificial chromosome (BAC) libraries representing the complete genomes of Mycobacterium tuberculosis H37Rv and the vaccine strain, Mycobacterium bovis BCG Pasteur, two major rearrangements were identified in the genome of M. bovis BCG Pasteur. These were shown to correspond to two tandem duplications, DU1 and DU2, of 29 668 bp and 36 161 bp, respectively. While DU1 resulted from a single duplication event, DU2 apparently arose from duplication of a 100 kb genomic segment that subsequently incurred an internal deletion of 64 kb. Several lines of evidence suggest that DU2 may continue to expand, since two copies were detected in a subpopulation of BCG Pasteur cells. BCG strains harbouring DU1 and DU2 are diploid for at le... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1686930 Thu, 07 Aug 2008 14:58:49 +0100 1686930 http://www.medworm.com/index.php?rid=1686929&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000630%2917%3A2%253C95%3A%3AAID-YEA16%253E3.0.CO%253B2-H A set of seven structurally related Sm proteins forms the core of the snRNP particles containing the spliceosomal U1, U2, U4 and U5 snRNAs. A search of the genomic sequence of Saccharomyces cerevisiae has identified a number of open reading frames that potentially encode structurally similar proteins termed Lsm (L¯ike Sm¯) proteins. With the aim of analysing all possible interactions between the Lsm proteins and any protein encoded in the yeast genome, we performed exhaustive and iterative genomic two-hybrid screens, starting with the Lsm proteins as baits. Indeed, extensive interactions amongst eight Lsm proteins were found that suggest the existence of a Lsm complex or complexes. These Lsm interactions apparently involve the conserved Sm domain that also mediates int... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1686929 Thu, 07 Aug 2008 14:58:49 +0100 1686929 http://www.medworm.com/index.php?rid=1686928&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000630%2917%3A2%253C88%3A%3AAID-YEA20%253E3.0.CO%253B2-Y The availability of complete genome sequences necessitates the development of standardized functional assays to analyse the tens of thousands of predicted gene products in high-throughput experimental settings. Such approaches are collectively referred to as ‘functional genomics’. One approach to investigate the properties of a proteome of interest is by systematic analysis of protein–protein interactions. So far, the yeast two-hybrid system is the most commonly used method for large-scale, high-throughput identification of potential protein–protein interactions. Here, we discuss several technical features of variants of the two-hybrid systems in light of data recently obtained from different protein interaction mapping projects for the budding yeast Saccharomyc... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1686928 Thu, 07 Aug 2008 14:58:49 +0100 1686928 http://www.medworm.com/index.php?rid=1686927&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000630%2917%3A2%253C81%3A%3AAID-YEA22%253E3.0.CO%253B2-Z In this review we examine the current state of analytical methods in proteomics. The conventional methodology using two-dimensional electrophoresis gels and mass spectrometry is discussed, with particular reference to the advantages and shortcomings thereof. Two recently published methods which offer an alternative approach are presented and discussed, with emphasis on how they can provide information not available via two-dimensional gel electrophoresis. These two methods are the isotope-coded affinity tags approach of Gygi et al. and the two-dimensional liquid chromatography–tandem mass spectrometry approach as presented by Link et al. We conclude that both of these new techniques represent significant advances in analytical methodology for proteome analysis. Furthermore, we belie... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1686927 Thu, 07 Aug 2008 14:58:49 +0100 1686927 http://www.medworm.com/index.php?rid=1503095&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F634283 Cohesin is a protein complex that regulates sister chromatid cohesin during cell division. Malfunction in chromatid cohesin results in chromosome missegregation and aneuploidy. Here, we report that mutations of MCD1 and PDS5, two major components of cohesin in budding yeast, cause apoptotic cell death, which is characterized by externalization of phosphatidylserine at cytoplasmic membrane, chromatin condensation and fragmentation, and ROS production. Microarray analysis suggests that the cell death caused by mutation of MCD1 or PDS5 is due to the internal stress response, contrasting to the environmental or external stress response induced by external stimuli, such as hydrogen peroxide. A common feature shared by the internal stress response and external stress response is the response to ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1503095 Mon, 09 Jun 2008 22:51:27 +0100 1503095 http://www.medworm.com/index.php?rid=1492736&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F879023 Cryptosporidium parvum and C. hominis are related protozoan pathogens which infect the intestinal epithelium of humans and other vertebrates. To explore the evolution of these parasites, and identify genes under positive selection, we performed a pairwise whole-genome comparison between all orthologous protein coding genes in C. parvum and C. hominis. Genome-wide calculation of the ratio of nonsynonymous versus synonymous nucleotide substitutions (dN/dS) was performed to detect the impact of positive and purifying selection. Of 2465 pairs of orthologous genes, a total of 27 (1.1%) showed a high ratio of nonsynonymous substitutions, consistent with positive selection. A majority of these genes were annotated as hypothetical proteins. In addition, proteins with transmembrane and signal p... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1492736 Wed, 04 Jun 2008 17:45:02 +0100 1492736 http://www.medworm.com/index.php?rid=1489904&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F1097-0061%2820000630%2917%3A2%253C79%3A%3AAID-YEA21%253E3.0.CO%253B2-X (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489904 Tue, 03 Jun 2008 22:25:36 +0100 1489904 http://www.medworm.com/index.php?rid=1489903&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253C71%3A%3AAID-YEA7%253E3.0.CO%253B2-K (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489903 Tue, 03 Jun 2008 22:25:36 +0100 1489903 http://www.medworm.com/index.php?rid=1489902&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253C56%3A%3AAID-YEA12%253E3.0.CO%253B2-H (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489902 Tue, 03 Jun 2008 22:25:36 +0100 1489902 http://www.medworm.com/index.php?rid=1489901&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253C48%3A%3AAID-YEA2%253E3.0.CO%253B2-H (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489901 Tue, 03 Jun 2008 22:25:36 +0100 1489901 http://www.medworm.com/index.php?rid=1489900&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253C43%3A%3AAID-YEA1%253E3.0.CO%253B2-Z In addition, the group is taking advantage of the completion of the C. elegans genome sequence to develop whole genome DNA microarrays for expression profiling. At the Sanger Centre, DNA microarrays are providing opportunities to examine how development and physiology are regulated globally, because most nematode genes have now been identified at the sequence level. The group are being assisted in this endeavour by Dr Stuart Kim (Stanford, CA). (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489900 Tue, 03 Jun 2008 22:25:36 +0100 1489900 http://www.medworm.com/index.php?rid=1489899&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253C37%3A%3AAID-YEA11%253E3.0.CO%253B2-P (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489899 Tue, 03 Jun 2008 22:25:36 +0100 1489899 http://www.medworm.com/index.php?rid=1489898&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253C22%3A%3AAID-YEA5%253E3.0.CO%253B2-S Conclusions: Comparison of observed data to computer simulations suggests that 4000–16 000 chromosomal rearrangements have occured since Fugu and human shared a common ancestor, implying a faster rate of rearrangement than seen in human/mouse comparisons. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489898 Tue, 03 Jun 2008 22:25:36 +0100 1489898 http://www.medworm.com/index.php?rid=1489897&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253C16%3A%3AAID-YEA6%253E3.0.CO%253B2-E Pharmacogenomics is defined as the study of the association between genetics and drug response. This is a rapidly expanding field with the hope that, within a few years, prospective genotyping will lead to patients being prescribed drugs which are both safer and more effective (‘the right drug for the right patient’, or personalized medicine). There are many existing examples in the literature of strong associations between genetic variation and drug response, and some of these even form the basis of accepted clinical tests. The molecular basis for some of these associations is described, and includes examples of variation in genes responsible for absorption and metabolism of the drug, and in target and disease genes. However, there are many issues surrounding the legal, regu... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489897 Tue, 03 Jun 2008 22:25:36 +0100 1489897 http://www.medworm.com/index.php?rid=1489896&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253C6%3A%3AAID-YEA15%253E3.0.CO%253B2-V Visualization of data is important for many data-rich disciplines. In biology, where data sets are becoming larger and more complex, grephical analysis is felt to be ever more pertinent. Although some patterns and trends in data sets may only be determined by sophisticated computional analysis, viewing data by eye can provide us with an extraordinary amount of information in an instant. Recent advances in bioinformatic technologies allow us to link graphical tools to data sources with ease, so we can visualize our data sets dynamically. Here, an overview of graghical software tools for comparative genome analysis is given, showing that a range of simple tools can provide us with powerful view of the differences and similarities between genome. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489896 Tue, 03 Jun 2008 22:25:36 +0100 1489896 http://www.medworm.com/index.php?rid=1489895&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253C1%3A%3AAID-YEA3%253E3.0.CO%253B2-V The rapidly accumulating genome sequence data from the plant Arabidopsis thaliana allows more detailed analysis of genome content and organisation than ever bafore possible in plants. The genome shows a surprisingly high level of genetic redundancy, with as many as 75% of gene products showing signficant homology to another protien of A. thaliana. Many duplicated genes occur in arrays of conserved order and indicate that A. thaliana is likely to have had a tetraploid ancestor. Analysis of the divergence of duplicated genome segments leads to the prediction of two major modes of plant genome evolution: macro-scale duplication and rearrangement of chromosomes and micro-scale translocation, duplication and loss of individual genes or small groups of genes. (Source: Comparative and Functi... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489895 Tue, 03 Jun 2008 22:25:36 +0100 1489895 http://www.medworm.com/index.php?rid=1489894&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253CVII%3A%3AAID-YEA14%253E3.0.CO%253B2-B (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489894 Tue, 03 Jun 2008 22:25:36 +0100 1489894 http://www.medworm.com/index.php?rid=1489893&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1002%2F%28SICI%291097-0061%28200004%2917%3A1%253CV%3A%3AAID-YEA13%253E3.0.CO%253B2-C (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489893 Tue, 03 Jun 2008 22:25:36 +0100 1489893 http://www.medworm.com/index.php?rid=1489892&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F49356 By combining crystallographic information with protein-interaction data obtained through traditional experimental means, this paper determines the most appropriate method for generating protein-interaction networks that incorporate data derived from protein complexes. We propose that a combined method should be considered; in which complexes composed of five chains or less are decomposed using the matrix model, whereas the spoke model is used to derive pairwise interactions for those with six chains or more. The results presented here should improve the accuracy and relevance of studies investigating the topology of protein-interaction networks. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489892 Tue, 03 Jun 2008 22:25:36 +0100 1489892 http://www.medworm.com/index.php?rid=1489891&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F43070 It has been suggested that there are special evolutionary forces that act on sex chromosomes. Hemizygosity of the X chromosome in male mammals has led to selection for male-advantage genes, and against genes posing extreme risks of tumor development. A similar bias against cancer genes should also apply to the Z chromosome that is present as a single copy in female birds. Using comparative database analysis, we found that there was no significant underrepresentation of cancer genes on the chicken Z, nor on the Z-orthologous regions of human chromosomes 5 and 9. This result does not support the hypothesis that genes involved in cancer are selected against on the sex chromosomes. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489891 Tue, 03 Jun 2008 22:25:36 +0100 1489891 http://www.medworm.com/index.php?rid=1489890&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F58721 Previous studies in the yeast Saccharomyces cerevisiae have shown that genes encoding subunits of macromolecular complexes have similar evolutionary rates (K) and expression levels (E). Besides, it is known that the expression of a gene is a strong predictor of its rate of evolution (i.e., E and K are correlated). Here we show that intracomplex variation of subunit expression correlates with intracomplex variation of their evolutionary rates (using two different measures of dispersion). However, a similar trend was observed for randomized complexes. Therefore, using a mathematical transformation, we created new variables capturing intracomplex variation of both E and K. The values of these new compound variables were smaller for real complexes than for randomized ones. This shows that prot... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489890 Tue, 03 Jun 2008 22:25:36 +0100 1489890 http://www.medworm.com/index.php?rid=1489889&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F47161 We have identified four repeats and ten domains that are novel in proteins encoded by the Bacillus anthracis str. Ames proteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residue YEFF domain, (4) 109-amino-acid-residue IMxxH domain, (5) 103-amino-acid-residue VxxT domain, (6) 84-amino-acid-residue ExW domain, (7) 104-amino-acid-residue NTGFIG do... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489889 Tue, 03 Jun 2008 22:25:36 +0100 1489889 http://www.medworm.com/index.php?rid=1489888&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F90578 Conclusions. The SCS normalisation results using 16 macroarray data sets from a Bacillus subtilis experiment confirm that the method is capable of reducing undesirable experimental variation whilst retaining important biological information. The ease and speed of implementation mean that this method can be easily adapted to other multicondition time/strain series single colour array data. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489888 Tue, 03 Jun 2008 22:25:36 +0100 1489888 http://www.medworm.com/index.php?rid=1489887&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F47304 This meeting report summarizes the proceedings of the “eGenomics: Cataloguing our Complete Genome Collection III” workshop held September 11–13, 2006, at the National Institute for Environmental eScience (NIEeS), Cambridge, United Kingdom. This 3rd workshop of the Genomic Standards Consortium was divided into two parts. The first half of the three-day workshop was dedicated to reviewing the genomic diversity of our current and future genome and metagenome collection, and exploring linkages to a series of existing projects through formal presentations. The second half was dedicated to strategic discussions. Outcomes of the workshop include a revised “Minimum Information about a Genome Sequence” (MIGS) specification (v1.1), consens... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489887 Tue, 03 Jun 2008 22:25:36 +0100 1489887 http://www.medworm.com/index.php?rid=1489886&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F25751 To elucidate the evolution of cyanobacterial envelopes and the relation between gene content and environmental adaptation, cell envelope structures and components of unicellular and filamentous cyanobacteria were analyzed in comparative genomics. Hundreds of envelope biogenesis genes were divided into 5 major groups and annotated according to their conserved domains and phylogenetic profiles. Compared to unicellular species, the gene numbers of filamentous cyanobacteria expanded due to genome enlargement effect, but only few gene families amplified disproportionately, such as those encoding waaG and glycosyl transferase 2. Comparison of envelope genes among various species suggested that the significant variance of certain cyanobacterial envelope biogenesis genes should be the response to ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489886 Tue, 03 Jun 2008 22:25:36 +0100 1489886 http://www.medworm.com/index.php?rid=1489885&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F21676 Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare) proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns wi... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489885 Tue, 03 Jun 2008 22:25:36 +0100 1489885 http://www.medworm.com/index.php?rid=1489884&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F89596 Two-dimensional gel-electrophoresis (2-DE) images show the expression levels of several hundreds of proteins where each protein is represented as a blob-shaped spot of grey level values. The spot detection, that is, the segmentation process has to be efficient as it is the first step in the gel processing. Such extraction of information is a very complex task. In this paper, we propose a novel spot detector that is basically a morphology-based method with the use of a seeded region growing as a central paradigm and which relies on the spot correlation information. The method is tested on our synthetic as well as on real gels with human samples from SWISS-2DPAGE (two-dimensional polyacrylamide gel electrophoresis) database. A comparison of results is done with a method called pixel value co... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489884 Tue, 03 Jun 2008 22:25:36 +0100 1489884 http://www.medworm.com/index.php?rid=1489883&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F60964 Tandemly arrayed genes (TAGs) account for about one third of the duplicated genes in eukaryotic genomes, yet there has not been any systematic study of their gene expression patterns. Taking advantage of recently published large-scale microarray data sets, we studied the expression divergence of 361 two-member TAGs in human and 212 two-member TAGs in mouse and examined the effect of sequence divergence, gene orientation, and chromosomal proximity on the divergence of TAG expression patterns. Our results show that there is a weak negative correlation between sequence divergence of TAG members and their expression similarity. There is also a weak negative correlation between chromosomal proximity of TAG members and their expression similarity. We did not detect any significant relationship b... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489883 Tue, 03 Jun 2008 22:25:36 +0100 1489883 http://www.medworm.com/index.php?rid=1489882&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F35604 The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489882 Tue, 03 Jun 2008 22:25:36 +0100 1489882 http://www.medworm.com/index.php?rid=1489881&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2007%2F57513 Nasopharyngeal carcinoma (NPC) is a rare malignancy in most parts of the world, but is one of the most common cancers in Southeast Asia. Both genetic and environmental factors contribute to the tumorigenesis of NPC, most notably the consumption of certain salted food items and Epstein-Barr virus infection. This review will focus on the current progress of the genetic analysis of NPC (genetic susceptibilities and somatic alterations). We will review the current advances in genomic technologies and their shaping of the future direction of NPC research. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489881 Tue, 03 Jun 2008 22:25:36 +0100 1489881 http://www.medworm.com/index.php?rid=1489880&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F451930 We have identified two genomic islands, that is, BCEGI-1 and BCEGI-2, in the genome of Bacillus cereus ATCC 10987, based on comparative analysis with Bacillus cereus ATCC 14579. Furthermore, by using the cumulative GC profile and performing homology searches between the two genomes, the integration sites of the two genomic islands were determined at single-nucleotide resolution. BCEGI-1 is integrated between 159705 bp and 198000 bp, whereas BCEGI-2 is integrated between the end of ORF BCE4594 and the start of the intergenic sequence immediately following BCE4626, that is, from 4256803 bp to 4285534 bp. BCEGI-1 harbors two bacterial Tn7 transposons, which have two sets of genes encoding TnsA, B, C, and... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489880 Tue, 03 Jun 2008 22:25:36 +0100 1489880 http://www.medworm.com/index.php?rid=1489879&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F254836 To identify key regulators of subminimum inhibitory concentration (sub-MIC) antibiotic response in the Pasteurella multocida proteome, we applied systems approaches. Using 2D-LC-ESI-MS2, we achieved 53% proteome coverage. To study the differential protein expression in response to sub-MIC antibiotics in the context of protein interaction networks, we inferred P. multocida Pm70 protein interaction network from orthologous proteins. We then overlaid the differential protein expression data onto the P. multocida protein interaction network to study the bacterial response. We identified proteins that could enhance antimicrobial activity. Overall compensatory response to antibiotics was characterized by altered expression of proteins involved in purine metabolism, stress response, and cell ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489879 Tue, 03 Jun 2008 22:25:36 +0100 1489879 http://www.medworm.com/index.php?rid=1489878&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F565631 There has been much interest in CpG islands (CGIs), clusters of CpG dinucleotides in GC-rich regions, because they are considered gene markers and involved in gene regulation. To date, there has been no genome-wide analysis of CGIs in the fish genome. We first evaluated the performance of three popular CGI identification algorithms in four fish genomes (tetraodon, stickleback, medaka, and zebrafish). Our results suggest that Takai and Jones' (2002) algorithm is most suitable for comparative analysis of CGIs in the fish genome. Then, we performed a systematic analysis of CGIs in the four fish genomes using Takai and Jones' algorithm, compared to other vertebrate genomes. We found that both the number of CGIs and the CGI density vary greatly among these genomes. Remarkably, each fish... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489878 Tue, 03 Jun 2008 22:25:36 +0100 1489878 http://www.medworm.com/index.php?rid=1489877&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F609684 We report on the clinical, cytogenetic, and molecular findings in a boy with autism carrying a de novo translocation t(7;16)(p22.1;p11.2). The chromosome 16 breakpoint disrupts the paralogous SLC6A8 gene also called SLC6A10 or CT2. Predicted translation of exons and RT-PCR analysis reveal specific expression of the creatine transporter paralogous in testis and brain. Several studies reported on the role of X-linked creatine transporter mutations in individuals with mental retardation, with or without autism. The existence of disruption in SLC6A8 paralogous gene associated with idiopathic autism suggests that this gene may be involved in the autistic phenotype in our patient. (Source: Comparative and Functional Genomics) Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489877 Tue, 03 Jun 2008 22:25:36 +0100 1489877 http://www.medworm.com/index.php?rid=1489876&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F571023 RNA methylation, which is a form of posttranscriptional modification, is catalyzed by S-adenosyl-L-methionone-dependent RNA methyltransterases (RNA MTases). We have identified a novel silkworm gene, BmRNAMTase, containing a 369-bp open reading frame that encodes a putative protein containing 122 amino acid residues and having a molecular weight of 13.88 kd. We expressed a recombinant His-tagged BmRNAMTase in E. coli BL21 (DE3), purified the fusion protein by metal-chelation affinity chromatography, and injected a New Zealand rabbit with the purified protein to generate anti-BmRNAMTase polyclonal antibodies. Immunohistochemistry revealed that BmRNAMTase is abundant in the cytoplasm of Bm5 cells. In addition, using RNA interference to reduce the intracellular activity and content of BmRNAMTa... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489876 Tue, 03 Jun 2008 22:25:36 +0100 1489876 http://www.medworm.com/index.php?rid=1489875&cid=s_37045_176_f&fid=37045&url=http%3A%2F%2Fwww.hindawi.com%2FGetArticle.aspx%3Fdoi%3D10.1155%2F2008%2F623145 Orientia tsutsugamushi, the causative agent of scrub typhus, is an obligate intracellular bacterium that belongs to the order of Rickettsiales. Recently, we have reported that O. tsutsugamushi has a unique genomic structure, consisting of highly repetitive sequences, and suggested that it may provide valuable insight into the evolution of intracellular bacteria. Here, we have used genomic information to construct the major metabolic pathways of O. tsutsugamushi and performed a comparative analysis of the metabolic genes and pathways of O. tsutsugamushi with other members of the Rickettsiales order. While O. tsutsugamushi has the ... Comparative and Functional Genomics journals http://www.medworm.com/rss/comments.php?id=1489875 Tue, 03 Jun 2008 22:25:36 +0100 1489875