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@ARTICLE{Kasahara:1008687,
      author       = {Kasahara, Keitaro and Leygeber, Markus and Seiffarth,
                      Johannes and Ruzaeva, Karina and Drepper, Thomas and Nöh,
                      Katharina and Kohlheyer, Dietrich},
      title        = {{E}nabling oxygen-controlled microfluidic cultures for
                      spatiotemporal microbial single-cell analysis},
      journal      = {Frontiers in microbiology},
      volume       = {14},
      issn         = {1664-302X},
      address      = {Lausanne},
      publisher    = {Frontiers Media},
      reportid     = {FZJ-2023-02478},
      pages        = {1198170},
      year         = {2023},
      abstract     = {Microfluidic cultivation devices that facilitate O2 control
                      enable unique studies of the complex interplay between
                      environmental O2 availability and microbial physiology at
                      the single-cell level. Therefore, microbial single-cell
                      analysis based on time-lapse microscopy is typically used to
                      resolve microbial behavior at the single-cell level with
                      spatiotemporal resolution. Time-lapse imaging then provides
                      large image-data stacks that can be efficiently analyzed by
                      deep learning analysis techniques, providing new insights
                      into microbiology. This knowledge gain justifies the
                      additional and often laborious microfluidic experiments.
                      Obviously, the integration of on-chip O2 measurement and
                      control during the already complex microfluidic cultivation,
                      and the development of image analysis tools, can be a
                      challenging endeavor. A comprehensive experimental approach
                      to allow spatiotemporal single-cell analysis of living
                      microorganisms under controlled O2 availability is presented
                      here. To this end, a gas-permeable polydimethylsiloxane
                      microfluidic cultivation chip and a low-cost 3D-printed
                      mini-incubator were successfully used to control O2
                      availability inside microfluidic growth chambers during
                      time-lapse microscopy. Dissolved O2 was monitored by imaging
                      the fluorescence lifetime of the O2-sensitive dye RTDP using
                      FLIM microscopy. The acquired image-data stacks from
                      biological experiments containing phase contrast and
                      fluorescence intensity data were analyzed using in-house
                      developed and open-source image-analysis tools. The
                      resulting oxygen concentration could be dynamically
                      controlled between $0\%$ and $100\%.$ The system was
                      experimentally tested by culturing and analyzing an E. coli
                      strain expressing green fluorescent protein as an indirect
                      intracellular oxygen indicator. The presented system allows
                      for innovative microbiological research on microorganisms
                      and microbial ecology with single-cell resolution.},
      cin          = {IBG-1 / IMET},
      ddc          = {570},
      cid          = {I:(DE-Juel1)IBG-1-20101118 / I:(DE-Juel1)IMET-20090612},
      pnm          = {2171 - Biological and environmental resources for
                      sustainable use (POF4-217) / DFG project 491111487 -
                      Open-Access-Publikationskosten / 2022 - 2024 /
                      Forschungszentrum Jülich (OAPKFZJ) (491111487)},
      pid          = {G:(DE-HGF)POF4-2171 / G:(GEPRIS)491111487},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {37408642},
      UT           = {WOS:001022849200001},
      doi          = {10.3389/fmicb.2023.1198170},
      url          = {https://juser.fz-juelich.de/record/1008687},
}