An optimized procedure greatly improves EST vector contamination removal

<p>Abstract</p> <p>Background</p> <p>The enormous amount of sequence data available in the public domain database has been a gold mine for researchers exploring various themes in life sciences, and hence the quality of such data is of serious concern to researchers. Removal of vector contamination is one of the most significant operations to obtain accurate sequence data containing only a cDNA insert from the basecalls output by an automatic DNA sequencer. Popular bioinformatics programs to accomplish vector trimming include LUCY, cross_match and SeqClean.</p> <p>Results</p> <p>In a recent study, where the program SeqClean was used to remove vector contamination from our test set of EST data compiled through various library construction systems, however, a significant number of errors remained after preliminary trimming. These errors were later almost completely corrected by simply using a re-linearized form of the cloning vector to compare against the target ESTs. The modified trimming procedure for SeqClean was also compared with the trimming efficiency of the other two popular programs, LUCY2, and cross_match. Using SeqClean with a re-linearized form of the cloning vector significantly surpassed the other two programs in all tested conditions, while the performance of the other two programs was not influenced by the modified procedure. Vector contamination in dbEST was also investigated in this study: 2203 out of the 48212 ESTs sampled from dbEST (2007-04-18 freeze) were found to match sequences in UNIVEC.</p> <p>Conclusion</p> <p>Vector contamination remains a serious concern to the data quality in the public sequence database nowadays. Based on the results presented here, we feel that our modified procedure with SeqClean should be recommended to all researchers for the task of vector removal from EST or genomic sequences.</p

Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells

<p>Abstract</p> <p>Background</p> <p><it>Echinacea </it>spp. extracts and the derived phytocompounds have been shown to induce specific immune cell activities and are popularly used as food supplements or nutraceuticals for immuno-modulatory functions. Dendritic cells (DCs), the most potent antigen presenting cells, play an important role in both innate and adaptive immunities. In this study, we investigated the specific and differential gene expression in human immature DCs (iDCs) in response to treatment with a butanol fraction containing defined bioactive phytocompounds extracted from stems and leaves of <it>Echinacea purpurea</it>, that we denoted [BF/S+L/Ep].</p> <p>Results</p> <p>Affymetrix DNA microarray results showed significant up regulation of specific genes for cytokines (IL-8, IL-1β, and IL-18) and chemokines (CXCL 2, CCL 5, and CCL 2) within 4 h after [BF/S+L/Ep] treatment of iDCs. Bioinformatics analysis of genes expressed in [BF/S+L/Ep]-treated DCs revealed a key-signaling network involving a number of immune-modulatory molecules leading to the activation of a downstream molecule, adenylate cyclase 8. Proteomic analysis showed increased expression of antioxidant and cytoskeletal proteins after treatment with [BF/S+L/Ep] and cichoric acid.</p> <p>Conclusion</p> <p>This study provides information on candidate target molecules and molecular signaling mechanisms for future systematic research into the immune-modulatory activities of an important traditional medicinal herb and its derived phytocompounds.</p

Metabolic syndrome in a Taiwanese metropolitan adult population

<p>Abstract</p> <p>Background</p> <p>Metabolic syndrome (MS) is a combination of medical disorders that increase one's risk for cardiovascular disease and diabetes. Little information exists on the prevalence of MS in a general adult population in Taiwan.</p> <p>Methods</p> <p>We did a cross-sectional survey in a representative sample of 2,359 Chinese adults aged 40 years and over who lived in a metropolitan city, Taiwan in 2004–05. MS was defined by Adult Treatment Panel III criteria modified for Asians.</p> <p>Results</p> <p>The prevalence of MetS was 35.32% and 43.23% in men aged 40–64 years and 65 years and over, respectively, and 24.19% and 51.82% in women aged 40–64 years and 65 years and over. Older age, postmenopausal status, higher body mass index, current smoking, low education attainment, low household income, no alcohol consumption, lower level of occupation physical activity, and a family history of diabetes were associated with increased odds of MetS.</p> <p>Conclusion</p> <p>MetS was present in more than 30% of the Taiwan adult population aged 40 years and over in a metropolitan area; there were substantial variations by age and body mass index groups.</p

Stimulatory effect of Echinacea purpurea extract on the trafficking activity of mouse dendritic cells: revealed by genomic and proteomic analyses

<p>Abstract</p> <p>Background</p> <p>Several <it>Echinacea </it>species have been used as nutraceuticals or botanical drugs for "immunostimulation", but scientific evidence supporting their therapeutic use is still controversial. In this study, a phytocompound mixture extracted from the butanol fraction (BF) of a stem and leaf (S+L) extract of <it>E. purpurea </it>([BF/S+L/Ep]) containing stringently defined bioactive phytocompounds was obtained using standardized and published procedures. The transcriptomic and proteomic effects of this phytoextract on mouse bone marrow-derived dendritic cells (BMDCs) were analyzed using primary cultures.</p> <p>Results</p> <p>Treatment of BMDCs with [BF/S+L/Ep] did not significantly influence the phenotypic maturation activity of dendritic cells (DCs). Affymetrix DNA microarray and bioinformatics analyses of genes differentially expressed in DCs treated with [BF/S+L/Ep] for 4 or 12 h revealed that the majority of responsive genes were related to cell adhesion or motility (<it>Cdh10</it>, <it>Itga6</it>, <it>Cdh1</it>, <it>Gja1 </it>and <it>Mmp8</it>), or were chemokines (<it>Cxcl2, Cxcl7) </it>or signaling molecules (<it>Nrxn1, Pkce </it>and <it>Acss1</it>). TRANSPATH database analyses of gene expression and related signaling pathways in treated-DCs predicted the JNK, PP2C-α, AKT, ERK1/2 or MAPKAPK pathways as the putative targets of [BF/S+L/Ep]. In parallel, proteomic analysis showed that the expressions of metabolic-, cytoskeleton- or NF-κB signaling-related proteins were regulated by treatment with [BF/S+L/Ep]. <it>In vitro </it>flow cytometry analysis of chemotaxis-related receptors and <it>in vivo </it>cell trafficking assay further showed that DCs treated with [BF/S+L/Ep] were able to migrate more effectively to peripheral lymph node and spleen tissues than DCs treated as control groups.</p> <p>Conclusion</p> <p>Results from this study suggest that [BF/S+L/Ep] modulates DC mobility and related cellular physiology in the mouse immune system. Moreover, the signaling networks and molecules highlighted here are potential targets for nutritional or clinical application of <it>Echinacea </it>or other candidate medicinal plants.</p

Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies

<p>Abstract</p> <p>Background</p> <p>To elucidate the molecular complications in many complex diseases, we argue for the priority to construct a model representing the normal physiological state of a cell/tissue.</p> <p>Results</p> <p>By analyzing three independent microarray datasets on normal human tissues, we established a quantitative molecular model GET, which consists of 24 tissue-specific <it>G</it>ene <it>E</it>xpression <it>T</it>emplates constructed from a set of 56 genes, for predicting 24 distinct tissue types under disease-free condition. 99.2% correctness was reached when a large-scale validation was performed on 61 new datasets to test the tissue-prediction power of GET. Network analysis based on molecular interactions suggests a potential role of these 56 genes in tissue differentiation and carcinogenesis.</p> <p>Applying GET to transcriptomic datasets produced from tissue development studies the results correlated well with developmental stages. Cancerous tissues and cell lines yielded significantly lower correlation with GET than the normal tissues. GET distinguished melanoma from normal skin tissue or benign skin tumor with 96% sensitivity and 89% specificity.</p> <p>Conclusions</p> <p>These results strongly suggest that a normal tissue or cell may uphold its normal functioning and morphology by maintaining specific chemical stoichiometry among genes. The state of stoichiometry can be depicted by a compact set of representative genes such as the 56 genes obtained here. A significant deviation from normal stoichiometry may result in malfunction or abnormal growth of the cells.</p

Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies

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Molecular characterization, overexpression and comparison of esterases-encoding LipRT, Lip4 and Lip20 from moderately thermophilic and mesophilic bacteria

Thermostable enzymes have the potential as the biocatalyst for industrial applications. To compare the relationship of enzymatic thermostability, the moderately thermophilic and mesophilic bacteria were utilized to explore the properties of esterases. By using the shotgun libraries of mesophilic Thalassomonas agarivorans, and Aeromonas sp., and moderately thermophilic Ralstonia sp., esterases-encoding Lip20, Lip4 and LipRT for α/β-hydrolase fold were cloned, sequenced, and characterized. According to the recombinant proteins overexpressed by Escherichia coli, these results indicated that Lip20, Lip4 and LipRT preferred to hydrolyze short-length p-nitrophenyl (p-NP) esters. The optimal temperature required for the activity of Lip20, Lip4 and LipRT was 30, 40 and 60°C, respectively, corresponding to the trend of bacterial growth temperature. Even at low temperature, cold-adapted Lip4 from Aeromonas sp. revealed well enzymatic activity. In addition, after 60 min incubation between 40-60°C, over 92% residual activity can be retained by the thermostable analysis of LipRT from Ralstonia sp.. Inspecting the predicted structures and amino acid composition, we found that the high helix content was exhibited in LipRT. Also, high frequency residues of Val, Phe and Arg for increasing hydrophobic and salt-bridge interactions were observed. These factors could improve LipRT thermal stabilization and lead to become more rigid

Molecular characterization, overexpression and comparison of esterases-encoding LipRT, Lip4 and Lip20 from moderately thermophilic and mesophilic bacteria

Thermostable enzymes have the potential as the biocatalyst for industrial applications. To compare the relationship of enzymatic thermostability, the moderately thermophilic and mesophilic bacteria were utilized to explore the properties of esterases. By using the shotgun libraries of mesophilic Thalassomonas agarivorans, and Aeromonas sp., and moderately thermophilic Ralstonia sp., esterases-encoding Lip20, Lip4 and LipRT for α/β-hydrolase fold were cloned, sequenced, and characterized. According to the recombinant proteins overexpressed by Escherichia coli, these results indicated that Lip20, Lip4 and LipRT preferred to hydrolyze short-length p-nitrophenyl (p-NP) esters. The optimal temperature required for the activity of Lip20, Lip4 and LipRT was 30, 40 and 60°C, respectively, corresponding to the trend of bacterial growth temperature. Even at low temperature, cold-adapted Lip4 from Aeromonas sp. revealed well enzymatic activity. In addition, after 60 min incubation between 40-60°C, over 92% residual activity can be retained by the thermostable analysis of LipRT from Ralstonia sp.. Inspecting the predicted structures and amino acid composition, we found that the high helix content was exhibited in LipRT. Also, high frequency residues of Val, Phe and Arg for increasing hydrophobic and salt-bridge interactions were observed. These factors could improve LipRT thermal stabilization and lead to become more rigid

An optimized procedure greatly improves EST vector contamination removal-0

<p><b>Copyright information:</b></p><p>Taken from "An optimized procedure greatly improves EST vector contamination removal"</p><p>http://www.biomedcentral.com/1471-2164/8/416</p><p>BMC Genomics 2007;8():416-416.</p><p>Published online 13 Nov 2007</p><p>PMCID:PMC2194723.</p><p></p>the EST. According to the original SeqClean design, the vector contaminant is recognized only if some or all of the similar vector sequence is identified within this range. The boxes in blue indicate the vector-derived sequence. The yellow open boxes represent cDNA inserts and the green bars show the low quality regions. The small stars indicate where the number 1 base is located by CVS coordinates. The boxes in red specify the product of SeqClean trimming. Comments for each of the three listed trimming situations are denoted to their right. Condition A indicates those ESTs which were mistakenly trashed. Condition B shows incomplete trimming and condition C is an example of correct trimming. Example ESTs corresponding to each of the three conditions are shown in the table below, where the position numbering followed the coordinates of the untrimmed EST sequences