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  • Public Library of Science  (42)
  • Molecular Diversity Preservation International  (28)
  • Oxford University Press  (25)
  • American Association for the Advancement of Science (AAAS)
  • 1
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    Protein-mediated protection as the predominant mechanism for defining processed mRNA termini in land plant chloroplasts (2012)
    Oxford University Press
    Details
    Publication Date: 2012-04-15
    Description: Most chloroplast mRNAs are processed from larger precursors. Several mechanisms have been proposed to mediate these processing events, including site-specific cleavage and the stalling of exonucleases by RNA structures. A protein barrier mechanism was proposed based on analysis of the pentatricopeptide repeat (PPR) protein PPR10: PPR10 binds two intercistronic regions and impedes 5'- and 3'-exonucleases, resulting in processed RNAs with PPR10 bound at the 5'- or 3'-end. In this study, we provide evidence that protein barriers are the predominant means for defining processed mRNA termini in chloroplasts. First, we map additional RNA termini whose arrangement suggests biogenesis via a PPR10-like mechanism. Second, we show that the PPR protein HCF152 binds to the immediate 5'- or 3'-termini of transcripts that require HCF152 for their accumulation, providing evidence that HCF152 defines RNA termini by blocking exonucleases. Finally, we build on the observation that the PPR10 and HCF152 binding sites accumulate as small chloroplast RNAs to infer binding sites of other PPR proteins. We show that most processed mRNA termini are represented by small RNAs whose sequences are highly conserved. We suggest that each such small RNA is the footprint of a PPR-like protein that protects the adjacent RNA from degradation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Frequent Gain and Loss of Intronic Splicing Regulatory Elements during the Evolution of Vertebrates (2012)
    Oxford University Press
    Details
    Publication Date: 2012-07-18
    Description: Splicing regulatory elements (SREs) are sequences bound by proteins that influence splicing of nearby splice sites. Constitutively spliced introns have evolved to utilize many different splicing factors. The evolutionary processes that influenced which splicing factors are used for splicing of individual introns are generally unclear. We demonstrate that in the lineage that gave rise to mammals, many introns lost U-rich sequences and gained G-rich sequences, both of which resemble known SREs. The apparent conversion of U-rich to G-rich SREs suggests that the associated splicing factors are functionally equivalent. In support of this we demonstrated that U-rich and G-rich SREs are both capable of promoting splicing of an SRE-dependent splicing reporter. Furthermore, we demonstrate, using the heterologous MS2 tethering system (bacterial MS2 coat fusion-protein and its RNA stem-loop binding site), that both the U-rich SRE-binding protein (TIA1) and the G-rich SRE-binding protein (HNRNPF) can promote splicing of the same intron. We also observed that gain of G-rich SREs is significantly associated with G/C-rich genomic isochores, suggesting that gain or loss of SREs was driven by the same processes that ultimately resulted in the formation of mammalian genomic isochores. We propose the following model for the gain and loss of mammalian SREs. Ancestral U-rich SREs located in genomic regions that were experiencing high rates of A/T to G/C conversion would have suffered frequent deleterious mutations. However, this same process resulted in increased formation of functionally equivalent G-rich SREs, and acquisition of new G-rich SREs decreased purifying selection on the U-rich SREs, which were then free to decay.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Seasonal carbohydrate dynamics and growth in Douglas-fir trees experiencing chronic, fungal-mediated reduction in functional leaf area (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-29
    Description: Stored non-structural carbohydrates (NSCs) could play an important role in tree survival in the face of a changing climate and associated stress-related mortality. We explored the effects of the stomata-blocking and defoliating fungal disease called Swiss needle cast on Douglas-fir carbohydrate reserves and growth to evaluate the extent to which NSCs can be mobilized under natural conditions of low water stress and restricted carbon supply in relation to potential demands for growth. We analyzed the concentrations of starch, sucrose, glucose and fructose in foliage, twig wood and trunk sapwood of 15 co-occurring Douglas-fir trees expressing a gradient of Swiss needle cast symptom severity quantified as previous-year functional foliage mass. Growth (mean basal area increment, BAI) decreased by ~80% and trunk NSC concentration decreased by 60% with decreasing functional foliage mass. The ratio of relative changes in NSC concentration and BAI, an index of the relative priority of storage versus growth, more than doubled with increasing disease severity. In contrast, twig and foliage NSC concentrations remained nearly constant with decreasing functional foliage mass. These results suggest that under disease-induced reductions in carbon supply, Douglas-fir trees retain NSCs (either actively or due to sequestration) at the expense of trunk radial growth. The crown retains the highest concentrations of NSC, presumably to maintain foliage growth and shoot extension in the spring, partially compensating for rapid foliage loss in the summer and fall.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 4
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    Fatty acid biosynthesis redirected to medium chains in transgenic oilseed plants (1992)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1992-07-03
    Description: Medium-chain fatty acids (FAs), found in storage lipids of certain plants, are an important renewable resource. Seeds of undomesticated California bay accumulate laurate (12:0), and a 12:0-acyl-carrier protein thioesterase (BTE) has been purified from this tissue. Sequencing of BTE enabled the cloning of a complementary DNA coding for a plastid-targeted preprotein. Expression of the complementary DNA in the seeds of Arabidopsis thaliana resulted in BTE activity, and medium chains accumulated at the expense of long-chain (greater than or equal to 16) FAs. Laurate became the most abundant FA species and was deposited in the storage triacylglycerols. These results demonstrate a mechanism for medium-chain FA synthesis in plants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Voelker, T A -- Worrell, A C -- Anderson, L -- Bleibaum, J -- Fan, C -- Hawkins, D J -- Radke, S E -- Davies, H M -- New York, N.Y. -- Science. 1992 Jul 3;257(5066):72-4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Calgene, Inc., Davis, CA 95616.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1621095" target="_blank"〉PubMed〈/a〉
    Keywords: Acetyltransferases/genetics/*metabolism ; Acyl-Carrier Protein S-Acetyltransferase ; Amino Acid Sequence ; DNA/genetics ; Fatty Acids/*biosynthesis/isolation & purification ; Genetic Engineering ; Lauric Acids/*metabolism ; Molecular Sequence Data ; Plants/genetics/*metabolism ; Plants, Genetically Modified ; Plasmids ; Seeds/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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  • 5
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    Widespread production of extracellular superoxide by heterotrophic bacteria (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-05-04
    Description: Superoxide and other reactive oxygen species (ROS) originate from several natural sources and profoundly influence numerous elemental cycles, including carbon and trace metals. In the deep ocean, the permanent absence of light precludes currently known ROS sources, yet ROS production mysteriously occurs. Here, we show that taxonomically and ecologically diverse heterotrophic bacteria from aquatic and terrestrial environments are a vast, unrecognized, and light-independent source of superoxide, and perhaps other ROS derived from superoxide. Superoxide production by a model bacterium within the ubiquitous Roseobacter clade involves an extracellular oxidoreductase that is stimulated by the reduced form of nicotinamide adenine dinucleotide (NADH), suggesting a surprising homology with eukaryotic organisms. The consequences of ROS cycling in immense aphotic zones representing key sites of nutrient regeneration and carbon export must now be considered, including potential control of carbon remineralization and metal bioavailability.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Diaz, Julia M -- Hansel, Colleen M -- Voelker, Bettina M -- Mendes, Chantal M -- Andeer, Peter F -- Zhang, Tong -- New York, N.Y. -- Science. 2013 Jun 7;340(6137):1223-6. doi: 10.1126/science.1237331. Epub 2013 May 2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23641059" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Carbon Cycle ; *Heterotrophic Processes ; Mercury/*metabolism ; Molecular Sequence Data ; NAD/metabolism ; Oxidoreductases/metabolism ; Phylogeny ; Roseobacter/classification/*metabolism ; Superoxides/*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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  • 6
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    Comment on "Detection, stimulation, and inhibition of neuronal signals with high-density nanowire transistor arrays" (2009)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2009-03-17
    Description: Patolsky et al. (Reports, 25 August 2006, p. 1100) used silicon nanowires to record action potentials in rat neuronal axons and found increases in conductance of about 85 nanosiemens. We point out that the data correspond to voltage changes of about -85 millivolts on the nanowire and that conceivable mechanisms of axon-nanowire interaction lead to signals that are opposite in sign or smaller by orders of magnitude.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fromherz, Peter -- Voelker, Moritz -- New York, N.Y. -- Science. 2009 Mar 13;323(5920):1429; author reply 1429. doi: 10.1126/science.1155416.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Membrane and Neurophysics, Max Planck Institute for Biochemistry, D82152 Martinsried/Munich, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19286538" target="_blank"〉PubMed〈/a〉
    Keywords: *Action Potentials ; Animals ; Axons/*physiology ; Electric Conductivity ; Electric Stimulation ; Ion Channel Gating ; *Nanowires ; Neural Inhibition ; Neurons/*physiology ; Rats ; Semiconductors ; Silicon ; Sodium/metabolism ; Static Electricity ; Transistors, Electronic
    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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    Paleoceanography. Onset of Mediterranean outflow into the North Atlantic (2014)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2014-06-14
    Description: Sediments cored along the southwestern Iberian margin during Integrated Ocean Drilling Program Expedition 339 provide constraints on Mediterranean Outflow Water (MOW) circulation patterns from the Pliocene epoch to the present day. After the Strait of Gibraltar opened (5.33 million years ago), a limited volume of MOW entered the Atlantic. Depositional hiatuses indicate erosion by bottom currents related to higher volumes of MOW circulating into the North Atlantic, beginning in the late Pliocene. The hiatuses coincide with regional tectonic events and changes in global thermohaline circulation (THC). This suggests that MOW influenced Atlantic Meridional Overturning Circulation (AMOC), THC, and climatic shifts by contributing a component of warm, saline water to northern latitudes while in turn being influenced by plate tectonics.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hernandez-Molina, F Javier -- Stow, Dorrik A V -- Alvarez-Zarikian, Carlos A -- Acton, Gary -- Bahr, Andre -- Balestra, Barbara -- Ducassou, Emmanuelle -- Flood, Roger -- Flores, Jose-Abel -- Furota, Satoshi -- Grunert, Patrick -- Hodell, David -- Jimenez-Espejo, Francisco -- Kim, Jin Kyoung -- Krissek, Lawrence -- Kuroda, Junichiro -- Li, Baohua -- Llave, Estefania -- Lofi, Johanna -- Lourens, Lucas -- Miller, Madeline -- Nanayama, Futoshi -- Nishida, Naohisa -- Richter, Carl -- Roque, Cristina -- Pereira, Helder -- Sanchez Goni, Maria Fernanda -- Sierro, Francisco J -- Singh, Arun Deo -- Sloss, Craig -- Takashimizu, Yasuhiro -- Tzanova, Alexandrina -- Voelker, Antje -- Williams, Trevor -- Xuan, Chuang -- New York, N.Y. -- Science. 2014 Jun 13;344(6189):1244-50. doi: 10.1126/science.1251306.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Earth Sciences, Royal Holloway, University of London, Egham, Surrey TW20 0EX, UK. javier.hernandez-molina@rhul.ac.uk. ; Institute of Petroleum Engineering, Heriot-Watt University, Edinburgh EH14 4AS, Scotland, UK. ; International Ocean Discovery Program, Department of Oceanography, Texas A&M University, College Station, TX 77845, USA. ; Department of Geography and Geology, Sam Houston State University, Huntsville, TX 77341, USA. ; Institute of Geosciences, University of Frankfurt, 60438 Frankfurt, Germany. ; Institute of Marine Sciences, University of California, Santa Cruz, CA 95064, USA. ; EPOC, Universite de Bordeaux, 33615 Pessac Cedex, France. ; School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794, USA. ; Departamento de Geologia, Universidad de Salamanca, 3008 Salamanca, Spain. ; Department of Natural History Sciences, Hokkaido University, N10W8, Kita-ku, Sapporo 060-0810, Japan. ; Institute for Earth Sciences, University of Graz, A-8010 Graz, Austria. ; Godwin Laboratory for Palaeoclimate Research, University of Cambridge, Cambridge CB2 3EQ, UK. ; Department of Biogeochemistry, JAMSTEC, 237-0061 Yokosuka, Japan. ; Korea Institute of Ocean Science & Technology, Ansan 426-744, Korea. ; School of Earth Sciences, Ohio State University, Columbus, OH 43210, USA. ; Institute for Frontier Research on Earth Evolution (IFREE), JAMSTEC, 2-15 Natsushima-Cho, Yokosuka-city, Kanagawa 237-0061, Japan. ; Department of Micropalaeontology, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, P.R. China. ; Instituto Geologico y Minero de Espana, Rios Rosas 23, 28003 Madrid, Spain. ; Geosciences Montpellier, Universite Montpellier II, 34090 Montpellier, France, and Department of Geology, University of Leicester, Leicester LE1 7RH, UK. ; Institute of Earth Sciences, Utrecht University, 3584 CD Utrecht, Netherlands. ; Department of Mechanical Engineering, California Institute of Technology, Pasadena, CA 91125, USA. ; Institute of Geology and Geoinformation, Geological Survey of Japan (AIST), Ibaraki 305-8567, Japan. ; School of Geosciences, University of Louisiana, Lafayette, LA 70504, USA. ; Divisao de Geologia e Georecursos Marinhos, IPMA, 1749-077 Lisboa, Portugal. ; Grupo de Biologia e Geologia, Escola Secundaria de Loule, 8100-740 Loule, Portugal. ; Ecole Pratique des Hautes Etudes, EPOC, Universite de Bordeaux, 33615 Pessac, France. ; Department of Geology, Banaras Hindu University, Varanasi 221005, India. ; School of Earth, Environmental and Biological Sciences, Queensland University of Technology, Brisbane, Queensland 4001, Australia. ; Department of Geology, Faculty of Education, Niigata University, Niigata 950-2181, Japan. ; Department of Geological Sciences, Brown University, Providence, RI 02912, USA. ; Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY 10964, USA. ; Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Waterfront Campus, Southampton SO14 3ZH, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24926012" target="_blank"〉PubMed〈/a〉
    Keywords: Atlantic Ocean ; *Climate Change ; Mediterranean Sea ; Paleontology ; *Seawater ; *Water Movements
    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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    Impacts of dwarf mistletoe on the physiology of host Tsuga heterophylla trees as recorded in tree-ring C and O stable isotopes (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-08
    Description: Dwarf mistletoes, obligate, parasitic plants with diminutive aerial shoots, have long-term effects on host tree water relations, hydraulic architecture and photosynthetic gas exchange and can eventually induce tree death. To investigate the long-term (1886–2010) impacts of dwarf mistletoe on the growth and gas exchange characteristics of host western hemlock, we compared the diameter growth and tree-ring cellulose stable carbon (C) and oxygen (O) isotope ratios ( 13 C cell , 18 O cell ) of heavily infected and uninfected trees. The relative basal area growth of infected trees was significantly greater than that of uninfected trees in 1886–90, but declined more rapidly in infected than uninfected trees through time and became significantly lower in infected than uninfected trees in 2006–10. Infected trees had significantly lower 13 C cell and 18 O cell than uninfected trees. Differences in 18 O cell between infected and uninfected trees were unexpected given that stomatal conductance and environmental variables that were expected to influence the 18 O values of leaf water were similar for both groups. However, estimates of mesophyll conductance ( g m ) were significantly lower and estimates of effective path length for water movement ( L ) were significantly higher in leaves of infected trees, consistent with their lower values of 18 O cell . This study reconstructs the long-term physiological responses of western hemlock to dwarf mistletoe infection. The long-term diameter growth and 13 C cell trajectories suggested that infected trees were growing faster than uninfected trees prior to becoming infected and subsequently declined in growth and leaf-level photosynthetic capacity compared with uninfected trees as the dwarf mistletoe infection became severe. This study further points to limitations of the dual-isotope approach for identifying sources of variation in 13 C cell and indicates that changes in leaf internal properties such as g m and L that affect 18 O cell must be considered.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 9
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    Microstructure, Texture, and Strength Development during High-Pressure Torsion of CrMnFeCoNi High-Entropy Alloy (2020)
    Molecular Diversity Preservation International
    Details
    Publication Date: 2020-04-24
    Description: The equiatomic face-centered cubic high-entropy alloy CrMnFeCoNi was severely deformed at room and liquid nitrogen temperature by high-pressure torsion up to shear strains of about 170. Its microstructure was analyzed by X-ray line profile analysis and transmission electron microscopy and its texture by X-ray microdiffraction. Microhardness measurements, after severe plastic deformation, were done at room temperature. It is shown that at a shear strain of about 20, a steady state grain size of 24 nm, and a dislocation density of the order of 1016 m−2 is reached. The dislocations are mainly screw-type with low dipole character. Mechanical twinning at room temperature is replaced by a martensitic phase transformation at 77 K. The texture developed at room temperature is typical for sheared face-centered cubic nanocrystalline metals, but it is extremely weak and becomes almost random after high-pressure torsion at 77 K. The strength of the nanocrystalline material produced by high-pressure torsion at 77 K is lower than that produced at room temperature. The results are discussed in terms of different mechanisms of deformation, including dislocation generation and propagation, twinning, grain boundary sliding, and phase transformation.
    Electronic ISSN: 2073-4352
    Topics: Physics
    Published by Molecular Diversity Preservation International
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  • 10
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    Adaptive genetic diversity and evidence of population genetic structure in the endangered Sierra Madre Sparrow (Xenospiza baileyi) (2020)
    Public Library of Science
    Details
    Publication Date: 2020-04-30
    Electronic ISSN: 1932-6203
    Topics: Medicine , Natural Sciences in General
    Published by Public Library of Science
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