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  • Oxford University Press  (30,734)
  • 2010-2014  (30,734)
  • 2013  (19,048)
  • 2011  (11,686)
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  • 2010-2014  (30,734)
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  • 1
    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
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  • 2
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.
    Description: Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.
    Description: University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.).
    Repository Name: Woods Hole Open Access Server
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  • 3
    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 Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.
    Description: The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.
    Description: National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.].
    Keywords: Next-generation sequencing ; Sequencing error ; Adapter ligation ; PCR ; Quality score
    Repository Name: Woods Hole Open Access Server
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  • 4
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    Oxford University Press
    In:  Encyclopedia of Climate and Weather, 2. ed.
    Publication Date: 2022-03-21
    Type: info:eu-repo/semantics/bookPart
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  • 5
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    Oxford University Press
    In:  Encyclopedia of Climate and Weather, 2. ed.
    Publication Date: 2022-03-21
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  • 6
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    Oxford University Press
    In:  Encyclopedia of Climate and Weather, 2. ed.
    Publication Date: 2022-03-21
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  • 7
    Publication Date: 2020-11-20
    Description: Siwi caldera, in the Vanuatu arc (Tanna island), is a rare volcanic complex where both persistent eruptive activity (Yasur volcano)and rapid block resurgence (Yenkahe horst) can be investigated simultaneously during a post-caldera stage. Here we provide new constraints on the feeding system of this volcanic complex, based on a detailed study of the petrology, geochemistry and volatile content of Yasur^Siwi bulk-rocks and melt inclusions, combined with measurements of the chemical composition and mass fluxes of Yasur volcanic gases. Major and trace element analyses of Yasur^ Siwi volcanic rocks, together with literature data for other volcanic centers, point to a single magmatic series and possibly long-lived feeding of Tanna volcanism by a homogeneous arc basalt. Olivine-hosted melt inclusions show that the parental basaltic magma, which produces basaltic-trachyandesites to trachyandesites by 50^70% crystal fractionation, is moderately enriched in volatiles ( 1wt % H2O, 0·1wt % S and 0·055 wt % Cl). The basaltic-trachyandesite magma, emplaced at between 4^5 km depth and the surface, preserves a high temperature (1107 158C) and constant H2O content ( 1wt %) until very shallow depths, where it degasses extensively and crystallizes. These conditions, maintained over the past 1400 years of Yasur activity, require early water loss during basalt differentiation, prevalent open-system degassing, and a relatively high heat flow ( 109W). Yasur volcano releases on average 13·4 103 tons d 1 of H2O and 680 tons d 1 of SO2, but moderate amounts of CO2 (840 tons d 1), HCl (165 tons d 1), and HF (23 tons d 1). Combined with melt inclusion data, these gas outputs constrain a bulk magma degassing rate of 5 107 m3 a 1, about a half of which is due to degassing of the basaltic-trachyandesite. We compute that 25 km3 of this magma have degassed without erupting and have accumulated beneath Siwi caldera over the past 1000 years, which is one order of magnitude larger than the accumulated volume uplift of the Yenkahe resurgent block. Hence, basalt supply and gradual storage of unerupted degassed basaltictrachyandesite could easily account for (or contribute to) the Yenkahe block resurgence.
    Description: Published
    Description: 1077-1105
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: restricted
    Keywords: Vanuatu arc ; Yasur ; gas fluxes ; volatiles ; melt inclusions ; resurgent block ; volcano thermal budget ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 8
    Publication Date: 2020-07-31
    Description: The aim of this study was to examine sponge orange band (SOB) disease affecting the prominent Caribbean sponge Xestospongia muta. Scanning and transmission electron microscopy revealed that SOB is accompanied by the massive destruction of the pinacoderm. Chlorophyll a content and the main secondary metabolites, tetrahydrofurans, characteristic of X. muta, were significantly lower in bleached than in healthy tissues. Denaturing gradient gel electrophoresis using cyanobacteria-specific 16S rRNA gene primers revealed a distinct shift from the Synechococcus/Prochlorococcus clade of sponge symbionts towards several clades of unspecific cyanobacteria, including lineages associated with coral disease (i.e. Leptolyngbya sp.). Underwater infection experiments were conducted by transplanting bleached cores into healthy individuals, but revealed no signs of SOB development. This study provided no evidence for the involvement of a specific microbial pathogen as an etiologic agent of disease; hence, the cause of SOB disease in X. muta remains unidentified.
    Type: Article , PeerReviewed
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  • 9
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    Federation of European Microbiological Societies | Oxford University Press
    In:  FEMS Microbiology Ecology, 84 (1). pp. 1-23.
    Publication Date: 2020-07-31
    Description: The vast majority of microbes inhabiting the subseafloor remain uncultivated and their energy sources unknown. Thus, a focus of ocean drilling expeditions over the past decade has been to characterize the distribution of microbes associated with specific metabolic reactions. An important question has been whether microbes involved in key microbial processes, such as sulfate reduction and methanogenesis, differ fundamentally from their counterparts in surface environments. To this end, functional genes of anaerobic methane cycling (mcrA), sulfate reduction (dsrAB), acetogenesis (fhs), and dehalorespiration (rdhA) have been examined. A compilation of existing functional gene data suggests that subseafloor microbes involved in anaerobic methane cycling, sulfate reduction, acetogenesis, and dehalorespiration are not fundamentally different from their counterparts in the surface world. Moreover, quantifications of mcrA and dsrAB suggest that, unless the majority of subseafloor microbes involved in methane cycling and sulfate reduction are too genetically divergent to be detected with conventional methods, these processes only support a small fraction (〈 1%) of total microbial biomass in the deep biosphere. Ecological explanations for the observed trends, target processes and methods for future investigations, and strategies for tackling the unresolved issue of microbial contamination in samples obtained by ocean drilling are discussed.
    Type: Article , PeerReviewed
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  • 10
    Publication Date: 2020-07-24
    Description: The concentration of CO2 in global surface ocean waters is increasing due to rising atmospheric CO2 emissions, resulting in lower pH and a lower saturation state of carbonate ions. Such changes in seawater chemistry are expected to impact calcification in calcifying marine organisms. However, other physiological processes related to calcification might also be affected, including enzyme activity. In a mesocosm experiment, macroalgal communities were exposed to three CO2 concentrations (380, 665, and 1486 µatm) to determine how the activity of two enzymes related to inorganic carbon uptake and nutrient assimilation in Corallina officinalis, an abundant calcifying rhodophyte, will be affected by elevated CO2 concentrations. The activity of external carbonic anhydrase, an important enzyme functioning in macroalgal carbon-concentrating mechanisms, was inversely related to CO2 concentration after long-term exposure (12 weeks). Nitrate reductase, the enzyme responsible for reduction of nitrate to nitrite, was stimulated by CO2 and was highest in algae grown at 665 µatm CO2. Nitrate and phosphate uptake rates were inversely related to CO2, while ammonium uptake was unaffected, and the percentage of inorganic carbon in the algal skeleton decreased with increasing CO2. The results indicate that the processes of inorganic carbon and nutrient uptake and assimilation are affected by elevated CO2 due to changes in enzyme activity, which change the energy balance and physiological status of C. officinalis, therefore affecting its competitive interactions with other macroalgae. The ecological implications of the physiological changes in C. officinalis in response to elevated CO2 are discussed.
    Type: Article , PeerReviewed
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