Periodic Fermentor Yield and Enhanced Product Enrichment from Autonomous Oscillations

Stowers, Chris C.; Robertson, J. Brian; Ban, Hyunju; Tanner, Robert D.; Boczko, Erik M.

doi:10.1007/s12010-008-8486-7

Cited by 10 publications

(15 citation statements)

References 32 publications

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“…This phenomenon is attributed to the observation that the daughter cell is smaller at division than the mother. 6 The magnitude of the size difference depends on the yeast strain, the growth environments and the replicative age of the mother. The larger the mother daughter size disparity the faster an initially synchronous culture will dephase.…”

Section: Resultsmentioning

confidence: 99%

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Measurement of the volume growth rate of single budding yeast with the MOSFET-based microfluidic Coulter counter

Sun

Stowers²,

Boczko

et al. 2010

Lab Chip

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We report on measurements of the volume growth rate of ten individual budding yeast cells using a recently developed MOSFET-based microfluidic Coulter counter. The MOSFET-based microfluidic Coulter counter is very sensitive, provides signals that are immune from the baseline drift, and can work with cell culture media of complex composition. These desirable features allow us to directly measure the volume growth rate of single cells of Saccharomyces cerevisiae LYH3865 strain budding yeast in YNB culture media over a whole cell cycle. Results indicate that all budding yeast follow a sigmoid volume growth profile with reduced growth rates at the initial stage before the bud emerges and the final stage after the daughter gets mature. Analysis of the data indicates that even though all piecewise linear, Gomperitz, and Hill’s function models can fit the global growth profile equally well, the data strongly support local exponential growth phenomenon. Accurate volume growth measurements are important for applications in systems biology where quantitative parameters are required for modeling and simulation.

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Section: Resultsmentioning

confidence: 99%

“…The calculation of the design parameters and the volume filtration cutoffs require accurate models of individual yeast growth rates as a function of the cell cycle. 6 …”

Section: Introductionmentioning

confidence: 99%

Measurement of the volume growth rate of single budding yeast with the MOSFET-based microfluidic Coulter counter

Sun

Stowers²,

Boczko

et al. 2010

Lab Chip

Self Cite

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show abstract

“…For instance in Figure 1 we show data from such an experiment for the yeast strain Cen.PK 113 [44, 45, 40]. It is seen in this experiment that dissolved O 2 levels oscillate between about 5% to 55%, with a period of a little less than 4 hours.…”

Section: The Yeast Cell Cycle and Experimental Observationsmentioning

confidence: 91%

ODE, RDE and SDE models of cell cycle dynamics and clustering in yeast

Boczko

Gedeon

Stowers

et al. 2009

Journal of Biological Dynamics

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Biologists have long observed periodic-like oxygen consumption oscillations in yeast populations under certain conditions and several unsatisfactory explanations for this phenomenon have been proposed. These "autonomous oscillations" have often appeared with periods that are nearly integer divisors of the calculated doubling time of the culture.We hypothesize that these oscillations could be caused by a weak form of cell cycle synchronization that we call clustering. We develop some novel ordinary differential equation models of the cell cycle. For these models, and for random and stochastic perturbations, we give both rigorous proofs and simulations showing that both positive and negative growth rate feedback within the cell cycle are possible agents that can cause clustering of populations within the cell cycle. It occurs for a variety of models and for a broad selection of parameter values. These results suggest that the clustering phenomenon is robust and is likely to be observed in nature. Since there are necessarily an integer number of clusters, clustering would lead to periodic-like behavior with periods that are nearly integer divisors of the period of the cell cycle.Related experiments have shown conclusively that cell cycle clustering occurs in some oscillating yeast cultures.

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“…Since Saccharomyces cerevisiae is a model organism, it is important to understand the interconnectedness of the CDC and metabolism [1,6,15,24,27,29]. Also, yeast are used in many bio-engineering processes and understanding their metabolism and cell cycle is of interest in some applications [14,25,31]. …”

Section: Introductionmentioning

confidence: 99%

Cell cycle dynamics in a response/signalling feedback system with a gap

Gong

Buckalew

Young

et al. 2014

Journal of Biological Dynamics

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We consider a dynamical model of cell cycles of n cells in a culture in which cells in one specific phase (S for signalling) of the cell cycle produce chemical agents that influence the growth/cell cycle progression of cells in another phase (R for responsive). In the case that the feedback is negative, it is known that subpopulations of cells tend to become clustered in the cell cycle; while for a positive feedback, all the cells tend to become synchronized. In this paper, we suppose that there is a gap between the two phases. The gap can be thought of as modelling the physical reality of a time delay in the production and action of the signalling agents. We completely analyse the dynamics of this system when the cells are arranged into two cell cycle clusters. We also consider the stability of certain important periodic solutions in which clusters of cells have a cyclic arrangement and there are just enough clusters to allow interactions between them. We find that the inclusion of a small gap does not greatly alter the global dynamics of the system; there are still large open sets of parameters for which clustered solutions are stable. Thus, we add to the evidence that clustering can be a robust phenomenon in biological systems. However, the gap does effect the system by enhancing the stability of the stable clustered solutions. We explain this phenomenon in terms of contraction rates (Floquet exponents) in various invariant subspaces of the system. We conclude that in systems for which these models are reasonable, a delay in signalling is advantageous to the emergence of clustering.

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Periodic Fermentor Yield and Enhanced Product Enrichment from Autonomous Oscillations

Cited by 10 publications

References 32 publications

Measurement of the volume growth rate of single budding yeast with the MOSFET-based microfluidic Coulter counter

Measurement of the volume growth rate of single budding yeast with the MOSFET-based microfluidic Coulter counter

ODE, RDE and SDE models of cell cycle dynamics and clustering in yeast

Cell cycle dynamics in a response/signalling feedback system with a gap

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