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  • 1
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    Recombinant human kallistatin inhibits angiogenesis by blocking VEGF signaling pathway (2013)
    Wiley
    Details
    Publication Date: 2013-10-16
    Description: Kallistatin has been recognized as an endogenous angiogenic inhibitor. However, the underlying molecular mechanism remains poorly understood. Taking it into account that vascular endothelial growth factor (VEGF) has been implicated in all aspects of normal and pathological vasculogenesis and angiogenesis, in this study, we investigated whether VEGF signaling pathway was impacted by the anti-angiogenic effect of recombinant human kallistatin (rhKal). It has been found the rhKal inhibited proliferation as well as induced apoptosis of cultured human umbilical vein endothelial cells (HUVECs) in both concentration- and time-dependent manners. The rhKal also suppressed the VEGF-induced migration and tube formation of HUVECs. Furthermore, our data revealed that the rhKal suppressed the VEGF165-stimulated tyrosine phosphorylation of VEGFR-2 as well as its downstream signal molecular activation. The inhibition of receptor phosphorylation was correlated with a decrease in VEGF-triggered phosphorylation of angiogenesis signal molecules AKT and ERK, but not stress-related JNK. Taken together, these findings added the knowledge for us to understand the anti-angiogenic mechanism of kallistatin, which suggested that the rhKal could be worth as a candidate compound for further development for the purpose of anti-angiogenic therapies. J. Cell. Biochem. © 2013 Wiley Periodicals, Inc.
    Electronic ISSN: 0091-7419
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Wiley
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  • 2
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    Chromatin architecture reorganization during stem cell differentiation (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-02-20
    Description: Higher-order chromatin structure is emerging as an important regulator of gene expression. Although dynamic chromatin structures have been identified in the genome, the full scope of chromatin dynamics during mammalian development and lineage specification remains to be determined. By mapping genome-wide chromatin interactions in human embryonic stem (ES) cells and four human ES-cell-derived lineages, we uncover extensive chromatin reorganization during lineage specification. We observe that although self-associating chromatin domains are stable during differentiation, chromatin interactions both within and between domains change in a striking manner, altering 36% of active and inactive chromosomal compartments throughout the genome. By integrating chromatin interaction maps with haplotype-resolved epigenome and transcriptome data sets, we find widespread allelic bias in gene expression correlated with allele-biased chromatin states of linked promoters and distal enhancers. Our results therefore provide a global view of chromatin dynamics and a resource for studying long-range control of gene expression in distinct human cell lineages.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4515363/" 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/PMC4515363/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dixon, Jesse R -- Jung, Inkyung -- Selvaraj, Siddarth -- Shen, Yin -- Antosiewicz-Bourget, Jessica E -- Lee, Ah Young -- Ye, Zhen -- Kim, Audrey -- Rajagopal, Nisha -- Xie, Wei -- Diao, Yarui -- Liang, Jing -- Zhao, Huimin -- Lobanenkov, Victor V -- Ecker, Joseph R -- Thomson, James A -- Ren, Bing -- R01 ES024984/ES/NIEHS NIH HHS/ -- T32 GM007198/GM/NIGMS NIH HHS/ -- U01 ES017166/ES/NIEHS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2015 Feb 19;518(7539):331-6. doi: 10.1038/nature14222.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA [2] Medical Scientist Training Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. ; Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA. ; 1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA [2] Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA. ; The Morgridge Institute for Research, 309 North Orchard Street, Madison, Wisconsin 53715, USA. ; Tsinghua University-Peking University Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China. ; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA. ; Laboratory of Immunogenetics, National Institute of Allergy and Infectious Diseases, Twinbrook I NIAID Facility, Room 1417, 5640 Fishers Lane, Rockville, Maryland 20852, USA. ; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA. ; 1] The Morgridge Institute for Research, 309 North Orchard Street, Madison, Wisconsin 53715, USA [2] Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706, USA [3] Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California 93106, USA. ; 1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093-0653, USA [2] University of California, San Diego School of Medicine, Department of Cellular and Molecular Medicine, Institute of Genomic Medicine, 9500 Gilman Drive, La Jolla, California 92093-0653, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25693564" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Allelic Imbalance/genetics ; *Cell Differentiation/genetics ; Cell Lineage/genetics ; Chromatin/*chemistry/genetics/*metabolism ; *Chromatin Assembly and Disassembly/genetics ; Embryonic Stem Cells/*cytology/*metabolism ; Enhancer Elements, Genetic/genetics ; Epigenesis, Genetic/*genetics ; Epigenomics ; Gene Regulatory Networks ; Humans ; Promoter Regions, Genetic/genetics ; Reproducibility of Results
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Fusion pore formation and expansion [Biophysics and Computational Biology] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-01-23
    Description: Fusion pore formation and expansion, crucial steps for neurotransmitter release and vesicle recycling in soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE)-dependent vesicle fusion, have not been well studied in vitro due to the lack of a reliable content-mixing fusion assay. Using methods detecting the intervesicular mixing of small and large...
    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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  • 4
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    LNCediting: a database for functional effects of RNA editing in lncRNAs (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-05
    Description: RNA editing is a widespread post-transcriptional mechanism that can make a single base change on specific nucleotide sequence in an RNA transcript. RNA editing events can result in missense codon changes and modulation of alternative splicing in mRNA, and modification of regulatory RNAs and their binding sites in noncoding RNAs. Recent computational studies accurately detected more than 2 million A-to-I RNA editing sites from next-generation sequencing (NGS). However, the vast majority of these RNA editing sites have unknown functions and are in noncoding regions of the genome. To provide a useful resource for the functional effects of RNA editing in long noncoding RNAs (lncRNAs), we systematically analyzed the A-to-I editing sites in lncRNAs across human, rhesus, mouse, and fly, and observed an appreciable number of RNA editing sites which can significantly impact the secondary structures of lncRNAs and lncRNA–miRNA interactions. All the data were compiled into LNCediting, a user-friendly database ( http://bioinfo.life.hust.edu.cn/LNCediting/ ). LNCediting provides customized tools to predict functional effects of novel editing sites in lncRNAs. We hope that it will become an important resource for exploring functions of RNA editing sites in lncRNAs.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Colletotrichum species causing anthracnose disease of chili in China (2017)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi (1878-9080) vol.38 (2017) p.20
    Details
    Publication Date: 2016-08-25
    Description: Anthracnose caused by Colletotrichum species is a serious disease of more than 30 plant genera. Several Colletotrichum species have been reported to infect chili in different countries. Although China is the largest chiliproducing country, little is known about the species that have been infecting chili locally. Therefore, we collected samples of diseased chili from 29 provinces of China, from which 1285 strains were isolated. The morphological characters of all strains were observed and compared, and multi-locus phylogenetic analyses (ITS, ACT, CAL, CHS-1, GAPDH, TUB2, and HIS3) were performed on selected representative strains. Fifteen Colletotrichum species were identified, with C. fioriniae, C. fructicola, C. gloeosporioides, C. scovillei, and C. truncatum being prevalent. Three new species, C. conoides, C. grossum, and C. liaoningense, were recognised and described in this paper. Colletotrichum aenigma, C. cliviae, C. endophytica, C. hymenocallidis, C. incanum, C. karstii, and C. viniferum were reported for the first time from chili. Pathogenicity of all species isolated from chili was confirmed, except for C. endophytica. The current study improves the understanding of species causing anthracnose on chili and provides useful information for the effective control of the disease in China.
    Keywords: DNA phylogeny ; multi-gene analysis ; plant pathogen ; systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: Article / Letter to the editor
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  • 6
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    Fusarium incarnatum-equiseti complex from China (2019)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 43, pp. 70-89
    Details
    Publication Date: 2024-01-12
    Description: The Fusarium incarnatum-equiseti species complex (FIESC) is shown to encompass 33 phylogenetic species, across a wide range of habitats/hosts around the world. Here, 77 pathogenic and endophytic FIESC strains collected from China were studied to investigate the phylogenetic relationships within FIESC, based on a polyphasic approach combining morphological characters, multi-locus phylogeny and distribution patterns. The importance of standardised cultural methods to the identification and classification of taxa in the FIESC is highlighted. Morphological features of macroconidia, including the shape, size and septum number, were considered as diagnostic characters within the FIESC. A multi-locus dataset encompassing the 5.8S nuclear ribosomal gene with the two flanking internal transcribed spacers (ITS), translation elongation factor (EF-1\xce\xb1), calmodulin (CAM), partial RNA polymerase largest subunit (RPB1) and partial RNA polymerase second largest subunit (RPB2), was generated to distinguish species within the FIESC. Nine novel species were identified and described. The RPB2 locus is demonstrated to be a primary barcode with high success rate in amplification, and to have the best species delimitation compared to the other four tested loci.
    Keywords: Fusarium ; new taxa ; species complex ; systematics ; taxonomy
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 7
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    Colletotrichum species causing anthracnose disease of chili in China (2017)
    In:  Persoonia - Molecular Phylogeny and Evolution of Fungi vol. 38, pp. 20-37
    Details
    Publication Date: 2024-01-12
    Description: Anthracnose caused by Colletotrichum species is a serious disease of more than 30 plant genera. Several Colletotrichum species have been reported to infect chili in different countries. Although China is the largest chiliproducing country, little is known about the species that have been infecting chili locally. Therefore, we collected samples of diseased chili from 29 provinces of China, from which 1285 strains were isolated. The morphological characters of all strains were observed and compared, and multi-locus phylogenetic analyses (ITS, ACT, CAL, CHS-1, GAPDH, TUB2, and HIS3) were performed on selected representative strains. Fifteen Colletotrichum species were identified, with C. fioriniae, C. fructicola, C. gloeosporioides, C. scovillei, and C. truncatum being prevalent. Three new species, C. conoides, C. grossum, and C. liaoningense, were recognised and described in this paper. Colletotrichum aenigma, C. cliviae, C. endophytica, C. hymenocallidis, C. incanum, C. karstii, and C. viniferum were reported for the first time from chili. Pathogenicity of all species isolated from chili was confirmed, except for C. endophytica. The current study improves the understanding of species causing anthracnose on chili and provides useful information for the effective control of the disease in China.
    Keywords: DNA phylogeny ; multi-gene analysis ; plant pathogen ; systematics
    Repository Name: National Museum of Natural History, Netherlands
    Type: info:eu-repo/semantics/article
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  • 8
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    Oxidation-induced intramolecular disulfide bond inactivates mitogen-activated protein kinase kinase 6 by inhibiting ATP binding (2010)
    National Academy of Sciences
    Details
    Publication Date: 2010-11-15
    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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  • 9
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    Evidence for C-H cleavage by an iron-superoxide complex in the glycol cleavage reaction catalyzed by myo-inositol oxygenase (2006)
    National Academy of Sciences
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    Publication Date: 2006-04-10
    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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  • 10
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    Tuning conformation, assembly, and charge transport properties of conjugated polymers by printing flow (2019)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2019
    Description: 〈p〉Intrachain charge transport is unique to conjugated polymers distinct from inorganic and small molecular semiconductors and is key to achieving high-performance organic electronics. Polymer backbone planarity and thin film morphology sensitively modulate intrachain charge transport. However, simple, generic nonsynthetic approaches for tuning backbone planarity and the ensuing multiscale assembly process do not exist. We first demonstrate that printing flow is capable of planarizing the originally twisted polymer backbone to substantially increase the conjugation length. This conformation change leads to a marked morphological transition from chiral, twinned domains to achiral, highly aligned morphology, hence a fourfold increase in charge carrier mobilities. We found a surprising mechanism that flow extinguishes a lyotropic twist-bend mesophase upon backbone planarization, leading to the observed morphology and electronic structure transitions.〈/p〉
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
    Published by American Association for the Advancement of Science (AAAS)
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