Browsing by Subject "Budding yeast"
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Item Open Access Bayesian Statistical Models of Cell-Cycle Progression at Single-Cell and Population Levels(2014) Mayhew, Michael BenjaminCell division is a biological process fundamental to all life. One aspect of the process that is still under investigation is whether or not cells in a lineage are correlated in their cell-cycle progression. Data on cell-cycle progression is typically acquired either in lineages of single cells or in synchronized cell populations, and each source of data offers complementary information on cell division. To formally assess dependence in cell-cycle progression, I develop a hierarchical statistical model of single-cell measurements and extend a previously proposed model of population cell division in the budding yeast, Saccharomyces cerevisiae. Both models capture correlation and cell-to-cell heterogeneity in cell-cycle progression, and parameter inference is carried out in a fully Bayesian manner. The single-cell model is fit to three published time-lapse microscopy datasets and the population-based model is fit to simulated data for which the true model is known. Based on posterior inferences and formal model comparisons, the single-cell analysis demonstrates that budding yeast mother and daughter cells do not appear to correlate in their cell-cycle progression in two of the three experimental settings. In contrast, mother cells grown in a less preferred sugar source, glycerol/ethanol, did correlate in their rate of cell division in two successive cell cycles. Population model fitting to simulated data suggested that, under typical synchrony experimental conditions, population-based measurements of the cell-cycle were not informative for correlation in cell-cycle progression or heterogeneity in daughter-specific G1 phase progression.
Item Open Access Principles that Govern Competition or Co-existence in Rho-GTPase Driven Polarization(2019) Chiou, Jian-gengRho-GTPases are master regulators of polarity establishment and cell morphology. Positive feedback enables concentration of Rho-GTPases into clusters at the cell cortex, from where they regulate the cytoskeleton. Different cell types reproducibly generate either one (e.g. the front of a migrating cell) or several clusters (e.g. the multiple dendrites of a neuron), but the mechanistic basis for unipolar or multipolar outcomes is unclear. The design principles of Rho-GTPase circuits are captured by two-component reaction-diffusion models based on conserved aspects of Rho-GTPase biochemistry. Some such models display rapid winner-takes-all competition between clusters, yielding a unipolar outcome. Other models allow prolonged co-existence of clusters. We investigate the behavior of a simple class of models and show that while the timescale of competition varies enormously depending on model parameters, a single factor explains a large majority of this variation. The dominant factor concerns the degree to which the maximal active GTPase concentration in a cluster approaches a “saturation point” determined by model parameters. We further show that the Rho-GTPase polarity machinery in the budding yeast S. cerevisiae, which normally generates only one bud through competition, can be manipulated to generate multiple buds
in ways consistent with this theoretical framework. We suggest that both saturation and the effect of saturation on competition reflect fundamental properties of the Rho-GTPase polarity machinery, regardless of the specific feedback mechanism, which predict whether the system will generate unipolar or multipolar outcomes.
Item Open Access Regulation of Morphogenetic Events in Saccharomyces cerevisiae(2018) Lai, Hung-HsuehTip growth in fungi involves highly polarized secretion and modification of the cell wall at the growing tip. The genetic requirements for initiating polarized growth are perhaps best understood for the model budding yeast, Saccharomyces cerevisiae. Once the cell is committed to enter the cell cycle by activation of G1 cyclin/cyclin-dependent kinase (CDK) complexes, the polarity regulator Cdc42 becomes concentrated at the presumptive bud site, actin cables are oriented towards that site, and septin filaments assemble into a ring around the polarity site. Several minutes later, the bud emerges. Here, we investigated the mechanisms that regulate the timing of these events at the single cell level and the role of polarisome during pheromone-induced polarized growth. We employed genetics and live cell microscopy to characterize cellular events. Septin recruitment was delayed relative to polarity establishment, and our findings suggest that a CDK-dependent septin “priming” facilitates septin recruitment by Cdc42. Bud emergence was delayed relative to the initiation of polarized secretion, and our findings suggest that the delay reflects the time needed to weaken the cell wall sufficiently to bud. Rho1 activation by Rom2 occurred at around the time of bud emergence, perhaps in response to local cell wall weakening. This report reveals regulatory mechanisms underlying the morphogenetic events in the budding yeast.
Item Open Access Single-Cell Analysis of Transcriptional Dynamics During Cell Cycle Arrest(2017) Winski, David J.In the past decade, a challenge to the canonical model of cell cycle transcriptional control has been posed by a series of high-throughput gene expression studies in budding yeast. Using genetic methods to inhibit or lock the activity of the cyclin-CDK/APC oscillator, these population studies demonstrated that a significant proportion of cell cycle transcription persists in the absence of cyclin-CDK/APC oscillations. To account for these findings, a network of serially activating transcription factors with sources of negative feedback from transcriptional repressors (referred to as a \say{TF network}) was proposed to drive cyclin-CDK/APC independent gene expression.
However, population studies of cell cycle gene expression are limited due to loss of phase synchrony that limits the timescale of measurement of gene expression and due to expression averaging that limits assessment of heterogeneity of expression within the population. To circumvent these limitations I used a single-cell timelapse microscopy approach to assess transcriptional dynamics of cell cycle regulated genes during extended cell cycle arrests in both the Gl/S and early mitosis (metaphase) phases of the cell cycle.
During G1/S arrest, transcriptional dynamics of four cell cycle regulated genes was assessed and activation of out-of-phase cell cycle transcription was observed in two of these genes. Though budding oscillations were observed in G1/S arrested cells, robust transcriptional oscillations were not seen for any of the four genes and budding dynamics were uncoupled from transcriptional dynamics after the first bud emergence. During cell cycle arrest in early mitosis, transcriptional dynamics of ten cell cycle regulated genes was assessed and activation of out-of-phase transcription was observed for four genes. All four genes activated once with canonical ordering but robust oscillations were not observed during mitotic arrest. Together these studies demonstrate activation, but not oscillation, of cell cycle transcription in the absence of cyclin-CDK/APC oscillations.
Item Open Access Understanding the Effects of Genetic Variation on Osmo-adaptation Dynamics Across S. cerevisiae using Bulk Segregant Analysis and Whole Genome Sequencing(2017) Aydin, SelcanAdapting to environmental changes (i.e. an increase in osmolarity) is critical for cell survival. How cells respond and adapt to osmotic stress has been well-studied in the model eukaryote Saccharomyces cerevisiae. Although the molecular and systems properties of osmo-adaptation have been well studied, few studies have focused on the effects of genetic variation. Understanding how genetic variation affects molecular pathways and their dynamics, which translates to variation in cellular and organismal phenotypes, is a key step towards understanding important phenomena such as complex gene by gene interactions and the mapping of genotype to phenotype. The challenge is to causally connect genetic differences with cellular function and differences in complex traits between individuals. As a first step towards addressing this challenge, my dissertation research investigates how natural genetic variation affects osmo-adaptation dynamics in budding yeast, Saccharomyces cerevisiae.
First, I characterized the natural variation in osmo-adaptation dynamics across S. cerevisiae. I showed that individual strains were highly variable in adaptation time and relative maximum growth rate after adapting to stress. Analysis of a broad set of genes involved in osmo-adaptation did not reveal any obvious genetic differences that could account for the observed variation. To identify alleles associated with the variation, I measured osmo-adaptation dynamics in progeny generated from a cross between two closely related lab strains. Identified alleles were outside the core signaling pathway and affected both adaptation time and relative maximum growth rate. Finally, I built a novel mapping panel and measured osmo-adaptation dynamics to obtain a more global, species-wide view. The panel showed an increased amount of variation in osmo-adaptation dynamics and a subset of progeny were phenotypically more extreme than their parents. Mapping the variation in this panel will generate a comprehensive list of alleles that affect osmo-adaptation. The strains in the mapping panel have a low number of mutations predicted to have strong effects in HOG pathway genes. Given our earlier results from the pairwise cross, I expect that many osmo-adaptation alleles discovered from the mapping panel will be outside the HOG pathway.