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  • 11
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    Three-dimensional optical metamaterial with a negative refractive index (2008)
    Nature Publishing Group (NPG)
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    Publication Date: 2008-08-12
    Description: Metamaterials are artificially engineered structures that have properties, such as a negative refractive index, not attainable with naturally occurring materials. Negative-index metamaterials (NIMs) were first demonstrated for microwave frequencies, but it has been challenging to design NIMs for optical frequencies and they have so far been limited to optically thin samples because of significant fabrication challenges and strong energy dissipation in metals. Such thin structures are analogous to a monolayer of atoms, making it difficult to assign bulk properties such as the index of refraction. Negative refraction of surface plasmons was recently demonstrated but was confined to a two-dimensional waveguide. Three-dimensional (3D) optical metamaterials have come into focus recently, including the realization of negative refraction by using layered semiconductor metamaterials and a 3D magnetic metamaterial in the infrared frequencies; however, neither of these had a negative index of refraction. Here we report a 3D optical metamaterial having negative refractive index with a very high figure of merit of 3.5 (that is, low loss). This metamaterial is made of cascaded 'fishnet' structures, with a negative index existing over a broad spectral range. Moreover, it can readily be probed from free space, making it functional for optical devices. We construct a prism made of this optical NIM to demonstrate negative refractive index at optical frequencies, resulting unambiguously from the negative phase evolution of the wave propagating inside the metamaterial. Bulk optical metamaterials open up prospects for studies of 3D optical effects and applications associated with NIMs and zero-index materials such as reversed Doppler effect, superlenses, optical tunnelling devices, compact resonators and highly directional sources.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Valentine, Jason -- Zhang, Shuang -- Zentgraf, Thomas -- Ulin-Avila, Erick -- Genov, Dentcho A -- Bartal, Guy -- Zhang, Xiang -- England -- Nature. 2008 Sep 18;455(7211):376-9. doi: 10.1038/nature07247. Epub 2008 Aug 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NSF Nano-scale Science and Engineering Center (NSEC), 3112 Etcheverry Hall, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18690249" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 12
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    High-Q surface-plasmon-polariton whispering-gallery microcavity (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-01-23
    Description: Surface plasmon polaritons (SPPs) are electron density waves excited at the interfaces between metals and dielectric materials. Owing to their highly localized electromagnetic fields, they may be used for the transport and manipulation of photons on subwavelength scales. In particular, plasmonic resonant cavities represent an application that could exploit this field compression to create ultrasmall-mode-volume devices. A key figure of merit in this regard is the ratio of cavity quality factor, Q (related to the dissipation rate of photons confined to the cavity), to cavity mode volume, V (refs 10, 11). However, plasmonic cavity Q factors have so far been limited to values less than 100 both for visible and near-infrared wavelengths. Significantly, such values are far below the theoretically achievable Q factors for plasmonic resonant structures. Here we demonstrate a high-Q SPP whispering-gallery microcavity that is made by coating the surface of a high-Q silica microresonator with a thin layer of a noble metal. Using this structure, Q factors of 1,376 +/- 65 can be achieved in the near infrared for surface-plasmonic whispering-gallery modes at room temperature. This nearly ideal value, which is close to the theoretical metal-loss-limited Q factor, is attributed to the suppression and minimization of radiation and scattering losses that are made possible by the geometrical structure and the fabrication method. The SPP eigenmodes, as well as the dielectric eigenmodes, are confined within the whispering-gallery microcavity and accessed evanescently using a single strand of low-loss, tapered optical waveguide. This coupling scheme provides a convenient way of selectively exciting and probing confined SPP eigenmodes. Up to 49.7 per cent of input power is coupled by phase-matching control between the microcavity SPP and the tapered fibre eigenmodes.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Min, Bumki -- Ostby, Eric -- Sorger, Volker -- Ulin-Avila, Erick -- Yang, Lan -- Zhang, Xiang -- Vahala, Kerry -- England -- Nature. 2009 Jan 22;457(7228):455-8. doi: 10.1038/nature07627.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Thomas J. Watson Laboratory of Applied Physics, California Institute of Technology, Pasadena, California 91125, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19158793" target="_blank"〉PubMed〈/a〉
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    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 13
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    Histone modifications at human enhancers reflect global cell-type-specific gene expression (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-03-20
    Description: The human body is composed of diverse cell types with distinct functions. Although it is known that lineage specification depends on cell-specific gene expression, which in turn is driven by promoters, enhancers, insulators and other cis-regulatory DNA sequences for each gene, the relative roles of these regulatory elements in this process are not clear. We have previously developed a chromatin-immunoprecipitation-based microarray method (ChIP-chip) to locate promoters, enhancers and insulators in the human genome. Here we use the same approach to identify these elements in multiple cell types and investigate their roles in cell-type-specific gene expression. We observed that the chromatin state at promoters and CTCF-binding at insulators is largely invariant across diverse cell types. In contrast, enhancers are marked with highly cell-type-specific histone modification patterns, strongly correlate to cell-type-specific gene expression programs on a global scale, and are functionally active in a cell-type-specific manner. Our results define over 55,000 potential transcriptional enhancers in the human genome, significantly expanding the current catalogue of human enhancers and highlighting the role of these elements in cell-type-specific gene expression.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910248/" 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/PMC2910248/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Heintzman, Nathaniel D -- Hon, Gary C -- Hawkins, R David -- Kheradpour, Pouya -- Stark, Alexander -- Harp, Lindsey F -- Ye, Zhen -- Lee, Leonard K -- Stuart, Rhona K -- Ching, Christina W -- Ching, Keith A -- Antosiewicz-Bourget, Jessica E -- Liu, Hui -- Zhang, Xinmin -- Green, Roland D -- Lobanenkov, Victor V -- Stewart, Ron -- Thomson, James A -- Crawford, Gregory E -- Kellis, Manolis -- Ren, Bing -- R01 HG004037/HG/NHGRI NIH HHS/ -- R01 HG004037-02/HG/NHGRI NIH HHS/ -- U01 HG003151/HG/NHGRI NIH HHS/ -- U01 HG003151-01/HG/NHGRI NIH HHS/ -- U01 HG003151-01S1/HG/NHGRI NIH HHS/ -- U01 HG003151-02/HG/NHGRI NIH HHS/ -- U01 HG003151-03/HG/NHGRI NIH HHS/ -- U01 HG003151-03S1/HG/NHGRI NIH HHS/ -- U01 HG003151-03S2/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- England -- Nature. 2009 May 7;459(7243):108-12. doi: 10.1038/nature07829. Epub 2009 Mar 18.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Ludwig Institute for Cancer Research, UCSD School of 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/19295514" target="_blank"〉PubMed〈/a〉
    Keywords: Binding Sites ; Cell Line ; *Cell Physiological Phenomena ; Chromatin/genetics ; *Gene Expression Regulation ; Genome, Human/genetics ; HeLa Cells ; Histones/*metabolism ; Humans ; K562 Cells ; Promoter Regions, Genetic/genetics ; Transcription Factors/*genetics/metabolism
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  • 14
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    Plasmon lasers at deep subwavelength scale (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-09-01
    Description: Laser science has been successful in producing increasingly high-powered, faster and smaller coherent light sources. Examples of recent advances are microscopic lasers that can reach the diffraction limit, based on photonic crystals, metal-clad cavities and nanowires. However, such lasers are restricted, both in optical mode size and physical device dimension, to being larger than half the wavelength of the optical field, and it remains a key fundamental challenge to realize ultracompact lasers that can directly generate coherent optical fields at the nanometre scale, far beyond the diffraction limit. A way of addressing this issue is to make use of surface plasmons, which are capable of tightly localizing light, but so far ohmic losses at optical frequencies have inhibited the realization of truly nanometre-scale lasers based on such approaches. A recent theoretical work predicted that such losses could be significantly reduced while maintaining ultrasmall modes in a hybrid plasmonic waveguide. Here we report the experimental demonstration of nanometre-scale plasmonic lasers, generating optical modes a hundred times smaller than the diffraction limit. We realize such lasers using a hybrid plasmonic waveguide consisting of a high-gain cadmium sulphide semiconductor nanowire, separated from a silver surface by a 5-nm-thick insulating gap. Direct measurements of the emission lifetime reveal a broad-band enhancement of the nanowire's exciton spontaneous emission rate by up to six times owing to the strong mode confinement and the signature of apparently threshold-less lasing. Because plasmonic modes have no cutoff, we are able to demonstrate downscaling of the lateral dimensions of both the device and the optical mode. Plasmonic lasers thus offer the possibility of exploring extreme interactions between light and matter, opening up new avenues in the fields of active photonic circuits, bio-sensing and quantum information technology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Oulton, Rupert F -- Sorger, Volker J -- Zentgraf, Thomas -- Ma, Ren-Min -- Gladden, Christopher -- Dai, Lun -- Bartal, Guy -- Zhang, Xiang -- England -- Nature. 2009 Oct 1;461(7264):629-32. doi: 10.1038/nature08364. Epub 2009 Aug 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉NSF Nanoscale Science and Engineering Centre, 3112 Etcheverry Hall, University of California, Berkeley, California 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19718019" target="_blank"〉PubMed〈/a〉
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  • 15
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    In situ observation of incompressible Mott-insulating domains in ultracold atomic gases (2009)
    Nature Publishing Group (NPG)
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    Publication Date: 2009-08-21
    Description: The observation of the superfluid to Mott insulator phase transition of ultracold atoms in optical lattices was an enabling discovery in experimental many-body physics, providing the first tangible example of a quantum phase transition (one that occurs even at zero temperature) in an ultracold atomic gas. For a trapped gas, the spatially varying local chemical potential gives rise to multiple quantum phases within a single sample, complicating the interpretation of bulk measurements. Here we report spatially resolved, in-situ imaging of a two-dimensional ultracold atomic gas as it crosses the superfluid to Mott insulator transition, providing direct access to individual characteristics of the insulating, superfluid and normal phases. We present results for the local compressibility in all phases, observing a strong suppression in the insulator domain and suppressed density fluctuations for the Mott insulator, in accordance with the fluctuation-dissipation theorem. Furthermore, we obtain a direct measure of the finite temperature of the system. Taken together, these methods enable a complete characterization of multiple phases in a strongly correlated Bose gas, and of the interplay between quantum and thermal fluctuations in the quantum critical regime.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gemelke, Nathan -- Zhang, Xibo -- Hung, Chen-Lung -- Chin, Cheng -- England -- Nature. 2009 Aug 20;460(7258):995-8. doi: 10.1038/nature08244.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The James Franck Institute and Department of Physics, University of Chicago, Chicago, Illinois 60637, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19693080" target="_blank"〉PubMed〈/a〉
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  • 16
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    A methyl transferase links the circadian clock to the regulation of alternative splicing (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-10-22
    Description: Circadian rhythms allow organisms to time biological processes to the most appropriate phases of the day-night cycle. Post-transcriptional regulation is emerging as an important component of circadian networks, but the molecular mechanisms linking the circadian clock to the control of RNA processing are largely unknown. Here we show that PROTEIN ARGININE METHYL TRANSFERASE 5 (PRMT5), which transfers methyl groups to arginine residues present in histones and Sm spliceosomal proteins, links the circadian clock to the control of alternative splicing in plants. Mutations in PRMT5 impair several circadian rhythms in Arabidopsis thaliana and this phenotype is caused, at least in part, by a strong alteration in alternative splicing of the core-clock gene PSEUDO RESPONSE REGULATOR 9 (PRR9). Furthermore, genome-wide studies show that PRMT5 contributes to the regulation of many pre-messenger-RNA splicing events, probably by modulating 5'-splice-site recognition. PRMT5 expression shows daily and circadian oscillations, and this contributes to the mediation of the circadian regulation of expression and alternative splicing of a subset of genes. Circadian rhythms in locomotor activity are also disrupted in dart5-1, a mutant affected in the Drosophila melanogaster PRMT5 homologue, and this is associated with alterations in splicing of the core-clock gene period and several clock-associated genes. Our results demonstrate a key role for PRMT5 in the regulation of alternative splicing and indicate that the interplay between the circadian clock and the regulation of alternative splicing by PRMT5 constitutes a common mechanism that helps organisms to synchronize physiological processes with daily changes in environmental conditions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sanchez, Sabrina E -- Petrillo, Ezequiel -- Beckwith, Esteban J -- Zhang, Xu -- Rugnone, Matias L -- Hernando, C Esteban -- Cuevas, Juan C -- Godoy Herz, Micaela A -- Depetris-Chauvin, Ana -- Simpson, Craig G -- Brown, John W S -- Cerdan, Pablo D -- Borevitz, Justin O -- Mas, Paloma -- Ceriani, M Fernanda -- Kornblihtt, Alberto R -- Yanovsky, Marcelo J -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Nov 4;468(7320):112-6. doi: 10.1038/nature09470. Epub 2010 Oct 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉IFEVA, Facultad de Agronomia, UBA-CONICET, C1417DSE Buenos Aires, Argentina.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20962777" target="_blank"〉PubMed〈/a〉
    Keywords: Alternative Splicing/*genetics ; Animals ; Arabidopsis/enzymology/genetics/*physiology/radiation effects ; Arabidopsis Proteins/genetics/*metabolism ; Base Sequence ; Circadian Clocks/genetics/*physiology ; Circadian Rhythm/genetics/*physiology ; Darkness ; Drosophila Proteins/genetics/*metabolism ; Drosophila melanogaster/enzymology/genetics/*physiology/radiation effects ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; Light ; Methylation ; Mutation ; Period Circadian Proteins/genetics ; Phenotype ; Protein Methyltransferases/genetics/*metabolism ; Protein-Arginine N-Methyltransferases/genetics/*metabolism ; RNA Precursors/genetics/metabolism ; RNA Splice Sites/genetics ; RNA, Messenger/genetics/metabolism ; Spliceosomes/metabolism ; Transcription Factors/genetics
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  • 17
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    Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-03-26
    Description: Although pioneered by human geneticists as a potential solution to the challenging problem of finding the genetic basis of common human diseases, genome-wide association (GWA) studies have, owing to advances in genotyping and sequencing technology, become an obvious general approach for studying the genetics of natural variation and traits of agricultural importance. They are particularly useful when inbred lines are available, because once these lines have been genotyped they can be phenotyped multiple times, making it possible (as well as extremely cost effective) to study many different traits in many different environments, while replicating the phenotypic measurements to reduce environmental noise. Here we demonstrate the power of this approach by carrying out a GWA study of 107 phenotypes in Arabidopsis thaliana, a widely distributed, predominantly self-fertilizing model plant known to harbour considerable genetic variation for many adaptively important traits. Our results are dramatically different from those of human GWA studies, in that we identify many common alleles of major effect, but they are also, in many cases, harder to interpret because confounding by complex genetics and population structure make it difficult to distinguish true associations from false. However, a-priori candidates are significantly over-represented among these associations as well, making many of them excellent candidates for follow-up experiments. Our study demonstrates the feasibility of GWA studies in A. thaliana and suggests that the approach will be appropriate for many other organisms.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023908/" 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/PMC3023908/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Atwell, Susanna -- Huang, Yu S -- Vilhjalmsson, Bjarni J -- Willems, Glenda -- Horton, Matthew -- Li, Yan -- Meng, Dazhe -- Platt, Alexander -- Tarone, Aaron M -- Hu, Tina T -- Jiang, Rong -- Muliyati, N Wayan -- Zhang, Xu -- Amer, Muhammad Ali -- Baxter, Ivan -- Brachi, Benjamin -- Chory, Joanne -- Dean, Caroline -- Debieu, Marilyne -- de Meaux, Juliette -- Ecker, Joseph R -- Faure, Nathalie -- Kniskern, Joel M -- Jones, Jonathan D G -- Michael, Todd -- Nemri, Adnane -- Roux, Fabrice -- Salt, David E -- Tang, Chunlao -- Todesco, Marco -- Traw, M Brian -- Weigel, Detlef -- Marjoram, Paul -- Borevitz, Justin O -- Bergelson, Joy -- Nordborg, Magnus -- GM057994/GM/NIGMS NIH HHS/ -- GM073822/GM/NIGMS NIH HHS/ -- GM078536/GM/NIGMS NIH HHS/ -- GM62932/GM/NIGMS NIH HHS/ -- P42ES007373/ES/NIEHS NIH HHS/ -- R01 GM057994/GM/NIGMS NIH HHS/ -- R01 GM057994-05A1/GM/NIGMS NIH HHS/ -- R01 GM062932/GM/NIGMS NIH HHS/ -- R01 GM062932-05/GM/NIGMS NIH HHS/ -- R01 GM073822/GM/NIGMS NIH HHS/ -- R01 GM073822-01A1/GM/NIGMS NIH HHS/ -- R01 GM078536-01A1/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2010 Jun 3;465(7298):627-31. doi: 10.1038/nature08800. Epub 2010 Mar 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular and Computational Biology, University of Southern California, Los Angeles, California 90089, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20336072" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Arabidopsis/*classification/*genetics ; Arabidopsis Proteins/genetics ; Flowers/genetics ; Genes, Plant/genetics ; Genetic Loci/genetics ; Genome, Plant/*genetics ; *Genome-Wide Association Study ; Genotype ; Immunity, Innate/genetics ; Inbreeding ; *Phenotype ; Polymorphism, Single Nucleotide/genetics
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  • 18
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    The dynamic genome of Hydra (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-03-17
    Description: The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4479502/" 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/PMC4479502/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapman, Jarrod A -- Kirkness, Ewen F -- Simakov, Oleg -- Hampson, Steven E -- Mitros, Therese -- Weinmaier, Thomas -- Rattei, Thomas -- Balasubramanian, Prakash G -- Borman, Jon -- Busam, Dana -- Disbennett, Kathryn -- Pfannkoch, Cynthia -- Sumin, Nadezhda -- Sutton, Granger G -- Viswanathan, Lakshmi Devi -- Walenz, Brian -- Goodstein, David M -- Hellsten, Uffe -- Kawashima, Takeshi -- Prochnik, Simon E -- Putnam, Nicholas H -- Shu, Shengquiang -- Blumberg, Bruce -- Dana, Catherine E -- Gee, Lydia -- Kibler, Dennis F -- Law, Lee -- Lindgens, Dirk -- Martinez, Daniel E -- Peng, Jisong -- Wigge, Philip A -- Bertulat, Bianca -- Guder, Corina -- Nakamura, Yukio -- Ozbek, Suat -- Watanabe, Hiroshi -- Khalturin, Konstantin -- Hemmrich, Georg -- Franke, Andre -- Augustin, Rene -- Fraune, Sebastian -- Hayakawa, Eisuke -- Hayakawa, Shiho -- Hirose, Mamiko -- Hwang, Jung Shan -- Ikeo, Kazuho -- Nishimiya-Fujisawa, Chiemi -- Ogura, Atshushi -- Takahashi, Toshio -- Steinmetz, Patrick R H -- Zhang, Xiaoming -- Aufschnaiter, Roland -- Eder, Marie-Kristin -- Gorny, Anne-Kathrin -- Salvenmoser, Willi -- Heimberg, Alysha M -- Wheeler, Benjamin M -- Peterson, Kevin J -- Bottger, Angelika -- Tischler, Patrick -- Wolf, Alexander -- Gojobori, Takashi -- Remington, Karin A -- Strausberg, Robert L -- Venter, J Craig -- Technau, Ulrich -- Hobmayer, Bert -- Bosch, Thomas C G -- Holstein, Thomas W -- Fujisawa, Toshitaka -- Bode, Hans R -- David, Charles N -- Rokhsar, Daniel S -- Steele, Robert E -- P 21108/Austrian Science Fund FWF/Austria -- R24 RR015088/RR/NCRR NIH HHS/ -- England -- Nature. 2010 Mar 25;464(7288):592-6. doi: 10.1038/nature08830. Epub 2010 Mar 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20228792" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Anthozoa/genetics ; Comamonadaceae/genetics ; DNA Transposable Elements/genetics ; Gene Transfer, Horizontal/genetics ; Genome/*genetics ; Genome, Bacterial/genetics ; Hydra/*genetics/microbiology/ultrastructure ; Molecular Sequence Data ; Neuromuscular Junction/ultrastructure
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  • 19
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    International network of cancer genome projects (2010)
    Nature Publishing Group (NPG)
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    Publication Date: 2010-04-16
    Description: The International Cancer Genome Consortium (ICGC) was launched to coordinate large-scale cancer genome studies in tumours from 50 different cancer types and/or subtypes that are of clinical and societal importance across the globe. Systematic studies of more than 25,000 cancer genomes at the genomic, epigenomic and transcriptomic levels will reveal the repertoire of oncogenic mutations, uncover traces of the mutagenic influences, define clinically relevant subtypes for prognosis and therapeutic management, and enable the development of new cancer therapies.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902243/" 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/PMC2902243/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉International Cancer Genome Consortium -- Hudson, Thomas J -- Anderson, Warwick -- Artez, Axel -- Barker, Anna D -- Bell, Cindy -- Bernabe, Rosa R -- Bhan, M K -- Calvo, Fabien -- Eerola, Iiro -- Gerhard, Daniela S -- Guttmacher, Alan -- Guyer, Mark -- Hemsley, Fiona M -- Jennings, Jennifer L -- Kerr, David -- Klatt, Peter -- Kolar, Patrik -- Kusada, Jun -- Lane, David P -- Laplace, Frank -- Youyong, Lu -- Nettekoven, Gerd -- Ozenberger, Brad -- Peterson, Jane -- Rao, T S -- Remacle, Jacques -- Schafer, Alan J -- Shibata, Tatsuhiro -- Stratton, Michael R -- Vockley, Joseph G -- Watanabe, Koichi -- Yang, Huanming -- Yuen, Matthew M F -- Knoppers, Bartha M -- Bobrow, Martin -- Cambon-Thomsen, Anne -- Dressler, Lynn G -- Dyke, Stephanie O M -- Joly, Yann -- Kato, Kazuto -- Kennedy, Karen L -- Nicolas, Pilar -- Parker, Michael J -- Rial-Sebbag, Emmanuelle -- Romeo-Casabona, Carlos M -- Shaw, Kenna M -- Wallace, Susan -- Wiesner, Georgia L -- Zeps, Nikolajs -- Lichter, Peter -- Biankin, Andrew V -- Chabannon, Christian -- Chin, Lynda -- Clement, Bruno -- de Alava, Enrique -- Degos, Francoise -- Ferguson, Martin L -- Geary, Peter -- Hayes, D Neil -- Johns, Amber L -- Kasprzyk, Arek -- Nakagawa, Hidewaki -- Penny, Robert -- Piris, Miguel A -- Sarin, Rajiv -- Scarpa, Aldo -- van de Vijver, Marc -- Futreal, P Andrew -- Aburatani, Hiroyuki -- Bayes, Monica -- Botwell, David D L -- Campbell, Peter J -- Estivill, Xavier -- Grimmond, Sean M -- Gut, Ivo -- Hirst, Martin -- Lopez-Otin, Carlos -- Majumder, Partha -- Marra, Marco -- McPherson, John D -- Ning, Zemin -- Puente, Xose S -- Ruan, Yijun -- Stunnenberg, Hendrik G -- Swerdlow, Harold -- Velculescu, Victor E -- Wilson, Richard K -- Xue, Hong H -- Yang, Liu -- Spellman, Paul T -- Bader, Gary D -- Boutros, Paul C -- Flicek, Paul -- Getz, Gad -- Guigo, Roderic -- Guo, Guangwu -- Haussler, David -- Heath, Simon -- Hubbard, Tim J -- Jiang, Tao -- Jones, Steven M -- Li, Qibin -- Lopez-Bigas, Nuria -- Luo, Ruibang -- Muthuswamy, Lakshmi -- Ouellette, B F Francis -- Pearson, John V -- Quesada, Victor -- Raphael, Benjamin J -- Sander, Chris -- Speed, Terence P -- Stein, Lincoln D -- Stuart, Joshua M -- Teague, Jon W -- Totoki, Yasushi -- Tsunoda, Tatsuhiko -- Valencia, Alfonso -- Wheeler, David A -- Wu, Honglong -- Zhao, Shancen -- Zhou, Guangyu -- Lathrop, Mark -- Thomas, Gilles -- Yoshida, Teruhiko -- Axton, Myles -- Gunter, Chris -- Miller, Linda J -- Zhang, Junjun -- Haider, Syed A -- Wang, Jianxin -- Yung, Christina K -- Cros, Anthony -- Liang, Yong -- Gnaneshan, Saravanamuttu -- Guberman, Jonathan -- Hsu, Jack -- Chalmers, Don R C -- Hasel, Karl W -- Kaan, Terry S H -- Lowrance, William W -- Masui, Tohru -- Rodriguez, Laura Lyman -- Vergely, Catherine -- Bowtell, David D L -- Cloonan, Nicole -- deFazio, Anna -- Eshleman, James R -- Etemadmoghadam, Dariush -- Gardiner, Brooke B -- Kench, James G -- Sutherland, Robert L -- Tempero, Margaret A -- Waddell, Nicola J -- Wilson, Peter J -- Gallinger, Steve -- Tsao, Ming-Sound -- Shaw, Patricia A -- Petersen, Gloria M -- Mukhopadhyay, Debabrata -- DePinho, Ronald A -- Thayer, Sarah -- Shazand, Kamran -- Beck, Timothy -- Sam, Michelle -- Timms, Lee -- Ballin, Vanessa -- Lu, Youyong -- Ji, Jiafu -- Zhang, Xiuqing -- Chen, Feng -- Hu, Xueda -- Yang, Qi -- Tian, Geng -- Zhang, Lianhai -- Xing, Xiaofang -- Li, Xianghong -- Zhu, Zhenggang -- Yu, Yingyan -- Yu, Jun -- Tost, Jorg -- Brennan, Paul -- Holcatova, Ivana -- Zaridze, David -- Brazma, Alvis -- Egevard, Lars -- Prokhortchouk, Egor -- Banks, Rosamonde Elizabeth -- Uhlen, Mathias -- Viksna, Juris -- Ponten, Fredrik -- Skryabin, Konstantin -- Birney, Ewan -- Borg, Ake -- Borresen-Dale, Anne-Lise -- Caldas, Carlos -- Foekens, John A -- Martin, Sancha -- Reis-Filho, Jorge S -- Richardson, Andrea L -- Sotiriou, Christos -- Thoms, Giles -- van't Veer, Laura -- Birnbaum, Daniel -- Blanche, Helene -- Boucher, Pascal -- Boyault, Sandrine -- Masson-Jacquemier, Jocelyne D -- Pauporte, Iris -- Pivot, Xavier -- Vincent-Salomon, Anne -- Tabone, Eric -- Theillet, Charles -- Treilleux, Isabelle -- Bioulac-Sage, Paulette -- Decaens, Thomas -- Franco, Dominique -- Gut, Marta -- Samuel, Didier -- Zucman-Rossi, Jessica -- Eils, Roland -- Brors, Benedikt -- Korbel, Jan O -- Korshunov, Andrey -- Landgraf, Pablo -- Lehrach, Hans -- Pfister, Stefan -- Radlwimmer, Bernhard -- Reifenberger, Guido -- Taylor, Michael D -- von Kalle, Christof -- Majumder, Partha P -- Pederzoli, Paolo -- Lawlor, Rita A -- Delledonne, Massimo -- Bardelli, Alberto -- Gress, Thomas -- Klimstra, David -- Zamboni, Giuseppe -- Nakamura, Yusuke -- Miyano, Satoru -- Fujimoto, Akihiro -- Campo, Elias -- de Sanjose, Silvia -- Montserrat, Emili -- Gonzalez-Diaz, Marcos -- Jares, Pedro -- Himmelbauer, Heinz -- Bea, Silvia -- Aparicio, Samuel -- Easton, Douglas F -- Collins, Francis S -- Compton, Carolyn C -- Lander, Eric S -- Burke, Wylie -- Green, Anthony R -- Hamilton, Stanley R -- Kallioniemi, Olli P -- Ley, Timothy J -- Liu, Edison T -- Wainwright, Brandon J -- 077198/Wellcome Trust/United Kingdom -- 088340/Wellcome Trust/United Kingdom -- 093867/Wellcome Trust/United Kingdom -- 6613/Cancer Research UK/United Kingdom -- K08 DK071329/DK/NIDDK NIH HHS/ -- K08 DK071329-04/DK/NIDDK NIH HHS/ -- K08 DK071329-05/DK/NIDDK NIH HHS/ -- P01 CA117969/CA/NCI NIH HHS/ -- P01 CA117969-04S1/CA/NCI NIH HHS/ -- P01 CA117969-05/CA/NCI NIH HHS/ -- P50 CA102701/CA/NCI NIH HHS/ -- P50 CA102701-08/CA/NCI NIH HHS/ -- P50 CA127003/CA/NCI NIH HHS/ -- P50 CA127003-04/CA/NCI NIH HHS/ -- P50 CA127003-05/CA/NCI NIH HHS/ -- R01 HG001806-02/HG/NHGRI NIH HHS/ -- England -- Nature. 2010 Apr 15;464(7291):993-8. doi: 10.1038/nature08987.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20393554" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Methylation ; DNA Mutational Analysis/trends ; Databases, Genetic ; Genes, Neoplasm/genetics ; Genetics, Medical/*organization & administration/trends ; Genome, Human/*genetics ; Genomics/*organization & administration/trends ; Humans ; Intellectual Property ; *International Cooperation ; Mutation ; Neoplasms/classification/*genetics/pathology/therapy
    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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  • 20
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    A mechanically stabilized receptor-ligand flex-bond important in the vasculature (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-08-21
    Description: Haemostasis in the arteriolar circulation mediated by von Willebrand factor (VWF) binding to platelets is an example of an adhesive interaction that must withstand strong hydrodynamic forces acting on cells. VWF is a concatenated, multifunctional protein that has binding sites for platelets as well as subendothelial collagen. Binding of the A1 domain in VWF to the glycoprotein Ib alpha subunit (GPIbalpha) on the surface of platelets mediates crosslinking of platelets to one another and the formation of a platelet plug for arterioles. The importance of VWF is illustrated by its mutation in von Willebrand disease, a bleeding diathesis. Here, we describe a novel mechanochemical specialization of the A1-GPIbalpha bond for force-resistance. We have developed a method that enables, for the first time, repeated measurements of the binding and unbinding of a receptor and ligand in a single molecule (ReaLiSM). We demonstrate two states of the receptor-ligand bond, that is, a flex-bond. One state is seen at low force; a second state begins to engage at 10 pN with a approximately 20-fold longer lifetime and greater force resistance. The lifetimes of the two states, how force exponentiates lifetime, and the kinetics of switching between the two states are all measured. For the first time, single-molecule measurements on this system are in agreement with bulk phase measurements. The results have important implications not only for how platelets bound to VWF are able to resist force to plug arterioles, but also how increased flow activates platelet plug formation.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4117310/" 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/PMC4117310/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kim, Jongseong -- Zhang, Cheng-Zhong -- Zhang, Xiaohui -- Springer, Timothy A -- HL-48675/HL/NHLBI NIH HHS/ -- P01 HL048675/HL/NHLBI NIH HHS/ -- England -- Nature. 2010 Aug 19;466(7309):992-5. doi: 10.1038/nature09295.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Immune Disease Institute, Children's Hospital Boston and Department of Pathology, Harvard Medical School, 3 Blackfan Circle, Boston, Massachusetts 02115, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20725043" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Arterioles/cytology/*physiology ; Blood Coagulation/*physiology ; Blood Platelets/chemistry/cytology/*metabolism ; Cell Line ; Hemorheology ; Humans ; Kinetics ; Ligands ; Membrane Glycoproteins/chemistry/*metabolism ; Mice ; Models, Chemical ; Models, Molecular ; Platelet Glycoprotein GPIb-IX Complex ; Protein Binding ; Protein Structure, Tertiary ; Tensile Strength ; von Willebrand Factor/chemistry/*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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