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  • Oxford University Press  (544)
  • 2010-2014  (347)
  • 2005-2009  (138)
  • 1990-1994  (59)
  • 1
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    Overcoming the challenges of studying conservation physiology in large whales : a review of available methods (2013)
    Oxford University Press
    Details
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 1 (2013): cot006, doi:10.1093/conphys/cot006.
    Description: Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples (‘blow’), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.
    Description: This work was supported by the United States Office of Naval Research (award #N000141110435 to K.E.H., award #N000141110540 to R.M.R., and award #N0001412WX20890 to L.C.Y. and C.E.D.); the United Kingdom Natural Environmental Research Council (supporting A.J.H.); the National Center for Research Resources, a component of the United States National Institutes of Health (NIH; supporting C.E.D.); the NIH Roadmap for Medical Research (UL1 RR024146 supporting C.E.D.); The Hartwell Foundation (supporting C.E.D.) and the 2012 Marine Mammal Breath Workshop, which was funded by the National Oceanic and Atmospheric Administration’s Marine Mammal Health and Stranding Response Program.
    Keywords: Blow ; Biopsy dart ; Cetacea ; Faecal samples ; Non-invasive ; Visual health assessment
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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  • 2
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    Single-Link Cluster Analysis As A Method to Evaluate Spatial and Temporal Properties of Earthquake Catalogues (1990)
    Oxford University Press
    Details
    Publication Date: 1990-01-01
    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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  • 3
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    The expressive power of first-order topological languages (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-26
    Description: We consider the expressive power of the first-order structure 〈, C 〉 where is either of two of different domains of extended regions in Euclidean space, and C(x,y) is the topological relation ‘Region x is in contact with region y .’ We prove two main theorems: Let $$\mathcal{P}$$ [Q] be the domain of bounded, non-empty, rational polyhedra in two- or three-dimensional Euclidean space. A relation over $$\mathcal{P}$$ [Q] is definable in the structure 〈 $$\mathcal{P}$$ [Q], C 〉 if and only if is arithmetic and invariant under rational PL-homeomorphisms of the space to itself. We also extend this result to a number of other domains, including the domain of all polyhedra and the domain of semi-algebraic regions. Let $$\mathcal{R}$$ be the space of bounded, non-empty, closed regular regions in n -dimensional Euclidean space. Any analytical relation over lower dimensional (i.e. empty interior) compact point sets that is invariant under homeomorphism is implicitly definable in the structure 〈 $$\mathcal{R}$$ , C 〉.
    Print ISSN: 0955-792X
    Electronic ISSN: 1465-363X
    Topics: Computer Science , Mathematics
    Published by Oxford University Press
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  • 4
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    The ATLAS3D project - XVII. Linking photometric and kinematic signatures of stellar discs in early-type galaxies (2013)
    Oxford University Press
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    Publication Date: 2013-06-09
    Description: We analyse the morphological structures in galaxies of the ATLAS 3D sample by fitting a single Sérsic profile and decomposing all non-barred objects (180 of 260 objects) in two components parametrized by an exponential and a general Sérsic function. The aim of this analysis is to look for signatures of discs in light distributions of nearby early-type galaxies and compare them to kinematic properties. Using Sérsic index from single-component fits for a distinction between slow and fast rotators, or even late- and early-type galaxies, is not recommended. Assuming that objects with n  〉 3 are slow rotators (or ellipticals), there is only a 22 per cent probability to correctly classify objects as slow rotators (or 37 per cent of previously classified as ellipticals). We show that exponential sub-components, as well as light profiles fitted with only a single component of a low Sérsic index, can be linked with the kinematic evidence for discs in early-type galaxies. The median disc-to-total light ratio for fast and slow rotators is 0.41 and 0.0, respectively. Similarly, the median Sérsic indices of the bulge (general Sérsic component) are 1.7 and 4.8 for fast and slow rotators, respectively. Overall, discs or disc-like structures are present in 83 per cent of early-type galaxies which do not have bars, and they show a full range of disc-to-total light ratios. Discs in early-type galaxies contribute with about 40 per cent to the total mass of the analysed (non-barred) objects. The decomposition into discs and bulges can be used as a rough approximation for the separation between fast and slow rotators, but it is not a substitute, as there is only a 59 per cent probability to correctly recognize slow rotators. We find trends between the angular momentum and the disc-to-total light ratios and the Sérsic index of the bulge, in the sense that high angular momentum galaxies have large disc-to-total light ratios and small bulge indices, but there is none between the angular momentum and the global Sérsic index. We investigate the inclination effects on the decomposition results and confirm that strong exponential profiles can be distinguished even at low inclinations, but medium-size discs are difficult to quantify using photometry alone at inclinations lower than ~50°. Kinematics (i.e. projected angular momentum) remains the best approach to mitigate the influence of the inclination effects. We also find weak trends with mass and environmental density, where disc-dominated galaxies are typically less massive and found at all densities, including the densest region sampled by the ATLAS 3D sample.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    The ATLAS3D project - XVI. Physical parameters and spectral line energy distributions of the molecular gas in gas-rich early-type galaxies (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-09
    Description: We present a detailed study of the physical properties of the molecular gas in a sample of 18 molecular gas-rich early-type galaxies (ETGs) from the ATLAS 3D sample. Our goal is to better understand the star formation processes occurring in those galaxies, starting here with the dense star-forming gas. We use existing integrated 12 CO (1–0, 2–1), 13 CO (1–0, 2–1), HCN (1–0) and HCO + (1–0) observations and new 12 CO (3–2) single-dish data. From these, we derive for the first time the average kinetic temperature, H 2 volume density and column density of the emitting gas in a significant sample of ETGs, using a non-local thermodynamical equilibrium theoretical model. Since the CO lines trace different physical conditions than of those the HCN and HCO + lines, the two sets of lines are treated separately. For most of the molecular gas-rich ETGs studied here, the CO transitions can be reproduced with kinetic temperatures of 10–20 K, H 2 volume densities of 10 3–4 cm –3 and CO column densities of $10^{18\text{--}20}$ cm –2 . The physical conditions corresponding to the HCN and HCO + gas component have large uncertainties and must be considered as indicative only. We also compare for the first time the predicted CO spectral line energy distributions and gas properties of our molecular gas-rich ETGs with those of a sample of nearby well-studied disc galaxies. The gas excitation conditions in 13 of our 18 ETGs appear analogous to those in the centre of the Milky Way, hence the star formation activity driving these conditions is likely of a similar strength and nature. Such results have never been obtained before for ETGs and open a new window to explore further star-formation processes in the Universe. The conclusions drawn should nevertheless be considered carefully, as they are based on a limited number of observations and on a simple model. In the near future, with higher CO transition observations, it should be possible to better identify the various gas components present in ETGs, as well as more precisely determine their associated physical conditions. To achieve these goals, we show here from our theoretical study, that mid- J CO lines [such as the 12 CO (6–5) line] are particularly useful.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    The ATLAS3D project - XVIII. CARMA CO imaging survey of early-type galaxies (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-09
    Description: We present the Combined Array for Research in Millimeter Astronomy (CARMA) ATLAS 3D molecular gas imaging survey, a systematic study of the distribution and kinematics of molecular gas in CO-rich early-type galaxies. Our full sample of 40 galaxies (30 newly mapped and 10 taken from the literature) is complete to a 12 CO(1–0) integrated flux of 18.5 Jy km s –1 , 1 and it represents the largest, best studied sample of its type to date. A comparison of the CO distribution of each galaxy to the g  – r colour image (representing dust) shows that the molecular gas and dust distributions are in good agreement and trace the same underlying interstellar medium. The galaxies exhibit a variety of CO morphologies, including discs (50 per cent), rings (15 per cent), bars+rings (10 per cent), spiral arms (5 per cent) and mildly (12.5 per cent) and strongly (7.5 per cent) disrupted morphologies. There appear to be weak trends between galaxy mass and CO morphology, whereby the most massive galaxies in the sample tend to have molecular gas in a disc morphology. We derive a lower limit to the total accreted molecular gas mass across the sample of 2.48  x 10 10 M , or approximately 8.3  x 10 8 M per minor merger within the sample, consistent with minor merger stellar mass ratios.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    The ATLAS3D project - XIX. The hot gas content of early-type galaxies: fast versus slow rotators (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-09
    Description: For early-type galaxies, the ability to sustain a corona of hot, X-ray-emitting gas could have played a key role in quenching their star formation history. A halo of hot gas may act as an effective shield against the acquisition of cold gas and can quickly absorb stellar mass loss material. Yet, since the discovery by the Einstein Observatory of such X-ray haloes around early-type galaxies, the precise amount of hot gas around these galaxies still remains a matter of debate. By combining homogeneously derived photometric and spectroscopic measurements for the early-type galaxies observed as part of the ATLAS 3D integral field survey with measurements of their X-ray luminosity based on X-ray data of both low and high spatial resolution (for 47 and 19 objects, respectively) we conclude that the hot gas content of early-type galaxies can depend on their dynamical structure. Specifically, whereas slow rotators generally have X-ray haloes with luminosity L X, gas and temperature T values that are well in line with what is expected if the hot gas emission is sustained by the thermalization of the kinetic energy carried by the stellar mass loss material, fast rotators tend to display L X, gas values that fall consistently below the prediction of this model, with similar T values that do not scale with the stellar kinetic energy (traced by the stellar velocity dispersion) as observed in the case of slow rotators. Such a discrepancy between the hot gas content of slow and fast rotators would appear to reduce, or even disappear, for large values of the dynamical mass (above ~3  x 10 11 M ), with younger fast rotators displaying also somewhat larger L X, gas values possibly owing to the additional energy input from recent supernovae explosions. Considering that fast rotators are likely to be intrinsically flatter than slow rotators, and that the few L X, gas -deficient slow rotators also happen to be relatively flat, the observed L X, gas deficiency in these objects would support the hypothesis whereby flatter galaxies have a harder time in retaining their hot gas, although we suggest that the degree of rotational support could further hamper the efficiency with which the kinetic energy of the stellar mass loss material is thermalized in the hot gas. We discuss the implications that a different hot gas content could have on the fate of both acquired and internally produced gaseous material, considering in particular how the L X, gas deficiency of fast rotators would make them more capable to recycle the stellar mass loss material into new stars than slow rotators. This would be consistent with the finding that molecular gas and young stellar populations are detected only in fast rotators across the entire ATLAS 3D sample, and that fast rotators tend to have a larger specific dust mass content than slow rotators.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Study of PcaV from Streptomyces coelicolor yields new insights into ligand-responsive MarR family transcription factors (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-02
    Description: MarR family proteins constitute a group of 〉12 000 transcriptional regulators encoded in bacterial and archaeal genomes that control gene expression in metabolism, stress responses, virulence and multi-drug resistance. There is much interest in defining the molecular mechanism by which ligand binding attenuates the DNA-binding activities of these proteins. Here, we describe how PcaV, a MarR family regulator in Streptomyces coelicolor, controls transcription of genes encoding β-ketoadipate pathway enzymes through its interaction with the pathway substrate, protocatechuate. This transcriptional repressor is the only MarR protein known to regulate this essential pathway for aromatic catabolism. In in vitro assays, protocatechuate and other phenolic compounds disrupt the PcaV–DNA complex. We show that PcaV binds protocatechuate in a 1:1 stoichiometry with the highest affinity of any MarR family member. Moreover, we report structures of PcaV in its apo form and in complex with protocatechuate. We identify an arginine residue that is critical for ligand coordination and demonstrate that it is also required for binding DNA. We propose that interaction of ligand with this arginine residue dictates conformational changes that modulate DNA binding. Our results provide new insights into the molecular mechanism by which ligands attenuate DNA binding in this large family of transcription factors.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Lack of CCM1 induces hypersprouting and impairs response to flow (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: Cerebral cavernous malformation (CCM) is a disease of vascular malformations known to be caused by mutations in one of three genes: CCM1 , CCM2 or CCM3 . Despite several studies, the mechanism of CCM lesion onset remains unclear. Using a Ccm1 knockout mouse model, we studied the morphogenesis of early lesion formation in the retina in order to provide insight into potential mechanisms. We demonstrate that lesions develop in a stereotypic location and pattern, preceded by endothelial hypersprouting as confirmed in a zebrafish model of disease. The vascular defects seen with loss of Ccm1 suggest a defect in endothelial flow response. Taken together, these results suggest new mechanisms of early CCM disease pathogenesis and provide a framework for further study.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    The Comparative Toxicogenomics Database: update 2013 (2012)
    Oxford University Press
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    Publication Date: 2012-12-20
    Description: The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/ ) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical–gene, chemical–disease and gene–disease interactions manually curated from the literature are integrated to generate expanded networks and predict many novel associations between different data types. CTD now contains over 15 million toxicogenomic relationships. To navigate this sea of data, we added several new features, including DiseaseComps (which finds comparable diseases that share toxicogenomic profiles), statistical scoring for inferred gene–disease and pathway–chemical relationships, filtering options for several tools to refine user analysis and our new Gene Set Enricher (which provides biological annotations that are enriched for gene sets). To improve data visualization, we added a Cytoscape Web view to our ChemComps feature, included color-coded interactions and created a ‘slim list’ for our MEDIC disease vocabulary (allowing diseases to be grouped for meta-analysis, visualization and better data management). CTD continues to promote interoperability with external databases by providing content and cross-links to their sites. Together, this wealth of expanded chemical–gene–disease data, combined with novel ways to analyze and view content, continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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