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  • 1
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    American Association for the Advancement of Science (AAAS)
    Publication Date: 2018-10-13
    Description: The transition from nanocluster to nanocrystal is a central issue in nanoscience. The atomic structure determination of metal nanoparticles in the transition size range is challenging and particularly important in understanding the quantum size effect at the atomic level. On the basis of the rationale that the intra- and interparticle weak interactions play critical roles in growing high-quality single crystals of metal nanoparticles, we have reproducibly obtained ideal crystals of Au 144 (SR) 60 and successfully solved its structure by x-ray crystallography (XRC); this structure was theoretically predicted a decade ago and has long been pursued experimentally but without success until now. Here, XRC reveals an interesting Au 12 hollow icosahedron in thiolated gold nanoclusters for the first time. The Au–Au bond length, close to that of bulk gold, shows better thermal extensibility than the other Au–Au bond lengths in Au 144 (SR) 60 , providing an atomic-level perspective because metal generally shows better thermal extensibility than nonmetal materials. Thus, our work not only reveals the mysterious, long experimentally pursued structure of a transition-sized nanoparticle but also has important implications for the growth of high-quality, single-crystal nanoparticles, as well as for the understanding of the thermal extensibility of metals from the perspective of chemical bonding.
    Electronic ISSN: 2375-2548
    Topics: Natural Sciences in General
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  • 2
    Publication Date: 2013-10-22
    Description: A large number of cis-regulatory sequences have been annotated in the human genome, but defining their target genes remains a challenge. One strategy is to identify the long-range looping interactions at these elements with the use of chromosome conformation capture (3C)-based techniques. However, previous studies lack either the resolution or coverage to permit a whole-genome, unbiased view of chromatin interactions. Here we report a comprehensive chromatin interaction map generated in human fibroblasts using a genome-wide 3C analysis method (Hi-C). We determined over one million long-range chromatin interactions at 5-10-kb resolution, and uncovered general principles of chromatin organization at different types of genomic features. We also characterized the dynamics of promoter-enhancer contacts after TNF-alpha signalling in these cells. Unexpectedly, we found that TNF-alpha-responsive enhancers are already in contact with their target promoters before signalling. Such pre-existing chromatin looping, which also exists in other cell types with different extracellular signalling, is a strong predictor of gene induction. Our observations suggest that the three-dimensional chromatin landscape, once established in a particular cell type, is relatively stable and could influence the selection or activation of target genes by a ubiquitous transcription activator in a cell-specific manner.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838900/" 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/PMC3838900/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jin, Fulai -- Li, Yan -- Dixon, Jesse R -- Selvaraj, Siddarth -- Ye, Zhen -- Lee, Ah Young -- Yen, Chia-An -- Schmitt, Anthony D -- Espinoza, Celso A -- Ren, Bing -- P50 GM085764/GM/NIGMS NIH HHS/ -- P50 GM085764-03/GM/NIGMS NIH HHS/ -- T32 GM008666/GM/NIGMS NIH HHS/ -- U01 ES017166/ES/NIEHS NIH HHS/ -- England -- Nature. 2013 Nov 14;503(7475):290-4. doi: 10.1038/nature12644. Epub 2013 Oct 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, USA [2].〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24141950" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Line ; Chromatin/chemistry/genetics/*metabolism ; *Chromosome Mapping ; Enhancer Elements, Genetic/physiology ; Gene Expression Regulation ; *Genome, Human ; Humans ; Imaging, Three-Dimensional ; Promoter Regions, Genetic/physiology ; Protein Binding ; Signal Transduction ; Tumor Necrosis Factor-alpha/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2014-12-05
    Description: The El Nino Southern Oscillation (ENSO) creates strong variations in sea surface temperature in the eastern equatorial Pacific, leading to major climatic and societal impacts. In particular, ENSO influences the yearly variations of tropical cyclone (TC) activities in both the Pacific and Atlantic basins through atmospheric dynamical factors such as vertical wind shear and stability. Until recently, however, the direct ocean thermal control of ENSO on TCs has not been taken into consideration because of an apparent mismatch in both timing and location: ENSO peaks in winter and its surface warming occurs mostly along the Equator, a region without TC activity. Here we show that El Nino--the warm phase of an ENSO cycle--effectively discharges heat into the eastern North Pacific basin two to three seasons after its wintertime peak, leading to intensified TCs. This basin is characterized by abundant TC activity and is the second most active TC region in the world. As a result of the time involved in ocean transport, El Nino's equatorial subsurface 'heat reservoir', built up in boreal winter, appears in the eastern North Pacific several months later during peak TC season (boreal summer and autumn). By means of this delayed ocean transport mechanism, ENSO provides an additional heat supply favourable for the formation of strong hurricanes. This thermal control on intense TC variability has significant implications for seasonal predictions and long-term projections of TC activity over the eastern North Pacific.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jin, F-F -- Boucharel, J -- Lin, I-I -- England -- Nature. 2014 Dec 4;516(7529):82-5. doi: 10.1038/nature13958.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Atmospheric Sciences, SOEST, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA [2] Laboratory for Climate Studies, Beijing Climate Center, Chinese Meteorological Agency, Beijing 100081, China. ; Department of Atmospheric Sciences, SOEST, University of Hawaii at Manoa, Honolulu, Hawaii 96822, USA. ; Department of Atmospheric Sciences, National Taiwan University, Taipei 10617, Taiwan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25471884" target="_blank"〉PubMed〈/a〉
    Keywords: *Cyclonic Storms ; *El Nino-Southern Oscillation ; *Hot Temperature ; Models, Theoretical ; Pacific Ocean ; Seasons ; Water Movements
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
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    Nature Publishing Group (NPG)
    Publication Date: 2015-10-30
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jin, F-F -- Boucharel, J -- Lin, I-I -- England -- Nature. 2015 Oct 29;526(7575):E5-6. doi: 10.1038/nature15547.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of Hawaii at Manoa, Honolulu, Hawaii 96822, USAjff@hawaii.edu. ; ARC Centre of Excellence for Climate System Science, University of New South Wales, Sydney, New South Wales 2052, Australiabouch@hawaii.edu. ; Department of Atmospheric Sciences, National Taiwan University, Taipei 10617, Taiwan.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26511583" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2018-11-02
    Description: Elevated expression of the c-Met receptor plays a crucial role in cancers. In non–small cell lung cancer (NSCLC), aberrant activation of the c-Met signaling pathway contributes to tumorigenesis and cancer progression and may mediate acquired resistance to epidermal growth factor receptor–targeted therapy. c-Met is therefore emerging as a promising therapeutic target for NSCLC, and methods for noninvasive in vivo assessment of c-Met expression would improve NSCLC treatment and diagnosis. Methods: We developed a new c-Met–binding peptide (cMBP) radiotracer, 99m Tc-hydrazine nicotinamide (HYNIC)-cMBP, for SPECT imaging. Cell uptake assays were performed on 2 NSCLC cell lines with different c-Met expressions: H1993 (high expression) and H1299 (no expression). In vivo tumor specificity was assessed by SPECT imaging in tumor-bearing mice at 0.5, 1, 2, and 4 h after injection of the probe. Blocking assays, biodistribution, and autoradiography were also conducted to determine probe specificity. Results: 99m Tc-HYNIC-cMBP was prepared with high efficiency and showed higher uptake in H1993 cells than in H1299 cells. Biodistribution and autoradiography also showed significantly higher percentages of the injected dose for 99m Tc-HYNIC-cMBP in H1993 tumors than in H1299 tumors at 0.5 h (4.74 ± 1.43%/g and 1.00 ± 0.37%/g, respectively; P 〈 0.05). H1993 tumors were clearly visualized at 0.5 h in SPECT images, whereas H1299 tumors were not observed at any time. The specificity of 99m Tc-HYNIC-cMBP for c-Met was demonstrated by a competitive block with an excess of nonradiolabeled peptide. Conclusion: For c-Met–targeted SPECT imaging of NSCLC, we developed 99m Tc-HYNIC-cMBP, a tracer that specifically binds to c-Met with favorable pharmacokinetics in vitro and in vivo.
    Print ISSN: 0022-3123
    Topics: Medicine
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  • 6
    Publication Date: 2018-10-17
    Description: Alternative pre-mRNA splicing remarkably expands protein diversity in eukaryotes. Drosophila PGRP-LC can generate three major 3' splice isoforms that exhibit distinct innate immune recognition and defenses against various microbial infections. However, the regulatory mechanisms underlying the uniquely biased splicing pattern at the 3' variable region remain unclear. Here we show that competing RNA pairings control the unique splicing of the 3' variable region of Drosophila PGRP-LC pre-mRNA. We reveal three roles by which these RNA pairings jointly regulate the 3' variant selection through activating the proximal 3' splice site and concurrently masking the intron-proximal 5' splice site, in combination with physical competition of RNA pairing. We also reveal that competing RNA pairings regulate alternative splicing of the highly complex 3' variable regions of Drosophila CG42235 and Pip . Our findings will facilitate a better understanding of the regulatory mechanisms of highly complex alternative splicing as well as highly variable 3' processing.
    Print ISSN: 1355-8382
    Electronic ISSN: 1469-9001
    Topics: Biology , Medicine
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  • 7
    Publication Date: 2013-11-19
    Description: The El Nino/Southern Oscillation (ENSO) is the Earth's most prominent source of interannual climate variability, exerting profound worldwide effects. Despite decades of research, its behaviour continues to challenge scientists. In the eastern equatorial Pacific Ocean, the anomalously cool sea surface temperatures (SSTs) found during La Nina events and the warm waters of modest El Nino events both propagate westwards, as in the seasonal cycle. In contrast, SST anomalies propagate eastwards during extreme El Nino events, prominently in the post-1976 period, spurring unusual weather events worldwide with costly consequences. The cause of this propagation asymmetry is currently unknown. Here we trace the cause of the asymmetry to the variations in upper ocean currents in the equatorial Pacific, whereby the westward-flowing currents are enhanced during La Nina events but reversed during extreme El Nino events. Our results highlight that propagation asymmetry is favoured when the westward mean equatorial currents weaken, as is projected to be the case under global warming. By analysing past and future climate simulations of an ensemble of models with more realistic propagation, we find a doubling in the occurrences of El Nino events that feature prominent eastward propagation characteristics in a warmer world. Our analysis thus suggests that more frequent emergence of propagation asymmetry will be an indication of the Earth's warming climate.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Santoso, Agus -- McGregor, Shayne -- Jin, Fei-Fei -- Cai, Wenju -- England, Matthew H -- An, Soon-Il -- McPhaden, Michael J -- Guilyardi, Eric -- England -- Nature. 2013 Dec 5;504(7478):126-30. doi: 10.1038/nature12683. Epub 2013 Nov 17.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Australian Research Council (ARC) Centre of Excellence for Climate System Science and Climate Change Research Centre, Level 4 Mathews Building, The University of New South Wales, Sydney 2052, Australia.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24240279" target="_blank"〉PubMed〈/a〉
    Keywords: *Computer Simulation ; El Nino-Southern Oscillation/history ; Global Warming ; History, 20th Century ; Pacific Ocean ; Seasons ; Water Movements ; Weather
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 8
    Publication Date: 2018-06-08
    Description: We read with great interest the article by Mocellin et al , 1 who conducted a comprehensive meta-analysis that nominated 11 germline variants at nine loci significantly associated with gastric cancer (GC) with high level of summary evidence. Moreover, they also identified 38 single nucleotide polymorphisms (SNPs) with intermediate quality significant associations. Most of these loci were resulted from hypothesis-driven studies based on biological relevance, but most of these studies were small sample size and might lead to publication bias. In order to further evaluate their relevance with GC in individual large studies, we analysed these variants directly or their strong linkage disequilibrium SNPs using existing genome-wide association study (GWAS) datasets (including 2631 cases and 4373 controls) in Chinese populations, including those from Nanjing and Beijing populations conducted by our group 2 and from Henan and Shanxi populations conducted by the USA National Cancer Institute. 3 After exclusion...
    Keywords: Gut
    Print ISSN: 0017-5749
    Electronic ISSN: 1468-3288
    Topics: Medicine
    Published by BMJ Publishing Group
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  • 9
    Publication Date: 2018-06-14
    Description: In this study, a new network pharmacology approach based on the components absorbed into the blood was used to investigate the pharmacodynamic material basis and the pharmacologic mechanism of the Fufang-Xialian-Capsule ( FXL ) in treating chronic atrophic gastritis (CAG). Initially, we confirmed the components absorbed into the blood by ultra-high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry. Then, the network approach, which was based on the results of components absorbed into the blood, was used to analyse the pharmacodynamic material basis and the pharmacologic mechanism of FXL on treating CAG. As a result, 22 absorbed components were found in rat plasma. Given the results of the absorption analysis of the components, eight pathways associated with CAG development were found. The targets linked to these pathways are the drug targets of FXL in CAG treatment. The components associated with these targets are the potential pharmacodynamic material basis and exert synergy in regulating pathways during CAG treatment.
    Keywords: analytical chemistry
    Electronic ISSN: 2054-5703
    Topics: Natural Sciences in General
    Published by Royal Society
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  • 10
    Publication Date: 2013-05-10
    Description: Bacterial biofilms are surface-associated, multicellular, morphologically complex microbial communities. Biofilm-forming bacteria such as the opportunistic pathogen Pseudomonas aeruginosa are phenotypically distinct from their free-swimming, planktonic counterparts. Much work has focused on factors affecting surface adhesion, and it is known that P. aeruginosa secretes the Psl exopolysaccharide, which promotes surface attachment by acting as 'molecular glue'. However, how individual surface-attached bacteria self-organize into microcolonies, the first step in communal biofilm organization, is not well understood. Here we identify a new role for Psl in early biofilm development using a massively parallel cell-tracking algorithm to extract the motility history of every cell on a newly colonized surface. By combining this technique with fluorescent Psl staining and computer simulations, we show that P. aeruginosa deposits a trail of Psl as it moves on a surface, which influences the surface motility of subsequent cells that encounter these trails and thus generates positive feedback. Both experiments and simulations indicate that the web of secreted Psl controls the distribution of surface visit frequencies, which can be approximated by a power law. This Pareto-type behaviour indicates that the bacterial community self-organizes in a manner analogous to a capitalist economic system, a 'rich-get-richer' mechanism of Psl accumulation that results in a small number of 'elite' cells becoming extremely enriched in communally produced Psl. Using engineered strains with inducible Psl production, we show that local Psl concentrations determine post-division cell fates and that high local Psl concentrations ultimately allow elite cells to serve as the founding population for initial microcolony development.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4109411/" 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/PMC4109411/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Zhao, Kun -- Tseng, Boo Shan -- Beckerman, Bernard -- Jin, Fan -- Gibiansky, Maxsim L -- Harrison, Joe J -- Luijten, Erik -- Parsek, Matthew R -- Wong, Gerard C L -- 1R01HL087920/HL/NHLBI NIH HHS/ -- P30 DK089507/DK/NIDDK NIH HHS/ -- R01 AI061396/AI/NIAID NIH HHS/ -- R01 AI077628/AI/NIAID NIH HHS/ -- R01 AI081983/AI/NIAID NIH HHS/ -- R01 AI097511/AI/NIAID NIH HHS/ -- R01 HL087920/HL/NHLBI NIH HHS/ -- R01AI077628/AI/NIAID NIH HHS/ -- R01AI081983/AI/NIAID NIH HHS/ -- R56AI061396/AI/NIAID NIH HHS/ -- England -- Nature. 2013 May 16;497(7449):388-91. doi: 10.1038/nature12155. Epub 2013 May 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Bioengineering, University of California, Los Angeles, California 90095, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23657259" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Bacterial Adhesion/physiology ; Biofilms/*growth & development ; Cell Tracking ; Feedback, Physiological ; Fluorescent Dyes ; Polysaccharides, Bacterial/*metabolism ; Pseudomonas aeruginosa/*cytology/*growth & development ; Staining and Labeling
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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