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HFSPO Fellowship Takuya Ohmura

Research Project
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01.08.2021
 - 31.03.2022

In their natural environment and during infections, bacteria are commonly organized in surface-attached communities termed biofilms, which are held together by a self-produced extracellular matrix. These biofilms can develop from single cells into macroscopic three-dimensional communities with characteristic morphology and cellular differentiation, reminiscent of eukaryotic multicellular development. Recently, single-cell level live-imaging of complete biofilm development has become possible, which now permits the experimental testing of detailed simulation predictions for biofilm development, and places the grand challenge of a quantitative and predictive understanding of biofilm development within reach. The key ingredients of the required simulations are the cell-cell interaction mechanisms and behavioral states of cells, yet both are generally unknown. To overcome this barrier, I will develop techniques for spatiotemporal transcriptome data generation and analysis during Vibrio cholerae biofilm development, which will allow me to obtain spatiotemporal maps of cellular interaction mechanisms and cellular states. These spatiotemporal maps will then be used as input for individual-based simulations I will develop, to identify which of the vast possibilities of cellular interactions and properties are necessary and sufficient for biofilm development. This interplay of experiments and simulations based on spatiotemporal transcriptome data and single-cell microscopy will ultimately not only identify the key cellular interaction mechanisms, but also the cellular interaction principles that are required irrespective of the underlying molecular mechanisms.

Funding

HFSPO Fellowship Takuya Ohmura

Weitere Europäische Forschungsprojekte (Eurostars, ESF, Interreg etc.) (GrantsTool), 08.2021-03.2022 (8)
PI : Drescher, Knut.

Publications

Jelli, Eric et al. (2023) ‘Single-cell segmentation in bacterial biofilms with an optimized deep learning method enables tracking of cell lineages and measurements of growth rates’, Molecular Microbiology, 119(6), pp. 659–676. Available at: https://doi.org/10.1111/mmi.15064.

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Members (1)

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Knut Drescher

Principal Investigator