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  • 1
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    Targeted Capture of Phylogenetically Informative Ves SINE Insertions in Genus Myotis (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-25
    Description: Identification of retrotransposon insertions in nonmodel taxa can be technically challenging and costly. This has inhibited progress in understanding retrotransposon insertion dynamics outside of a few well-studied species. To address this problem, we have extended a retrotransposon-based capture and sequence method (ME-Scan [mobile element scanning]) to identify insertions belonging to the Ves family of short interspersed elements (SINEs) across seven species of the bat genus Myotis. We identified between 120,000 and 143,000 SINE insertions in six taxa lacking a draft genome by comparing to the M. lucifugus reference genome. On average, each Ves insertion was sequenced to 129.6 x coverage. When mapped back to the M. lucifugus reference genome, all insertions were confidently assigned within a 10-bp window. Polymorphic Ves insertions were identified in each taxon based on their mapped locations. Using cross-species comparisons and the identified insertion positions, a presence–absence matrix was created for approximately 796,000 insertions. Dollo parsimony analysis of more than 85,000 phylogenetically informative insertions recovered strongly supported, monophyletic clades that correspond with the biogeography of each taxa. This phylogeny is similar to previously published mitochondrial phylogenies, with the exception of the placement of M. vivesi. These results support the utility of our variation on ME-Scan to identify polymorphic retrotransposon insertions in taxa without a reference genome and for large-scale retrotransposon-based phylogenetics.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Pollution policy [Environmental Sciences] (2013)
    National Academy of Sciences
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    Publication Date: 2013-01-16
    Description: In Europe and, increasingly, the rest of the world, the key policy tool for the control of air pollution is the critical load, a level of pollution below which there are no known significant harmful effects on the environment. Critical loads are used to map sensitive regions and habitats, permit...
    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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  • 3
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    Why imatinib remains an exception of cancer research (2012)
    Wiley
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    Publication Date: 2012-09-28
    Description: The archetype driving the drug targeting approach to cancer therapy is the success of imatinib against chronic phase chronic myeloid leukemia (CML-CP). Molecular targeting success of this magnitude has yet to be repeated for most solid tumors. To answer why imatinib remains an exception of cancer research, we summarize key features and patterns of evolution that contrast CML-CP from prostate cancer, an example of a solid tumor that also shares a signature fusion gene. Distinctive properties of CML-CP include: a large cell population size that is not geographically constrained, a highly penetrant dominant oncogene that sweeps the entire cell population, subsequent progressive and ordered clonal genetic changes, and the effectiveness of molecular targeting within the chronic phase, which is comparable to the benign phase of solid tumors. CML-CP progression resembles a clonal, stepwise model of evolution, whereas the pattern of solid tumor evolution is highly dynamic and stochastic. The distinguishing features and evolutionary pattern of CML-CP support why the success of imatinib does not carry over to most solid tumors. Changing the focus of cancer research from a gene-based view to a genome-based concept will provide insight into solid tumor evolutionary dynamics. J. Cell. Physiol. © 2012 Wiley Periodicals, Inc.
    Electronic ISSN: 1097-4652
    Topics: Biology , Medicine
    Published by Wiley
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  • 4
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    Controls on precipitation and cloudiness in simulations of trade-wind cumulus as observed during RICO (2011)
    Wiley
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    Publication Date: 2011-07-19
    Description: Twelve large-eddy simulations, with a wide range of microphysical representations, are compared to each other and to independent measurements. The measurements and the initial and forcing data for the simulations are taken from the undisturbed period of the Rain in Cumulus over the Ocean (RICO) field study. A regional downscaling of meteorological analyses is performed so as to provide forcing data consistent with the measurements. The ensemble average of the simulations plausibly reproduces many features of the observed clouds, including the vertical structure of cloud fraction, profiles of cloud and rain water, and to a lesser degree the population density of rain drops. The simulations do show considerable departures from one another in the representation of the cloud microphysical structure and the ensuant surface precipitation rates, increasingly so for the more simplified microphysical models. There is a robust tendency for simulations that develop rain to produce a shallower, somewhat more stable cloud layer. Relations between cloud cover and precipitation are ambiguous.
    Electronic ISSN: 1942-2466
    Topics: Geography , Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 5
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    On the connection between tropical circulation, convective mixing, and climate sensitivity (2014)
    Wiley
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    Publication Date: 2014-09-06
    Description: The connection between the large-scale tropical circulation of the atmosphere, convective mixing, and climate sensitivity is explored in a wide range of climates through a perturbed-parameter ensemble of a comprehensive Earth-System Model. Four parameters related to the representation of atmospheric moist convection are found to dominate the response of the model. Their values govern the strength of the tropical circulation, the surface temperature, atmospheric humidity, and the strength of the tropical overturning circulation, largely through their influence on the atmospheric stability. The same convective parameters, albeit in different combinations, also have a strong influence on the equilibrium climate sensitivity of the model, which ranges from a little over 3 ∘ C to more than 10 ∘ C. The importance of the most poorly represented processes in determining important aspects of the behavior of the model argues for the need to move beyond statistical approaches to estimating climate sensitivity and focusing on the development of a better understanding and representation of convective mixing, particularly in the tropics.
    Print ISSN: 0035-9009
    Electronic ISSN: 1477-870X
    Topics: Geography , Physics
    Published by Wiley
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  • 6
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    The distribution and variability of low-level cloud in the North-Atlantic trades (2013)
    Wiley
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    Publication Date: 2013-11-29
    Description: In the North Atlantic trades variations in the distribution of low-level cloud are rich. Using two-years of observations from a remote sensing site located on the eastward coast of Barbados, the vertical distribution of cloud and its contribution to low-level cloud amount are explored. The vertical distribution of first detected cloud base heights is marked by a strong peak near the lifting condensation level (LCL) from passive optically thin shallow cumuli. Cloud with a base near this level dominates the total cloud cover with a contribution of about two-thirds. The other one-third comes from cloud with its cloud base further aloft at heights 〉 1 km, such as cumulus edges or stratiform cloud below the trade inversion. Cloud found aloft, regardless of where its base is located, contains more variance, in particular near the inversion and on timescales longer than a day. In turn, cloud near the LCL is surprisingly invariant on longer time scales, although consistent with existing theories. Because this component does not systematically vary, changes in cloud cover in response to changes in meteorology or climate may be limited to changes in its contribution from cloud aloft.
    Print ISSN: 0035-9009
    Electronic ISSN: 1477-870X
    Topics: Geography , Physics
    Published by Wiley
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  • 7
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    Response of Schwann cells to action potentials in development (2000)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2000-03-24
    Description: Sensory axons become functional late in development when Schwann cells (SC) stop proliferating and differentiate into distinct phenotypes. We report that impulse activity in premyelinated axons can inhibit proliferation and differentiation of SCs. This neuron-glial signaling is mediated by adenosine triphosphate acting through P2 receptors on SCs and intracellular signaling pathways involving Ca2+, Ca2+/calmodulin kinase, mitogen-activated protein kinase, cyclic adenosine 3',5'-monophosphate response element binding protein, and expression of c-fos and Krox-24. Adenosine triphosphate arrests maturation of SCs in an immature morphological stage and prevents expression of O4, myelin basic protein, and the formation of myelin. Through this mechanism, functional activity in the developing nervous system could delay terminal differentiation of SCs until exposure to appropriate axon-derived signals.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, B -- Fields, R D -- New York, N.Y. -- Science. 2000 Mar 24;287(5461):2267-71.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of Developmental Neurobiology, National Institutes of Health, National Institute of Child Health and Human Development, Building 49, Room 5A38, 49 Convent Drive, Bethesda, MD 20892, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/10731149" target="_blank"〉PubMed〈/a〉
    Keywords: Action Potentials ; Adenosine Triphosphate/metabolism ; Animals ; Axons/*physiology ; Calcium/metabolism ; Calcium-Calmodulin-Dependent Protein Kinases/metabolism ; Cell Differentiation ; Cell Division ; Cells, Cultured ; Coculture Techniques ; Cyclic AMP Response Element-Binding Protein/metabolism ; DNA-Binding Proteins/genetics/metabolism ; Early Growth Response Protein 1 ; Electric Stimulation ; Ganglia, Spinal/physiology ; Gene Expression Regulation, Developmental ; Genes, fos ; *Immediate-Early Proteins ; Mice ; Microscopy, Confocal ; Myelin Sheath/metabolism ; Neurons, Afferent/*physiology ; Phosphorylation ; Proto-Oncogene Proteins c-fos/metabolism ; Receptors, Purinergic P2/metabolism ; Schwann Cells/*cytology/*physiology ; Signal Transduction ; Transcription Factors/genetics/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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    Untangling aerosol effects on clouds and precipitation in a buffered system (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-10-02
    Description: It is thought that changes in the concentration of cloud-active aerosol can alter the precipitation efficiency of clouds, thereby changing cloud amount and, hence, the radiative forcing of the climate system. Despite decades of research, it has proved frustratingly difficult to establish climatically meaningful relationships among the aerosol, clouds and precipitation. As a result, the climatic effect of the aerosol remains controversial. We propose that the difficulty in untangling relationships among the aerosol, clouds and precipitation reflects the inadequacy of existing tools and methodologies and a failure to account for processes that buffer cloud and precipitation responses to aerosol perturbations.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, Bjorn -- Feingold, Graham -- England -- Nature. 2009 Oct 1;461(7264):607-13. doi: 10.1038/nature08281.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Meteorologie, KlimaCampus, 20251 Hamburg, Germany. bjorn.stevens@zmaw.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19794487" target="_blank"〉PubMed〈/a〉
    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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  • 9
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    New insights into neuron-glia communication (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-10-19
    Description: Two-way communication between neurons and nonneural cells called glia is essential for axonal conduction, synaptic transmission, and information processing and thus is required for normal functioning of the nervous system during development and throughout adult life. The signals between neurons and glia include ion fluxes, neurotransmitters, cell adhesion molecules, and specialized signaling molecules released from synaptic and nonsynaptic regions of the neuron. In contrast to the serial flow of information along chains of neurons, glia communicate with other glial cells through intracellular waves of calcium and via intercellular diffusion of chemical messengers. By releasing neurotransmitters and other extracellular signaling molecules, glia can affect neuronal excitability and synaptic transmission and perhaps coordinate activity across networks of neurons.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1226318/" 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/PMC1226318/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Fields, R Douglas -- Stevens-Graham, Beth -- Z01 HD000713-11/HD/NICHD NIH HHS/ -- New York, N.Y. -- Science. 2002 Oct 18;298(5593):556-62.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Neurocytology and Physiology Section, National Institute of Child Health and Human Development, Bethesda, MD 20892, USA. fields@helix.nih.gov〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12386325" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Astrocytes/cytology/physiology ; Brain/cytology/physiology ; *Cell Communication ; Humans ; Microglia/cytology/physiology ; Myelin Sheath/physiology ; Nerve Regeneration ; Nervous System Diseases/pathology/physiopathology ; Neuroglia/*physiology ; Neurons/*physiology ; Neurotransmitter Agents/metabolism ; Oligodendroglia/cytology/physiology ; Schwann Cells/cytology/physiology ; Signal Transduction ; Stem Cells/cytology/physiology ; Synapses/physiology ; 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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  • 10
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    Aerosols: Uncertain then, irrelevant now (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-11-10
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stevens, Bjorn -- England -- Nature. 2013 Nov 7;503(7474):47-8. doi: 10.1038/503047a.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Meteorology, KlimaCampus, Hamburg 20146, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24201277" target="_blank"〉PubMed〈/a〉
    Keywords: Aerosols/*analysis ; *Climate ; *Models, Theoretical ; *Uncertainty
    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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