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  • 1
    Publikationsdatum: 2022-05-25
    Beschreibung: © 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.
    Beschreibung: 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.
    Beschreibung: 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.
    Schlagwort(e): Blow ; Biopsy dart ; Cetacea ; Faecal samples ; Non-invasive ; Visual health assessment
    Repository-Name: Woods Hole Open Access Server
    Materialart: Article
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  • 2
    Publikationsdatum: 2022-05-25
    Beschreibung: © 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.
    Beschreibung: 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/.
    Beschreibung: 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.).
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  • 3
    Publikationsdatum: 2022-05-25
    Beschreibung: © 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.
    Beschreibung: 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.
    Beschreibung: National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.].
    Schlagwort(e): Next-generation sequencing ; Sequencing error ; Adapter ligation ; PCR ; Quality score
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  • 4
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    Oxford University Press
    In:  EPIC3Journal of Experimental Botany, Oxford University Press, ISSN: 0022-0957
    Publikationsdatum: 2019-07-17
    Repository-Name: EPIC Alfred Wegener Institut
    Materialart: Article , isiRev
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  • 5
    Publikationsdatum: 2019-07-17
    Beschreibung: Enhancement of ocean alkalinity using calcium compounds, e.g., lime has been proposed to mitigate further increase of atmospheric CO2 and ocean acidification due to anthropogenic CO2 emissions. Using a global model, we show that such alkalinization has the potential to preserve pH and the saturation state of carbonate minerals at close to today’s values. Effects of alkalinization persist after termination: Atmospheric CO2 and pH do not return to unmitigated levels. Only scenarios in which large amounts of alkalinity (i.e., in a ratio of 2:1 with respect to emitted CO2) are added over large ocean areas can boost oceanic CO2 uptake sufficiently to avoid further ocean acidification on the global scale, thereby elevating some key biogeochemical parameters, e.g., pH significantly above preindustrial levels. Smaller-scale alkalinization could counteract ocean acidification on a subregional or even local scale, e.g., in upwelling systems. The decrease of atmospheric CO2 would then be a small side effect.
    Repository-Name: EPIC Alfred Wegener Institut
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  • 6
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    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 40(22), pp. 5882-5887, ISSN: 0094-8276
    Publikationsdatum: 2019-07-17
    Beschreibung: Optical televiewer luminosity logs are compared with densities measured gravimetrically on 520 snow, firn and ice samples from two locations of similar annual temperature (~-14 °C) and contrasting accumulation rates (0.23 and 0.43 m w.e. per year) on the Roi Baudouin Ice Shelf, Antarctica. At the scale of ≥10-1 m, an inverse exponential relationship (R2 = 0.96) is recorded between density and luminosity, indicating (i) that OPTV luminosity provides an effective proxy for density at such ice shelves, and (ii) that densities may be reconstructed from boreholes drilled elsewhere by hot water without the need for core material. Our analysis also suggests that this relationship may hold for newly-formed ice as well as for snow and firn. At the scale of ≤10-1 m, both luminosity and density show similar patterns, but precise correlation is confounded by detailed differences between the two records.
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  • 7
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    Wiley
    In:  EPIC3Journal of Geophysical Research-Atmospheres, Wiley, 118(20), pp. 11888-11903, ISSN: 0148-0227
    Publikationsdatum: 2019-07-17
    Beschreibung: We present a climatology of the diurnal variation of short-lived atmospheric compounds, such as ClO, BrO, HO2, and HOCl, as well as longer-lived species: O3, the hydrogen chloride isotopes H35Cl and H37Cl, and HNO3. Measurements were taken by the Superconducting Submillimeter-wave Limb-Emission Sounder (SMILES). This spectrally resolving radiometer, with very low observation noise and altitude range from the lower stratosphere to the lower thermosphere (20–100km), was measuring vertical profiles of absorption spectra along a non-sun-synchronous orbit, thus observing at all local times. We used the retrieved volume mixing ratio profiles to compile climatologies that are a function of pressure, a horizontal coordinate (latitude or equivalent latitude), and a temporal coordinate (solar zenith angle or local solar time). The main product presented are climatologies with a high resolution of the temporal coordinate (diurnal variation climatologies). In addition, we provide climatologies with a high resolution of the horizontal coordinate (zonal climatologies).The diurnal variation climatologies are based on data periods of 2 months and the zonal climatologies on monthly data periods. Consideration of the SMILES time-space sampling patterns with respect to the averaging coordinates is a key issue for climatology creation, especially in case of diurnal variation climatologies. Biases induced by inhomogeneous sampling are minimized by carefully choosing the size of averaging bins. The sampling biases of the diurnal variation climatology of ClO and BrO are investigated in a comparison of homogeneously sampled model data versus SMILES-sampled model data from the stratospheric Lagrangian chemistry and transport model ATLAS. In most cases, the relative sampling error is in the range of 0–20%. The strongest impact of sampling biases is found where the species' temporal gradients are strongest (mostly at sunrise and sunset), with a relative error of 60–100%. The SMILES climatology data sets are available via the SMILES data distribution home page.
    Repository-Name: EPIC Alfred Wegener Institut
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  • 8
    Publikationsdatum: 2019-07-16
    Beschreibung: Estimates of the relative motion between the Hawaiian and Louisville hot spots have consequences for understanding the role and character of deep Pacific-mantle return flow. The relative motion between these primary hot spots can be inferred by comparing the age records for their seamount trails. We report 40Ar/39Ar ages for 18 lavas from 10 seamounts along the Hawaiian-Emperor Seamount Chain (HESC), showing that volcanism started in the sharp portion of the Hawaiian-Emperor Bend (HEB) at ≥47.5 Ma and continued for ≥5 Myr. The slope of the along-track distance from the currently active Hawaiian hot spot plotted versus age is constant (57 ± 2 km/Myr) between ∼57 and 25 Ma in the central ∼1900 km of the seamount chain, including the HEB. This model predicts an age for the oldest Emperor Seamounts that matches published ages, implying that a linear age-distance relationship might extend back to at least 82 Ma. In contrast, Hawaiian age progression was much faster since at least ∼15 Ma and possibly as early as ∼27 Ma. Linear age-distance relations for the Hawaii-Emperor and Louisville seamount chains predict ∼300 km overall hot spot relative motion between 80 and 47.5 Ma, in broad agreement with numerical models of plumes in a convecting mantle, and paleomagnetic data. We show that a change in hot spot relative motion may also have occurred between ∼55 Ma and ∼50 Ma. We interpret this change in hot spot motion as evidence that the HEB reflects a combination of hot spot and plate motion changes driven by the same plate/mantle reorganization.
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  • 9
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    Wiley
    In:  EPIC3Geophysical Research Letters, Wiley, 40(21), pp. 5735-5739, ISSN: 0094-8276
    Publikationsdatum: 2019-07-16
    Beschreibung: The western Ross Sea is one of the key sites for cross-shelf water exchange around Antarctica. The mech- anism through which tides affect the cross-shelf exchange in the northwestern Ross Sea is investigated using numeri- cal simulations. Tides are found to increase the high-salinity shelf water (HSSW) outflow through the impact on the warm water intrusion of open ocean origin. The residual tidal currents are onshore along the Modified Circumpolar Deep Water pathway and therefore enhance its intrusion. Lighter ambient water adjacent to the HSSW increases the cross-flow density gradient, thus strengthening the HSSW export. At the same time, the onshore residual current and increased dilution of the HSSW have the potential to reduce the export rate. Owing to the existence of opposite tidal effects, the strongest HSSW export happens at the inter- mediate tidal forcing strength. The amplification of tides on cross-shelf exchange indicates that the relevant dynam- ical processes should be simulated or parameterized in climate models in order to adequately predict the ocean.
    Repository-Name: EPIC Alfred Wegener Institut
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  • 10
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    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 193(3), pp. 1399-1414, ISSN: 0956-540X
    Publikationsdatum: 2019-07-16
    Beschreibung: The Boreas Basin is located in the Norwegian-Greenland Sea between Northeast Greenland and Svalbard. Towards the east, it is bounded by the ultraslow mid-ocean Knipovich Ridge. Here, we present a 340-km-long seismic refraction line acquired during the expedition ARK-XXIV/3 of research vessel Polarstern in 2009, using 18 ocean bottom seismometers. It crosses the central Boreas Basin from the Knipovich Ridge to the Northeast Greenland margin. Thus, the line provides the first reliable crustal structure information of this basin. In addition, the gravity data acquired parallel to the seismic refraction line are used to calculate a 2.5-D gravity model. The P-wave velocity model shows an unusual ∼3-km-thin oceanic crust with seismic velocities less than 6.3 km s−1, indicating the absence of a significant oceanic layer 3. Mantle velocities vary between 7.5 kms−1 in the uppermost mantle and 8.0 km s−1 at approximately 15 km depth. The low velocities within the upper mantle may be explained by 13 per cent serpentinisation, which is negligible at about 15 km depth. Furthermore, the S-wave velocity model shows low Vp/Vs ratios in the mantle, indicating a highly serpentinised mantle at shallow depths. The gravity model has crustal densities between 2.3 and 2.9 g cm−3, which also point towards the absence of a significant thick oceanic layer 3. The results of our seismic refraction line and other geophysical data indicate that the entire Boreas Basin opened at ultraslow spreading rates since at least ∼28 Ma. No evidence for an extinct spreading ridge in the centre of the Boreas Basin was found.
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