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  • Articles  (283)
  • Biology  (151)
  • Geosciences  (135)
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  • Articles  (283)
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  • 1
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    Effects of MreB paralogs on poly-{gamma}-glutamic acid synthesis and cell morphology in Bacillus amyloliquefaciens (2016)
    Oxford University Press
    Details
    Publication Date: 2016-08-27
    Description: Actin-like MreB paralogs play important roles in cell shape maintenance, cell wall synthesis and the regulation of the D,L-endopeptidases, CwlO and LytE. The gram-positive bacteria, Bacillus amyloliquefaciens LL3, is a poly--glutamic acid (-PGA) producing strain that contains three MreB paralogs: MreB, Mbl and MreBH. In B. amyloliquefaciens , CwlO and LytE can degrade -PGA. In this study, we aimed to test the hypothesis that modulating transcript levels of MreB paralogs would alter the synthesis and degradation of -PGA. The results showed that overexpression or inhibition of MreB, Mbl or MreBH had distinct effects on cell morphology and the molecular weight of the -PGA products. In fermentation medium, cells of mreB inhibition mutant were 50.2% longer than LL3, and the -PGA titer increased by 55.7%. However, changing the expression level of mbl showed only slight effects on the morphology, -PGA molecular weight and titer. In the mreBH inhibition mutant, -PGA production and its molecular weight increased by 56.7% and 19.4%, respectively. These results confirmed our hypothesis that suppressing the expression of MreB paralogs might reduce -PGA degradation, and that improving the cell size could strengthen -PGA synthesis. This is the first report of enhanced -PGA production via suppression of actin-like MreB paralogs.
    Keywords: Biotechnology & Synthetic Biology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    SBF-1 exerts strong anticervical cancer effect through inducing endoplasmic reticulum stress-associated cell death via targeting sarco/endoplasmic reticulum Ca2+-ATPase 2 (2014)
    Springer Nature
    Details
    Publication Date: 2014-12-19
    Description: SBF-1 exerts strong anticervical cancer effect through inducing endoplasmic reticulum stress-associated cell death via targeting sarco/endoplasmic reticulum Ca2+-ATPase 2 Cell Death and Disease 5, e1581 (December 2014). doi:10.1038/cddis.2014.538 Authors: W Li, Z Ouyang, Q Zhang, L Wang, Y Shen, X Wu, Y Gu, Y Shu, B Yu, X Wu, Y Sun & Q Xu
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 3
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    DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-05
    Description: The human disease methylation database (DiseaseMeth,  http://bioinfo.hrbmu.edu.cn/diseasemeth/ ) is an interactive database that aims to present the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. Recently, the high-throughput microarray and sequencing technologies have promoted the production of methylome data that contain comprehensive knowledge of human diseases. In this DiseaseMeth update, we have increased the number of samples from 3610 to 32 701, the number of diseases from 72 to 88 and the disease–gene associations from 216 201 to 679 602. DiseaseMeth version 2.0 provides an expanded comprehensive list of disease–gene associations based on manual curation from experimental studies and computational identification from high-throughput methylome data. Besides the data expansion, we also updated the search engine and visualization tools. In particular, we enhanced the differential analysis tools, which now enable online automated identification of DNA methylation abnormalities in human disease in a case-control or disease–disease manner. To facilitate further mining of the disease methylome, three new web tools were developed for cluster analysis, functional annotation and survival analysis. DiseaseMeth version 2.0 should be a useful resource platform for further understanding the molecular mechanisms of human diseases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    A new genus Liaous of early Anisian Stage (Middle Triassic) brachiopods from southwestern China: systematics, reassessment of classification of the Spiriferinioidea, community paleoecology, and paleoenvironmental implications (2016)
    Paleontological Society
    Details
    Publication Date: 2016-05-12
    Description: This paper describes a new genus Liaous , with L. shaiwensis He and Chen n. gen. n. sp. as the type species, from the Xinyuan Formation of Anisian age in Ziyun, southern Guizhou, China. The phylogenetic tree revealed by the parsimony analysis shows that Liaous is closely allied to both Mentzelia Quenstedt, 1871 and Paramentzelia Xu, 1978 of the subfamily Mentzeliinae. A new classification scheme for the Spiriferinoidea is also proposed based on a phylogenetic tree of the superfamily indicated by parsimony analysis. The Spiriferinoidea includes three families and nine subfamilies. Three new subfamilies—Madoinae He and Chen, new subfam., Qinghaispiriferininae He and Chen, new subfam., and Triadispirinae He and Chen, new subfam. are proposed. Liaous shaiwensis He and Chen n. gen. n. sp. is found in the Posidonia wengensis - Liaous shaiwensis (P-L) paleocommunity, which is dominated by r-strategists (i.e., organisms defined by a fauna with a high dominance and small body sizes) and has a low diversity and high dominance. The P-L paleocommunity therefore has little similarity to its coeval communities from the Anisian Stage of South China and instead it appears more similar to the Lower Triassic shelly faunas in community structures. This paleocommunity is interpreted to have inhabited a relatively deep, low-energy, dysaerobic offshore basin/slope setting with the influence of episodic storms.
    Print ISSN: 0022-3360
    Electronic ISSN: 1937-2337
    Topics: Geosciences
    Published by Paleontological Society
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  • 5
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    Mesophyll diffusion and CO2 fertilization on land [Environmental Sciences] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-11-05
    Description: In C3 plants, CO2 concentrations drop considerably along mesophyll diffusion pathways from substomatal cavities to chloroplasts where CO2 assimilation occurs. Global carbon cycle models have not explicitly represented this internal drawdown and therefore overestimate CO2 available for carboxylation and underestimate photosynthetic responsiveness to atmospheric CO2. An explicit consideration of mesophyll...
    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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  • 6
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    Suppression of BRCA1 sensitizes cells to proteasome inhibitors (2014)
    Springer Nature
    Details
    Publication Date: 2014-12-19
    Description: Suppression of BRCA1 sensitizes cells to proteasome inhibitors Cell Death and Disease 5, e1580 (December 2014). doi:10.1038/cddis.2014.537 Authors: Y Gu, P Bouwman, D Greco, J Saarela, B Yadav, J Jonkers & S G Kuznetsov
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 7
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    ASDB: a resource for probing protein functions with small molecules (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-01
    Description: : Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies. Therefore, we create the Annotated Scaffold Database (ASDB), a computer-readable and systematic target-annotated scaffold database, to serve such needs. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets and medical indications. The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets. The scaffolds consist of 3032 scaffolds derived from drugs and 5163 scaffolds derived from natural products. For given scaffolds, scaffold-target networks can be generated from the database to demonstrate the relations of scaffolds and targets. Availability and implementation: ASDB is freely available at http://www.rcdd.org.cn/asdb/ with the major web browsers. Contact: junxu@biochemomes.com or xujun9@mail.sysu.edu.cn 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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    Genetic variants in lncRNA HOTAIR are associated with risk of colorectal cancer (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-17
    Description: Long non-coding RNA HOX transcript antisenseRNA ( HOTAIR ) has been widely identified to participate in tumour pathogenesis, acting as a promoter in colorectal cancer carcinogenesis. However, the association between genetic variants in HOTAIR and cancer risk has not yet been reported. In the present study, we performed a two-stage case–control study to investigate the association between HOTAIR tagSNPs and the risk of colorectal cancer. We found that individuals with rs7958904 CC genotype had a significantly decreased risk of colorectal cancer in both Stage 1 and 2, compared with those carrying GG genotype [odds ratio (OR) = 0.70, 95% confidence interval (CI) = 0.51–0.97 in Stage 1; OR = 0.58, 95% CI = 0.37–0.91 in Stage 2; OR = 0.67, 95% CI = 0.51–0.87 in combined stage]. The subsequently stratified analyses showed that the protective effect of rs7958904 was more pronounced in several subgroups. In summary, our study showed that genetic variants in HOTAIR were associated with risk of colorectal cancer and rs7958904 may act as a potential biomarker for predicting the risk of colorectal cancer.
    Print ISSN: 0267-8357
    Electronic ISSN: 1464-3804
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 9
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    Integrin {alpha}5 activation by flow [Physiology] (2016)
    National Academy of Sciences
    Details
    Publication Date: 2016-01-21
    Description: Local flow patterns determine the uneven distribution of atherosclerotic lesions. Membrane lipid rafts and integrins are crucial for shear stress-regulated endothelial function. In this study, we investigate the role of lipid rafts and integrin α5 in regulating the inflammatory response in endothelial cells (ECs) under atheroprone versus atheroprotective flow. Lipid...
    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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    Cirrus cloud simulations using WRF with improved radiation parameterization and increased vertical resolution (2011)
    Wiley
    Details
    Publication Date: 2011-03-30
    Description: The capability of Weather Research and Forecasting (WRF) model in the simulation of cirrus clouds has been examined, with a focus on the effects of radiative processes and vertical model resolution. We incorporate in WRF a new radiation module, referred to as the Fu-Liou-Gu scheme, which is an improvement and refinement based on the Fu-Liou scheme, particularly in reference to parameterization of the single-scattering properties of ice crystal size and shape. We conducted a number of real-time WRF simulations for cirrus cases that were observed in the coastal and western United States on 29–30 March 2007, and we compared these with available observations from Moderate Resolution Imaging Spectroradiometer (MODIS) and GOES visible and IR images over the same areas. Simulation results show that WRF is capable of generating reasonable cirrus cloud fields and their movement and dissipation processes, especially those associated with the large-scale frontal system. Radiative processes are important in cirrus cloud simulations by affecting the vertical thermal structure and hence convection. The newly implemented radiation module, the Fu-Liou-Gu scheme, has been demonstrated to work well in WRF and can be effectively used for studies related to cirrus cloud formation and evolution and aerosol-cloud-radiation interactions. With the newly implemented radiation scheme, the simulations of cloud cover and cloud and ice water path (CWP and IWP) have been improved for cirrus clouds, with a more consistent comparison with the corresponding MODIS observations in terms of CWP and IWP means and CWP frequency distribution, especially for optically thin cirrus with an improvement of about 20% in simulated mean IWP. The model-simulated ice crystal sizes have also been shown to be comparable to those determined from MODIS cloud products. Finally, we have demonstrated that model vertical resolution plays a significant role in cirrus cloud simulation in terms of altering vertical velocity field and the associated regional circulation.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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