Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data

<p>Abstract</p> <p>Background</p> <p>It was proposed that differentially-expressed genes, aside from genetic variations affecting protein processing and functioning, between hybrid and its parents provide essential candidates for studying heterosis or hybrid vigor. Based our serial analysis of gene expression (SAGE) data from an elite Chinese super-hybrid rice (<it>LYP9</it>) and its parental cultivars (<it>93-11 </it>and <it>PA64s</it>) in three major tissue types (leaves, roots and panicles) at different developmental stages, we analyzed the transcriptome and looked for candidate genes related to rice heterosis.</p> <p>Results</p> <p>By using an improved strategy of tag-to-gene mapping and two recently annotated genome assemblies (<it>93-11 and PA64s</it>), we identified 10,268 additional high-quality tags, reaching a grand total of 20,595 together with our previous result. We further detected 8.5% and 5.9% physically-mapped genes that are differentially-expressed among the triad (in at least one of the three stages) with <it>P</it>-values less than 0.05 and 0.01, respectively. These genes distributed in 12 major gene expression patterns; among them, 406 up-regulated and 469 down-regulated genes (<it>P </it>< 0.05) were observed. Functional annotations on the identified genes highlighted the conclusion that up-regulated genes (some of them are known enzymes) in hybrid are mostly related to enhancing carbon assimilation in leaves and roots. In addition, we detected a group of up-regulated genes related to male sterility and 442 down-regulated genes related to signal transduction and protein processing, which may be responsible for rice heterosis.</p> <p>Conclusion</p> <p>We improved tag-to-gene mapping strategy by combining information from transcript sequences and rice genome annotation, and obtained a more comprehensive view on genes that related to rice heterosis. The candidates for heterosis-related genes among different genotypes provided new avenue for exploring the molecular mechanism underlying heterosis.</p

DeteX: A highly accurate software for detecting SNV and InDel in single and paired NGS data in cancer research

Background: Genetic testing is becoming more and more accepted in the auxiliary diagnosis and treatment of tumors. Due to the different performance of the existing bioinformatics software and the different analysis results, the needs of clinical diagnosis and treatment cannot be met. To this end, we combined Bayesian classification model (BC) and fisher exact test (FET), and develop an efficient software DeteX to detect SNV and InDel mutations. It can detect the somatic mutations in tumor-normal paired samples as well as mutations in a single sample.Methods: Combination of Bayesian classification model (BC) and fisher exact test (FET).Results: We detected SNVs and InDels in 11 TCGA glioma samples, 28 clinically targeted capture samples and 2 NCCL-EQA standard samples with DeteX, VarDict, Mutect, VarScan and GatkSNV. The results show that, among the three groups of samples, DeteX has higher sensitivity and precision whether it detects SNVs or InDels than other callers and the F1 value of DeteX is the highest. Especially in the detection of substitution and complex mutations, only DeteX can accurately detect these two kinds of mutations. In terms of single-sample mutation detection, DeteX is much more sensitive than the HaplotypeCaller program in Gatk. In addition, although DeteX has higher mutation detection capabilities, its running time is only .609 of VarDict, which is .704 and .343 longer than VarScan and MuTect, respectively.Conclusion: In this study, we developed DeteX to detect SNV and InDel mutations in single and paired samples. DeteX has high sensitivity and precision especially in the detection of substitution and complex mutations. In summary, DeteX from NGS data is a good SNV and InDel caller

Specific 12β-Hydroxylation of Cinobufagin by Filamentous Fungi

Biotransformation of natural products has great potential for producing new drugs and could provide in vitro models of mammalian metabolism. Microbial transformation of the cytotoxic steroid cinobufagin was investigated. Cinobufagin could be specifically hydroxylated at the 12β-position by the fungus Alternaria alternata. Six products from a scaled-up fermentation were obtained by silica gel column chromatography and reversed-phase liquid chromatography and were identified as 12β-hydroxyl cinobufagin, 12β-hydroxyl desacetylcinobufagin, 3-oxo-12β-hydroxyl cinobufagin, 3-oxo-12β-hydroxyl desacetylcinobufagin, 12-oxo-cinobufagin, and 3-oxo-12α-hydroxyl cinobufagin. The last five products are new compounds. 12β-Hydroxylation of cinobufagin by A. alternata is a fast catalytic reaction and was complete within 8 h of growth with the substrate. This reaction was followed by dehydrogenation of the 3-hydroxyl group and then deacetylation at C-16. Hydroxylation at C-12β also was the first step in the metabolism of cinobufagin by a variety of fungal strains. In vitro cytotoxicity assays suggest that 12β-hydroxyl cinobufagin and 3-oxo-12α-hydroxyl cinobufagin exhibit somewhat decreased but still significant cytotoxic activities. The 12β-hydroxylated bufadienolides produced by microbial transformation are difficult to obtain by chemical synthesis

Biological Databases for Hematology Research

With the advances of genome-wide sequencing technologies and bioinformatics approaches, a large number of datasets of normal and malignant erythropoiesis have been generated and made public to researchers around the world. Collection and integration of these datasets greatly facilitate basic research and clinical diagnosis and treatment of blood disorders. Here we provide a brief introduction of the most popular omics data resources of normal and malignant hematopoiesis, including some integrated web tools, to help users get better equipped to perform common analyses. We hope this review will promote the awareness and facilitate the usage of public database resources in the hematology research

Functional Categories of up-regulated and down-regulated genes in panicles, leaves, and roots

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data"</p><p>http://www.biomedcentral.com/1471-2229/7/49</p><p>BMC Plant Biology 2007;7():49-49.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2077334.</p><p></p

Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data-4

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data"</p><p>http://www.biomedcentral.com/1471-2229/7/49</p><p>BMC Plant Biology 2007;7():49-49.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2077334.</p><p></p>ion, glycolic acid oxidation, and fatty acid β-oxdidation pathways are shown. The enzymes (denotes key or rate-limiting enzymes) are: E1, fructose-1,6-bisphosphatase; E2, fructose-bisphosphate aldolase; E3, glyceraldehyde 3-phosphate dehydrogenase; E4, phosphoglycerate kinase; E5, pyruvate kinase; E6, alcohol dehydrogenase; E7, catalase; E8, acyl-CoA dehydrogenase; E9, succinyl-CoA ligase; E10, malate dehydrogenase; E11, ribulose bisphosphate carboxylase; E12, transketolase; E13, ribulose-phosphate 3-epimerase; E14, phosphoribulokinase; E15, beta-phosphoglucomutase, 1,4-alpha-glucan branching enzyme; E16, sucrose phosphate synthase; E17, sucrose synthase. Proteins and enzymes in the light reaction complex are plastocyanin, ferredoxin [2Fe-2S], chlorophyll A-B binding protein, photosystem II protein PsbX, photosystem II protein PsbW, photosystem II protein PsbY, photosystem II oxygen evolving complex protein PsbP, photosystem II protein PsbR, photosystem II manganese-stabilizing protein PsbO, photosystem II oxygen evolving complex protein PsbQ, photosystem I reaction centre (subunit XI PsaL), photosystem I psaG/psaK protein, photosystem I reaction centre subunit N, photosystem I reaction center protein PsaF (subunit III), NADH:flavin oxidoreductase/NADH oxidase, and cytochrome b ubiquinol oxidase. The ratios of up- (+) or down (-) -regulated tags are indicated. Detailed information for light reaction complexes is listed in Additional file . Note that the key enzymes are either up- or down-regulated in three tissues; this behavior suggests active yet unique regulations in the hybrid

Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data-0

<p><b>Copyright information:</b></p><p>Taken from "Differential gene expression in an elite hybrid rice cultivar () and its parental lines based on SAGE data"</p><p>http://www.biomedcentral.com/1471-2229/7/49</p><p>BMC Plant Biology 2007;7():49-49.</p><p>Published online 19 Sep 2007</p><p>PMCID:PMC2077334.</p><p></p>A, UniGene, and ST; see Materials and Methods) were used for the construction of virtual transcripts. When the transcript sequences extend beyond the predicated coding sequence were available, the UTR sequences were aligned and determined (A). When the information was not available, the theoretical 3' UTR sequences were determined based on a stepwise (100-, 200-, 300-, 400-, and 500 bp) assessment of the genome sequences and added after the stop codons (B). Nearly 58.7% of the assigned tags have a 3'-UTR length of 300 bp