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  • 1
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    The Footprint of Polygenic Adaptation on Stress-Responsive Cis-Regulatory Divergence in the Arabidopsis Genus (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-19
    Description: Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis -acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, we identify cis -acting modifications with the help of an interspecific crossing scheme designed to distinguish modifications derived in each of the two sister species, Arabidopsis halleri and A. lyrata . Allele-specific expression levels were assessed in three environmental conditions chosen to reflect interspecific ecological differences: cold exposure, dehydration, and standard conditions. The functions described by Gene Ontology categories enriched in cis -acting mutations are markedly different in A. halleri and A. lyrata , suggesting that polygenic adaptation reshaped distinct polygenic molecular functions in the two species. In the A. halleri lineage, an excess of cis -acting changes affecting metal transport and homeostasis was observed, confirming that the well-known heavy metal tolerance of this species is the result of polygenic selection. In A. lyrata , we find a marked excess of cis -acting changes among genes showing a transcriptional response to cold stress in the outgroup species A. thaliana . The adaptive relevance of these changes will have to be validated. We finally observed that polygenic molecular functions enriched in derived cis -acting changes are more constrained at the amino acid level. Using the distribution of cis -acting variation to tackle the polygenic basis of adaptation thus reveals the contribution of mutations of small effect to Darwinian adaptation.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Three-dimensional non-linear magnetohydrodynamic modeling of massive gas injection triggered disruptions in JET (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-06-25
    Description: JOREK 3D non-linear MHD simulations of a D 2 Massive Gas Injection (MGI) triggered disruption in JET are presented and compared in detail to experimental data. The MGI creates an overdensity that rapidly expands in the direction parallel to the magnetic field. It also causes the growth of magnetic islands ( m / n = 2 / 1 and 3/2 mainly) and seeds the 1/1 internal kink mode. O-points of all island chains (including 1/1) are located in front of the MGI, consistently with experimental observations. A burst of MHD activity and a peak in plasma current take place at the same time as in the experiment. However, the magnitude of these two effects is much smaller than in the experiment. The simulated radiation is also much below the experimental level. As a consequence, the thermal quench is not fully reproduced. Directions for progress are identified. Radiation from impurities is a good candidate.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 3
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    Electronic band dispersion determination in azimuthally disordered transition-metal dichalcogenide monolayers (2019)
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    Publication Date: 2019
    Electronic ISSN: 2399-3650
    Topics: Physics
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  • 4
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    Engineering the provitamin A (beta-carotene) biosynthetic pathway into (carotenoid-free) rice endosperm (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-01-15
    Description: Rice (Oryza sativa), a major staple food, is usually milled to remove the oil-rich aleurone layer that turns rancid upon storage, especially in tropical areas. The remaining edible part of rice grains, the endosperm, lacks several essential nutrients, such as provitamin A. Thus, predominant rice consumption promotes vitamin A deficiency, a serious public health problem in at least 26 countries, including highly populated areas of Asia, Africa, and Latin America. Recombinant DNA technology was used to improve its nutritional value in this respect. A combination of transgenes enabled biosynthesis of provitamin A in the endosperm.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Ye, X -- Al-Babili, S -- Kloti, A -- Zhang, J -- Lucca, P -- Beyer, P -- Potrykus, I -- New York, N.Y. -- Science. 2000 Jan 14;287(5451):303-5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute for Plant Sciences, Swiss Federal Institute of Technology, CH-8092 Zurich, Switzerland. University of Freiburg, Center for Applied Biosciences, D-79104 Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10634784" target="_blank"〉PubMed〈/a〉
    Keywords: Alkyl and Aryl Transferases/genetics ; Carotenoids/metabolism ; Chromatography, High Pressure Liquid ; Crops, Agricultural/genetics/metabolism ; Genes, Plant ; *Genetic Engineering ; Genetic Vectors ; Geranylgeranyl-Diphosphate Geranylgeranyltransferase ; Intramolecular Lyases/genetics ; Oryza/enzymology/*genetics/*metabolism ; Oxidoreductases/genetics ; Plants, Genetically Modified ; Plasmids ; Seeds/enzymology/*metabolism ; Transformation, Genetic ; Transgenes ; beta Carotene/*biosynthesis
    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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  • 5
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    The structure of a retinal-forming carotenoid oxygenase (2005)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2005-04-12
    Description: Enzymes that produce retinal and related apocarotenoids constitute a sequence- and thus structure-related family, a member of which was analyzed by x-ray diffraction. This member is an oxygenase and contains an Fe2+-4-His arrangement at the axis of a seven-bladed beta-propeller chain fold covered by a dome formed by six large loops. The Fe2+ is accessible through a long nonpolar tunnel that holds a carotenoid derivative in one of the crystals. On binding, three consecutive double bonds of this carotenoid changed from a straight all-trans to a cranked cis-trans-cis conformation. The remaining trans bond is located at the dioxygen-ligated Fe2+ and cleaved by oxygen.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kloer, Daniel P -- Ruch, Sandra -- Al-Babili, Salim -- Beyer, Peter -- Schulz, Georg E -- R01 EY020551/EY/NEI NIH HHS/ -- New York, N.Y. -- Science. 2005 Apr 8;308(5719):267-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Organische Chemie und Biochemie, Albert-Ludwigs-Universitat, Albertstrasse 21, 79104 Freiburg im Breisgau, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/15821095" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Cloning, Molecular ; Crystallography, X-Ray ; Escherichia coli ; Humans ; Molecular Sequence Data ; Oxygenases/*chemistry ; Protein Conformation ; Recombinant Proteins ; Retinaldehyde/*chemistry ; Synechocystis/*enzymology/genetics
    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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  • 6
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    Coagulation factor X activates innate immunity to human species C adenovirus (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-09-29
    Description: Although coagulation factors play a role in host defense for "living fossils" such as horseshoe crabs, the role of the coagulation system in immunity in higher organisms remains unclear. We modeled the interface of human species C adenovirus (HAdv) interaction with coagulation factor X (FX) and introduced a mutation that abrogated formation of the HAdv-FX complex. In vivo genome-wide transcriptional profiling revealed that FX-binding-ablated virus failed to activate a distinct network of nuclear factor kappaB-dependent early-response genes that are activated by HAdv-FX complex downstream of TLR4/MyD88/TRIF/TRAF6 signaling. Our study implicates host factor "decoration" of the virus as a mechanism to trigger an innate immune sensor that responds to a misplacement of coagulation FX from the blood into intracellular macrophage compartments upon virus entry into the cell.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4762479/" 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/PMC4762479/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Doronin, Konstantin -- Flatt, Justin W -- Di Paolo, Nelson C -- Khare, Reeti -- Kalyuzhniy, Oleksandr -- Acchione, Mauro -- Sumida, John P -- Ohto, Umeharu -- Shimizu, Toshiyuki -- Akashi-Takamura, Sachiko -- Miyake, Kensuke -- MacDonald, James W -- Bammler, Theo K -- Beyer, Richard P -- Farin, Frederico M -- Stewart, Phoebe L -- Shayakhmetov, Dmitry M -- AI065429/AI/NIAID NIH HHS/ -- CA141439/CA/NCI NIH HHS/ -- P30ES07033/ES/NIEHS NIH HHS/ -- R01 AI065429/AI/NIAID NIH HHS/ -- R01 CA141439/CA/NCI NIH HHS/ -- New York, N.Y. -- Science. 2012 Nov 9;338(6108):795-8. doi: 10.1126/science.1226625. Epub 2012 Sep 27.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Medicine, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23019612" target="_blank"〉PubMed〈/a〉
    Keywords: Adenoviridae Infections/*immunology/metabolism/virology ; Adenoviruses, Human/genetics/*immunology/*metabolism ; Animals ; CHO Cells ; Capsid Proteins/chemistry/genetics/metabolism ; Cell Line, Tumor ; Cricetinae ; Cricetulus ; Cryoelectron Microscopy ; Cytokines/metabolism ; Factor X/chemistry/*metabolism ; Gene Expression Profiling ; Gene Expression Regulation ; Hepatocytes/virology ; Humans ; *Immunity, Innate ; Macrophages/metabolism/virology ; Mice ; Mice, Inbred C57BL ; Molecular Dynamics Simulation ; Mutation ; NF-kappa B/metabolism ; Signal Transduction ; Virus Internalization
    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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  • 7
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    The path from beta-carotene to carlactone, a strigolactone-like plant hormone (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-03-17
    Description: Strigolactones, phytohormones with diverse signaling activities, have a common structure consisting of two lactones connected by an enol-ether bridge. Strigolactones derive from carotenoids via a pathway involving the carotenoid cleavage dioxygenases 7 and 8 (CCD7 and CCD8) and the iron-binding protein D27. We show that D27 is a beta-carotene isomerase that converts all-trans-beta-carotene into 9-cis-beta-carotene, which is cleaved by CCD7 into a 9-cis-configured aldehyde. CCD8 incorporates three oxygens into 9-cis-beta-apo-10'-carotenal and performs molecular rearrangement, linking carotenoids with strigolactones and producing carlactone, a compound with strigolactone-like biological activities. Knowledge of the structure of carlactone will be crucial for understanding the biology of strigolactones and may have applications in combating parasitic weeds.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Alder, Adrian -- Jamil, Muhammad -- Marzorati, Mattia -- Bruno, Mark -- Vermathen, Martina -- Bigler, Peter -- Ghisla, Sandro -- Bouwmeester, Harro -- Beyer, Peter -- Al-Babili, Salim -- New York, N.Y. -- Science. 2012 Mar 16;335(6074):1348-51. doi: 10.1126/science.1218094.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Faculty of Biology, University of Freiburg, Freiburg, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22422982" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics/*metabolism ; Arabidopsis Proteins/genetics/metabolism ; Biosynthetic Pathways ; Carotenoids/chemistry/metabolism ; Dioxygenases/genetics/metabolism ; Germination ; Isomerases/genetics/metabolism ; Lactones/chemistry/*metabolism/pharmacology ; Molecular Structure ; Mutation ; Oryza/genetics/*metabolism ; Peas/genetics/*metabolism ; Phenotype ; Plant Growth Regulators/*biosynthesis/chemistry ; Plant Proteins/genetics/metabolism ; Stereoisomerism ; Striga/growth & development ; beta Carotene/*metabolism
    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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    L-H transition dynamics in fluid turbulence simulations with neoclassical force balance (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-07-24
    Description: Spontaneous transport barrier generation at the edge of a magnetically confined plasma is reproduced in flux-driven three-dimensional fluid simulations of electrostatic turbulence. Here, the role on the radial electric field of collisional friction between trapped and passing particles is shown to be the key ingredient. Especially, accounting for the self-consistent and precise dependence of the friction term on the actual plasma temperature allows for the triggering of a transport barrier, provided that the input power exceeds some threshold. In addition, the barrier is found to experience quasi-periodic relaxation events, reminiscent of edge localised modes. These results put forward a possible key player, namely, neoclassical physics via radial force balance, for the low- to high-confinement regime transition observed in most of controlled fusion devices.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 9
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    Convective radial energy flux due to resonant magnetic perturbations and magnetic curvature at the tokamak plasma edge (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-08-02
    Description: With the resonant magnetic perturbations (RMPs) consolidating as an important tool to control the transport barrier relaxation, the mechanism on how they work is still a subject to be clearly understood. In this work, we investigate the equilibrium states in the presence of RMPs for a reduced MHD model using 3D electromagnetic fluid numerical code with a single harmonic RMP (single magnetic island chain) and multiple harmonics RMPs in cylindrical and toroidal geometry. Two different equilibrium states were found in the presence of the RMPs with different characteristics for each of the geometries used. For the cylindrical geometry in the presence of a single RMP, the equilibrium state is characterized by a strong convective radial thermal flux and the generation of a mean poloidal velocity shear. In contrast, for toroidal geometry, the thermal flux is dominated by the magnetic flutter. For multiple RMPs, the high amplitude of the convective flux and poloidal rotation are basically the same in cylindrical geometry, but in toroidal geometry the convective thermal flux and the poloidal rotation appear only with the islands overlapping of the linear coupling between neighbouring poloidal wavenumbers m , m – 1, and m  + 1.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 10
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    Copper-Induced Deregulation of microRNA Expression in the Zebrafish Olfactory System (2013)
    American Chemical Society (ACS)
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    Publication Date: 2013-06-21
    Description: Environmental Science & Technology DOI: 10.1021/es400615q
    Print ISSN: 0013-936X
    Electronic ISSN: 1520-5851
    Topics: Chemistry and Pharmacology , Energy, Environment Protection, Nuclear Power Engineering
    Published by American Chemical Society (ACS)
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