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  • 1
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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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  • 2
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    Fungal small RNAs suppress plant immunity by hijacking host RNA interference pathways (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-10-05
    Description: Botrytis cinerea, the causative agent of gray mold disease, is an aggressive fungal pathogen that infects more than 200 plant species. Here, we show that some B. cinerea small RNAs (Bc-sRNAs) can silence Arabidopsis and tomato genes involved in immunity. These Bc-sRNAs hijack the host RNA interference (RNAi) machinery by binding to Arabidopsis Argonaute 1 (AGO1) and selectively silencing host immunity genes. The Arabidopsis ago1 mutant exhibits reduced susceptibility to B. cinerea, and the B. cinerea dcl1 dcl2 double mutant that can no longer produce these Bc-sRNAs displays reduced pathogenicity on Arabidopsis and tomato. Thus, this fungal pathogen transfers "virulent" sRNA effectors into host plant cells to suppress host immunity and achieve infection, which demonstrates a naturally occurring cross-kingdom RNAi as an advanced virulence mechanism.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096153/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4096153/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Weiberg, Arne -- Wang, Ming -- Lin, Feng-Mao -- Zhao, Hongwei -- Zhang, Zhihong -- Kaloshian, Isgouhi -- Huang, Hsien-Da -- Jin, Hailing -- R01 GM093008/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2013 Oct 4;342(6154):118-23. doi: 10.1126/science.1239705.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Plant Pathology and Microbiology, University of California, Riverside, CA 92521, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24092744" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*immunology/microbiology ; Arabidopsis Proteins/genetics ; Argonaute Proteins/genetics ; Botrytis/genetics/*pathogenicity ; Gene Expression Regulation, Plant ; Host-Pathogen Interactions/genetics/*immunology ; Lycopersicon esculentum/genetics/immunology/microbiology ; Mutation ; Plant Diseases/genetics/immunology/*microbiology ; *RNA Interference ; RNA, Fungal/*genetics ; RNA, Small Interfering/*genetics ; Virulence/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
    Electronic Resource
    Electronic Resource
    Nitrogen-doped ZnSe with selenium-rich growth by low-pressure organometallic chemical vapor deposition (1994)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 75 (1994), S. 7821-7824 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: A high-quality nitrogen-doped p-type ZnSe epilayer on (100) GaAs substrate was obtained under selenium-rich growth conditions by low-pressure organometallic chemical vapor deposition. Ammonia was used as the dopant source. The resistivity (0.5 Ω cm) and the free-carrier concentration (p=8.8×1017 cm−3) of as-grown ZnSe:N were derived from Hall measurements. With selenium-rich growth conditions, we can reduce the concentration of compensation defects (VSe-Zn-NSe which acts as a donor in ZnSe). Nitrogen is found to incorporate in ZnSe as a shallow level, which is examined by the dependence of free-to-acceptor emission on the NH3/H2Se molar ratio. The carrier concentration of as-grown ZnSe:N seems to change insignificantly within a wide range of growth temperatures. That is thought to be useful for device fabrication due to uniformity considerations.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.357029
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    Paper (German National Licenses)
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  • 4
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    Blue light reduces organ injury from I/R [Applied Biological Sciences] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-05-12
    Description: Evidence suggests that light and circadian rhythms profoundly influence the physiologic capacity with which an organism responds to stress. However, the ramifications of light spectrum on the course of critical illness remain to be determined. Here, we show that acute exposure to bright blue spectrum light reduces organ injury by...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 5
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    Transcribed pseudogene {psi}PPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-02
    Description: Pseudogenes, especially those that are transcribed, may not be mere genomic fossils, but their biological significance remains unclear. Postulating that in the human genome, as in animal models, pseudogenes may function as gene regulators through generation of endo-siRNAs (esiRNAs), antisense RNAs or RNA decoys, we performed bioinformatic and subsequent experimental tests to explore esiRNA-mediated mechanisms of pseudogene involvement in oncogenesis. A genome-wide survey revealed a partial retrotranscript pseudogene PPM1K containing inverted repeats capable of folding into hairpin structures that can be processed into two esiRNAs; these esiRNAs potentially target many cellular genes, including NEK8 . In 41 paired surgical specimens, we found significantly reduced expression of two predicted PPM1K -specific esiRNAs, and the cognate gene PPM1K , in hepatocellular carcinoma compared with matched non-tumour tissues, whereas the expression of target gene NEK8 was increased in tumours. Additionally, NEK8 and PPM1K were downregulated in stably transfected PPM1K -overexpressing cells, but not in cells transfected with an esiRNA1-deletion mutant of PPM1K . Furthermore, expression of NEK8 in PPM1K -transfected cells demonstrated that NEK8 can counteract the growth inhibitory effects of PPM1K . These findings indicate that a transcribed pseudogene can exert tumour-suppressor activity independent of its parental gene by generation of esiRNAs that regulate human cell growth.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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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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  • 7
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    CircNet: a database of circular RNAs derived from transcriptome sequencing data (2016)
    Oxford University Press
    Details
    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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  • 8
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    dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins (2016)
    Oxford University Press
    Details
    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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  • 9
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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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  • 10
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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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