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  • 1
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    Dissecting the chromatin interactome of microRNA genes (2014)
    Oxford University Press
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    Publication Date: 2014-03-13
    Description: Our knowledge of the role of higher-order chromatin structures in transcription of microRNA genes ( MIRs ) is evolving rapidly. Here we investigate the effect of 3D architecture of chromatin on the transcriptional regulation of MIRs . We demonstrate that MIRs have transcriptional features that are similar to protein-coding genes. RNA polymerase II–associated ChIA-PET data reveal that many groups of MIRs and protein-coding genes are organized into functionally compartmentalized chromatin communities and undergo coordinated expression when their genomic loci are spatially colocated. We observe that MIRs display widespread communication in those transcriptionally active communities. Moreover, miRNA–target interactions are significantly enriched among communities with functional homogeneity while depleted from the same community from which they originated, suggesting MIRs coordinating function-related pathways at posttranscriptional level. Further investigation demonstrates the existence of spatial MIR–MIR chromatin interacting networks. We show that groups of spatially coordinated MIRs are frequently from the same family and involved in the same disease category. The spatial interaction network possesses both common and cell-specific subnetwork modules that result from the spatial organization of chromatin within different cell types. Together, our study unveils an entirely unexplored layer of MIR regulation throughout the human genome that links the spatial coordination of MIRs to their co-expression and function.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Enhanced optical conductivity induced by surface states in ABC-stacked few-layer graphene (2011)
    American Physical Society (APS)
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    Publication Date: 2011-06-23
    Description: Author(s): Jia-An Yan, W. Y. Ruan, and M. Y. Chou The surface states of ABC-stacked few-layer graphene (FLG) are studied based on density-functional theory. These states form flat bands near the Fermi level, with the k -space range increasing with the layer number. Based on a tight-binding model, the characteristics of these surface states and their... [Phys. Rev. B 83, 245418] Published Wed Jun 22, 2011
    Keywords: Surface physics, nanoscale physics, low-dimensional systems
    Print ISSN: 1098-0121
    Electronic ISSN: 1095-3795
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
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    Antiferromagnetic ordering in spin-chain multiferroic Gd2BaNiO5 studied by electronic spin resonance (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-06-10
    Description: High-field electron spin resonance (ESR) has been employed to study the antiferromagnetic (AFM) ordering state ( T  
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data [Medical Sciences] (2011)
    National Academy of Sciences
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    Publication Date: 2011-07-20
    Description: We present the analysis of the evolution of tumors in a case of hepatocellular carcinoma. This case is particularly informative about cancer growth dynamics and the underlying driving mutations. We sampled nine different sections from three tumors and seven more sections from the adjacent nontumor tissues. Selected sections were subjected to exon as well as whole-genome sequencing. Putative somatic mutations were then individually validated across all 9 tumor and 7 nontumor sections. Among the mutations validated, 24 were amino acid changes; in addition, 22 large indels/copy number variants (〉1 Mb) were detected. These somatic mutations define four evolutionary lineages among tumor cells. Separate evolution and expansion of these lineages were recent and rapid, each apparently having only one lineage-specific protein-coding mutation. Hence, by using a cell-population genetic definition, this approach identified three coding changes (CCNG1, P62, and an indel/fusion gene) as tumor driver mutations. These three mutations, affecting cell cycle control and apoptosis, are functionally distinct from mutations that accumulated earlier, many of which are involved in inflammation/immunity or cell anchoring. These distinct functions of mutations at different stages may reflect the genetic interactions underlying tumor growth.
    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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  • 5
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    Full-polarized Tomographic Diffraction Microscopy Achieves a Resolution about One-Fourth of the Wavelength (2013)
    American Physical Society (APS)
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    Publication Date: 2013-12-13
    Description: Author(s): T. Zhang, Y. Ruan, G. Maire, D. Sentenac, A. Talneau, K. Belkebir, P. C. Chaumet, and A. Sentenac We present a marker-free microscope that records the phase, amplitude, and polarization state of the field diffracted by the sample for different illumination directions. The data are processed with an appropriate inversion method to yield the sample permittivity map. We observe that the full-polari... [Phys. Rev. Lett. 111, 243904] Published Thu Dec 12, 2013
    Keywords: Nonlinear Dynamics, Fluid Dynamics, Classical Optics, etc.
    Print ISSN: 0031-9007
    Electronic ISSN: 1079-7114
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    Untangling the contributions of image charge and laser profile for optimal photoemission of high-brightness electron beams (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-11-04
    Description: Using our model for the simulation of photoemission of high brightness electron beams, we investigate the virtual cathode physics and the limits to spatio-temporal and spectroscopic resolution originating from the image charge on the surface and from the profile of the exciting laser pulse. By contrasting the effect of varying surface properties (leading to expanding or pinned image charge), laser profiles (Gaussian, uniform, and elliptical), and aspect ratios (pancake- and cigar-like) under different extraction field strengths and numbers of generated electrons, we quantify the effect of these experimental parameters on macroscopic pulse properties such as emittance, brightness (4D and 6D), coherence length, and energy spread. Based on our results, we outline optimal conditions of pulse generation for ultrafast electron microscope systems that take into account constraints on the number of generated electrons and on the required time resolution.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    Direct imaging of transient molecular structures with ultrafast diffraction (2001)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2001-02-13
    Description: Ultrafast electron diffraction (UED) has been developed to study transient structures in complex chemical reactions initiated with femtosecond laser pulses. This direct imaging of reactions was achieved using our third-generation apparatus equipped with an electron pulse (1.07 +/- 0.27 picoseconds) source, a charge-coupled device camera, and a mass spectrometer. Two prototypical gas-phase reactions were studied: the nonconcerted elimination reaction of a haloethane, wherein the structure of the intermediate was determined, and the ring opening of a cyclic hydrocarbon containing no heavy atoms. These results demonstrate the vastly improved sensitivity, resolution, and versatility of UED for studying ultrafast structural dynamics in complex molecular systems.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ihee, H -- Lobastov, V A -- Gomez, U M -- Goodson, B M -- Srinivasan, R -- Ruan, C Y -- Zewail, A H -- New York, N.Y. -- Science. 2001 Jan 19;291(5503):458-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11161194" target="_blank"〉PubMed〈/a〉
    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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  • 8
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    Biodiversity and biogeography of phages in modern stromatolites and thrombolites (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-04
    Description: Viruses, and more particularly phages (viruses that infect bacteria), represent one of the most abundant living entities in aquatic and terrestrial environments. The biogeography of phages has only recently been investigated and so far reveals a cosmopolitan distribution of phage genetic material (or genotypes). Here we address this cosmopolitan distribution through the analysis of phage communities in modern microbialites, the living representatives of one of the most ancient life forms on Earth. On the basis of a comparative metagenomic analysis of viral communities associated with marine (Highborne Cay, Bahamas) and freshwater (Pozas Azules II and Rio Mesquites, Mexico) microbialites, we show that some phage genotypes are geographically restricted. The high percentage of unknown sequences recovered from the three metagenomes (〉97%), the low percentage similarities with sequences from other environmental viral (n = 42) and microbial (n = 36) metagenomes, and the absence of viral genotypes shared among microbialites indicate that viruses are genetically unique in these environments. Identifiable sequences in the Highborne Cay metagenome were dominated by single-stranded DNA microphages that were not detected in any other samples examined, including sea water, fresh water, sediment, terrestrial, extreme, metazoan-associated and marine microbial mats. Finally, a marine signature was present in the phage community of the Pozas Azules II microbialites, even though this environment has not been in contact with the ocean for tens of millions of years. Taken together, these results prove that viruses in modern microbialites display biogeographical variability and suggest that they may be derived from an ancient community.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Desnues, Christelle -- Rodriguez-Brito, Beltran -- Rayhawk, Steve -- Kelley, Scott -- Tran, Tuong -- Haynes, Matthew -- Liu, Hong -- Furlan, Mike -- Wegley, Linda -- Chau, Betty -- Ruan, Yijun -- Hall, Dana -- Angly, Florent E -- Edwards, Robert A -- Li, Linlin -- Thurber, Rebecca Vega -- Reid, R Pamela -- Siefert, Janet -- Souza, Valeria -- Valentine, David L -- Swan, Brandon K -- Breitbart, Mya -- Rohwer, Forest -- England -- Nature. 2008 Mar 20;452(7185):340-3. doi: 10.1038/nature06735. Epub 2008 Mar 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, San Diego State University, San Diego, California 92182, USA. cdesnues@yahoo.fr〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18311127" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteriophages/classification/genetics/*isolation & purification/*physiology ; Bahamas ; *Biodiversity ; Capsid/chemistry ; Computational Biology ; DNA, Viral/analysis/genetics ; *Ecosystem ; Fresh Water/microbiology/virology ; Genome, Viral/genetics ; Genomics ; *Geography ; Geologic Sediments/microbiology/virology ; Mexico ; Molecular Sequence Data ; Phylogeny ; Proteome/metabolism ; Seawater/microbiology/virology ; *Water Microbiology
    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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  • 9
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    Functional metagenomic profiling of nine biomes (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-03-14
    Description: Microbial activities shape the biogeochemistry of the planet and macroorganism health. Determining the metabolic processes performed by microbes is important both for understanding and for manipulating ecosystems (for example, disruption of key processes that lead to disease, conservation of environmental services, and so on). Describing microbial function is hampered by the inability to culture most microbes and by high levels of genomic plasticity. Metagenomic approaches analyse microbial communities to determine the metabolic processes that are important for growth and survival in any given environment. Here we conduct a metagenomic comparison of almost 15 million sequences from 45 distinct microbiomes and, for the first time, 42 distinct viromes and show that there are strongly discriminatory metabolic profiles across environments. Most of the functional diversity was maintained in all of the communities, but the relative occurrence of metabolisms varied, and the differences between metagenomes predicted the biogeochemical conditions of each environment. The magnitude of the microbial metabolic capabilities encoded by the viromes was extensive, suggesting that they serve as a repository for storing and sharing genes among their microbial hosts and influence global evolutionary and metabolic processes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dinsdale, Elizabeth A -- Edwards, Robert A -- Hall, Dana -- Angly, Florent -- Breitbart, Mya -- Brulc, Jennifer M -- Furlan, Mike -- Desnues, Christelle -- Haynes, Matthew -- Li, Linlin -- McDaniel, Lauren -- Moran, Mary Ann -- Nelson, Karen E -- Nilsson, Christina -- Olson, Robert -- Paul, John -- Brito, Beltran Rodriguez -- Ruan, Yijun -- Swan, Brandon K -- Stevens, Rick -- Valentine, David L -- Thurber, Rebecca Vega -- Wegley, Linda -- White, Bryan A -- Rohwer, Forest -- England -- Nature. 2008 Apr 3;452(7187):629-32. doi: 10.1038/nature06810. Epub 2008 Mar 12.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biology, San Diego State University, San Diego, California 92182, USA. elizabeth_dinsdale@hotmail.com〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18337718" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthozoa/physiology ; Archaea/genetics/isolation & purification/metabolism ; Bacteria/*genetics/isolation & purification/*metabolism ; Chemotaxis/genetics ; Computational Biology ; Culicidae/physiology ; *Ecosystem ; Fishes/physiology ; Fresh Water ; *Gene Expression Profiling ; Genome, Archaeal ; Genome, Bacterial ; Genome, Viral ; *Genomics ; Microbiology ; Seawater ; Viruses/*genetics/isolation & purification/*metabolism
    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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  • 10
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    An oestrogen-receptor-alpha-bound human chromatin interactome (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-11-06
    Description: Genomes are organized into high-level three-dimensional structures, and DNA elements separated by long genomic distances can in principle interact functionally. Many transcription factors bind to regulatory DNA elements distant from gene promoters. Although distal binding sites have been shown to regulate transcription by long-range chromatin interactions at a few loci, chromatin interactions and their impact on transcription regulation have not been investigated in a genome-wide manner. Here we describe the development of a new strategy, chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) for the de novo detection of global chromatin interactions, with which we have comprehensively mapped the chromatin interaction network bound by oestrogen receptor alpha (ER-alpha) in the human genome. We found that most high-confidence remote ER-alpha-binding sites are anchored at gene promoters through long-range chromatin interactions, suggesting that ER-alpha functions by extensive chromatin looping to bring genes together for coordinated transcriptional regulation. We propose that chromatin interactions constitute a primary mechanism for regulating transcription in mammalian genomes.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774924/" 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/PMC2774924/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fullwood, Melissa J -- Liu, Mei Hui -- Pan, You Fu -- Liu, Jun -- Xu, Han -- Mohamed, Yusoff Bin -- Orlov, Yuriy L -- Velkov, Stoyan -- Ho, Andrea -- Mei, Poh Huay -- Chew, Elaine G Y -- Huang, Phillips Yao Hui -- Welboren, Willem-Jan -- Han, Yuyuan -- Ooi, Hong Sain -- Ariyaratne, Pramila N -- Vega, Vinsensius B -- Luo, Yanquan -- Tan, Peck Yean -- Choy, Pei Ye -- Wansa, K D Senali Abayratna -- Zhao, Bing -- Lim, Kar Sian -- Leow, Shi Chi -- Yow, Jit Sin -- Joseph, Roy -- Li, Haixia -- Desai, Kartiki V -- Thomsen, Jane S -- Lee, Yew Kok -- Karuturi, R Krishna Murthy -- Herve, Thoreau -- Bourque, Guillaume -- Stunnenberg, Hendrik G -- Ruan, Xiaoan -- Cacheux-Rataboul, Valere -- Sung, Wing-Kin -- Liu, Edison T -- Wei, Chia-Lin -- Cheung, Edwin -- Ruan, Yijun -- 1U54HG004557-01/HG/NHGRI NIH HHS/ -- R01 HG004456/HG/NHGRI NIH HHS/ -- R01 HG004456-01/HG/NHGRI NIH HHS/ -- R01 HG004456-02/HG/NHGRI NIH HHS/ -- R01 HG004456-03/HG/NHGRI NIH HHS/ -- R01HG003521-01/HG/NHGRI NIH HHS/ -- R01HG004456-01/HG/NHGRI NIH HHS/ -- U54 HG004557/HG/NHGRI NIH HHS/ -- U54 HG004557-01/HG/NHGRI NIH HHS/ -- U54 HG004557-02/HG/NHGRI NIH HHS/ -- U54 HG004557-03/HG/NHGRI NIH HHS/ -- U54 HG004557-04/HG/NHGRI NIH HHS/ -- England -- Nature. 2009 Nov 5;462(7269):58-64. doi: 10.1038/nature08497.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19890323" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Line ; Chromatin/*genetics/*metabolism ; Chromatin Immunoprecipitation ; Cross-Linking Reagents ; Estrogen Receptor alpha/*metabolism ; Formaldehyde ; Genome, Human/*genetics ; Humans ; Promoter Regions, Genetic/genetics ; Protein Binding ; Reproducibility of Results ; Sequence Analysis, DNA ; Transcription, Genetic ; Transcriptional Activation
    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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