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  • Articles  (35)
  • Biology  (35)
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  • Articles  (35)
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  • 1
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    Prespawning herring distribution in the Irish Celtic Sea between 2005 and 2012 (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-20
    Description: Knowledge of the spatial distribution of species is fundamental to understanding trophic interactions and ecosystem structure. Intraspecies-specific dynamics and environmental factors shape species distribution within an ecosystem. Distribution patterns and the realized habitat of Atlantic herring ( Clupea harengus ), a key fish species in the Celtic Sea, were examined using distribution data collected during annual acoustic stock assessment surveys during 2005–2012. Distribution patterns during migration to spawning grounds were analysed using geostatistical methods, including modelling of variograms and comparing the centre of gravity (CG). Distribution patterns were further linked to oceanographic variables collected with the acoustic data to describe habitat. Herring density was greatest inshore along the spawning grounds and lower farther offshore. Herring shoals were clustered and randomly distributed during spawning migration. Variograms of fish densities described the global structure, with high local variability of the same order of magnitude as variability at a regional scale, indicating that no continuous structure can be found within the study area. The CG values showed that the average position of the population was located northeast. The realized habitat for herring encompassed a wide range of temperatures and salinities; therefore, oceanographic features were not a limiting factor for herring distribution during spawning migration. The present study changes the perception of the spatial distribution of the Celtic Sea herring stock from a more continuous distribution to a discrete model, with implications for trophic ecosystem modelling on local scales. Future studies of herring distribution and its influence within the Celtic Sea ecosystem would benefit from using the approach employed in the present study for analysing aggregation patterns.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 2
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    Altered axonal targeting and short-term plasticity in the hippocampus of Disc1 mutant mice [Neuroscience] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-12-07
    Description: Carefully designed animal models of genetic risk factors are likely to aid our understanding of the pathogenesis of schizophrenia. Here, we study a mouse strain with a truncating lesion in the endogenous Disc1 ortholog designed to model the effects of a schizophrenia-predisposing mutation and offer a detailed account of the consequences that this mutation has on the development and function of a hippocampal circuit. We uncover widespread and cumulative cytoarchitectural alterations in the dentate gyrus during neonatal and adult neurogenesis, which include errors in axonal targeting and are accompanied by changes in short-term plasticity at the mossy fiber/CA3 circuit. We also provide evidence that cAMP levels are elevated as a result of the Disc1 mutation, leading to altered axonal targeting and dendritic growth. The identified structural alterations are, for the most part, not consistent with the growth-promoting and premature maturation effects inferred from previous RNAi-based Disc1 knockdown. Our results provide support to the notion that modest disturbances of neuronal connectivity and accompanying deficits in short-term synaptic dynamics is a general feature of schizophrenia-predisposing mutations.
    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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    Boarfish (Capros aper) target strength modelled from magnetic resonance imaging (MRI) scans of its swimbladder (2013)
    Oxford University Press
    Details
    Publication Date: 2013-10-15
    Description: Fässler, S. M. M., O'Donnell, C., and Jech, J.M. 2013. Boarfish ( Capros aper ) target strength modelled from magnetic resonance imaging (MRI) scans of its swimbladder. – ICES Journal of Marine Science, 70: . Boarfish ( Capros aper ) abundance has increased dramatically in the Northeast Atlantic from the early 1970s after successive years of good recruitment attributed to an increase in sea surface temperature. Due to increased commercial fishing over recent years, an acoustic boarfish survey funded by the Killybegs Fishermen's Organisation was initiated by the Marine Institute to establish a baseline for the future management of this stock. In the absence of any species-specific boarfish target strength ( TS ), acoustic backscatter was estimated by a Kirchhoff-ray mode model using reconstructed three-dimensional swimbladder shapes which were computed from magnetic resonance imaging scans of whole fish. The model predicted TS as a function of size, fish tilt angle, and operating frequency. Standardized directivity patterns revealed the increasing importance of changes in the inclination of the dorsal swimbladder surface at higher frequencies (120 and 200 kHz) and a less directive response at lower frequencies (18 and 38 kHz). The model predicted a TS -to-total fish length relationship of TS = 20 log 10 ( L ) – 66.2. The intercept is ~1 dB higher than in the general physoclist relationship, potentially reflecting the bulky nature of the boarfish swimbladder with its relatively large circumference.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 4
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    Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-20
    Description: The study of genetic influences on drug response and efficacy (‘pharmacogenetics’) has existed for over 50 years. Yet, we still lack a complete picture of how genetic variation, both common and rare, affects each individual's responses to medications. Exome sequencing is a promising alternative method for pharmacogenetic discovery as it provides information on both common and rare variation in large numbers of individuals. Using exome data from 2203 AA and 4300 Caucasian individuals through the NHLBI Exome Sequencing Project, we conducted a survey of coding variation within 12 Cytochrome P450 ( CYP ) genes that are collectively responsible for catalyzing nearly 75% of all known Phase I drug oxidation reactions. In addition to identifying many polymorphisms with known pharmacogenetic effects, we discovered over 730 novel nonsynonymous alleles across the 12 CYP genes of interest. These alleles include many with diverse functional effects such as premature stop codons, aberrant splicesites and mutations at conserved active site residues. Our analysis considering both novel, predicted functional alleles as well as known, actionable CYP alleles reveals that rare, deleterious variation contributes markedly to the overall burden of pharmacogenetic alleles within the populations considered, and that the contribution of rare variation to this burden is over three times greater in AA individuals as compared with Caucasians. While most of these impactful alleles are individually rare, 7.6–11.7% of individuals interrogated in the study carry at least one newly described potentially deleterious alleles in a major drug-metabolizing CYP .
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 5
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    Climate change and latitudinal patterns of intertidal thermal stress (2002)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2002-11-02
    Description: The interaction of climate and the timing of low tides along the West Coast of the United States creates a complex mosaic of thermal environments, in which northern sites can be more thermally stressful than southern sites. Thus, climate change may not lead to a poleward shift in the distribution of intertidal organisms, as has been proposed, but instead will likely cause localized extinctions at a series of "hot spots." Patterns of exposure to extreme climatic conditions are temporally variable, and tidal predictions suggest that in the next 3 to 5 years "hot spots" are likely to appear at several northern sites.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Helmuth, Brian -- Harley, Christopher D G -- Halpin, Patricia M -- O'Donnell, Michael -- Hofmann, Gretchen E -- Blanchette, Carol A -- New York, N.Y. -- Science. 2002 Nov 1;298(5595):1015-7.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉University of South Carolina, Department of Biological Sciences and Marine Sciences Program, Columbia, SC 29208, USA. helmuth@biol.sc.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/12411702" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bivalvia/*physiology ; *Body Temperature ; *Climate ; *Ecosystem ; Environment ; Geography ; Pacific Ocean ; Pacific States ; Seasons ; *Seawater ; Temperature ; *Water Movements
    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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  • 6
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    The replisome uses mRNA as a primer after colliding with RNA polymerase (2008)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2008-11-21
    Description: Replication forks are impeded by DNA damage and protein-nucleic acid complexes such as transcribing RNA polymerase. For example, head-on collision of the replisome with RNA polymerase results in replication fork arrest. However, co-directional collision of the replisome with RNA polymerase has little or no effect on fork progression. Here we examine co-directional collisions between a replisome and RNA polymerase in vitro. We show that the Escherichia coli replisome uses the RNA transcript as a primer to continue leading-strand synthesis after the collision with RNA polymerase that is displaced from the DNA. This action results in a discontinuity in the leading strand, yet the replisome remains intact and bound to DNA during the entire process. These findings underscore the notable plasticity by which the replisome operates to circumvent obstacles in its path and may explain why the leading strand is synthesized discontinuously in vivo.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2605185/" 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/PMC2605185/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pomerantz, Richard T -- O'Donnell, Mike -- R01 GM038839/GM/NIGMS NIH HHS/ -- R01 GM038839-21/GM/NIGMS NIH HHS/ -- R37 GM038839/GM/NIGMS NIH HHS/ -- R37 GM038839-20/GM/NIGMS NIH HHS/ -- England -- Nature. 2008 Dec 11;456(7223):762-6. doi: 10.1038/nature07527. Epub 2008 Nov 19.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, New York 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19020502" target="_blank"〉PubMed〈/a〉
    Keywords: DNA Polymerase III/*metabolism ; DNA Replication ; DNA, Bacterial/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli/genetics/*metabolism ; Models, Molecular ; *Rna ; RNA, Bacterial/*metabolism ; RNA, Messenger/*metabolism
    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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  • 7
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    Structural biology. Getting DNA to unwind (2007)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2007-09-01
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Georgescu, Roxana E -- O'Donnell, Mike -- GM38839/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Aug 31;317(5842):1181-2.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Laboratory of DNA Replication, Howard Hughes Medical Institute, Rockefeller University, New York, NY 10065, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17761872" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphate/metabolism ; Aeropyrum/*chemistry/metabolism ; Archaeal Proteins/*chemistry/metabolism ; Binding Sites ; DNA, Archaeal/*chemistry/metabolism ; Dimerization ; Models, Molecular ; Nucleic Acid Conformation ; Origin Recognition Complex/*chemistry/*metabolism ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; Replication Origin ; Sulfolobus solfataricus/*chemistry/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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    Direct restart of a replication fork stalled by a head-on RNA polymerase (2010)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2010-01-30
    Description: In vivo studies suggest that replication forks are arrested by encounters with head-on transcription complexes. Yet, the fate of the replisome and RNA polymerase (RNAP) after a head-on collision is unknown. We found that the Escherichia coli replisome stalls upon collision with a head-on transcription complex, but instead of collapsing, the replication fork remains highly stable and eventually resumes elongation after displacing the RNAP from DNA. We also found that the transcription-repair coupling factor Mfd promotes direct restart of the fork after the collision by facilitating displacement of the RNAP. These findings demonstrate the intrinsic stability of the replication apparatus and a previously unknown role for the transcription-coupled repair pathway in promoting replication past a RNAP block.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2861996/" 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/PMC2861996/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Pomerantz, Richard T -- O'Donnell, Mike -- R01 GM038839/GM/NIGMS NIH HHS/ -- R01 GM038839-23/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2010 Jan 29;327(5965):590-2. doi: 10.1126/science.1179595.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Rockefeller University, Howard Hughes Medical Institute, 1230 York Avenue, New York, NY 10021, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20110508" target="_blank"〉PubMed〈/a〉
    Keywords: Bacterial Proteins/metabolism ; DNA Repair ; *DNA Replication ; DNA, Bacterial/*metabolism ; DNA-Directed DNA Polymerase/metabolism ; DNA-Directed RNA Polymerases/*metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/metabolism ; Templates, Genetic ; Transcription Factors/metabolism ; Transcription, Genetic
    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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  • 9
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    How a DNA polymerase clamp loader opens a sliding clamp (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-12-24
    Description: Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281585/" 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/PMC3281585/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelch, Brian A -- Makino, Debora L -- O'Donnell, Mike -- Kuriyan, John -- F32 GM087888/GM/NIGMS NIH HHS/ -- F32 GM087888-02/GM/NIGMS NIH HHS/ -- F32-087888/PHS HHS/ -- R01 GM038839/GM/NIGMS NIH HHS/ -- R01 GM038839-26/GM/NIGMS NIH HHS/ -- R01 GM045547/GM/NIGMS NIH HHS/ -- R01 GM045547-20/GM/NIGMS NIH HHS/ -- R01-GM308839/GM/NIGMS NIH HHS/ -- R01-GM45547/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Dec 23;334(6063):1675-80. doi: 10.1126/science.1211884.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194570" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Bacteriophage T4 ; Binding Sites ; Crystallography, X-Ray ; DNA, A-Form/*chemistry/metabolism ; DNA, Viral/*chemistry/metabolism ; DNA-Directed DNA Polymerase/chemistry/*metabolism ; Hydrolysis ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Static Electricity ; Templates, Genetic ; Trans-Activators/*chemistry/metabolism ; Viral Proteins/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 10
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    Water and climate risks to power generation with carbon capture and storage (2016)
    Institute of Physics (IOP)
    Details
    Publication Date: 2016-02-13
    Description: Carbon capture and storage (CCS) provides the opportunity to minimize atmospheric carbon emissions from fossil fuel power plants. However, CCS increases cooling water use and few studies have simulated the potential impacts of low flows on CCS power plant reliability. We present a framework to simulate the impacts of natural hydrological variability and climatic changes on water availability for portfolios of CCS capacity and cooling technologies. The methods are applied to the River Trent, the UK’s largest inland cooling water source for electricity generation capacity. Under a medium emissions climate change scenario, the projected median reductions in river flow by the 2040s was 43% for Q 99.9 very low flows and 31% in licensable abstractions between Q 99.9 and Q 91 . With CCS developments, cooling water abstractions are projected to increase, likely exceeding available water for all users by the 2030s–2040s. Deficits are r...
    Print ISSN: 1748-9318
    Electronic ISSN: 1748-9326
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering
    Published by Institute of Physics (IOP)
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