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  • 1
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    The Dfam database of repetitive DNA families (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org . Seed alignments, profile HMMs, hit lists and other underlying data are available for download.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Extracting Inner‐Heliosphere Solar Wind Speed Information From Heliospheric Imager Observations (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract We present evidence that variability in the STEREO‐A Heliospheric Imager (HI) data is correlated with in situ solar wind speed estimates from WIND, STEREO‐A, and STEREO‐B. For 2008–2012, we compute the variability in HI differenced images in a plane‐of‐sky shell between 20 to 22.5 solar radii and, for a range of position angles, compare daily means of HI variability and in situ solar wind speed estimates. We show that the HI variability data and in situ solar wind speeds have similar temporal autocorrelation functions. Carrington rotation periodicities are well documented for in situ solar wind speeds, but, to our knowledge, this is the first time they have been presented in statistics computed from HI images. In situ solar wind speeds from STEREO‐A, STEREO‐B, and WIND are all are correlated with the HI variability, with a lag that varies in a manner consistent with the longitudinal separation of the in situ monitor and the HI instrument. Unlike many approaches to processing HI observations, our method requires no manual feature tracking; it is automated, is quick to compute, and does not suffer the subjective biases associated with manual classifications. These results suggest we could possibly estimate solar wind speeds in the low heliosphere directly from HI observations. This motivates further investigation, as this could be a significant asset to the space weather forecasting community; it might provide an independent observational constraint on heliospheric solar wind forecasts, through, for example, data assimilation. Finally, these results are another argument for the potential utility of including a HI on an operational space weather mission.
    Print ISSN: 1539-4964
    Electronic ISSN: 1542-7390
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    Stellar diameters and temperatures - VI. High angular resolution measurements of the transiting exoplanet host stars HD 189733 and HD 209458 and implications for models of cool dwarfs (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-21
    Description: We present direct radii measurements of the well-known transiting exoplanet host stars HD 189733 and HD 209458 using the CHARA Array interferometer. We find the limb-darkened angular diameters to be LD  = 0.3848 ± 0.0055 and 0.2254 ± 0.0072 mas for HD 189733 and HD 209458, respectively. HD 189733 and HD 209458 are currently the only two transiting exoplanet systems where detection of the respective planetary companion's orbital motion from high-resolution spectroscopy has revealed absolute masses for both star and planet. We use our new measurements together with the orbital information from radial velocity and photometric time series data, Hipparcos distances, and newly measured bolometric fluxes to determine the stellar effective temperatures ( T eff  = 4875 ± 43, 6092 ± 103 K), stellar linear radii ( R *  = 0.805 ± 0.016, 1.203 ± 0.061 R ), mean stellar densities ( *  = 1.62 ± 0.11, 0.58 ± 0.14 ), planetary radii ( R p  = 1.216 ± 0.024, 1.451 ± 0.074 R Jup ), and mean planetary densities ( p  = 0.605 ± 0.029, 0.196 ± 0.033 Jup ) for HD 189733b and HD 209458b, respectively. The stellar parameters for HD 209458, an F9 dwarf, are consistent with indirect estimates derived from spectroscopic and evolutionary modelling. However, we find that models are unable to reproduce the observational results for the K2 dwarf, HD 189733. We show that, for stellar evolutionary models to match the observed stellar properties of HD 189733, adjustments lowering the solar-calibrated mixing-length parameter to α MLT =1.34 need to be employed.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Stellar diameters and temperatures - VI. High angular resolution measurements of the transiting exoplanet host stars HD 189733 and HD 209458 and implications for models of cool dwarfs (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-29
    Description: We present direct radii measurements of the well-known transiting exoplanet host stars HD 189733 and HD 209458 using the CHARA Array interferometer. We find the limb-darkened angular diameters to be LD  = 0.3848 ± 0.0055 and 0.2254 ± 0.0072 mas for HD 189733 and HD 209458, respectively. HD 189733 and HD 209458 are currently the only two transiting exoplanet systems where detection of the respective planetary companion's orbital motion from high-resolution spectroscopy has revealed absolute masses for both star and planet. We use our new measurements together with the orbital information from radial velocity and photometric time series data, Hipparcos distances, and newly measured bolometric fluxes to determine the stellar effective temperatures ( T eff  = 4875 ± 43, 6092 ± 103 K), stellar linear radii ( R *  = 0.805 ± 0.016, 1.203 ± 0.061 R ), mean stellar densities ( *  = 1.62 ± 0.11, 0.58 ± 0.14 ), planetary radii ( R p  = 1.216 ± 0.024, 1.451 ± 0.074 R Jup ), and mean planetary densities ( p  = 0.605 ± 0.029, 0.196 ± 0.033 Jup ) for HD 189733b and HD 209458b, respectively. The stellar parameters for HD 209458, an F9 dwarf, are consistent with indirect estimates derived from spectroscopic and evolutionary modelling. However, we find that models are unable to reproduce the observational results for the K2 dwarf, HD 189733. We show that, for stellar evolutionary models to match the observed stellar properties of HD 189733, adjustments lowering the solar-calibrated mixing-length parameter to α MLT =1.34 need to be employed.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Diurnal dopamine [Neuroscience] (2014)
    National Academy of Sciences
    Details
    Publication Date: 2014-07-02
    Description: The majority of neurotransmitter systems shows variations in state-dependent cell firing rates that are mechanistically linked to variations in extracellular levels, or tone, of their respective neurotransmitter. Diurnal variation in dopamine tone has also been demonstrated within the striatum, but this neurotransmitter is unique, in that variation in dopamine tone...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Role of serotonin in the paradoxical calming effect of psychostimulants on hyperactivity (1999)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1999-01-15
    Description: The mechanism by which psychostimulants act as calming agents in humans with attention-deficit hyperactivity disorder (ADHD) or hyperkinetic disorder is currently unknown. Mice lacking the gene encoding the plasma membrane dopamine transporter (DAT) have elevated dopaminergic tone and are hyperactive. This activity was exacerbated by exposure to a novel environment. Additionally, these mice were impaired in spatial cognitive function, and they showed a decrease in locomotion in response to psychostimulants. This paradoxical calming effect of psychostimulants depended on serotonergic neurotransmission. The parallels between the DAT knockout mice and individuals with ADHD suggest that common mechanisms may underlie some of their behaviors and responses to psychostimulants.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gainetdinov, R R -- Wetsel, W C -- Jones, S R -- Levin, E D -- Jaber, M -- Caron, M G -- MH-40159/MH/NIMH NIH HHS/ -- New York, N.Y. -- Science. 1999 Jan 15;283(5400):397-401.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute Laboratories, Department of Cell Biology, Duke University Medical Center, Durham, NC 27710, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9888856" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Attention Deficit Disorder with Hyperactivity/drug ; therapy/physiopathology/psychology ; Behavior, Animal/drug effects ; Carrier Proteins/antagonists & inhibitors/drug effects/genetics/metabolism ; Central Nervous System Stimulants/*pharmacology ; Corpus Striatum/*metabolism ; Dopamine/metabolism/physiology ; Dopamine Plasma Membrane Transport Proteins ; Fluoxetine/pharmacology ; Humans ; Hyperkinesis/*drug therapy/physiopathology/psychology ; Maze Learning ; Membrane Glycoproteins/drug effects/metabolism ; *Membrane Transport Proteins ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Motor Activity/drug effects ; *Nerve Tissue Proteins ; Norepinephrine Plasma Membrane Transport Proteins ; Serotonin/metabolism/*physiology ; Serotonin Plasma Membrane Transport Proteins ; Serotonin Uptake Inhibitors/pharmacology ; *Symporters ; *Synaptic Transmission
    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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    Structural insight into magnetochrome-mediated magnetite biomineralization (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-10-08
    Description: Magnetotactic bacteria align along the Earth's magnetic field using an organelle called the magnetosome, a biomineralized magnetite (Fe(II)Fe(III)2O4) or greigite (Fe(II)Fe(III)2S4) crystal embedded in a lipid vesicle. Although the need for both iron(II) and iron(III) is clear, little is known about the biological mechanisms controlling their ratio. Here we present the structure of the magnetosome-associated protein MamP and find that it is built on a unique arrangement of a self-plugged PDZ domain fused to two magnetochrome domains, defining a new class of c-type cytochrome exclusively found in magnetotactic bacteria. Mutational analysis, enzyme kinetics, co-crystallization with iron(II) and an in vitro MamP-assisted magnetite production assay establish MamP as an iron oxidase that contributes to the formation of iron(III) ferrihydrite eventually required for magnetite crystal growth in vivo. These results demonstrate the molecular mechanisms of iron management taking place inside the magnetosome and highlight the role of magnetochrome in iron biomineralization.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Siponen, Marina I -- Legrand, Pierre -- Widdrat, Marc -- Jones, Stephanie R -- Zhang, Wei-Jia -- Chang, Michelle C Y -- Faivre, Damien -- Arnoux, Pascal -- Pignol, David -- T32 GM066698/GM/NIGMS NIH HHS/ -- England -- Nature. 2013 Oct 31;502(7473):681-4. doi: 10.1038/nature12573. Epub 2013 Oct 6.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Commissariat a l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Biologie Environnementale et de Biotechnologies,, F-13108, France [2] Centre National de la Recherche Scientifique, Unite Mixte de Recherche Biologie Vegetale et Microbiologie Environnementales, Saint-Paul-lez-Durance, F-13108, France [3] Aix-Marseille Universite, Saint-Paul-lez-Durance, F-13108, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24097349" target="_blank"〉PubMed〈/a〉
    Keywords: Bacteria/*cytology/enzymology/genetics/*metabolism ; Bacterial Proteins/chemistry/genetics/metabolism ; Conserved Sequence ; Ferric Compounds/metabolism ; Ferrosoferric Oxide/*metabolism ; Genes, Bacterial/genetics ; Iron/metabolism ; Magnetosomes/*metabolism ; Models, Molecular ; Oxidation-Reduction ; Oxidoreductases/chemistry/genetics/metabolism ; Protein Multimerization ; Protein Structure, Tertiary ; Static Electricity
    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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  • 8
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    Developing vanadium valence state oxybarometers (spinel-melt, olivine-melt, spinel-olivine) and V/(Cr+Al) partitioning (spinel-melt) for martian olivine-phyric basalts (2013)
    Mineralogical Society of America
    Details
    Publication Date: 2013-11-19
    Description: A spiked (with REE, V, Sc) martian basalt Yamato 980459 (Y98) composition was used to synthesize olivine, spinel, and pyroxene at 1200 °C at five oxygen fugacities: IW–1, IW, IW+1, IW+2, and QFM. These run products were analyzed by electron microprobe, ion microprobe, and X-ray absorption near-edge spectroscopy to establish four oxybarometers based on vanadium partitioning behavior between the following pairs of phases: V spinel-melt, V/(Cr+Al) spinel-melt, olivine-melt, and spinel-olivine. The results for the spinel-melt, olivine-melt, and V/(Cr+Al) spinel-melt are applicable for the entire oxygen fugacity range while the spinel-olivine oxybarometer is only applicable between IW–1 and IW+1. The oxybarometer based on V partitioning between spinel-olivine is restricted to basalts that crystallized under low oxygen fugacities, some martian, all lunar, as well as samples from 4 Vesta. The true potential and power of the new spinel-olivine oxybarometer is that it does not require samples representative of a melt composition or samples with some remnant of quenched melt present. It just requires that the spinel-olivine pairs were in equilibrium when the partitioning of V occurred. We have applied the V spinel-olivine oxybarometer to the Y98 meteorite as a test of the method.
    Print ISSN: 0003-004X
    Electronic ISSN: 1945-3027
    Topics: Geosciences
    Published by Mineralogical Society of America
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  • 9
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    Stellar diameters and temperatures - V. 11 newly characterized exoplanet host stars (2014)
    Oxford University Press
    Details
    Publication Date: 2014-02-15
    Description: We use near-infrared interferometric data coupled with trigonometric parallax values and spectral energy distribution fitting to directly determine stellar radii, effective temperatures and luminosities for the exoplanet host stars 61 Vir, CrB, GJ 176, GJ 614, GJ 649, GJ 876, HD 1461, HD 7924, HD 33564, HD 107383 and HD 210702. Three of these targets are M dwarfs. Statistical uncertainties in the stellar radii and effective temperatures range from 0.5 to 5 per cent and from 0.2 to 2 per cent, respectively. For eight of these targets, this work presents the first directly determined values of radius and temperature; for the other three, we provide updates to their properties. The stellar fundamental parameters are used to estimate stellar mass and calculate the location and extent of each system's circumstellar habitable zone. Two of these systems have planets that spend at least parts of their respective orbits in the system habitable zone: two of GJ 876's four planets and the planet that orbits HD 33564. We find that our value for GJ 876's stellar radius is more than 20 per cent larger than previous estimates and frequently used values in the astronomical literature.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
    Electronic Resource
    Electronic Resource
    Immunosuppression in rainbow trout, Salmo gairdneri Richardson, caused by the haemoflagellate Cryptobia salmositica Katz, 1951 (1986)
    Oxford, UK : Blackwell Publishing Ltd
    Journal of fish diseases 9 (1986), S. 0 
    Details
    ISSN: 1365-2761
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology , Medicine
    Notes: Abstract. An experimental Cryptobia salmositica infection in rainbow trout, Salmo gairdneri Richardson, produced suppression of the humoral response against sheep red blood cells as measured by direct haemagglutination. Two-month and 5-month infections produced equal suppression. The parasite also produced suppression of the humoral response against a bacterial pathogen, Yersinia ruckeri. Anti-Y. ritckeri titres were significantly lower in most fish infected with C. salmositica than in non-infected fish. Immunosuppression became evident when C. salmositica first appeared in the blood (first 2 weeks of infection), Immunosuppression was confirmed by challenge with Y. ruckeri. Mortality at challenge occurred in 64·3% to 83·3% of the fish already infected with C. salmositica at the time of initial Y. ruckeri exposure. There was no mortality at challenge if fish were not infected with C. salmositica at initial bacterial exposure, nor in those concurrently infected with both pathogens. Antigenic competition may have caused the immunosuppression.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1365-2761.1986.tb01036.x
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