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  • Springer Nature  (88)
  • Oxford University Press  (75)
  • Nature Publishing Group (NPG)
  • 2010-2014  (121)
  • 2000-2004  (54)
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  • 1
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    Bod1 regulates protein phosphatase 2A at mitotic kinetochores (2013)
    Springer Nature
    Details
    Publication Date: 2013-10-27
    Description: Article PP2A-B56 regulates the stability of kinetochore-microtubule attachments by dephosphorylating several kinetochore proteins. Porter et al . identify Bod1 as a specific inhibitor of PP2A-B56 phosphatase activity and show that this activity is required for proper chromosome alignment during mitosis. Nature Communications doi: 10.1038/ncomms3677 Authors: Iain M. Porter, Katharina Schleicher, Michael Porter, Jason R. Swedlow
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 2
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    Bod1 regulates protein phosphatase 2A at mitotic kinetochores (2013)
    Springer Nature
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    Publication Date: 2013-10-25
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 3
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    Crop–climate models need an overhaul (2011)
    Springer Nature
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    Publication Date: 2011-06-19
    Description: Estimates of how much food we can grow in a warmer world are out of date. Researchers need to switch to more rigorous multi-model ensembles.
    Print ISSN: 1758-678X
    Electronic ISSN: 1758-6798
    Topics: Geosciences
    Published by Springer Nature
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  • 4
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    MaSC: mappability-sensitive cross-correlation for estimating mean fragment length of single-end short-read sequencing data (2013)
    Oxford University Press
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    Publication Date: 2013-02-13
    Description: Motivation: Reliable estimation of the mean fragment length for next-generation short-read sequencing data is an important step in next-generation sequencing analysis pipelines, most notably because of its impact on the accuracy of the enriched regions identified by peak-calling algorithms. Although many peak-calling algorithms include a fragment-length estimation subroutine, the problem has not been adequately solved, as demonstrated by the variability of the estimates returned by different algorithms. Results: In this article, we investigate the use of strand cross-correlation to estimate mean fragment length of single-end data and show that traditional estimation approaches have mixed reliability. We observe that the mappability of different parts of the genome can introduce an artificial bias into cross-correlation computations, resulting in incorrect fragment-length estimates. We propose a new approach, called mappability-sensitive cross-correlation (MaSC), which removes this bias and allows for accurate and reliable fragment-length estimation. We analyze the computational complexity of this approach, and evaluate its performance on a test suite of NGS datasets, demonstrating its superiority to traditional cross-correlation analysis. Availability: An open-source Perl implementation of our approach is available at http://www.perkinslab.ca/Software.html . Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 5
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    Estuarine and early-marine survival of transported and in-river migrant Snake River spring Chinook salmon smolts (2012)
    Springer Nature
    Details
    Publication Date: 2012-07-09
    Description: Estuarine and early-marine survival of transported and in-river migrant Snake River spring Chinook salmon smolts Scientific Reports 2, 11062012 doi: 10.1038/srep00448 Erin L. Rechisky David W. Welch Aswea D. Porter Melinda C. Jacobs-Scott Paul M. Winchell John L. McKern Many juvenile Snake River Chinook salmon are transported downriver to avoid hydroelectric dams in the Columbia River basin. As mortality to the final dam is ∼50%, transported fish should return as adults at roughly double the rate of nontransported fish; however, the benefit of transportation has not been realized consistently. “Delayed” mortality caused by transportation-induced stress is one hypothesis to explain reduced returns of transported fish. Differential timing of ocean entry is another. We used a large-scale acoustic telemetry array to test whether survival of transported juvenile spring Chinook is reduced relative to in-river migrant control groups after synchronizing ocean entry timing. During the initial 750 km, 1 month long migration after release, we found no evidence of decreased estuarine or ocean survival of transported groups; therefore, decreased survival to adulthood for transported Chinook is likely caused by factors other than delayed effects of transportation, such as earlier ocean entry.
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 6
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    Sequence requirements for RNA binding by HuR and AUF1 (2012)
    Oxford University Press
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    Publication Date: 2012-04-25
    Description: The stability of RNAs bearing AU-rich elements in their 3'-UTRs, and thus the level of expression of their protein products, is regulated by interactions with cytoplasmic RNA-binding proteins. Binding by HuR generally leads to mRNA stabilization and increased protein production, whereas binding by AUF1 isoforms generally lead to rapid degradation of the mRNA and reduced protein production. The exact nature of the interplay between these and other RNA-binding proteins remains unclear, although recent studies have shown close interactions between them and even suggested competition between the two for binding to their cognate recognition sequences. Other recent reports have suggested that the sequences recognized by the two proteins are different. We therefore performed a detailed in vitro analysis of the binding site(s) for HuR and AUF1 present in androgen receptor mRNA to define their exact target sequences, and show that the same sequence is contacted by both proteins. Furthermore, we analysed a proposed HuR target within the 3'-UTR of MTA1 mRNA, and show that the contacted bases lie outside of the postulated motif and are a better match to a classical ARE than the postulated motif. The defining features of these HuR binding sites are their U-richness and single strandedness.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
    Published by Oxford University Press on behalf of The Japanese Biochemical Society (JBS).
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  • 7
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    Suppression of thermal conductivity by rattling modes in thermoelectric sodium cobaltate (2013)
    Springer Nature
    Details
    Publication Date: 2013-10-24
    Description: Nature Materials 12, 1028 (2013). doi:10.1038/nmat3739 Authors: D. J. Voneshen, K. Refson, E. Borissenko, M. Krisch, A. Bosak, A. Piovano, E. Cemal, M. Enderle, M. J. Gutmann, M. Hoesch, M. Roger, L. Gannon, A. T. Boothroyd, S. Uthayakumar, D. G. Porter & J. P. Goff The need for both high electrical conductivity and low thermal conductivity creates a design conflict for thermoelectric systems, leading to the consideration of materials with complicated crystal structures. Rattling of ions in cages results in low thermal conductivity, but understanding the mechanism through studies of the phonon dispersion using momentum-resolved spectroscopy is made difficult by the complexity of the unit cells. We have performed inelastic X-ray and neutron scattering experiments that are in remarkable agreement with our first-principles density-functional calculations of the phonon dispersion for thermoelectric Na0.8CoO2, which has a large-period superstructure. We have directly observed an Einstein-like rattling mode at low energy, involving large anharmonic displacements of the sodium ions inside multi-vacancy clusters. These rattling modes suppress the thermal conductivity by a factor of six compared with vacancy-free NaCoO2. Our results will guide the design of the next generation of materials for applications in solid-state refrigerators and power recovery.
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 8
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    Nitrogen uptake over entire root systems of tree seedlings (2014)
    Oxford University Press
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    Publication Date: 2014-05-06
    Description: Uptake of nitrogen (N) by sequential root regions in six tree species was measured in roots of 16- to 26-month-old seedlings at 50 and 1500 µM NH 4 NO 3 concentration, at the cell level using oscillating microelectrodes and at the root region level using enriched 15 N application. Our objective was to determine the root regions making the greatest contribution to total N uptake in each species as measured by the two contrasting techniques. White and condensed tannin zones were the regions with the smallest surface area in all species, but these zones often had the highest net flux of NH 4 + and NO 3 – . For most species, little variation was found among root regions in N flux calculated using a 15 N mass balance approach, but where significant differences existed, high N flux was observed in white, cork or woody zones. When N fluxes measured by each of the two methods were multiplied by the estimated surface area or biomass of each root region, the effect of root region size had the greatest influence on regional N uptake. Root regions of greatest overall N uptake were the cork and woody zones, on average. Total N uptake may thus be greatest in older regions of tree seedling roots, despite low rates of uptake per unit area.
    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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    Modelling the ages and metallicities of early-type galaxies in Fundamental Plane space (2014)
    Oxford University Press
    Details
    Publication Date: 2014-10-26
    Description: Recent observations have probed the formation histories of nearby elliptical galaxies by tracking correlations between the stellar population parameters, age and metallicity, and the structural parameters that enter the Fundamental Plane, size R e , and velocity dispersion . These studies have found intriguing correlations between these four parameters. In this work, we make use of a semi-analytic model, based on halo merger trees extracted from the Bolshoi cosmological simulation, that predicts the structural properties of spheroid-dominated galaxies based on an analytic model that has been tested and calibrated against an extensive suite of hydrodynamic+ N -body binary merger simulations. We predict the R e , , luminosity, age, and metallicity of spheroid-dominated galaxies, enabling us to compare directly to observations. Our model predicts a strong correlation between age and for early-type galaxies, and no significant correlation between age and radius, in agreement with observations. In addition, we predict a strong correlation between metallicity and , and a weak correlation between metallicity and R e , in qualitative agreement with observations. We find that the correlations with arise as a result of the strong link between and the galaxy's assembly time. Minor mergers produce a large change in radius while leaving nearly the same, which explains the weaker trends with radius.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Enrichment of pathogenic alleles in the brittle cornea gene, ZNF469, in keratoconus (2014)
    Oxford University Press
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    Publication Date: 2014-09-20
    Description: Keratoconus, a common inherited ocular disorder resulting in progressive corneal thinning, is the leading indication for corneal transplantation in the developed world. Genome-wide association studies have identified common SNPs 100 kb upstream of ZNF469 strongly associated with corneal thickness. Homozygous mutations in ZNF469 and PR domain-containing protein 5 ( PRDM5 ) genes result in brittle cornea syndrome (BCS) Types 1 and 2, respectively. BCS is an autosomal recessive generalized connective tissue disorder associated with extreme corneal thinning and a high risk of corneal rupture. Some individuals with heterozygous PRDM5 mutations demonstrate a carrier ocular phenotype, which includes a mildly reduced corneal thickness, keratoconus and blue sclera. We hypothesized that heterozygous variants in PRDM5 and ZNF469 predispose to the development of isolated keratoconus. We found a significant enrichment of potentially pathologic heterozygous alleles in ZNF469 associated with the development of keratoconus ( P = 0.00102) resulting in a relative risk of 12.0. This enrichment of rare potentially pathogenic alleles in ZNF469 in 12.5% of keratoconus patients represents a significant mutational load and highlights ZNF469 as the most significant genetic factor responsible for keratoconus identified to date.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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