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  • 1
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    Comments on 'MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets' (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-08
    Description: Contact: zyhe@dlut.edu.cn
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Oligonucleotides targeting TCF4 triplet repeat expansion inhibit RNA foci and mis-splicing in Fuchs’ dystrophy (2018)
    Oxford University Press
    Details
    Publication Date: 2018-03-06
    Description: Fuchs’ endothelial corneal dystrophy (FECD) is the most common repeat expansion disorder. FECD impacts 4% of U.S. population and is the leading indication for corneal transplantation. Most cases are caused by an expanded intronic CUG tract in the TCF4 gene that forms nuclear foci, sequesters splicing factors and impairs splicing. We investigated the sense and antisense RNA landscape at the FECD gene and find that the sense-expanded repeat transcript is the predominant species in patient corneas. In patient tissue, sense foci number were negatively correlated with age and showed no correlation with sex. Each endothelial cell has ∼2 sense foci and each foci is single RNA molecule. We designed antisense oligonucleotides (ASOs) to target the mutant-repetitive RNA and demonstrated potent inhibition of foci in patient-derived cells. Ex vivo treatment of FECD human corneas effectively inhibits foci and reverses pathological changes in splicing. FECD has the potential to be a model for treating many trinucleotide repeat diseases and targeting the TCF4 expansion with ASOs represents a promising therapeutic strategy to prevent and treat FECD.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    A genetic variant in ERCC2 is associated with gastric cancer prognosis in a Chinese population (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-14
    Description: Endogenous and exogenous factors can induce DNA damage, leading to increased risk of cancer. Nucleotide excision repair (NER) is considered as the most versatile DNA repair pathway to deal with a variety of different DNA lesions. ERCC1 and ERCC2 are the two important proteins in NER pathway. In this study, we investigated the association of three functional single nucleotide polymorphisms (SNPs) ( ERCC1 rs11615, ERCC2 rs13181 and ERCC2 rs1799793) with the clinical outcome of 940 gastric cancer patients in a Chinese population. Multiplex SNaPshot technology was used to genotype these three SNPs. Our results revealed that individuals with ERCC2 rs13181TG/GG genotypes had a decreased risk of death compared with those with TT genotype [log-rank P = 0.008; adjusted hazard ratio = 0.68, 95% confidence interval = 0.51–0.91] and this protective effect was more pronounced among the subgroups of patients with tumour size ≤ 5cm (0.59, 0.39–0.89), non-cardia gastric tumour (0.69, 0.48–0.98), no lymph node metastasis (0.55, 0.32–0.96), no distant metastasis (0.70, 0.52–0.95) and chemotherapy (0.39, 0.21–0.72). We conclude that ERCC2 rs13181 polymorphism could play different roles in the overall survival of gastric cancer. Further larger studies should be conducted to validate our findings.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 4
    Electronic Resource
    Electronic Resource
    Evaluation of dual differential absorption lidar based on Raman-shifted Nd:YAG or KrF laser for tropospheric ozone measurements (1996)
    Springer
    Applied physics 62 (1996), S. 143-147 
    Details
    ISSN: 1432-0649
    Keywords: 42.68.Ay ; 42.68.Ge ; 42.80
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract Based on Raman-shifted Nd:YAG or KrF laser, a method of three-wavelength Dual DIfferential Absorption Lidar (DIAL) for tropospheric ozone measurements is proposed. A theoretical analysis and numerical simulations of the measurement error have been performed. The results show that this method can reduce the error in ozone measurements caused by the aerosol layer in the troposphere by a factor of ten. The proposed method is also shown to be insensitive to aerosol optical properties, and therefore, one does not need to know the wavelength dependence of aerosol scattering. The dual-DIAL with 277.1, 291.8, 313.2 nm radiation based on a Raman-shifted KrF laser can be used both during day- and night-time. The dual-DIAL with 289.0, 299.1, 316.1 nm radiation based on Raman-shifted Nd:YAG laser can only be used during night-time.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01081116
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    Paper (German National Licenses)
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  • 5
    Electronic Resource
    Electronic Resource
    Environmental Factors and the Succession of Aquatic Insects in a Shallow Chinese Lake (2000)
    Springer
    Bulletin of environmental contamination and toxicology 64 (2000), S. 701-707 
    Details
    ISSN: 1432-0800
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s001280000060
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  • 6
    Electronic Resource
    Electronic Resource
    A light-inducible Myb-like gene that is specifically expressed in red Perilla frutescens and presumably acts as a determining factor of the anthocyanin forma (1999)
    Springer
    Molecular genetics and genomics 262 (1999), S. 65-72 
    Details
    ISSN: 1617-4623
    Keywords: Key words Anthocyanin biosynthesis ; Light induction ; MYB transcriptional factor ; Perilla frutescens
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The Myb-p1 gene was isolated by screening for differentially expressed Myb-related genes in red (anthocyanin-producing) and green (anthocyanin non-producing) forms of Perilla frutescens. Expression of Myb-p1 is increased 10-fold in the red relative to the green form of P. frutescens, and the gene is induced by light. MYB-P1 has only one DNA-binding region, which corresponds to repeat III in the general structure of MYB proteins. In the yeast two-hybrid system, it was shown that MYB-P1 interacted with MYC-RP, a MYC-related transcriptional regulatory protein involved in the control of anthocyanin biosynthesis in P. frutescens. In yeast, MYB-P1 was able to bind to a dihydroflavonol reductase (DFR) gene promoter isolated from red P. frutescens. These data suggest that Myb-p1 may be involved in the regulation of anthocyanin biosynthesis and could therefore be responsible for determining anthocyanin formation in red P. frutescens.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/PL00008639
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  • 7
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    The novel long non-coding RNA CRG regulates Drosophila locomotor behavior (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-14
    Description: Long non-coding RNAs (lncRNAs) that have no protein-coding capacity make up a large proportion of the transcriptome of various species. Many lncRNAs are expressed within the animal central nervous system in spatial- and temporal-specific patterns, indicating that lncRNAs play important roles in cellular processes, neural development, and even in cognitive and behavioral processes. However, relatively little is known about their in vivo functions and underlying molecular mechanisms in the nervous system. Here, we report a neural-specific Drosophila lncRNA, CASK regulatory gene ( CRG ), which participates in locomotor activity and climbing ability by positively regulating its neighboring gene CASK (Ca 2+ /calmodulin-dependent protein kinase). CRG deficiency led to reduced locomotor activity and a defective climbing ability—phenotypes that are often seen in CASK mutant. CRG mutant also showed reduced CASK expression level while CASK over-expression could rescue the CRG mutant phenotypes in reciprocal. At the molecular level, CRG was required for the recruitment of RNA polymerase II to the CASK promoter regions, which in turn enhanced CASK expression. Our work has revealed new functional roles of lncRNAs and has provided insights to explore the pathogenesis of neurological diseases associated with movement disorders.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Genome-Wide Disruption of Gene Expression in Allopolyploids but Not Hybrids of Rice Subspecies (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-23
    Description: Hybridization and polyploidization are prominent processes in plant evolution. Hybrids and allopolyploids typically exhibit radically altered gene expression patterns relative to their parents, a phenomenon termed "transcriptomic shock." To distinguish the effects of hybridization from polyploidization on coregulation of divergent alleles, we analyzed expression of parental copies (homoeologs) of 11,608 genes using RNA-seq-based transcriptome profiling in reciprocal hybrids and tetraploids constructed from subspecies japonica and indica of Asian rice ( Oryza sativa L.). The diploid hybrids and their derived allopolyploids differ dramatically in morphology, despite having the same suite of genes and genic proportions. Allelic and homoeolog-specific transcripts were unequivocally diagnosed in the hybrids and tetraploids based on parent-specific SNPs. Compared with the in silico hybrid (parental mix), the range of progenitor expression divergence was significantly reduced in both reciprocally generated F1 hybrids, presumably due to the ameliorating effects of a common trans environment on divergent cis -factors. In contrast, parental expression differences were greatly elaborated at the polyploid level, which we propose is a consequence of stoichiometric disruptions associated with the numerous chromosomal packaging and volumetric changes accompanying nascent polyploidy. We speculate that the emergent property of "whole genome doubling" has repercussions that reverberate throughout the transcriptome and downstream, ultimately generating altered phenotypes. This perspective may yield insight into the nature of adaptation and the origin of evolutionary novelty accompanying polyploidy.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Amplified stretch of bottlebrush-coated DNA in nanofluidic channels (2013)
    Oxford University Press
    Details
    Publication Date: 2013-11-02
    Description: The effect of a cationic-neutral diblock polypeptide on the conformation of single DNA molecules confined in rectangular nanochannels is investigated with fluorescence microscopy. An enhanced stretch along the channel is observed with increased binding of the cationic block of the polypeptide to DNA. A maximum stretch of 85% of the contour length can be achieved inside a channel with a cross-sectional diameter of 200 nm and at a 2-fold excess of polypeptide with respect to DNA charge. With site-specific fluorescence labelling, it is demonstrated that this maximum stretch is sufficient to map large-scale genomic organization. Monte Carlo computer simulation shows that the amplification of the stretch inside the nanochannels is owing to an increase in bending rigidity and thickness of bottlebrush-coated DNA. The persistence lengths and widths deduced from the nanochannel data agree with what has been estimated from the analysis of atomic force microscopy images of dried complexes on silica.
    Keywords: Phsyical and Biochemical Characterisation of DNA
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
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    Comparative Genomics Provide Insights into Evolution of Trichoderma Nutrition Style (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-23
    Description: Saprotrophy on plant biomass is a recently developed nutrition strategy for Trichoderma . However, the physiology and evolution of this new nutrition strategy is still elusive. We report the deep sequencing and analysis of the genome of Trichoderma longibrachiatum , an efficient cellulase producer. The 31.7-Mb genome, smallest among the sequenced Trichoderma species, encodes fewer nutrition-related genes than saprotrophic T. reesei ( Tr ), including glycoside hydrolases and nonribosomal peptide synthetase–polyketide synthase. Homology and phylogenetic analyses suggest that a large number of nutrition-related genes, including GH18 chitinases, β-1,3/1,6-glucanases, cellulolytic enzymes, and hemicellulolytic enzymes, were lost in the common ancestor of T. longibrachiatum ( Tl ) and Tr . d N /d S () calculation indicates that all the nutrition-related genes analyzed are under purifying selection. Cellulolytic enzymes, the key enzymes for saprotrophy on plant biomass, are under stronger purifying selection pressure in Tl and Tr than in mycoparasitic species, suggesting that development of the nutrition strategy of saprotrophy on plant biomass has increased the selection pressure. In addition, aspartic proteases, serine proteases, and metalloproteases are subject to stronger purifying selection pressure in Tl and Tr , suggesting that these enzymes may also play important roles in the nutrition. This study provides insights into the physiology and evolution of the nutrition strategy of Trichoderma .
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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