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Observing Nutrient Gradients, Gene Expression and Growth Variation Using the "Yeast Machine" Microfluidic Device.

Zoran S Marinkovic1,2,3, Clément Vulin1,4,5, Mislav Acman1,3

  • 1Laboratoire Matière et Systèmes Complexes, UMR 7057 CNRS & Université de Paris, 10 rue Alice Domon et Léonie Duquet, 75013 Paris, France.

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|March 4, 2021
PubMed
Summary

Researchers developed a microfluidic device, the "yeast machine," to study yeast colony dynamics. This tool reveals how nutrient gradients form within colonies, impacting growth and gene expression at single-cell resolution.

Keywords:
Emerging propertiesGene expressionMetabolismMicrobial ecologyMicrofluidicsSpatial organizationYeast colony

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Area of Science:

  • Microbiology
  • Systems Biology
  • Biophysics

Background:

  • Microbial communities exhibit complex spatiotemporal dynamics influenced by spatial position and time.
  • Standard research environments (e.g., bulk liquid cultures) fail to capture these dynamics.
  • Studying biofilms and colonies is challenging for single-cell spatiotemporal analysis.

Purpose of the Study:

  • To develop a microfluidic device for observing yeast colony development.
  • To investigate how intercellular metabolic interactions shape colony structure.
  • To understand nutrient gradient formation and its effect on yeast growth.

Main Methods:

  • Design and implementation of a microfluidic device with yeast colony arrays.
  • Utilizing Saccharomyces cerevisiae as a model organism.
  • Monitoring fluorescently labeled hexose transporters to visualize glucose gradients.
  • Quantifying intra-colony growth rates and gene expression patterns.

Main Results:

  • Demonstrated the emergence of glucose gradients within yeast colonies.
  • Quantified spatial patterns of gene expression related to glucose availability.
  • Observed the formation of amino acid gradients within colonies.
  • Showcased the device's capability to study nutrient gradients at single-cell resolution.

Conclusions:

  • The "yeast machine" enables detailed study of spatiotemporal dynamics in microbial colonies.
  • Intercellular metabolic interactions and nutrient gradients significantly influence colony morphogenesis.
  • This approach can be extended to study multi-species systems and ecological timescales.