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  • 1
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    The Effects of Microsatellite Selection on Linked Sequence Diversity (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-24
    Description: The genome-wide scan for selection is an important method for identifying loci involved in adaptive evolution. However, theory that underlies standard scans for selection assumes a simple mutation model. In particular, recurrent mutation of the selective target is not considered. Although this assumption is reasonable for single-nucleotide variants (SNVs), a microsatellite targeted by selection will reliably violate this assumption due to high mutation rate. Moreover, the mutation rate of microsatellites is generally high enough to ensure that recurrent mutation is pervasive rather than occasional. It is therefore unclear if positive selection targeting microsatellites can be detected using standard scanning statistics. Examples of functional variation at microsatellites underscore the significance of understanding the genomic effects of microsatellite selection. Here, we investigate the joint effects of selection and complex mutation on linked sequence diversity, comparing simulations of microsatellite selection and SNV-based selective sweeps. We find that selection on microsatellites is generally difficult to detect using popular summaries of the site frequency spectrum, and, under certain conditions, using popular methods such as the integrated haplotype statistic and SweepFinder. However, comparisons of the number of haplotypes (K) and segregating sites (S) often provide considerable power to detect selection on microsatellites. We apply this knowledge to a scan of autosomes in the human CEU population (CEPH population sampled from Utah). In addition to the most commonly reported targets of selection in European populations, we identify numerous novel genomic regions that bear highly anomalous haplotype configurations. Using one of these regions—intron 1 of MAGI2 —as an example, we show that the anomalous configuration is coincident with a perfect CA repeat of length 22. We conclude that standard genome-wide scans will commonly fail to detect mutationally complex targets of selection but that comparisons of K and S will, in many cases, facilitate their identification.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Cajon pass scientific drilling project: Drilling overview (1990)
    Springer
    In:  Professional Paper, Open-File Rept., Super-Deep Continental Drilling and Deep Geophysical Sounding, Berlin, Springer, vol. 22, no. 16, pp. 40-56, (ISBN 0080419208)
    Details
    Publication Date: 1990
    Keywords: Review article ; Project report/description ; Borehole geophys. ; scientific drilling
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    BIBLIOGRAPHY SEISMOLOGY
  • 3
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    Finding a Missing Gene: EFG1 Regulates Morphogenesis in Candida tropicalis (2015)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2015-05-12
    Description: Fungi from the genus Candida are common members of the human microbiota; however, they are also important opportunistic pathogens in immunocompromised hosts. Several morphological transitions have been linked to the ability of these fungi to occupy the different ecological niches in the human body. The transcription factor Efg1 from the APSES family plays a central role in the transcription circuits underlying several of these morphological changes. In Candida albicans , for example, Efg1 is a central regulator of filamentation, biofilm formation, and white-opaque switching, processes associated with survival in the human host. Orthologs of Efg1 are present throughout the Candida clade but, surprisingly, the genome sequence of Candida tropicalis failed to uncover a gene coding for Efg1. One possibility was that the paralog of Efg1, Efh1, had assumed the function of Efg1 in C. tropicalis . However, we show that this gene has only a minor role in the morphological transitions mentioned above. Instead, we report here that C. tropicalis does have an ortholog of the EFG1 gene found in other Candida species. The gene is located in a different genomic position than EFG1 in C. albicans , in a region that contains a gap in the current genome assembly of C. tropicalis . We show that the newly identified C. tropicalis EFG1 gene regulates filamentation, biofilm formation, and white-opaque switching. Our results highlight the conserved role of Efg1 in controlling morphogenesis in Candida species and remind us that published genome sequences are drafts that require continuous curation and careful scrutiny.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 4
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    CALHM1 mediates Ca2+o regulation of excitability [Physiology] (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-07-11
    Description: Extracellular Ca2+ (Ca2+ o) plays important roles in physiology. Changes of Ca2+o concentration ([Ca2+]o) have been observed to modulate neuronal excitability in various physiological and pathophysiological settings, but the mechanisms by which neurons detect [Ca2+]o are not fully understood. Calcium homeostasis modulator 1 (CALHM1) expression was shown to induce cation currents in cells and elevate cytoplasmic Ca2+ concentration ([Ca2+]i) in response to removal of Ca2+o and its subsequent addback. However, it is unknown whether CALHM1 is a pore-forming ion channel or modulates endogenous ion channels. Here we identify CALHM1 as the pore-forming subunit of a plasma membrane Ca2+-permeable ion channel with distinct ion permeability properties and unique coupled allosteric gating regulation by voltage and [Ca2+]o. Furthermore, we show that CALHM1 is expressed in mouse cortical neurons that respond to reducing [Ca2+]o with enhanced conductance and action potential firing and strongly elevated [Ca2+]i upon Ca2+o removal and its addback. In contrast, these responses are strongly muted in neurons from mice with CALHM1 genetically deleted. These results demonstrate that CALHM1 is an evolutionarily conserved ion channel family that detects membrane voltage and extracellular Ca2+ levels and plays a role in cortical neuronal excitability and Ca2+ homeostasis, particularly in response to lowering [Ca2+]o and its restoration to normal levels.
    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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  • 5
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    Controls on dissolved cobalt in surface waters of the Sargasso Sea: Comparisons with iron and aluminum (2012)
    Wiley
    Details
    Publication Date: 2012-05-19
    Description: Dissolved cobalt (dCo), iron (dFe) and aluminum (dAl) were determined in water column samples along a meridional transect (∼31°N to 24°N) south of Bermuda in June 2008. A general north-to-south increase in surface concentrations of dFe (0.3–1.6 nM) and dAl (14–42 nM) was observed, suggesting that aerosol deposition is a significant source of dFe and dAl, whereas no clear trend was observed for near-surface dCo concentrations. Shipboard aerosol samples indicate fractional solubility values of 8–100% for aerosol Co, which are significantly higher than corresponding estimates of the solubility of aerosol Fe (0.44–45%). Hydrographic observations and analysis of time series rain samples from Bermuda indicate that wet deposition accounts for most (〉80%) of the total aeolian flux of Co, and hence a significant proportion of the atmospheric input of dCo to our study region. Our aerosol data imply that the atmospheric input of dCo to the Sargasso Sea is modest, although this flux may be more significant in late summer. The water column dCo profiles reveal a vertical distribution that predominantly reflects ‘nutrient-type’ behavior, versus scavenged-type behavior for dAl, and a hybrid of nutrient- and scavenged-type behavior for dFe. Mesoscale eddies also appear to impact on the vertical distribution of dCo. The effects of biological removal of dCo from the upper water column were apparent as pronounced sub-surface minima (21 ± 4 pM dCo), coincident with maxima in Prochlorococcus abundance. These observations imply that Prochlorococcus plays a major role in removing dCo from the euphotic zone, and that the availability of dCo may regulate Prochlorococcus growth in the Sargasso Sea.
    Print ISSN: 0886-6236
    Electronic ISSN: 1944-9224
    Topics: Biology , Chemistry and Pharmacology , Geography , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    Major element and oxygen isotope geochemistry of vapour-phase garnet from the Topopah Spring Tuff at Yucca Mountain, Nevada, USA (2014)
    Mineralogical Society of Great Britain and Ireland
    Details
    Publication Date: 2014-10-23
    Description: Twenty vapour-phase garnets were studied in two samples of the Topopah Spring Tuff of the Paintbrush Group from Yucca Mountain, in southern Nevada. The Miocene-age Topopah Spring Tuff is a 350 m thick, devitrified, moderately to densely welded ash-flow tuff that is zoned compositionally from high-silica rhyolite to latite. During cooling of the tuff, escaping vapour produced lithophysae (former gas cavities) lined with an assemblage of tridymite (commonly inverted to cristobalite or quartz), sanidine and locally, hematite and/or garnet. Vapour-phase topaz and economic deposits associated commonly with topaz-bearing rhyolites (characteristically enriched in F) were not found in the Topopah Spring Tuff at Yucca Mountain. Based on their occurrence only in lithophysae, the garnets are not primary igneous phenocrysts, but rather crystals that grew from a F-poor magma-derived vapour trapped during and after emplacement of the tuff. The garnets are euhedral, vitreous, reddish brown, trapezohedral, as large as 2 mm in diameter and fractured. The garnets also contain inclusions of tridymite. Electron microprobe analyses of the garnets reveal that they are almandine-spessartine (48.0 and 47.9 mol.%, respectively), have an average composition of (Fe 1.46 Mn 1.45 Mg 0.03 Ca 0.10 )(Al 1.93 Ti 0.02 )Si 3.01 O 12 and are comparatively homogeneous in Fe and Mn concentrations from core to rim. Composited garnets from each sample site have 18 O values of 7.2 and 7.4. The associated quartz (after tridymite) has 18 O values of 17.4 and 17.6, values indicative of reaction with later, low-temperature water. Unaltered tridymite from higher in the stratigraphic section has a 18 O of 11.1 which, when coupled with the garnet 18 O values in a quartz-garnet fractionation equation, indicates isotopic equilibration (vapour-phase crystallization) at temperatures of ~600°C. This high-temperature mineralization, formed during cooling of the tuffs, is distinct from the later and commonly recognized low-temperature stage (generally 50–70°C) of calcite, quartz and opal secondary mineralization, formed from downward-percolating meteoric water, that locally coats fracture footwalls and lithophysal floors.
    Print ISSN: 0026-461X
    Electronic ISSN: 1471-8022
    Topics: Geosciences
    Published by Mineralogical Society of Great Britain and Ireland
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  • 7
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    Direct observation of heterogeneous chemistry in the atmosphere (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-03-04
    Description: The heterogeneous replacement of chloride by nitrate in individual sea-salt particles was monitored continuously over time in the troposphere with the use of aerosol time-of-flight mass spectrometry. Modeling calculations show that the observed chloride displacement process is consistent with a heterogeneous chemical reaction between sea-salt particles and gas-phase nitric acid, leading to sodium nitrate production in the particle phase accompanied by liberation of gaseous HCl from the particles. Such single-particle measurements, combined with a single-particle model, make it possible to monitor and explain heterogeneous gas/particle chemistry as it occurs in the atmosphere.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gard -- Kleeman -- Gross -- Hughes -- Allen -- Morrical -- Fergenson -- Dienes -- E Galli M -- Johnson -- Cass -- Prather -- New York, N.Y. -- Science. 1998 Feb 20;279(5354):1184-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉E. E. Gard, D. S. Gross, B. D. Morrical, D. P. Fergenson, T. Dienes, M. E. Galli, K. A. Prather, Department of Chemistry, University of California, Riverside, CA 92521, USA. M. J. Kleeman, L. S. Hughes, J. O. Allen, R. J. Johnson, G. R. Cass, Departme.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9469803" target="_blank"〉PubMed〈/a〉
    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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    Long-run and Short-run Co-movements in Energy Prices and the Prices of Agricultural Feedstocks for Biofuel (2014)
    Oxford University Press
    Details
    Publication Date: 2014-07-23
    Description: Recent expansions in biofuel production have led to concerns about an emerging "new relationship" between energy prices and the prices of agricultural feedstock for biofuel. We provide new econometric evidence on this relationship using common trend-common cycle decompositions to estimate long-run and short-run co-movement across various energy and agricultural prices. We also test for the presence of regime changes that may alter the relationship between energy and agricultural feedstock prices under certain conditions. We find that co-movements between energy and agricultural feedstock prices tend to dissipate in the long-run, which has important implications for biofuel and food policy.
    Keywords: O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q20 - General
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 9
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    The Comparative Toxicogenomics Database: update 2017 (2017)
    Oxford University Press
    Details
    Publication Date: 2017-01-05
    Description: The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/ ) provides information about interactions between chemicals and gene products, and their relationships to diseases. Core CTD content (chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature) are integrated with each other as well as with select external datasets to generate expanded networks and predict novel associations. Today, core CTD includes more than 30.5 million toxicogenomic connections relating chemicals/drugs, genes/proteins, diseases, taxa, Gene Ontology (GO) annotations, pathways, and gene interaction modules. In this update, we report a 33% increase in our core data content since 2015, describe our new exposure module (that harmonizes exposure science information with core toxicogenomic data) and introduce a novel dataset of GO-disease inferences (that identify common molecular underpinnings for seemingly unrelated pathologies). These advancements centralize and contextualize real-world chemical exposures with molecular pathways to help scientists generate testable hypotheses in an effort to understand the etiology and mechanisms underlying environmentally influenced diseases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 10
    Electronic Resource
    Electronic Resource
    Molecular structure of .mu.-diphenylacetylene-[1-{carbonyl(.eta.4-tetraphenylcyclobutadiene)molybdenum(0)}-2-{dicarbonyl-.mu.-(.eta.4-tetraphenylcyclopentadienone)-molybdenum(0)}], (OC)2(Ph4C5O)Mo(Ph2C2)Mo(C4Ph4)(CO), a complex with a molybdenum:molybdenum bond and a bridging cyclopentadienone group (1977)
    s.l. : American Chemical Society
    Inorganic chemistry 16 (1977), S. 2354-2359 
    Details
    ISSN: 1520-510X
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ic50175a041
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    Paper (German National Licenses)
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