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  • Wiley  (4)
  • 2015-2019  (4)
  • 1
    In: Molecular Ecology Resources, Wiley, Vol. 18, No. 2 ( 2018-03), p. 204-216
    Abstract: Next‐generation sequencing is a common method for analysing microbial community diversity and composition. Configuring an appropriate sequence processing strategy within the variety of tools and methods is a nontrivial task and can considerably influence the resulting community characteristics. We analysed the V4 region of 18S rRNA gene sequences of marine samples by 454‐pyrosequencing. Along this process, we generated several data sets with QIIME , mothur, and a custom‐made pipeline based on DNAS tar and the phylogenetic tree‐based PhyloAssigner. For all processing strategies, default parameter settings and punctual variations were used. Our results revealed strong differences in total number of operational taxonomic units ( OTU s), indicating that sequence preprocessing and clustering had a major impact on protist diversity estimates. However, diversity estimates of the abundant biosphere (abundance of ≥1%) were reproducible for all conducted processing pipeline versions. A qualitative comparison of diatom genera emphasized strong differences between the pipelines in which phylogenetic placement of sequences came closest to light microscopy‐based diatom identification. We conclude that diversity studies using different sequence processing strategies are comparable if the focus is on higher taxonomic levels, and if abundance thresholds are used to filter out OTU s of the rare biosphere.
    Type of Medium: Online Resource
    ISSN: 1755-098X , 1755-0998
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2018
    detail.hit.zdb_id: 2406833-0
    SSG: 12
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  • 2
    In: Global Change Biology, Wiley, Vol. 23, No. 4 ( 2017-04), p. 1499-1510
    Abstract: Thermal tolerance windows serve as a powerful tool for estimating the vulnerability of marine species and their life stages to increasing temperature means and extremes. However, it remains uncertain to which extent additional drivers, such as ocean acidification, modify organismal responses to temperature. This study investigated the effects of CO 2 ‐driven ocean acidification on embryonic thermal sensitivity and performance in Atlantic cod, Gadus morhua , from the Kattegat. Fertilized eggs were exposed to factorial combinations of two P CO 2 conditions (400  μ atm vs. 1100  μ atm) and five temperature treatments (0, 3, 6, 9 and 12 °C), which allow identifying both lower and upper thermal tolerance thresholds. We quantified hatching success, oxygen consumption ( M O 2 ) and mitochondrial functioning of embryos as well as larval morphometrics at hatch and the abundance of acid–base‐relevant ionocytes on the yolk sac epithelium of newly hatched larvae. Hatching success was high under ambient spawning conditions (3–6 °C), but decreased towards both cold and warm temperature extremes. Elevated P CO 2 caused a significant decrease in hatching success, particularly at cold (3 and 0 °C) and warm (12 °C) temperatures. Warming imposed limitations to M O 2 and mitochondrial capacities. Elevated P CO 2 stimulated M O 2 at cold and intermediate temperatures, but exacerbated warming‐induced constraints on M O 2 , indicating a synergistic interaction with temperature. Mitochondrial functioning was not affected by P CO 2 . Increased M O 2 in response to elevated P CO 2 was paralleled by reduced larval size at hatch. Finally, ionocyte abundance decreased with increasing temperature, but did not differ between P CO 2 treatments. Our results demonstrate increased thermal sensitivity of cod embryos under future P CO 2 conditions and suggest that acclimation to elevated P CO 2 requires reallocation of limited resources at the expense of embryonic growth. We conclude that ocean acidification constrains the thermal performance window of embryos, which has important implication for the susceptibility of cod to projected climate change.
    Type of Medium: Online Resource
    ISSN: 1354-1013 , 1365-2486
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2017
    detail.hit.zdb_id: 2020313-5
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    Wiley ; 2019
    In:  Rapid Communications in Mass Spectrometry Vol. 33, No. 2 ( 2019-01-30), p. 193-202
    In: Rapid Communications in Mass Spectrometry, Wiley, Vol. 33, No. 2 ( 2019-01-30), p. 193-202
    Abstract: High‐resolution mass spectrometry (HRMS) with high sample throughput has become an important analytical tool for the analysis of highly complex samples and data processing has become a major challenge for the user community. Evaluating direct‐infusion HRMS data without automated tools for batch processing can be a time‐consuming step in the analytical pipeline. Therefore, we developed a new browser‐based software tool for processing HRMS data. Methods The software, named UltraMassExplorer (UME), was written in the R programming language using the shiny library to build the graphical user interface. The performance of the integrated formula library search algorithm was tested using HRMS data derived from analyses of up to 50 extracts of marine dissolved organic matter. Results The software supports the processing of lists of calibrated masses of neutral, protonated or deprotonated molecules, with masses of up to 700 Da and a mass accuracy 〈 3 ppm. In the performance test, the number of assigned peaks per second increased with the number of submitted peaks and reached a maximum rate of 4745 assigned peaks per second. Conclusions UME offers a complete data evaluation pipeline comprising a fast molecular formula assignment algorithm allowing for the swift reanalysis of complete datasets, advanced filter functions and the export of data, metadata and publication‐quality graphics. Unique to UME is a fast and interactive connection between data and their visual representation. UME provides a new platform enabling an increased transparency, customization, documentation and comparability of datasets.
    Type of Medium: Online Resource
    ISSN: 0951-4198 , 1097-0231
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2002158-6
    detail.hit.zdb_id: 58731-X
    SSG: 11
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  • 4
    In: Journal of Phycology, Wiley, Vol. 51, No. 1 ( 2015-02), p. 93-108
    Abstract: Macroalgae of the order Laminariales (kelp) are important components of cold‐temperate coastal ecosystems. Major factors influencing their distribution are light (including UV radiation) and temperature. Therefore, future global environmental changes potentially will impact their zonation, distribution patterns, and primary productivity. Many physiological studies were performed on UV radiation and temperature stress in kelp but combinatory effects have not been analyzed and so far no study is available on the molecular processes involved in acclimation to these stresses. Therefore, sporophytes of Saccharina latissima were exposed for 2 weeks to 12 combinations of photosynthetically active radiation ( PAR ), UV radiation and temperature. Subsequently, microarray hybridizations were performed to determine changes in gene expression patterns. Several effects on the transcriptome were observed after exposure experiments. The strongest effect of temperature on gene expression was observed at 2°C. Furthermore, UV radiation had stronger effects on gene expression than high PAR , and caused stronger induction genes correlated with categories such as photosynthetic components and vitamin B 6 biosynthesis. Higher temperatures ameliorated the negative effects of UV radiation in S. latissima . Regulation of reactive oxygen species ( ROS ) scavenging seems to work in a compartment specific way. Gene expression profiles of ROS scavengers indicated a high amount of oxidative stress in response to the 2°C condition as well as to excessive light at 12°C. Interestingly, stress levels that did not lead to physiological alterations already caused by a transcriptomic response.
    Type of Medium: Online Resource
    ISSN: 0022-3646 , 1529-8817
    URL: Issue
    RVK:
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 281226-5
    detail.hit.zdb_id: 1478748-9
    SSG: 12
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