Continuous rate modeling of bacterial stochastic size dynamics

Nieto, César; Vargas-García, César Augusto; Pedraza, Juan Manuel

doi:10.1103/physreve.104.044415

Cited by 12 publications

(42 citation statements)

References 51 publications

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“…3c). Although it has a steady mean ⟨s⟩ and steady CV 2 (s), the distribution presents a limit cycle, as observed in previous studies [14], [25]. The complete time dynamics can be found in Supplementary videos 1 and 2 for the single lineage and population snapshots, respectively.…”

Section: B the Pbe For Growing And Dividing Cellssupporting

confidence: 56%

“…The mean population N ( t ) over time, the mean size ⟨ s ⟩, and the variance var( s ) are given by the following: As we explained in previous studies [14], we normalize the time by the doubling time such as τ d = 1, that is, µ = ln(2) and the size by the mean added size before division so, we chose k = µ = ln(2). Thus, all sizes are measured in units of µ/k .…”

Section: Population Balance Equationmentioning

confidence: 99%

“…In this article, we contrast the moments in the system (18) with those derived from data (simulations) by estimating the moment ⟨ s α ⟩ from C colonies, each with Z c cells, with cell size s z,c : with SL , referring to single lineage perspective, and PS referring to Population Snapshots. These formulae were also used to compare the solutions of numerical methods and stochastic simulation algorithms [14], [35].…”

Section: Population Balance Equationmentioning

confidence: 99%

“…Others study the transient dynamics of the distribution moments with limited precision [24]. Finally, further studies can obtain the distribution in exceptional cases and the transient moment dynamics with arbitrary accuracy, but limited to the case of a single lineage [14], [33].…”

Section: Population Balance Equationmentioning

confidence: 99%

“…As we explained in previous studies [14], we normalize the time by the doubling time such as τ d = 1, that is, µ = ln (2) and the size by the mean added size before division µ k = 1 so, we chose k = µ = ln (2). Thus, all sizes are measured in units of µ/k.…”

Section: B the Pbe For Growing And Dividing Cellsmentioning

confidence: 99%

See 4 more Smart Citations

Cell size regulation and proliferation fluctuations in single-cell derived colonies

Nieto

Vargas-García

Pedraza

et al. 2022

Preprint

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Exponentially growing cells regulate their size by controlling their timing of division. Since two daughter cells are born as a result of this cell splitting, cell size regulation has a direct connection with cell proliferation dynamics. Recent models found more clues about this connection by suggesting that division occurs at a size-dependent rate. In this article, we propose a framework that couples the stochastic transient dynamics of both the cell size and the number of cells in the initial expansion of a single-cell-derived colony. We describe the population from the two most common perspectives. The first is known as Single Lineage: where only one cell is followed in each colony, and the second is Population Snapshots: where all cells in different colonies are followed. At a low number of cells, we propose a third perspective; Single Colony, where one tracks only cells with a common ancestor. We observe how the statistics of these three approaches are different at low numbers and how the Single Colony perspective tends to Population Snapshots at high numbers. Analyzing colony-to-colony fluctuations in the number of cells, we report an intriguing find: the extent of fluctuations first increases with time and then decreases to approach zero at large numbers of cells. In contrast, in classical size-independent proliferation models, where cell division occurs based on a pure timing mechanism, fluctuations in cell number increase monotonically over time to approach a nonzero value. We systematically study these differences and the convergence speed using different size control strategies.

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Section: B the Pbe For Growing And Dividing Cellssupporting

confidence: 56%

Section: Population Balance Equationmentioning

confidence: 99%

Section: Population Balance Equationmentioning

confidence: 99%

Section: Population Balance Equationmentioning

confidence: 99%

Section: B the Pbe For Growing And Dividing Cellsmentioning

confidence: 99%

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Cell size regulation and proliferation fluctuations in single-cell derived colonies

Nieto

Vargas-García

Pedraza

et al. 2022

Preprint

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Modeling cell size control under dynamic environments

Nieto

Vargas-García

Pedraza³

et al. 2022

IFAC-PapersOnLine

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Mechanisms of cell size regulation in slow-growing Escherichia coli cells: discriminating models beyond the adder

Nieto,

Vargas-García,

Pedraza

et al. 2024

npj Syst Biol Appl

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Under ideal conditions, Escherichia coli cells divide after adding a fixed cell size, a strategy known as the adder. This concept applies to various microbes and is often explained as the division that occurs after a certain number of stages, associated with the accumulation of precursor proteins at a rate proportional to cell size. However, under poor media conditions, E. coli cells exhibit a different size regulation. They are smaller and follow a sizer-like division strategy where the added size is inversely proportional to the size at birth. We explore three potential causes for this deviation: degradation of the precursor protein and two models where the propensity for accumulation depends on the cell size: a nonlinear accumulation rate, and accumulation starting at a threshold size termed the commitment size. These models fit the mean trends but predict different distributions given the birth size. To quantify the precision of the models to explain the data, we used the Akaike information criterion and compared them to open datasets of slow-growing E. coli cells in different media. We found that none of the models alone can consistently explain the data. However, the degradation model better explains the division strategy when cells are larger, whereas size-related models (power-law and commitment size) account for smaller cells. Our methodology proposes a data-based method in which different mechanisms can be tested systematically.

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Continuous rate modeling of bacterial stochastic size dynamics

Cited by 12 publications

References 51 publications

Cell size regulation and proliferation fluctuations in single-cell derived colonies

Cell size regulation and proliferation fluctuations in single-cell derived colonies

Modeling cell size control under dynamic environments

Mechanisms of cell size regulation in slow-growing Escherichia coli cells: discriminating models beyond the adder

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