Morphologically Constrained and Data Informed Cell Segmentation of Budding Yeast

Bakker, Elco; Swain, Peter S.; Crane, Matthew M.

doi:10.1101/105106

Cited by 16 publications

(42 citation statements)

References 38 publications

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“…Switching between media is via an external mixer and syringe pumps. Bright-field and fluorescence images are acquired every 2.5 min, and cells are segmented by using the DISCO algorithm (33).…”

Section: Methodsmentioning

confidence: 99%

Distributed and dynamic intracellular organization of extracellular information

Granados

Pietsch

Cepeda-Humerez

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.

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Section: Methodsmentioning

confidence: 99%

Distributed and dynamic intracellular organization of extracellular information

Granados

Pietsch

Cepeda-Humerez

et al. 2018

Proc. Natl. Acad. Sci. U.S.A.

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“…BY strains with fluorescently-tagged transcription factors (33) were grown in ALCATRAS microfluidic devices (21) in synthetic complete medium with 2% glucose for at least 3 hours and then exposed to stress for another 5 hours (SI Appendix). Bright-field and fluorescence images were acquired every 2.5 min and cells were segmented using the DISCO algorithm (34).…”

Section: Time-lapse Microscopymentioning

confidence: 99%

Distributed and dynamic intracellular organization of extracellular information

Granados

Pietsch²,

Cepeda-Humerez

et al. 2017

Preprint

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Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for ten transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: generalists (Msn2/4, Tod6/Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. Each transcription factor reports differently, and it is only their collective response that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change, and we predict that such multi-dimensional representations are common in cellular decision-making. Significance StatementTo thrive in diverse environments, cells must represent extracellular change intracellularly despite stochastic biochemistry. Here we introduce a quantitative framework for investigating the organization of information within a cell. Combining single-cell measurements of intracellular dynamics with a new, scalable methodology for estimating mutual information between time-series and a discrete input, we demonstrate that extracellular information is encoded in the dynamics of the nuclear localization of transcription factors and that information is lost with alternative static statistics. Any one transcription factor is usually insufficient, but the collective dynamics of multiple transcription factors can represent complex extracellular change. We therefore show that a cell's internal representation of its environment can be both distributed across diverse proteins and dynamically encoded.

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“…For pHluorin2 ratiometric imaging, the Chroma GFP ET49002 filter set and a custom ET405/40X excitation and ET525/50m emission filter set (Chroma) were used. Following data acquisition, cells were segmented and tracked using previously published software (Bakker et al, 2018). Divisions were scored by eye, and errors in cell segmentation and tracking were corrected manually.…”

Section: Microfluidics and Fluorescence Microscopymentioning

confidence: 99%

Loss of vacuolar acidity results in iron sulfur cluster defects and divergent homeostatic responses during aging inSaccharomyces cerevisiae

Chen

Ven

Crane

et al. 2020

Preprint

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The loss of vacuolar/lysosomal acidity is an early event during aging that has been linked to mitochondrial dysfunction. However, it is unclear how loss of vacuolar acidity results in age-related dysfunction. Through unbiased genetic screens, we determined that increased iron uptake can suppress the mitochondrial respiratory deficiency phenotype of yeast vma mutants, which have lost vacuolar acidity due to genetic disruption of the vacuolar ATPase proton pump. Yeast vma mutants exhibited nuclear localization of Aft1, which turns on the iron regulon in response to iron sulfur cluster (ISC) deficiency. This led us to find that loss of vacuolar acidity with age in wildtype yeast causes ISC defects and a DNA damage response. Using microfluidics to investigate aging at the single cell level, we observe grossly divergent trajectories of iron homeostasis within an isogenic and environmentally homogeneous population. One subpopulation of cells fails to mount the expected compensatory iron regulon gene expression program, and suffers progressively severe ISC deficiency with little to no activation of the iron regulon. In contrast, other cells show robust iron regulon activity with limited ISC deficiency, which allows extended passage and survival through a period of genomic instability during aging. These divergent trajectories suggest that iron regulation and ISC homeostasis represent a possible target for aging interventions.

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Morphologically Constrained and Data Informed Cell Segmentation of Budding Yeast

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Cited by 16 publications

References 38 publications

Distributed and dynamic intracellular organization of extracellular information

Distributed and dynamic intracellular organization of extracellular information

Distributed and dynamic intracellular organization of extracellular information

Loss of vacuolar acidity results in iron sulfur cluster defects and divergent homeostatic responses during aging inSaccharomyces cerevisiae

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