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  • 11
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    Road effects on vegetation composition in a saline environment (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-13
    Description: Aims Road effects from maintenance and traffic have the potential to alter plant communities, but the exact relationships between these effects and changes in plant community composition have not often been studied in diverse environments. To determine the direction and level of community composition changes in saline environment due to road effects, we conducted a study along roads of different ages and in nearby non-road (i.e. natural) areas in the Yellow River Delta, China. Additionally, to potentially elucidate the mechanisms underlying the changes in the richness and composition of plant communities along roads, we evaluated physiochemical changes in soil of roadside and non-road areas. Methods Floristic and environmental data were collected along roadside of different ages and nearby non-road areas. To evaluate plant communities at each site, six 2 m x 2 m quadrats were placed at 3-m intervals along roads and six quadrats were arranged randomly in non-road areas. To determine the difference in plant community composition between roadside and non-road areas, we measured species richness and the abundance of each species, examined species turnover and floristic dissimilarity between the two areas and positioned plant species and sites in an abstract multivariate space. Plant community (species richness, percentage of halophytes) and soil physicochemical properties (pH, salinity, moisture content, bulk density, nitrate and ammonium nitrogen concentration) were compared between roadside and non-road areas (young roadside vs. corresponding non-road areas, old roadside vs. corresponding non-road areas) by using t -tests. Classification and ordination techniques were used to examine the relationship between vegetation and related environmental variables in both roadside and non-road areas. Important Findings For both the young and old roadside areas, species richness in roadside areas was significantly higher than in non-road areas and high floristic dissimilarity values indicated that roadside and non-road areas differed greatly in community composition. In both the young and old roadside areas, the plant communities in roadside areas had lower percentages of halophytes than non-road communities. Correspondence analysis and two-way indicator species analysis showed that halophytes dominated in the non-road areas, while a number of typical non-salt-tolerant species dominated in the roadside areas. Compared to non-road areas, activities associated with roads significantly decreased soil moisture, bulk density and salinity and increased soil pH and nitrate content. Forward selection for the environmental variables in canonical correspondence analysis showed that soil salinity was the most important factor related to the variation of species composition between roadside and non-road areas. Our study demonstrates that road effects have a significant impact on the associated vegetation and soil, and these changes are consistent across roads of different ages in our system.
    Print ISSN: 1752-993X
    Electronic ISSN: 1752-9921
    Topics: Biology
    Published by Oxford University Press
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  • 12
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    Geometrically locked vortex lattices in semiconductor quantum fluids (2012)
    Springer Nature
    Details
    Publication Date: 2012-12-05
    Description: Geometrically locked vortex lattices in semiconductor quantum fluids Nature Communications 3, 1243 (2012). doi:10.1038/ncomms2255 Authors: G. Tosi, G. Christmann, N.G. Berloff, P. Tsotsis, T. Gao, Z. Hatzopoulos, P.G. Savvidis & J.J. Baumberg
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 13
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    An integrated structure- and system-based framework to identify new targets of metabolites and known drugs (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-10
    Description: Motivation: The inherent promiscuity of small molecules towards protein targets impedes our understanding of healthy versus diseased metabolism. This promiscuity also poses a challenge for the pharmaceutical industry as identifying all protein targets is important to assess (side) effects and repositioning opportunities for a drug. Results: Here, we present a novel integrated structure- and system-based approach of drug-target prediction (iDTP) to enable the large-scale discovery of new targets for small molecules, such as pharmaceutical drugs, co-factors and metabolites (collectively called ‘drugs’). For a given drug, our method uses sequence order–independent structure alignment, hierarchical clustering and probabilistic sequence similarity to construct a probabilistic pocket ensemble (PPE) that captures promiscuous structural features of different binding sites on known targets. A drug’s PPE is combined with an approximation of its delivery profile to reduce false positives. In our cross-validation study, we use iDTP to predict the known targets of 11 drugs, with 63% sensitivity and 81% specificity. We then predicted novel targets for these drugs—two that are of high pharmacological interest, the peroxisome proliferator-activated receptor gamma and the oncogene B-cell lymphoma 2, were successfully validated through in vitro binding experiments. Our method is broadly applicable for the prediction of protein-small molecule interactions with several novel applications to biological research and drug development. Availability and implementation: The program, datasets and results are freely available to academic users at http://sfb.kaust.edu.sa/Pages/Software.aspx . Contact: xin.gao@kaust.edu.sa and stefan.arold@kaust.edu.sa 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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  • 14
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    Polariton condensate transistor switch (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-06-02
    Description: Author(s): T. Gao, P. S. Eldridge, T. C. H. Liew, S. I. Tsintzos, G. Stavrinidis, G. Deligeorgis, Z. Hatzopoulos, and P. G. Savvidis A polariton condensate transistor switch is realized through optical excitation of a microcavity ridge with two beams. The ballistically ejected polaritons from a condensate formed at the source are gated using the 20 times weaker second beam to switch on and off the flux of polaritons. In the absen... [Phys. Rev. B 85, 235102] Published Fri Jun 01, 2012
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 15
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    Zinc-finger antiviral protein inhibits HIV-1 infection by selectively targeting multiply spliced viral mRNAs for degradation [Cell Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-09-21
    Description: The zinc-finger antiviral protein (ZAP) was originally identified as a host factor that inhibits the replication of Moloney murine leukemia virus. Here we report that ZAP inhibits HIV-1 infection by promoting the degradation of specific viral mRNAs. Overexpression of ZAP rendered cells resistant to HIV-1 infection in a ZAP expression level-dependent manner, whereas depletion of endogenous ZAP enhanced HIV-1 infection. Both human and rat ZAP inhibited the propagation of replication-competent HIV-1. ZAP specifically targeted the multiply spliced but not unspliced or singly spliced HIV-1 mRNAs for degradation. We provide evidence indicating that ZAP selectively recruits cellular poly(A)-specific ribonuclease (PARN) to shorten the poly(A) tail of target viral mRNA and recruits the RNA exosome to degrade the RNA body from the 3′ end. In addition, ZAP recruits cellular decapping complex through its cofactor RNA helicase p72 to initiate degradation of the target viral mRNA from the 5′ end. Depletion of each of these mRNA degradation enzymes reduced ZAP's activity. Our results indicate that ZAP inhibits HIV-1 by recruiting both the 5′ and 3′ mRNA degradation machinery to specifically promote the degradation of multiply spliced HIV-1 mRNAs.
    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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  • 16
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    BMP9 procomplex structure and function [Biophysics and Computational Biology] (2015)
    National Academy of Sciences
    Details
    Publication Date: 2015-03-25
    Description: Bone morphogenetic proteins (BMPs) belong to the TGF-β family, whose 33 members regulate multiple aspects of morphogenesis. TGF-β family members are secreted as procomplexes containing a small growth factor dimer associated with two larger prodomains. As isolated procomplexes, some members are latent, whereas most are active; what determines these differences...
    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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  • 17
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    Androgen-stimulated eRNA enhances transcription [Cell Biology] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-05-21
    Description: The androgen receptor (AR) is a key factor that regulates the behavior and fate of prostate cancer cells. The AR-regulated network is activated when AR binds enhancer elements and modulates specific enhancer–promoter looping. Kallikrein-related peptidase 3 (KLK3), which codes for prostate-specific antigen (PSA), is a well-known AR-regulated gene and its...
    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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  • 18
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    Quantum oscillations in CuxBi2Se3 in high magnetic fields (2014)
    American Physical Society (APS)
    Details
    Publication Date: 2014-11-22
    Description: Author(s): B. J. Lawson, G. Li, F. Yu, T. Asaba, C. Tinsman, T. Gao, W. Wang, Y. S. Hor, and Lu Li CuxBi2Se3 has drawn much attention as the leading candidate to be the first topological superconductor and the realization of coveted Majorana particles in a condensed matter system. However, there has been increasing controversy about the nature of its superconducting phase. This study sheds light ... [Phys. Rev. B 90, 195141] Published Fri Nov 21, 2014
    Keywords: Electronic structure and strongly correlated systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 19
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    Polymer replicas of photonic porous silicon for sensing and drug delivery applications (2003)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2003-03-29
    Description: Elaborate one-dimensional photonic crystals are constructed from a variety of organic and biopolymers, which can be dissolved or melted, by templating the solution-cast or injection-molded materials in porous silicon or porous silicon dioxide multilayer (rugate dielectric mirror) structures. After the removal of the template by chemical dissolution, the polymer castings replicate the photonic features and the nanostructure of the master. We demonstrate that these castings can be used as vapor sensors, as deformable and tunable optical filters, and as self-reporting, bioresorbable materials.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Li, Yang Yang -- Cunin, Frederique -- Link, Jamie R -- Gao, Ting -- Betts, Ronald E -- Reiver, Sarah H -- Chin, Vicki -- Bhatia, Sangeeta N -- Sailor, Michael J -- New York, N.Y. -- Science. 2003 Mar 28;299(5615):2045-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Department 0358, La Jolla, CA 92093-0358, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12663921" target="_blank"〉PubMed〈/a〉
    Keywords: *Biocompatible Materials ; Caffeine ; *Drug Delivery Systems ; Ethanol ; Humans ; Hydrogen-Ion Concentration ; Hydrolysis ; Light ; *Nanotechnology ; Optics and Photonics ; Oxidation-Reduction ; Polyesters/chemistry ; Polyethylene/chemistry ; *Polymers ; Polystyrenes/chemistry ; Porosity ; *Silicon/chemistry ; Silicon Dioxide/chemistry ; Spectrum Analysis ; Volatilization
    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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  • 20
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    Galectin-1 induces hepatocellular carcinoma EMT and sorafenib resistance by activating FAK/PI3K/AKT signaling (2016)
    Springer Nature
    Details
    Publication Date: 2016-04-22
    Description: Galectin-1 induces hepatocellular carcinoma EMT and sorafenib resistance by activating FAK/PI3K/AKT signaling Cell Death and Disease 7, e2201 (April 2016). doi:10.1038/cddis.2015.324 Authors: P-F Zhang, K-S Li, Y-h Shen, P-T Gao, Z-R Dong, J-B Cai, C Zhang, X-Y Huang, M-X Tian, Z-Q Hu, D-M Gao, J Fan, A-W Ke & G-M Shi
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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