REGNET: Mining context-specific human transcription networks using composite genomic information

Background: Genome-wide expression profiles reflect the transcriptional networks specific to the given cell context. However, most statistical models try to estimate the average connectivity of the networks from a collection of gene expression data, and are unable to characterize the context-specific transcriptional regulations. We propose an approach for mining context-specific transcription networks from a large collection of gene expression fold-change profiles and composite gene-set information.Results: Using a composite gene-set analysis method, we combine the information of transcription factor binding sites, Gene Ontology or pathway gene sets and gene expression fold-change profiles for a variety of cell conditions. We then collected all the significant patterns and constructed a database of context-specific transcription networks for human (REGNET). As a result, context-specific roles of transcription factors as well as their functional targets are readily explored. To validate the approach, nine predicted targets of E2F1 in HeLa cells were tested using chromatin immunoprecipitation assay. Among them, five (Gadd45b, Dusp6, Mll5, Bmp2 and E2f3) were successfully bound by E2F1. c-JUN and the EMT transcription networks were also validated from literature.Conclusions: REGNET is a useful tool for exploring the ternary relationships among the transcription factors, their functional targets and the corresponding cell conditions. It is able to provide useful clues for novel cell-specific transcriptional regulations. The REGNET database is available at http://mgrc.kribb.re.kr/regnet.open0

EST sequencing and gene expression profiling in Scutellaria baicalensis

Scutellaria baicalensis is an important medicinal plant, but few genomic resources are available for this species, as well as for other non-model plants. One of the major new directions in genome research is to discover the full spectrum of genes transcribed from the whole genome. Here, we report extensive transcriptome data of the early growth stage of S. baicalensis. This transcriptome consensus sequence was constructed by de novo assembly of shotgun sequencing data, obtained using multiple next-generation DNA sequencing (NGS) platforms (Roche/454 GS_FLX+ and Illumina/Solexa HiSeq2000). We show that this new approach to obtain extensive mRNA is an efficient strategy for genome-wide transcriptome analysis. We obtained 1,226,938 and 161,417,646 reads using the GS_FLX and the Illumina/Solexa HiS-eq2000, respectively. De novo assembly of the high-quality GS_FLX and Illumina reads (95 % and 75 %) resulted in more than 82 Mb of mRNA consensus sequence, which we assembled into 51,188 contigs, with at least 500 bp per contig. Of these contigs, 39,581 contained known genes, as determined by BLASTX searches against non-redundant NCBI database. Of these, 20,498 different genes were expressed during the early growth stage of S. baicalensis. We have made the expressed sequences available on a public database. Our results demonstrate the utility of combining NGS technologies as a basis for the development of genomic tools in non-model, medicinal plant species. Knowledge of all described genes and quantitation of the expressed genes, including the transcription factors involved, will be useful in studies of the biology of S. baicalensis gene regulation

Correlation between Repeated Sprint Ability (RSA) and Hoff Test of High School Soccer Plyers

PURPOSE This study aimed to investigate the correlation between repeated sprint ability (RSA) and Hoff test performance in high school soccer players. METHODS Fourteen male high school football players participated in this study. After measuring body composition, the Bangsbo Sprint Test for RSA and Hoff test were performed. The tests were conducted in the field to create an experimental environment similar to that during actual training and competition. RESULTS A significant correlation was observed between the fatigue index (FI) in the RSA and running distance in the Hoff test (p<.05). A high level of correlation between the performance distance and body fat percentage and muscle mass in the Hoff test was observed (p<.001). There was no significant relationship between the best and average RSA records using the Hoff test. CONCLUSIONS It was confirmed that the running distance in the Hoff test developed for event specificity affects the FI in RSA. In subsequent studies, it will be necessary to examine the variables affecting the best and average RSA records

Analysis of peer-scaffolding patterns in four phases of problem-solving in web-based instruction

2008Various peer-scaffoldings in problem-solving have been studied as effective learning strategies in web‐based instruction and on‐line discussion. The web-based environment provides a medium for sharing knowledge and resources, which help learners engage in problem-solving and interactive learning. Learners, however, easily feel isolated in web-based environments because of the tremendous amount of resources and visual information that are easily available. In this regard, it is important to seriously consider peer-scaffolding strategies as effective problem-solving strategies. The purpose of the present study is to find patterns of peerscaffolding that constitute effective problem-solving strategies in web-based instruction. Six participants registered in the major leader training program at the National Academy Educational Administrators voluntarily participated in this experiment as part of their coursework. All participants provided their scaffoldings in on-line casual discussions. To collect data from peer group problem-solving interactions in collaborative activities among the six participations, their discourses content was analyzed to nvestigate patterns of peer-scaffolding. The results of this study were as follows: First, the results showed statistically non‐significant differences in peer-scaffoldings among three dimensions: it showed the highest proportion of peer-scaffoldings in the content dimension, followed by the affection dimension, and finally the strategy dimension. Second, comparing the eight types of scaffolding, the offering praise scaffolding was related to the most important scaffoldings for making peers cooperate with each other while they solve problems. Third, considering patterns of peer-scaffolding in the strategy dimension, the maintaining direction scaffolding represents a higher proportion of the understanding phase than the assigning role-taking scaffolding. Fourth, considering patterns of peer-scaffolding in the content dimension, the offering cue scaffolding represents a higher proportion of the solving phase than the other three peer-scaffoldings. Finally, considering patterns of peer-scaffolding in the affection dimension, the inviting participation scaffolding represents a higher proportion of the understanding phase than the offering praise scaffolding. After reviewing phases, the offering praise scaffolding represented a higher proportion than the inviting participation scaffolding

Improvement of retinoids production in recombinant E. coli using glyoxylic acid

Isoprenoids are the most chemically diverse compounds found in nature. They are present in all organisms and have essential roles in membrane structure, redox chemistry, reproductive cycles, growth regulation, signal transduction and defense mechanisms. In spite of their diversity of functions and structures, all isoprenoids are derived from the common building blocks of isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). Optimization of IPP synthesis pathway is of benefit to mass production of various isoprenoids. There are two pathways of 2-C-Methyl-D-erythritol-4-phosphate (MEP) and mevalonate (MVA) for IPP synthesis. Prokaryotes including E. coli generally use MEP pathway whereas MVA pathway is used in eukaryotes. To improve isoprenoid production, it was performed the deletion of genes in E. coli, which are involved in both formation of fermentation by-products such as organic acids and alcohols, and consumption of precursors of MEP and MVA pathways, pyruvate and acetyl-CoA. As a result, we were able to develop a strain with improved fermentation productivity and carbon source utilization efficiency, the mutant strain was called AceCo. Higher lycopene production was achieved in the AceCo strain compared to the wild type MG1655 strain due to no formation of the inhibitory by-products. However, retinoids production of AceCo strain decreased to a half of that of MG1655 strain. Please click Additional Files below to see the full abstract

Assessment of satellite rainfall nowcasting based on extrapolation technique

Póster presentado en: 3rd European Nowcasting Conference, celebrada en la sede central de AEMET en Madrid del 24 al 26 de abril de 2019

Thiol-linked peroxidase activity of human ceruloplasmin

AbstractHuman ceruloplasmin exhibited different antioxidant effects according to the electron donors in a metal-catalyzed oxidation system. Purified ceruloplasmin did not play a significant role in the protection of DNA strand breaks in the ascorbate/Fe3+/O2 system. However, when ascorbates were replaced with a thiol-reducing equivalent such as dithiothreitol, DNA strand breaks were significantly prevented by the same amount of ceruloplasmin. Ceruloplasmin did not catalyze the decomposition of H2O2 in the absence of reduced glutathione. On the contrary, ceruloplasmin showed a potent peroxidase ability to destroy H2O2 in the presence of reduced glutathione. In conclusion, the removal of H2O2 by human ceruloplasmin is not simply stoichiometric but thiol-dependent