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  • 1
    Electronic Resource
    Electronic Resource
    Structure of acid protease from Endothia parasitica in crosslinked form at 2.45-.ANG. resolution (1979)
    s.l. : American Chemical Society
    Biochemistry 18 (1979), S. 1638-1640 
    Details
    ISSN: 1520-4995
    Source: ACS Legacy Archives
    Topics: Biology , Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/bi00575a041
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    Paper (German National Licenses)
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  • 2
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    Temporal regulation of kin recognition maintains recognition-cue diversity and suppresses cheating (2015)
    Springer Nature
    Details
    Publication Date: 2015-05-30
    Description: Article It is unclear how variation in cues that enable recognition of kin and facilitate cooperation is maintained. Here, the authors show that rare variants of Dictyostelium discoideum are excluded from aggregates when the potential for social cheating is high, but subsequently rejoin the aggregate and produce spores. Nature Communications doi: 10.1038/ncomms8144 Authors: Hsing-I Ho, Gad Shaulsky
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 3
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    The structure of human SFPQ reveals a coiled-coil mediated polymer essential for functional aggregation in gene regulation (2015)
    Oxford University Press
    Details
    Publication Date: 2015-04-21
    Description: SFPQ, (a.k.a. PSF), is a human tumor suppressor protein that regulates many important functions in the cell nucleus including coordination of long non-coding RNA molecules into nuclear bodies. Here we describe the first crystal structures of Splicing Factor Proline and Glutamine Rich (SFPQ), revealing structural similarity to the related PSPC1/NONO heterodimer and a strikingly extended structure (over 265 Å long) formed by an unusual anti-parallel coiled-coil that results in an infinite linear polymer of SFPQ dimers within the crystals. Small-angle X-ray scattering and transmission electron microscopy experiments show that polymerization is reversible in solution and can be templated by DNA. We demonstrate that the ability to polymerize is essential for the cellular functions of SFPQ: disruptive mutation of the coiled-coil interaction motif results in SFPQ mislocalization, reduced formation of nuclear bodies, abrogated molecular interactions and deficient transcriptional regulation. The coiled-coil interaction motif thus provides a molecular explanation for the functional aggregation of SFPQ that directs its role in regulating many aspects of cellular nucleic acid metabolism.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Automatic semantic classification of scientific literature according to the hallmarks of cancer (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-02
    Description: Motivation: The hallmarks of cancer have become highly influential in cancer research. They reduce the complexity of cancer into 10 principles (e.g. resisting cell death and sustaining proliferative signaling) that explain the biological capabilities acquired during the development of human tumors. Since new research depends crucially on existing knowledge, technology for semantic classification of scientific literature according to the hallmarks of cancer could greatly support literature review, knowledge discovery and applications in cancer research. Results: We present the first step toward the development of such technology. We introduce a corpus of 1499 PubMed abstracts annotated according to the scientific evidence they provide for the 10 currently known hallmarks of cancer. We use this corpus to train a system that classifies PubMed literature according to the hallmarks. The system uses supervised machine learning and rich features largely based on biomedical text mining. We report good performance in both intrinsic and extrinsic evaluations, demonstrating both the accuracy of the methodology and its potential in supporting practical cancer research. We discuss how this approach could be developed and applied further in the future. Availability and implementation: The corpus of hallmark-annotated PubMed abstracts and the software for classification are available at: http://www.cl.cam.ac.uk/~sb895/HoC.html . Contact: simon.baker@cl.cam.ac.uk
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Atmospheric pressure route to epitaxial nitrogen-doped trilayer graphene on 4H-SiC (0001) substrate (2014)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2014-12-11
    Description: Large-area graphene film doped with nitrogen is of great interest for a wide spectrum of nanoelectronics applications, such as field effect devices, super capacitors, and fuel cells among many others. Here, we report on the structural and electronic properties of nitrogen doped trilayer graphene on 4H-SiC (0001) grown under atmospheric pressure. The trilayer nature of the growth is evidenced by scanning transmission electron microscopy. X-ray photoelectron spectroscopy shows the incorporation of 1.2% of nitrogen distributed in pyrrolic-N, and pyridinic-N configurations as well as a graphitic-N contribution. This incorporation causes an increase in the D band on the Raman signature indicating that the nitrogen is creating defects. Ultraviolet photoelectron spectroscopy shows a decrease of the work function of 0.3 eV due to the N-type doping of the nitrogen atoms in the carbon lattice and the edge defects. A top gate field effect transistor device has been fabricated and exhibits carrier mobilities up to 1300 cm 2 /V s for holes and 850 cm 2 /V s for electrons at room temperature.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 6
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    Implications of an r mode in XTE J1751-305: mass, radius and spin evolution (2014)
    Oxford University Press
    Details
    Publication Date: 2014-06-19
    Description: Recently Strohmayer and Mahmoodifar presented evidence for a coherent oscillation in the X-ray light curve of the accreting millisecond pulsar XTE J1751–305, using data taken by RXTE during the 2002 outburst of this source. They noted that a possible explanation includes the excitation of a non-radial oscillation mode of the neutron star, either in the form of a g mode or an r mode. The r-mode interpretation has connections with proposed spin-evolution scenarios for systems such as XTE J1751–305. Here, we examine in detail this interesting possible interpretation. Using the ratio of the observed oscillation frequency to the star's spin frequency, we derive an approximate neutron star mass–radius relation which yields reasonable values for the mass over the range of expected stellar radius (as constrained by observations of radius-expansion burst sources). However, we argue that the large mode amplitude suggested by the Strohmayer and Mahmoodifar analysis would inevitably lead to a large spin-down of the star, inconsistent with its observed spin evolution, regardless of whether the r mode itself is in a stable or unstable regime. We therefore conclude that the r-mode interpretation of the observed oscillation is not consistent with our current understanding of neutron star dynamics and must be considered unlikely. Finally we note that, subject to the availability of a sufficiently accurate timing model, a direct gravitational-wave search may be able to confirm or reject an r-mode interpretation unambiguously, should such an event, with a similar inferred mode amplitude, recur during the advanced detector era.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    Fluorinated Graphene as High Performance Dielectric Materials and the Applications for Graphene Nanoelectronics (2014)
    Springer Nature
    Details
    Publication Date: 2014-08-02
    Description: There is broad interest in surface functionalization of 2D materials and its related applications. In this work, we present a novel graphene layer transistor fabricated by introducing fluorinated graphene (fluorographene), one of the thinnest 2D insulator, as the gate dielectric material. For the first time, the dielectric properties of fluorographene, including its dielectric constant, frequency dispersion, breakdown electric field and thermal stability, were comprehensively investigated. We found that fluorographene with extremely thin thickness (5 nm) can sustain high resistance at temperature up to 400°C. The measured breakdown electric field is higher than 10 MV cm−1, which is the heightest value for dielectric materials in this thickness. Moreover, a proof-of-concept methodology, one-step fluorination of 10-layered graphene, is readily to obtain the fluorographene/graphene heterostructures, where the top-gated transistor based on this structure exhibits an average carrier mobility above 760 cm2/Vs, higher than that obtained when SiO2 and GO were used as gate dielectric materials. The demonstrated fluorographene shows excellent dielectric properties with fast and scalable processing, providing a universal applications for the integration of versatile nano-electronic devices. Scientific Reports 4 doi: 10.1038/srep05893
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 8
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    The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-12-14
    Description: The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Dehal, Paramvir -- Satou, Yutaka -- Campbell, Robert K -- Chapman, Jarrod -- Degnan, Bernard -- De Tomaso, Anthony -- Davidson, Brad -- Di Gregorio, Anna -- Gelpke, Maarten -- Goodstein, David M -- Harafuji, Naoe -- Hastings, Kenneth E M -- Ho, Isaac -- Hotta, Kohji -- Huang, Wayne -- Kawashima, Takeshi -- Lemaire, Patrick -- Martinez, Diego -- Meinertzhagen, Ian A -- Necula, Simona -- Nonaka, Masaru -- Putnam, Nik -- Rash, Sam -- Saiga, Hidetoshi -- Satake, Masanobu -- Terry, Astrid -- Yamada, Lixy -- Wang, Hong-Gang -- Awazu, Satoko -- Azumi, Kaoru -- Boore, Jeffrey -- Branno, Margherita -- Chin-Bow, Stephen -- DeSantis, Rosaria -- Doyle, Sharon -- Francino, Pilar -- Keys, David N -- Haga, Shinobu -- Hayashi, Hiroko -- Hino, Kyosuke -- Imai, Kaoru S -- Inaba, Kazuo -- Kano, Shungo -- Kobayashi, Kenji -- Kobayashi, Mari -- Lee, Byung-In -- Makabe, Kazuhiro W -- Manohar, Chitra -- Matassi, Giorgio -- Medina, Monica -- Mochizuki, Yasuaki -- Mount, Steve -- Morishita, Tomomi -- Miura, Sachiko -- Nakayama, Akie -- Nishizaka, Satoko -- Nomoto, Hisayo -- Ohta, Fumiko -- Oishi, Kazuko -- Rigoutsos, Isidore -- Sano, Masako -- Sasaki, Akane -- Sasakura, Yasunori -- Shoguchi, Eiichi -- Shin-i, Tadasu -- Spagnuolo, Antoinetta -- Stainier, Didier -- Suzuki, Miho M -- Tassy, Olivier -- Takatori, Naohito -- Tokuoka, Miki -- Yagi, Kasumi -- Yoshizaki, Fumiko -- Wada, Shuichi -- Zhang, Cindy -- Hyatt, P Douglas -- Larimer, Frank -- Detter, Chris -- Doggett, Norman -- Glavina, Tijana -- Hawkins, Trevor -- Richardson, Paul -- Lucas, Susan -- Kohara, Yuji -- Levine, Michael -- Satoh, Nori -- Rokhsar, Daniel S -- HD-37105/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2002 Dec 13;298(5601):2157-67.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12481130" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Animals ; Apoptosis ; Base Sequence ; Cellulose/metabolism ; Central Nervous System/physiology ; Ciona intestinalis/anatomy & histology/classification/*genetics/physiology ; Computational Biology ; Endocrine System/physiology ; Gene Dosage ; Gene Duplication ; Genes ; Genes, Homeobox ; *Genome ; Heart/embryology/physiology ; Immunity/genetics ; Molecular Sequence Data ; Multigene Family ; Muscle Proteins/genetics ; Organizers, Embryonic/physiology ; Phylogeny ; Polymorphism, Genetic ; Proteins/genetics/physiology ; *Sequence Analysis, DNA ; Sequence Homology, Nucleic Acid ; Species Specificity ; Thyroid Gland/physiology ; Urochordata/genetics ; Vertebrates/anatomy & histology/classification/genetics/physiology
    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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  • 9
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    Ge auto-doping and out-diffusion in InGaP grown on Ge substrate and their effects on the ordering of InGaP (2016)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2016-03-17
    Description: We report on the Ge auto-doping and out-diffusion in InGaP epilayer with Cu-Pt ordering grown on 4-in. Ge substrate. Ge profiles determined from secondary ion mass spectrometry indicate that the Ge out-diffusion depth is within 100 nm. However, the edge of the wafer suffers from stronger Ge gas-phase auto-doping than the center, leading to ordering deterioration in the InGaP epilayer. In the edge, we observed a residual Cu-Pt ordering layer left beneath the surface, suggesting that the ordering deterioration takes place after the deposition rather than during the deposition and In/Ga inter-diffusion enhanced by Ge vapor-phase auto-doping is responsible for the deterioration. We thus propose a di-vacancy diffusion model, in which the amphoteric Ge increases the di-vacancy density, resulting in a Ge density dependent diffusion. In the model, the In/Ga inter-diffusion and Ge out-diffusion are realized by the random hopping of In/Ga host atoms and Ge atoms to di-vacancies, respectively. Simulation based on this model well fits the Ge out-diffusion profiles, suggesting its validity. By comparing the Ge diffusion coefficient obtained from the fitting and the characteristic time constant of ordering deterioration estimated from the residual ordering layer, we found that the hopping rates of Ge and the host atoms are in the same order of magnitude, indicating that di-vacancies are bound in the vicinity of Ge atoms.
    Print ISSN: 0021-8979
    Electronic ISSN: 1089-7550
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 10
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    Self-recognition in social amoebae is mediated by allelic pairs of tiger genes (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-06-28
    Description: Free-living cells of the social amoebae Dictyostelium discoideum can aggregate and develop into multicellular fruiting bodies in which many die altruistically as they become stalk cells that support the surviving spores. Dictyostelium cells exhibit kin discrimination--a potential defense against cheaters, which sporulate without contributing to the stalk. Kin discrimination depends on strain relatedness, and the polymorphic genes tgrB1 and tgrC1 are potential components of that mechanism. Here, we demonstrate a direct role for these genes in kin discrimination. We show that a matching pair of tgrB1 and tgrC1 alleles is necessary and sufficient for attractive self-recognition, which is mediated by differential cell-cell adhesion. We propose that TgrB1 and TgrC1 proteins mediate this adhesion through direct binding. This system is a genetically tractable ancient model of eukaryotic self-recognition.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142563/" 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/PMC3142563/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hirose, Shigenori -- Benabentos, Rocio -- Ho, Hsing-I -- Kuspa, Adam -- Shaulsky, Gad -- F31 GM086131/GM/NIGMS NIH HHS/ -- R01 GM084992/GM/NIGMS NIH HHS/ -- R01 GM084992-03/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2011 Jul 22;333(6041):467-70. doi: 10.1126/science.1203903. Epub 2011 Jun 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21700835" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Amino Acid Sequence ; *Cell Adhesion ; Cell Aggregation ; Dictyostelium/*genetics/*physiology ; Gene Deletion ; *Genes, Protozoan ; Molecular Sequence Data ; Protein Binding ; Protozoan Proteins/*metabolism ; Spores, Protozoan/physiology
    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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