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Search: (WFRF:(Sørensen Søren J)) > (2015-2019)

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  • Gupta, Shashank, 1989-, et al. (author)
  • Amplicon sequencing provides more accurate microbiome information in healthy children compared to culturing
  • 2019
  • In: Communications Biology. - : Springer Nature. - 2399-3642. ; 2:1
  • Journal article (peer-reviewed)abstract
    • Next-Generation Sequencing (NGS) of 16S rRNA gene is now one of the most widely used application to investigate the microbiota at any given body site in research. Since NGS is more sensitive than traditional culture methods (TCMs), many studies have argued for them to replace TCMs. However, are we really ready for this transition? Here we compare the diagnostic efficiency of the two methods using a large number of samples (n = 1,748 fecal and n = 1,790 hypopharyngeal), among healthy children at different time points. Here we show that bacteria identified by NGS represented 75.70% of the unique bacterial species cultured in each sample, while TCM only identified 23.86% of the bacterial species found by amplicon sequencing. We discuss the pros and cons of both methods and provide perspective on how NGS can be implemented effectively in clinical settings.
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3.
  • Heins, Anna Lena, et al. (author)
  • Quantitative flow cytometry to understand population heterogeneity in response to changes in substrate availability in escherichia coli and saccharomyces cerevisiae chemostats
  • 2019
  • In: Frontiers in Bioengineering and Biotechnology. - : Frontiers Media SA. - 2296-4185. ; 7:AUG
  • Journal article (peer-reviewed)abstract
    • Microbial cells in bioprocesses are usually described with averaged parameters. But in fact, single cells within populations vary greatly in characteristics such as stress resistance, especially in response to carbon source gradients. Our aim was to introduce tools to quantify population heterogeneity in bioprocesses using a combination of reporter strains, flow cytometry, and easily comprehensible parameters. We calculated mean, mode, peak width, and coefficient of variance to describe distribution characteristics and temporal shifts in fluorescence intensity. The skewness and the slope of cumulative distribution function plots illustrated differences in distribution shape. These parameters are person-independent and precise. We demonstrated this by quantifying growth-related population heterogeneity of Saccharomyces cerevisiae and Escherichia coli reporter strains in steady-state of aerobic glucose-limited chemostat cultures at different dilution rates and in response to glucose pulses. Generally, slow-growing cells showed stronger responses to glucose excess than fast-growing cells. Cell robustness, measured as membrane integrity after exposure to freeze-thaw treatment, of fast-growing cells was strongly affected in subpopulations of low membrane robustness. Glucose pulses protected subpopulations of fast-growing but not slower-growing yeast cells against membrane damage. Our parameters could successfully describe population heterogeneity, thereby revealing physiological characteristics that might have been overlooked during traditional averaged analysis.
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