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  • 1
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    Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-20
    Description: Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience to these factors has been suggested to be due to enhanced damage prevention and repair mechanisms, as well as highly efficient antioxidant protection systems. Here, using mutation-accumulation experiments, we find that the GC-rich Deinococcus radiodurans has an overall background genomic mutation rate similar to that of E. coli , but differs in mutation spectrum, with the A/T to G/C mutation rate (based on a total count of 88 A:T-〉G:C transitions and 82 A:T-〉C:G transversions) per site per generation higher than that in the other direction (based on a total count of 157 G:C-〉A:T transitions and 33 G:C-〉T:A transversions). We propose that this unique spectrum is shaped mainly by the abundant uracil DNA glycosylases reducing G:C-〉A:T transitions, adenine methylation elevating A:T-〉C:G transversions, and absence of cytosine methylation decreasing G:C-〉A:T transitions. As opposed to the greater than 100 x elevation of the mutation rate in MMR – (DNA Mismatch Repair deficient) strains of most other organisms, MMR – D. radiodurans only exhibits a 4-fold elevation, raising the possibility that other DNA repair mechanisms compensate for a relatively low-efficiency DNA MMR pathway. As D. radiodurans has plentiful insertion sequence (IS) elements in the genome and the activities of IS elements are rarely directly explored, we also estimated the insertion (transposition) rate of the IS elements to be 2.50 x 10 –3 per genome per generation in the wild-type strain; knocking out MMR did not elevate the IS element insertion rate in this organism.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Wavelet Analysis of Polar Vortex Variability over the 20th Century (2015)
    Wiley
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    Publication Date: 2015-12-27
    Description: Recent increases in extreme weather events in the Northern Hemisphere have been linked to amplified planetary waves [Screen and Simmons, 2014]. Changes in planetary wave properties are linked to changes in climate; hence, finding a mechanism that links the planetary wave variability under climatic forcing and mid-latitude blocking events has engendered a great deal of interest. In this study, wavelet analysis is applied to time series of planetary wave phase speeds at high latitudes as a first step to assessing the potential for identifying these mechanisms in the observational record. A circumpolar multiannual cycle increase is found but signals also demonstrate a complex westward propagation pattern with periods of intense wave variability. Significant correlations between wavelet power at all timescales and albedo, snow cover, atmospheric ozone levels, and surface air temperature are demonstrated.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    Linkages between Arctic summer circulation regimes and regional sea ice anomalies (2016)
    Wiley
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    Publication Date: 2016-07-03
    Description: The downward trend in overall Arctic summer sea ice extent has been substantial, particularly in the last few decades. Departures in ice extent from year to year can be very large, however, in part due to the high variability in summer atmospheric circulation patterns. Anomalies in the Pacific sector ice cover can be partially compensated by anomalies of opposite sign in the Atlantic sector. An assessment of linkages between summer atmospheric patterns and sectoral anomalies in the area of maximum open water north of 70°N demonstrates that there is asymmetry in the mechanisms. Years with low ice extent and high open water fraction are uniformly associated with positive temperature anomalies and southerly flow in both the Atlantic and Pacific sectors. However, years with high extent and low open water fraction in both sectors reveal two dominant mechanisms. Some years with anomalously low maximum open water fraction are associated with negative temperature anomalies and southerly transport – a cool summer pattern that allows ice to persist over larger areas. However, other low open water years are characterized by an “ice factory” mechanism, whereby – even when melting – ice cover is continually replenished by advection from the north.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    Recessive NEK9 mutation causes a lethal skeletal dysplasia with evidence of cell cycle and ciliary defects (2016)
    Oxford University Press
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    Publication Date: 2016-07-06
    Description: Skeletal dysplasias are a clinically and genetically heterogeneous group of bone and cartilage disorders. Whilst 〉450 skeletal dysplasias have been reported, 30% are genetically uncharacterized. We report two Irish Traveller families with a previously undescribed lethal skeletal dysplasia characterized by fetal akinesia, shortening of all long bones, multiple contractures, rib anomalies, thoracic dysplasia, pulmonary hypoplasia and protruding abdomen. Single nucleotide polymorphism homozygosity mapping and whole exome sequencing identified a novel homozygous stop-gain mutation in NEK9 (c.1489C〉T; p.Arg497*) as the cause of this disorder. NEK9 encodes a never in mitosis gene A-related kinase involved in regulating spindle organization, chromosome alignment, cytokinesis and cell cycle progression. This is the first disorder to be associated with NEK9 in humans. Analysis of NEK9 protein expression and localization in patient fibroblasts showed complete loss of full-length NEK9 (107 kDa). Functional characterization of patient fibroblasts showed a significant reduction in cell proliferation and a delay in cell cycle progression. We also provide evidence to support possible ciliary associations for NEK9. Firstly, patient fibroblasts displayed a significant reduction in cilia number and length. Secondly, we show that the NEK9 orthologue in Caenorhabditis elegans , nekl-1 , is almost exclusively expressed in a subset of ciliated cells, a strong indicator of cilia-related functions. In summary, we report the clinical and molecular characterization of a lethal skeletal dysplasia caused by NEK9 mutation and suggest that this disorder may represent a novel ciliopathy.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Accelerated quantum dynamics (2015)
    American Physical Society (APS)
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    Publication Date: 2015-07-14
    Description: Author(s): Morgan H. Lynch In this paper we establish a formalism for the computation of observables due to acceleration-induced particle physics processes. General expressions for the transition rate, multiplicity, power, spectra, and displacement law of particles undergoing time-dependent acceleration and transitioning into… [Phys. Rev. D 92, 024019] Published Mon Jul 13, 2015
    Keywords: General Relativity and Gravitation
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
    Published by American Physical Society (APS)
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  • 6
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    Sustainability, Vol. 3, Pages 322-362: The Carbon and Global Warming Potential Impacts of Organic Farming: Does It Have a Significant Role in an Energy Constrained World? (2011)
    MDPI Publishing
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    Publication Date: 2011-01-29
    Description: About 130 studies were analyzed to compare farm-level energy use and global warming potential (GWP) of organic and conventional production sectors. Cross cutting issues such as tillage, compost, soil carbon sequestration and energy offsets were also reviewed. Finally, we contrasted E and GWP data from the wider food system. We concluded that the evidence strongly favours organic farming with respect to whole-farm energy use and energy efficiency both on a per hectare and per farm product basis, with the possible exception of poultry and fruit sectors. For GWP, evidence is insufficient except in a few sectors, with results per ha more consistently favouring organic farming than GWP per unit product. Tillage was consistently a negligible contributor to farm E use and additional tillage on organic farms does not appear to significantly deplete soil C. Energy offsets, biogas, energy crops and residues have a more limited role on organic farms compared to conventional ones, because of the nutrient and soil building uses of soil organic matter, and the high demand for organic foods in human markets. If farm E use represents 35% of total food chain E use, improvements shown of 20% or more in E efficiency through organic farm management would reduce food-chain E use by 7% or more. Among other food supply chain stages, wholesale/retail (including cooling and packaging) and processing often each contribute 30% or more to total food system E. Thus, additional improvements can be obtained with reduced processing, whole foods and food waste minimization.
    Electronic ISSN: 2071-1050
    Topics: Energy, Environment Protection, Nuclear Power Engineering
    Published by MDPI Publishing
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  • 7
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    Relationships between Antarctic cyclones and surface conditions as derived from high-resolution numerical weather prediction data (2011)
    Wiley
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    Publication Date: 2011-04-14
    Description: An Antarctic cyclone climatology was created based on simulations of the Antarctic Mesoscale Prediction System (AMPS) and the University of Melbourne Cyclone (UM) detection and tracking algorithm for the period 2001–2009. Over 17,000 cyclone tracks were included in the climatology, and 20% of these cyclones were mesoscale in terms of their size. Mesoscale systems were common south of the Antarctic Circumpolar Trough (ACT) over the coastal oceans of the Indian Ocean sector and in the Ross Sea, while large synoptic systems occurred most frequently in the ACT. A novel technique was applied to study the relationships between cyclone characteristics and surface properties over the Southern Ocean and the coastal areas of Antarctica. Our comprehensive study has revealed that up to half of the cyclones simulated by AMPS correlated with the surface latent heat flux, sensible heat flux, or temperature gradient. These cyclones either modified the surface or were being modified by it. In the former category, 85% of the systems were synoptic cyclones associated predominantly with baroclinicity and advection, and the atmospheric boundary layer had a little influence in the generation and development of cyclones. On the contrary, in the latter category, 36% of the systems were mesoscale cyclones gaining energy from instabilities in the boundary layer associated with strong turbulent fluxes.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
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    Pinning down the cosmic ray source mechanism with new IceCube data (2014)
    American Physical Society (APS)
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    Publication Date: 2014-04-05
    Description: Author(s): Luis A. Anchordoqui, Haim Goldberg, Morgan H. Lynch, Angela V. Olinto, Thomas C. Paul, and Thomas J. Weiler Very recently the IceCube Collaboration has reported an observation of 28 neutrino candidates with energies between 50 TeV and 2 PeV, constituting a 4.1σ excess compared to the atmospheric background. In this article we investigate the compatibility between the data and a hypothesized unbroken power... [Phys. Rev. D 89, 083003] Published Fri Apr 04, 2014
    Keywords: Astrophysics
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
    Published by American Physical Society (APS)
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  • 9
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    Role of land-surface changes in arctic summer warming (2005)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2005-09-24
    Description: A major challenge in predicting Earth's future climate state is to understand feedbacks that alter greenhouse-gas forcing. Here we synthesize field data from arctic Alaska, showing that terrestrial changes in summer albedo contribute substantially to recent high-latitude warming trends. Pronounced terrestrial summer warming in arctic Alaska correlates with a lengthening of the snow-free season that has increased atmospheric heating locally by about 3 watts per square meter per decade (similar in magnitude to the regional heating expected over multiple decades from a doubling of atmospheric CO2). The continuation of current trends in shrub and tree expansion could further amplify this atmospheric heating by two to seven times.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chapin, F S 3rd -- Sturm, M -- Serreze, M C -- McFadden, J P -- Key, J R -- Lloyd, A H -- McGuire, A D -- Rupp, T S -- Lynch, A H -- Schimel, J P -- Beringer, J -- Chapman, W L -- Epstein, H E -- Euskirchen, E S -- Hinzman, L D -- Jia, G -- Ping, C-L -- Tape, K D -- Thompson, C D C -- Walker, D A -- Welker, J M -- New York, N.Y. -- Science. 2005 Oct 28;310(5748):657-60. Epub 2005 Sep 22.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Arctic Biology; University of Alaska Fairbanks, Fairbanks, AK 99775, USA. terry.chapin@uaf.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/16179434" target="_blank"〉PubMed〈/a〉
    Keywords: Alaska ; Arctic Regions ; *Greenhouse Effect ; Picea ; Seasons ; Trees
    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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  • 10
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    Identification of a plastidial phenylalanine exporter that influences flux distribution through the phenylalanine biosynthetic network (2015)
    Springer Nature
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    Publication Date: 2015-09-12
    Description: Article Phenylalanine is synthesized in plant chloroplasts and is then exported to the cytosol, where it is a precursor for various secondary metabolites. Here, the authors identify PhpCAT as a plastid phenylalanine transporter required to maintain metabolic flux in petunia. Nature Communications doi: 10.1038/ncomms9142 Authors: Joshua R. Widhalm, Michael Gutensohn, Heejin Yoo, Funmilayo Adebesin, Yichun Qian, Longyun Guo, Rohit Jaini, Joseph H. Lynch, Rachel M. McCoy, Jacob T. Shreve, Jyothi Thimmapuram, David Rhodes, John A. Morgan, Natalia Dudareva
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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