Biology subjects

Vargas-Garcia, C.

Publications and source records attributed to Vargas-Garcia, C..

12 recordsLinked to original sources

bioRxiv2024

rpfF is not required for X. translucens pv. undulosa pathogenesis

Bacterial cells self-coordinate via a mechanism called quorum sensing. In Xanthomonas species the gene rpfF encodes the quorum sensing autoinducer synthase. Xanthomonas species are divided into two main phylogenetic groups called Clade I and Clade II. The rpf quorum sensing system has been well studied in multiple Clade II Xanthomonas species and deletion of rpfF resulted in a major loss of virulence on susceptible hosts. However, the only Clade I Xanthomonas species in which the rpfF system was previously studied was in the sugarcane pathogen X. albilineans. In X. albilineans the rpf cluster plays a relatively small role in pathogenesis. Xanthomonas translucens pv. undulosa (Xtu) is a Clade I Xanthomonas species that causes bacterial leaf streak (BLS) and black chaff of wheat and barley and has increased as a concern in recent decades. Neither major resistance nor chemical treatments are available to prevent disease caused by Xtu. Interference with rpf bacterial quorum sensing systems has demonstrated some success in other systems. It was unknown whether BLS caused by Xtu could be prevented via quorum sensing interference. We found that Xtu encodes an rpfF homolog and we created an rpfF knockout mutant to study the role of the rpf system in Xtu. We found that the rpfF mutant was unaffected in its pathogenesis as it caused BLS symptoms and multiplied within wheat plants to the same levels as the wildtype strain. The Xtu rpfF mutant grew normally in lag and log phases in vitro, however it exhibited a shorter stationary phase and an early death phase in plant-derived media. The importance of RpfF in Xtus life cycle is unknown, though it appears to carry out a role in population stability. Our research determined that rpfF is not a major Xtu pathogenicity factor. Therefore, we do not recommend the targeting of the rpf quorum sensing system as a preventative treatment for BLS of wheat.

molecular biology↗

bioRxiv2023

Mechanisms of Cell Size Regulation in Slow-Growing Escherichia coli Cells: Discriminating Models Beyond the Adder

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: precursor protein degradation, nonlinear accumulation rate, and a threshold size termed the commitment size. These models fit mean trends but predict different distributions given the birth size. To validate these models, we used the Akaike information criterion and compared them to open datasets of slow-growing E. coli cells in different media. the degradation model could explain the division strategy for media where cells are larger, while the commitment size model could account for smaller cells. The power-law model, finally, better fits the data at intermediate regimes.

systems biology↗

bioRxiv2022

The fission yeast cell size control system integrates pathways measuring cell surface area, volume, and time

Eukaryotic cells tightly control their size, but the relevant aspect of size is unknown in most cases. Fission yeast divide at a threshold cell surface area due in part to the protein kinase Cdr2. We find that fission yeast cells only divide by surface area under a size threshold but shift to volume-based divisions when they reach a larger size. The size threshold for changing from surface area to volume-based control is set by ploidy. Within this size control system, we identified the mitotic activator Cdc25 as a volume-based sizer molecule, while the mitotic cyclin Cdc13 accumulates as a timer. We propose an integrated model for cell size control based on multiple signaling pathways that report on distinct aspects of cell size and growth, including cell surface area (Cdr2), cell volume (Cdc25), and time (Cdc13). Combined modeling and experiments show how this system can generate both sizer and adder-like properties. HIGHLIGHTSO_LIFission yeast use surface area or volume-based cell size control depending on overall size and ploidy C_LIO_LIMitotic activator Cdc25 exhibits properties of a volume-based sizer molecule C_LIO_LIMitotic cyclin Cdc13 accumulates in the nucleus dependent on time, not size C_LIO_LICombined modeling and experiments identify conditions for sizer versus adder behavior C_LI

cell biology↗

bioRxiv2022

The role of division stochasticity on the robustness of bacterial size dynamics

Variables of bacterial division such as size at birth, growth rate, division time, and the position of the septal ring, all vary from cell to cell. Currently, it is unknown how these random fluctuations can combine to produce a robust mechanism of homeostasis. To address this question, we studied the dynamics of the cell division process from both experimental and theoretical perspectives. Our model predicts robustness in division times as sustained oscillations in metrics of the cell size distribution, such as the mean, variability, and the cell size autocorrelation function. These oscillations do not get damped, even considering stochasticity in division timing and the cell size at the beginning of the experiment. Damping appears just after inducing stochasticity in either the septum position or the growth rate. We compare the predictions of the full model with the size dynamics of E. coli bacteria growing in minimal media using either glucose or glycerol as carbon sources. We observe that growth in poorer media increases the noise in both partitioning position and growth rate. This additional noise results in oscillations with more damping. Although intracellular noise is known as a source of phenotypic variation, our results show that it can play a similar but subtler role in maintaining population-level homeostasis by causing rapid desynchronization of cell cycles..

systems biology↗

bioRxiv2022

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

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.

systems biology↗

bioRxiv2022

Threshold-crossing time statistics for gene expression in growing cells

Many intracellular events are triggered by attaining critical concentrations of their corresponding regulatory proteins. How cells ensure precision in the timing of the protein accumulation is a fundamental problem, and contrasting predictions of different models can help us understand the mechanisms involved in such processes. Here, we formulate the timing of protein threshold-crossing as a first passage time (FPT) problem focusing on how the mean FPT and its fluctuations depend on the threshold protein concentration. First, we model the protein-crossing dynamics from the perspective of three classical models of gene expression that do not explicitly accounts for cell growth but consider the dilution as equivalent to degradation: (birth-death process, discrete birth with continuous deterministic degradation, and Fokker-Planck approximation). We compare the resulting FPT statistics with a fourth model proposed by us (growing cell) that comprises size-dependent expression in an exponentially growing cell. When proteins accumulate in growing cells, their concentration reaches a steady value. We observe that if dilution by cell growth is modeled as degradation, cells can reach concentrations higher than this steady-state level at a finite time. In the growing cell model, on the other hand, the FPT moments diverge if the threshold is higher than the steady-state level. This effect can be interpreted as a transition between noisy dynamics when cells are small to an almost deterministic behavior when cells grow enough. We finally study the mean FPT that optimizes the timing precision. The growing cell model predicts a higher optimal FPT and less variability than the classical models.

systems biology↗

bioRxiv2020

PyEcoLib: a python library for simulating E. coli stochastic size dynamics

Recent studies describe bacterial division as a jump process triggered when it reaches a fixed number of stochastic discrete events at a rate depending on the cell-size. This theoretical approach enabled the computation of stochastic cell-size transient dynamics with arbitrary precision, with the possibility of being coupled to other continuous processes as gene expression. Here we synthesize most of this theory in the tool PyEcoLib, a python-based library to estimate bacterial cell size stochastic dynamics including continuous growth and division events. In this library, we include examples predicting statistical properties seen in experiments.

systems biology↗

bioRxiv2020

Continuous Rate Modelling of bacterial stochastic size dynamics

Bacterial division is an inherently stochastic process. However, theoretical tools to simulate and study the stochastic transient dynamics of cell-size are scarce. Here, we present a general theoretical approach based on the Chapman-Kolmogorov formalism to describe these stochastic dynamics including continuous growth and division events as jump processes. Using this approach, we analyze the effect of different sources of noise on the dynamics of the size distribution. Oscillations in the distribution central moments were found as consequence of the discrete translation invariance of the system with period of one doubling time, these oscillations are found in both the central moments of the size distribution and the auto-correlation function and do not disappear including stochasticity on division times or size heterogeneity on the population but only after include noise in either growth rate or septum position.

systems biology↗

bioRxiv2020

Division stochasticity can be transmitted to protein expression through chromosome replication

Stochastic fluctuations (noise) are a fundamental characteristic of protein production. Some sources of this stochasticity are still under debate. In this work, we explore how these fluctuations can originate from the stochasticity on division events. To do that, we consider the classical gene expression model with chromosome replication following the known Helmstetter & Cooper model. This model predicts intervals of the cell cycle where bacteria can have more than one copy of a particular gene. Considering the transcription rate as proportional to the number of chromosomes and division based on a continuous rate model, we explore how stochasticity in division or equivalently in cell size, could be transmitted to gene expression. Our simulations suggest that division can be an important source of such fluctuations only if chromosomes are replicating, otherwise, this noise is not well transmitted. This effect happens even if replication is deterministic. This work can be helpful for understanding cell cycle dynamics and their interplay with phenotypic variability.

systems biology↗

bioRxiv2020

Noise signature in added size suggests bacteria target a commitment size to enable division

Recent experiments suggested that sizer-like division strategy, a deviation from the adder paradigm might be produced by additional degradation events of cell division machinery molecules. We revisited single cell size data from a recently microfluidics setup using the above model. We observed that such additional degradation process, although reproduces size observations in the mean sense, it is unable to capture cell size fluctuations. We further extended recently proposed power law models to include commitment size. Our proposal is in agreement of both mean and fluctuation profiles seen in experiments. Our approach suggests further uses of noise profiles on dissecting cell size regulatory mechanisms. SIGNIFICANCEWe contrast cell division models against bacteria cell size data in minimal media. Our results seems to support the idea that division starts once bacteria meet a given commitment size.

systems biology↗

bioRxiv2018

Synaptic transmission may provide an evolutionary benefit to HIV through modulation of latency

Transmission of HIV is known to occur by two mechanisms in vivo: the free virus pathway, where viral particles bud off an infected cell before attaching to an uninfected cell, and the cell-cell pathway, where infected cells form virological synapses through close contact with an uninfected cell. It has also been shown that HIV replication includes a positive feedback loop controlled by the viral protein Tat, which may act as a stochastic switch in determining whether an infected cell enters latency. In this paper, we introduce a simple mathematical model of HIV replication containing both the free virus and cell-cell pathways. Using this model, we demonstrate that the high multiplicity of infection in cell-cell transmission results in a suppression of latent infection, and that this modulation of latency through balancing the two transmission mechanisms can provide an evolutionary benefit to the virus. This benefit increases with decreasing overall viral fitness, which may provide a within-host evolutionary pressure toward more cell-cell transmission in late-stage HIV infection.

microbiology↗

bioRxiv2017

Joint regulation of growth and division timing drives size homeostasis in proliferating animal cells

How organisms maintain cell size homeostasis is a long-standing problem that remains unresolved, especially in multicellular organisms. Recent experiments in diverse animal cell types demonstrate that within a cell population the extent of growth and cellular proliferation (i.e., fitness) is low for small and large cells, but high at intermediate sizes. Here we use mathematical models to explore size-control strategies that drive such a non-monotonic fitness profile resulting in an optimal cell size. Our analysis reveals that if cell size grows exponentially or linearly over time, then fitness always varies monotonically with size irrespective of how timing of division is regulated. Furthermore, if the cell divides upon attaining a critical size (as in the Sizer or size-checkpoint model), then fitness always increases with size irrespective of how growth rate is regulated. These results show that while several size control models can maintain cell size homeostasis, they fail to predict the optimal cell size, and hence unable to explain why cells prefer a certain size. Interestingly, fitness maximization at an optimal size requires two key ingredients: 1) The growth rate decreases with increasing size for large enough cells; and 2) The cell size at the time of division is a function of the newborn size. The latter condition is consistent with the Adder paradigm for division control (division is triggered upon adding a fixed size from birth), or a Sizer-Adder combination. Consistent with theory, Jurkat T cell growth rates, as measured via oxygen consumption or mitochondrial activity, increase with size for small cells, but decrease with size for large cells. In summary, regulation of both growth and cell division timing is critical for size control in animal cells, and this joint-regulation leads to an optimal size where cellular fitness is maximized. Address inquires to A. Singh, E-mail: absingh@udel.edu.

systems biology↗