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  • Oxford University Press  (253)
  • American Geophysical Union  (118)
  • Nature Publishing Group (NPG)
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  • 1
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    BBC microcomputer controlled field inversion gel electrophoresis (1988)
    Oxford University Press
    Details
    Publication Date: 1988-01-01
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Dynamic fine-scale sea icescape shapes adult emperor penguin foraging habitat in east Antarctica (2020)
    American Geophysical Union
    Details
    Publication Date: 2022-05-26
    Description: Author Posting. © American Geophysical Union, 2019. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geophysical Research Letters 46(20), (2019): 11206-11218, doi: 10.1029/2019GL084347.
    Description: The emperor penguin, an iconic species threatened by projected sea ice loss in Antarctica, has long been considered to forage at the fast ice edge, presumably relying on large/yearly persistent polynyas as their main foraging habitat during the breeding season. Using newly developed fine‐scale sea icescape data and historical penguin tracking data, this study for the first time suggests the importance of less recognized small openings, including cracks, flaw leads and ephemeral short‐term polynyas, as foraging habitats for emperor penguins. The tracking data retrieved from 47 emperor penguins in two different colonies in East Antarctica suggest that those penguins spent 23% of their time in ephemeral polynyas and did not use the large/yearly persistent, well‐studied polynyas, even if they occur much more regularly with predictable locations. These findings challenge our previous understanding of emperor penguin breeding habitats, highlighting the need for incorporating fine‐scale seascape features when assessing the population persistence in a rapidly changing polar environment.
    Description: This study was supported financially and logistically by the Australian Antarctic Division, the Australian Government's Cooperative Research Centre program through the Antarctic Climate & Ecosystems Cooperative Research Centre, and by the Australian Research Council's Special Research Initiative for Antarctic Gateway Partnership (Project ID SR140300001), the French Polar Institute (Institut Paul Emile Victor, IPEV) research projects, and the postdoctoral scholar award from Woods Hole Oceanographic Institution. S. J. acknowledges support from NSF award 1744794 and 1643901. C. B. and Y. R.‐C. acknowledge support from the BNP Paribas Foundation as part of program SENSEI (SENtinels of the SEa Ice). Y. R.‐C. and R. R. R. acknowledge support from the WWF‐UK through R. Downie. Special thanks go to Y. le Maho in charge of the research program in Terre Adelie in 1996/1997, M. LaRue for the field opportunity in the Ross Sea, illuminating sea icescapes and movements of emperor penguins during the breeding season, D. Ainley for interesting discussions, D. Iles for the proofreading and all colleagues and volunteers involved in the research on emperor penguins in Terre Adélie and at the Mawson Coast, especially D. Rodary and W. Bonneau. All animals in this study were treated in accordance with the IPEV and Polar Environment Committees guidelines, and Australian Antarctic Program Animal Ethics Committee permits. Data and data products related to the paper are available on the following repository http://www.usap‐dc.org/view/dataset/601209 with the doi: 10.15784/601209.
    Description: 2020-03-16
    Keywords: emperor penguin ; sea ice ; iceberg ; fast ice ; polynya ; foraging ecology
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 3
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    Do You Know Your Home’s Flood Risk? (2020)
    American Geophysical Union
    Details
    Publication Date: 2020-06-29
    Description: Search for your address in this new database and get an easy to understand indicator of the potential for flooding now and over the next several decades as climate change alters our environment.
    Print ISSN: 0096-3941
    Electronic ISSN: 2324-9250
    Topics: Geosciences
    Published by American Geophysical Union
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  • 4
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    A Statistical Study of Mid-Atlantic Ridge Earthquakes (1971)
    Oxford University Press
    Details
    Publication Date: 1971-10-01
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 5
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    Use of the HPRT gene to study nuclease-induced DNA double-strand break repair (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-21
    Description: Understanding the mechanisms of chromosomal double-strand break repair (DSBR) provides insight into genome instability, oncogenesis and genome engineering, including disease gene correction. Research into DSBR exploits rare-cutting endonucleases to cleave exogenous reporter constructs integrated into the genome. Multiple reporter constructs have been developed to detect various DSBR pathways. Here, using a single endogenous reporter gene, the X-chromosomal disease gene encoding hypoxanthine phosphoribosyltransferase ( HPRT ), we monitor the relative utilization of three DSBR pathways following cleavage by I-Sce I or CRISPR/Cas9 nucleases. For I-Sce I, our estimated frequencies of accurate or mutagenic non-homologous end-joining and gene correction by homologous recombination are 4.1, 1.5 and 0.16%, respectively. Unexpectedly, I-Sce I and Cas9 induced markedly different DSBR profiles. Also, using an I-Sce I-sensitive HPRT minigene, we show that gene correction is more efficient when using long double-stranded DNA than single- or double-stranded oligonucleotides. Finally, using both endogenous HPRT and exogenous reporters, we validate novel cell cycle phase-specific I-Sce I derivatives for investigating cell cycle variations in DSBR. The results obtained using these novel approaches provide new insights into template design for gene correction and the relationships between multiple DSBR pathways at a single endogenous disease gene.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    A role for human homologous recombination factors in suppressing microhomology-mediated end joining (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-09
    Description: DNA double-strand breaks (DSBs) are toxic lesions, which if improperly repaired can result in cell death or genomic instability. DSB repair is usually facilitated by the classical non-homologous end joining (C-NHEJ), or homologous recombination (HR) pathways. However, a mutagenic alternative NHEJ pathway, microhomology-mediated end joining (MMEJ), can also be deployed. While MMEJ is suppressed by C-NHEJ, the relationship between HR and MMEJ is less clear. Here, we describe a role for HR genes in suppressing MMEJ in human cells. By monitoring DSB mis-repair using a sensitive HPRT assay, we found that depletion of HR proteins, including BRCA2, BRCA1 or RPA, resulted in a distinct mutational signature associated with significant increases in break-induced mutation frequencies, deletion lengths and the annealing of short regions of microhomology (2–6 bp) across the break-site. This signature was dependent on CtIP, MRE11, POLQ and PARP, and thus indicative of MMEJ. In contrast to CtIP or MRE11, depletion of BRCA1 resulted in increased partial resection and MMEJ, thus revealing a functional distinction between these early acting HR factors. Together these findings indicate that HR factors suppress mutagenic MMEJ following DSB resection.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Opsin Repertoire and Expression Patterns in Horseshoe Crabs: Evidence from the Genome of Limulus polyphemus (Arthropoda: Chelicerata) (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-05
    Description: Horseshoe crabs are xiphosuran chelicerates, the sister group to arachnids. As such, they are important for understanding the most recent common ancestor of Euchelicerata and the evolution and diversification of Arthropoda. Limulus polyphemus is the most investigated of the four extant species of horseshoe crabs, and the structure and function of its visual system have long been a major focus of studies critical for understanding the evolution of visual systems in arthropods. Likewise, studies of genes encoding Limulus opsins, the protein component of the visual pigments, are critical for understanding opsin evolution and diversification among chelicerates, where knowledge of opsins is limited, and more broadly among arthropods. In the present study, we sequenced and assembled a high quality nuclear genomic sequence of L. polyphemus and used these data to annotate the full repertoire of Limulus opsins. We conducted a detailed phylogenetic analysis of Limulus opsins, including using gene structure and synteny information to identify relationships among different opsin classes. We used our phylogeny to identify significant genomic events that shaped opsin evolution and therefore the visual system of Limulus . We also describe the tissue expression patterns of the 18 opsins identified and show that transcripts encoding a number, including a peropsin, are present throughout the central nervous system. In addition to significantly extending our understanding of photosensitivity in Limulus and providing critical insight into the genomic evolution of horseshoe crab opsins, this work provides a valuable genomic resource for addressing myriad questions related to xiphosuran physiology and arthropod evolution.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 8
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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
    Details
    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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  • 9
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    Defining clusters of related industries (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-04
    Description: Clusters are geographic concentrations of industries related by knowledge, skills, inputs, demand and/or other linkages. There is an increasing need for cluster-based data to support research, facilitate comparisons of clusters across regions and support policymakers in defining regional strategies. This article develops a novel clustering algorithm that systematically generates and assesses sets of cluster definitions (i.e., groups of closely related industries). We implement the algorithm using 2009 data for U.S. industries (six-digit NAICS), and propose a new set of benchmark cluster definitions that incorporates measures of inter-industry linkages based on co-location patterns, input–output links, and similarities in labor occupations. We also illustrate the algorithm’s ability to compare alternative sets of cluster definitions by evaluating our new set against existing sets in the literature. We find that our proposed set outperforms other methods in capturing a wide range of inter-industry linkages, including the grouping of industries within the same three-digit NAICS.
    Keywords: C38-Classification Methods ; Cluster Analysis ; Factor Models
    Print ISSN: 1468-2702
    Electronic ISSN: 1468-2710
    Topics: Geography , Economics
    Published by Oxford University Press
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  • 10
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    Collisional excitation of [C II], [O I] and CO in massive galaxies (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-28
    Description: Many massive galaxies at the centres of relaxed galaxy clusters and groups have vast reservoirs of warm (~10 000 K) and cold (100 K) gas. In many such low-redshift systems this gas is lifted into the hot interstellar medium in filamentary structures, which are long lived and are typically not forming stars. Two important questions are how far do these reservoirs cool and if cold gas is abundant what is the cause of the low star formation efficiency? Heating and excitation of the filaments from collisions and mixing of hot particles in the surrounding X-ray gas describes well the optical and near infrared line ratios observed in the filaments. In this paper we examine the theoretical properties of dense, cold clouds emitting in the far infrared and sub-millimetre through the bright lines of [C  ii ] 157 μm , [O  i ] 63 μm and CO, exposed to such energetic ionizing particles. We find that optical depth effects and thermal pressure support alone cannot account for the line ratios; however, a very modest additional pressure support can fit the observed [O  i ] 63 μm/[C  ii ] 157 μm line ratios by decreasing the density of the gas. This may also help stabilize the filaments against collapse leading to the low rates of star formation. We make predictions for the line ratios expected from cold gas under these conditions and present diagnostic diagrams for comparison with further observations. We provide our code as an Appendix.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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