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  • 1
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    miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: MicroRNAs (miRNAs) are small non-coding RNAs of approximately 22 nucleotides, which negatively regulate the gene expression at the post-transcriptional level. This study describes an update of the miRTarBase ( http://miRTarBase.mbc.nctu.edu.tw/ ) that provides information about experimentally validated miRNA-target interactions (MTIs). The latest update of the miRTarBase expanded it to identify systematically Argonaute-miRNA-RNA interactions from 138 crosslinking and immunoprecipitation sequencing (CLIP-seq) data sets that were generated by 21 independent studies. The database contains 4966 articles, 7439 strongly validated MTIs (using reporter assays or western blots) and 348 007 MTIs from CLIP-seq. The number of MTIs in the miRTarBase has increased around 7-fold since the 2014 miRTarBase update. The miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA) are integrated to provide an effective overview of this exponential growth in the miRNA experimental data. These improvements make the miRTarBase one of the more comprehensively annotated, experimentally validated miRNA-target interactions databases and motivate additional miRNA research efforts.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    MethHC: a database of DNA methylation and gene expression in human cancer (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-16
    Description: We present MethHC ( http://MethHC.mbc.nctu.edu.tw ), a database comprising a systematic integration of a large collection of DNA methylation data and mRNA/microRNA expression profiles in human cancer. DNA methylation is an important epigenetic regulator of gene transcription, and genes with high levels of DNA methylation in their promoter regions are transcriptionally silent. Increasing numbers of DNA methylation and mRNA/microRNA expression profiles are being published in different public repositories. These data can help researchers to identify epigenetic patterns that are important for carcinogenesis. MethHC integrates data such as DNA methylation, mRNA expression, DNA methylation of microRNA gene and microRNA expression to identify correlations between DNA methylation and mRNA/microRNA expression from TCGA (The Cancer Genome Atlas), which includes 18 human cancers in more than 6000 samples, 6548 microarrays and 12 567 RNA sequencing data.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Performance analysis of a cascaded solar Organic Rankine Cycle with superheating (2016)
    Oxford University Press
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    Publication Date: 2016-05-27
    Description: A cascaded Organic Rankine Cycle (ORC) with scroll expanders is investigated in this paper, the system performances under various configurations are evaluated and the effect of superheating on the system efficiency is clarified. The efficiency of two-stage ORC system is 38.9% higher than that of single-stage system when R245fa is used as the working fluid, while the efficiency of two-stage ORC system is 10% lower than that of single stage when R134a is adopted. The specific work of single-stage ORC system with R245fa increases linearly with the degree of superheat. There is an optimal superheated degree for the system output power and efficiency, which is 35 K for the expansion ratio of 3.5 and 45 K for the expansion ratio of 5.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Oxford University Press
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  • 4
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    Electromagnetic energy conversion at dipolarization fronts: Multi-spacecraft results (2015)
    Wiley
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    Publication Date: 2015-05-09
    Description: Dipolarization fronts (DFs) are believed to play important roles in transferring plasmas, magnetic fluxes and energies in the magnetotail. Using the Cluster observations in 2003, electromagnetic energy conversion at the DFs is investigated by case and statistical studies. The case study indicates strongest energy conversion at the DF. The statistical study shows the similar features that the energy of the fields can be significantly transferred to the plasmas (load, J·E 〉0) at the DFs. These results are consistent with some recent simulations. Examining the electromagnetic fluctuations at the DFs, we suggest that the wave activities around the lower hybrid frequency may play an important role in the energy dissipation.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    CircNet: a database of circular RNAs derived from transcriptome sequencing data (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: Circular RNAs (circRNAs) represent a new type of regulatory noncoding RNA that only recently has been identified and cataloged. Emerging evidence indicates that circRNAs exert a new layer of post-transcriptional regulation of gene expression. In this study, we utilized transcriptome sequencing datasets to systematically identify the expression of circRNAs (including known and newly identified ones by our pipeline) in 464 RNA-seq samples, and then constructed the CircNet database ( http://circnet.mbc.nctu.edu.tw/ ) that provides the following resources: (i) novel circRNAs, (ii) integrated miRNA-target networks, (iii) expression profiles of circRNA isoforms, (iv) genomic annotations of circRNA isoforms (e.g. 282 948 exon positions), and (v) sequences of circRNA isoforms. The CircNet database is to our knowledge the first public database that provides tissue-specific circRNA expression profiles and circRNA–miRNA-gene regulatory networks. It not only extends the most up to date catalog of circRNAs but also provides a thorough expression analysis of both previously reported and novel circRNAs. Furthermore, it generates an integrated regulatory network that illustrates the regulation between circRNAs, miRNAs and genes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: Owing to the importance of the post-translational modifications (PTMs) of proteins in regulating biological processes, the dbPTM ( http://dbPTM.mbc.nctu.edu.tw/ ) was developed as a comprehensive database of experimentally verified PTMs from several databases with annotations of potential PTMs for all UniProtKB protein entries. For this 10th anniversary of dbPTM, the updated resource provides not only a comprehensive dataset of experimentally verified PTMs, supported by the literature, but also an integrative interface for accessing all available databases and tools that are associated with PTM analysis. As well as collecting experimental PTM data from 14 public databases, this update manually curates over 12 000 modified peptides, including the emerging S -nitrosylation, S -glutathionylation and succinylation, from approximately 500 research articles, which were retrieved by text mining. As the number of available PTM prediction methods increases, this work compiles a non-homologous benchmark dataset to evaluate the predictive power of online PTM prediction tools. An increasing interest in the structural investigation of PTM substrate sites motivated the mapping of all experimental PTM peptides to protein entries of Protein Data Bank (PDB) based on database identifier and sequence identity, which enables users to examine spatially neighboring amino acids, solvent-accessible surface area and side-chain orientations for PTM substrate sites on tertiary structures. Since drug binding in PDB is annotated, this update identified over 1100 PTM sites that are associated with drug binding. The update also integrates metabolic pathways and protein–protein interactions to support the PTM network analysis for a group of proteins. Finally, the web interface is redesigned and enhanced to facilitate access to this resource.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-27
    Description: Motivation: The establishment of quantitative gene regulatory networks (qGRNs) through existing network component analysis (NCA) approaches suffers from shortcomings such as usage limitations of problem constraints and the instability of inferred qGRNs. The proposed GeNOSA framework uses a global optimization algorithm (OptNCA) to cope with the stringent limitations of NCA approaches in large-scale qGRNs. Results: OptNCA performs well against existing NCA-derived algorithms in terms of utilization of connectivity information and reconstruction accuracy of inferred GRNs using synthetic and real Escherichia coli datasets. For comparisons with other non-NCA-derived algorithms, OptNCA without using known qualitative regulations is also evaluated in terms of qualitative assessments using a synthetic Saccharomyces cerevisiae dataset of the DREAM3 challenges. We successfully demonstrate GeNOSA in several applications including deducing condition-dependent regulations, establishing high-consensus qGRNs and validating a sub-network experimentally for dose–response and time–course microarray data, and discovering and experimentally confirming a novel regulation of CRP on AscG. Availability and implementation: All datasets and the GeNOSA framework are freely available from http://e045.life.nctu.edu.tw/GeNOSA . Contact: syho@mail.nctu.edu.tw Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 8
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    Molecular analysis of in situ diets of coral reef copepods: evidence of terrestrial plant detritus as a food source in Sanya Bay, China (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-25
    Description: Knowledge of copepod in situ diet is critical for accurate assessment of trophic linkages and transfer efficiencies of the marine food web but is limited due to technical challenges. Here we report, using a recently developed eukaryote-universal copepod-excluding ectobiotic ciliate-blocking protocol, to investigate the natural diets of the copepods Temora turbinata , Subeucalanus subcrassus and Canthocalanus pauper in coastal waters in Sanya Bay, China. Analysis of the resultant 18S rDNA clone libraries revealed diverse diet composition for all the three copepod species, with 11 prey species for C. pauper , 9 for T. turbinata and 9 for S. subcrassus . The ingested materials included land plants, green algae, Metazoa, Euglenozoa and Rhizaria, although species numbers from each of these lineages differed. Broussonetia sp. (land plant), which might have been ingested in the form of pollen or fresh detritus were common among all three copepods, and accounted for a significant proportion (〉55%) of the clones sequenced. These results suggest that copepods in Sanya coastal waters might use terrigenous detritus as supplementary food sources when phytoplankton production is limited. However, the significance of the plant detritus as a nutrition source of these copepods remains to be determined by analyzing carbon-based proportion and digestion/assimilation rate of the ingested plant materials.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Engineering of a 3'-sulpho-Gal{beta}1-4GlcNAc-specific probe by a single amino acid substitution of a fungal galectin (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-28
    Description: Among sulphated glycans, little is known about 3'-sulphation because of the lack of useful probes. In the course of molecular engineering of a fungal galectin from Agrocybe cylindracea , we found that a single substitution of Glu86 with alanine resulted in acquisition of specific binding for the 3'-sulpho-Galβ1-4GlcNAc structure. Extensive glyco-technological analysis revealed that this property was obtained in a ‘loss-of-function’ manner. Though this mutant (E86A) had low total affinity, it showed substantial binding to a naturally occurring N -glycan, of which the terminal galactose is 3-sulphated. Moreover, E86A specifically bound to HeLa cells, in which galactose-3- O -sulfotransferases (Gal3ST2 or Gal3ST3) were over-expressed.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 10
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    Two types of whistler waves in the hall reconnection region (2016)
    Wiley
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    Publication Date: 2016-07-05
    Description: Whistler waves are believed to play an important role during magnetic reconnection. Here we report the near-simultaneous occurrence of two types of the whistler-mode waves in the magnetotail Hall reconnection region. The first type is observed in the magnetic pileup region of downstream and propagates away to downstream along the field lines, and is possibly generated by the electron temperature anisotropy at the magnetic equator. The second type, propagating towards the X-line, is found around the separatrix region and probably is generated by the electron beam-driven whistler instability or Čerenkov emission from electron phase-space holes. These observations of two different types of whistler waves are consistent with recent kinetic simulations, and suggest that the observed whistler waves are a consequence of magnetic reconnection.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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