Publications

2021
Guo Y, Amir A. The effect of weak clonal interference on average fitness trajectories in the presence of macroscopic epistasis. 2021. biorxivAbstract
Adaptation dynamics on fitness landscapes is often studied theoretically in the strong-selection, weak-mutation (SSWM) regime. However, in a large population, multiple beneficial mutants can emerge before any of them fixes in the population. Competition between mutants is known as clonal interference, and how it affects the form of long-term fitness trajectories in the presence of epistasis is an open question. Here, by considering how changes in fixation probabilities arising from weak clonal interference affect the dynamics of adaptation on fitness-parameterized landscapes, we find that the change in the form of fitness trajectory arises only through changes in the supply of beneficial mutations (or equivalently, the beneficial mutation rate). Furthermore, a depletion of beneficial mutations as a population climbs up the fitness landscape can speed up the functional form of the fitness trajectory, while an enhancement of the beneficial mutation rate does the opposite of slowing down the form of the dynamics. Our findings suggest that by carrying out evolution experiments in both regimes (with and without clonal interference), one could potentially distinguish the different sources of macroscopic epistasis (fitness effect of mutations vs. change in fraction of beneficial mutations).
Parsa S, Zareei A, Santanach-Carreras E, Morris EJ, Amir A, Xiao L, Weitz DA. Unexpected scaling of interstitial velocities with permeability due to polymer retention in porous media. Physical Review Fluids. 2021;6 (8). Publisher's VersionAbstract
Polymer retention from the flow of a polymer solution through porous media results in substantial decrease of the permeability; however, the underlying physics of this effect is unknown. While the polymer retention leads to a decrease in pore volume, here we show that this cannot cause the full reduction in permeability. Instead, to determine the origin of this anomalous decrease in permeability, we use confocal microscopy to measure the pore-level velocities in an index-matched model porous medium. We show that they exhibit an exponential distribution and, upon polymer retention, this distribution is broadened yet retains the same exponential form. Surprisingly, the velocity distributions are scaled by the inverse square root of the permeabilities. We combine experiment and simulation to show these changes result from diversion of flow in the random porous-medium network rather than reduction in pore volume upon polymer retention.
Qiu L, Hutchinson JW, Amir A. Bending Instability of Rod-shaped Bacteria. 2021. arXivAbstract
A thin-walled tube, e.g., a drinking straw, manifests an instability when bent by localizing the curvature change in a small region. This instability has been extensively studied since the seminal work of Brazier nearly a century ago. However, the scenario of pressurized tubes has received much less attention. Motivated by rod-shaped bacteria such as E. coli, whose cell walls are much thinner than their radius and are subject to a substantial internal pressure, we study, theoretically, how this instability is affected by this internal pressure. In the parameter range relevant to the bacteria, we find that the internal pressure significantly postpones the onset of the instability, while the bending stiffness of the cell wall has almost no influence. This study suggests a new method to infer turgor pressure in rod-shaped bacteria from bending experiments.
Kar P, Tiruvadi-Krishnan S, Männik J, Männik J, Amir A. To bin or not to bin: analyzing single-cell growth data. 2021. biorxivAbstract
Collection of high-throughput data has become prevalent in biology. Large datasets allow the use of statistical constructs such as binning and linear regression to quantify relationships between variables and hypothesize underlying biological mechanisms based on it. We discuss several such examples in relation to single-cell data and cellular growth. In particular, we show instances where what appears to be ordinary use of these statistical methods leads to incorrect conclusions such as growth being non-exponential as opposed to exponential and vice versa. We propose that the data analysis and its interpretation should be done in the context of a generative model, if possible. In this way, the statistical methods can be validated either analytically or against synthetic data generated via the use of the model, leading to a consistent method for inferring biological mechanisms from data. On applying the validated methods of data analysis to infer cellular growth on our experimental data, we find the growth of length in E. coli to be non-exponential. Our analysis shows that in the later stages of the cell cycle the growth rate is faster than exponential.
Wong F, Wilson S, Helbig R, Hegde S, Aftenieva O, Zheng H, Liu C, Pilizota T, Garner EC, Amir A, et al. Understanding beta-lactam-induced lysis at the single-cell level. Frontiers in Microbiology. 2021;12 (1664-302X) :2085. Publisher's VersionAbstract
Mechanical rupture, or lysis, of the cytoplasmic membrane is a common cell death pathway in bacteria occurring in response to β-lactam antibiotics. A better understanding of the cellular design principles governing the susceptibility and response of individual cells to lysis could indicate methods of potentiating β-lactam antibiotics and clarify relevant aspects of cellular physiology. Here, we take a single-cell approach to bacterial cell lysis to examine three cellular features-turgor pressure, mechanosensitive channels, and cell shape changes-that are expected to modulate lysis. We develop a mechanical model of bacterial cell lysis and experimentally analyze the dynamics of lysis in hundreds of single Escherichia coli cells. We find that turgor pressure is the only factor, of these three cellular features, which robustly modulates lysis. We show that mechanosensitive channels do not modulate lysis due to insufficiently fast solute outflow, and that cell shape changes result in more severe cellular lesions but do not influence the dynamics of lysis. These results inform a single-cell view of bacterial cell lysis and underscore approaches of combatting antibiotic tolerance to β-lactams aimed at targeting cellular turgor.
Zareei A, Pan D, Amir A. Temporal Evolution of Flow in Pore-Networks: From Homogenization to Instability. 2021. arXivAbstract
We study the dynamics of flow-networks in porous media using a pore-network model. First, we consider a class of erosion dynamics assuming a constitutive law depending on flow rate, local velocities, or shear stress at the walls. We show that depending on the erosion law, the flow may become uniform and homogenized or become unstable and develop channels. By defining an order parameter capturing these different behaviors we show that a phase transition occurs depending on the erosion dynamics. Using a simple model, we identify quantitative criteria to distinguish these regimes and correctly predict the fate of the network, and discuss the experimental relevance of our result.
Tiruvadi-Krishnan S, Männik J, Kar P, Lin J, Amir A, Männik J. Replication-related control over cell division in Escherichia coli is growth-rate dependent. 2021. bioRxivAbstract
How replication and division processes are coordinated in the cell cycle is a fundamental yet poorly understood question in cell biology. In Escherichia coli different data sets and models have supported a range of conclusions from one extreme where these two processes are tightly linked to another extreme where these processes are completely independent of each other. Using high throughput optical microscopy and cell cycle modeling, we show that in slow growth conditions replication and division processes are strongly correlated, indicating a significant coupling between replication and division. This coupling weakens as the growth rate of cells increases. Our data suggest that the underlying control mechanism in slow growth conditions is related to unreplicated chromosome blocking the onset of constriction at the midcell. We show that the nucleoid occlusion protein SlmA does not play a role in this process and neither do other known factors involved in positioning bacterial Z-ring relative to the chromosome. Altogether this work reconciles different ideas from the past and brings out a more nuanced role of replication in controlling the division process in a growth-rate dependent manner.
Amir A. Thinking Probabilistically: Stochastic Processes, Disordered Systems, and Their Applications. Cambridge University Press; 2021. Publisher's Version
Dieterle PB, Amir A. Diffusive wave dynamics beyond the continuum limit. Physical Review E. 2021;104 (1). Publisher's VersionAbstract
Scientists have observed and studied diffusive waves in contexts as disparate as population genetics and cell signaling. Often, these waves are propagated by discrete entities or agents, such as individual cells in the case of cell signaling. For a broad class of diffusive waves, we characterize the transition between the collective propagation of diffusive waves -- in which the wave speed is well-described by continuum theory -- and the propagation of diffusive waves by individual agents. We show that this transition depends heavily on the dimensionality of the system in which the wave propagates and that disordered systems yield dynamics largely consistent with lattice systems. In some system dimensionalities, the intuition that closely packed sources more accurately mimic a continuum can be grossly violated.
Min J, Amir A. A transport approach to relate asymmetric protein segregation and population growth. JSTAT. 2021. Publisher's VersionAbstract
Many unicellular organisms allocate their key proteins asymmetrically between the mother and daughter cells, especially in a stressed environment. A recent theoretical model is able to predict when the asymmetry in segregation of key proteins enhances the population fitness, extrapolating the solution at two limits where the segregation is perfectly asymmetric (asymmetry a = 1) and when the asymmetry is small (0≤a≪1). We generalize the model by introducing stochasticity and use a transport equation to obtain a self-consistent equation for the population growth rate and the distribution of the amount of key proteins. We provide two ways of solving the self-consistent equation: numerically by updating the solution for the self-consistent equation iteratively and analytically by expanding moments of the distribution. With these more powerful tools, we can extend the previous model by Lin et al. to include stochasticity to the segregation asymmetry. We show the stochastic model is equivalent to the deterministic one with a modified effective asymmetry parameter (a_eff). We discuss the biological implication of our models and compare with other theoretical models.
Barber F, Min J, Murray AW, Amir A. Modeling the impact of single-cell stochasticity and size control on the population growth rate in asymmetrically dividing cells. PLOS Computational Biology. 2021;17 (6). Publisher's versionAbstract
Microbial populations show striking diversity in cell growth morphology and lifecycle; however, our understanding of how these factors influence the growth rate of cell populations remains limited. We use theory and simulations to predict the impact of asymmetric cell division, cell size regulation and single-cell stochasticity on the population growth rate. Our model predicts that coarse-grained noise in the single-cell growth rate λ decreases the population growth rate, as previously seen for symmetrically dividing cells. However, for a given noise in λ we find that dividing asymmetrically can enhance the population growth rate for cells with strong size control (between a “sizer” and an “adder”). To reconcile this finding with the abundance of symmetrically dividing organisms in nature, we propose that additional constraints on cell growth and division must be present which are not included in our model, and we explore the effects of selected extensions thereof. Further, we find that within our model, epigenetically inherited generation times may arise due to size control in asymmetrically dividing cells, providing a possible explanation for recent experimental observations in budding yeast. Taken together, our findings provide insight into the complex effects generated by non-canonical growth morphologies.
Lin J, Amir A. Disentangling Intrinsic and Extrinsic Gene Expression Noise in Growing Cells. Physical Review Letters. 2021;126 (7). Publisher's versionAbstract
Gene expression is a stochastic process. Despite the increase of protein numbers in growing cells, the protein concentrations are often found to be confined within small ranges throughout the cell cycle. Generally, the noise in protein concentration can be decomposed into an intrinsic and an extrinsic component, where the former vanishes for high expression levels. Considering the time trajectory of protein concentration as a random walker in the concentration space, an effective restoring force (with a corresponding “spring constant”) must exist to prevent the divergence of concentration due to random fluctuations. In this work, we prove that the magnitude of the effective spring constant is directly related to the fraction of intrinsic noise in the total protein concentration noise. We show that one can infer the magnitude of intrinsic, extrinsic, and measurement noises of gene expression solely based on time-resolved data of protein concentration, without any a priori knowledge of the underlying gene expression dynamics. We apply this method to experimental data of single-cell bacterial gene expression. The results allow us to estimate the average copy numbers and the translation burst parameters of the studied proteins.
Guo Y, Amir A. Exploring the effect of network topology, mRNA and protein dynamics on gene regulatory network stability. Nature Communications. 2021;12 (130). Publisher's versionAbstract
Homeostasis of protein concentrations in cells is crucial for their proper functioning, requiring steady-state concentrations to be stable to fluctuations. Since gene expression is regulated by proteins such as transcription factors (TFs), the full set of proteins within the cell constitutes a large system of interacting components, which can become unstable. We explore factors affecting stability by coupling the dynamics of mRNAs and proteins in a growing cell. We find that mRNA degradation rate does not affect stability, contrary to previous claims. However, global structural features of the network can dramatically enhance stability. Importantly, a network resembling a bipartite graph with a lower fraction of interactions that target TFs has a higher chance of being stable. Scrambling the E. coli transcription network, we find that the biological network is significantly more stable than its randomized counterpart, suggesting that stability constraints may have shaped network structure during the course of evolution.
2020
Dieterle PB, Min J, Irimia D, Amir A. Dynamics of diffusive cell signaling relays. eLife. 2020;9 (61771). Publisher's VersionAbstract

In biological contexts as diverse as development, apoptosis, and synthetic microbial consortia, collections of cells or sub-cellular components have been shown to overcome the slow signaling speed of simple diffusion by utilizing diffusive relays, in which the presence of one type of diffusible signaling molecule triggers participation in the emission of the same type of molecule. This collective effect gives rise to fast-traveling diffusive waves. Here, in the context of cell signaling, we show that system dimensionality – the shape of the extracellular medium and the distribution of cells within it – can dramatically affect the wave dynamics, but that these dynamics are insensitive to details of cellular activation. As an example, we show that neutrophil swarming experiments exhibit dynamical signatures consistent with the proposed signaling motif. We further show that cell signaling relays generate much steeper concentration profiles than does simple diffusion, which may facilitate neutrophil chemotaxis.

Levien E, Min J, Kondev J, Amir A. Non-genetic variability: survival strategy or nuisance?. 2020. arXivAbstract
The observation that phenotypic variability is ubiquitous in isogenic populations has led to a multitude of experimental and theoretical studies seeking to probe the causes and consequences of this variability. Whether it be in the context of antibiotic treatments or exponential growth in constant environments, non-genetic variability has shown to have significant effects on population dynamics. Here, we review research that elucidates the relationship between cell-to-cell variability and population dynamics. After summarizing the relevant experimental observations, we discuss models of bet-hedging and phenotypic switching. In the context of these models, we discuss how switching between phenotypes at the single-cell level can help populations survive in uncertain environments. Next, we review more fine-grained models of phenotypic variability where the relationship between single-cell growth rates, generation times and cell sizes is explicitly considered. Variability in these traits can have significant effects on the population dynamics, even in a constant environment. We show how these effects can be highly sensitive to the underlying model assumptions. We close by discussing a number of open questions, such as how environmental and intrinsic variability interact and what the role of non-genetic variability in evolutionary dynamics is.
Ash B, Amir A, Bar-Sinai Y, Oreg Y, Imry Y. Thermal conductance of one-dimensional disordered harmonic chains. Physical Review B. 2020;101 (12). Publisher's VersionAbstract
We study heat conduction mediated by longitudinal phonons in one-dimensional disordered harmonic chains. Using scaling properties of the phonon density of states and localization in disordered systems, we find nontrivial scaling of the thermal conductance with the system size. Our findings are corroborated by extensive numerical analysis. We show that, suprisingly, the thermal conductance of a system with strong disorder, characterized by a “heavy-tailed” probability distribution, and with large impedance mismatch between the bath and the system, scales normally with the system size, i.e., in a manner consistent with Fourier's law. We identify a dimensionless scaling parameter, related to the temperature scale and the localization length of the phonons, through which the thermal conductance for different models of disorder and different temperatures follows a universal behavior.
Levien E, GrandPre T, Amir A. Large Deviation Principle Linking Lineage Statistics to Fitness in Microbial Populations. Physical Review Letters. 2020;125 (4). Publisher's versionAbstract
In exponentially proliferating populations of microbes, the population doubles at a rate less than the average doubling time of a single-cell due to variability at the single-cell level. It is known that the distribution of generation times obtained from a single lineage is, in general, insufficient to determine a population’s growth rate. Is there an explicit relationship between observables obtained from a single lineage and the population growth rate? We show that a population’s growth rate can be represented in terms of averages over isolated lineages. This lineage representation is related to a large deviation principle that is a generic feature of exponentially proliferating populations. Due to the large deviation structure of growing populations, the number of lineages needed to obtain an accurate estimate of the growth rate depends exponentially on the duration of the lineages, leading to a nonmonotonic convergence of the estimate, which we verify in both synthetic and experimental data sets.
Amir A. An elementary renormalization-group approach to the generalized central limit theorem and extreme value distributions. Journal of Statistical Mechanics: Theory and Experiment. 2020;2020. Publisher's VersionAbstract
The generalized central limit theorem is a remarkable generalization of the central limit theorem, showing that the sum of a large number of independent, identically-distributed (i.i.d) random variables with infinite variance may converge under appropriate scaling to a distribution belonging to a special family known as Lévy stable distributions. Similarly, the maximum of i.i.d. variables may converge to a distribution belonging to one of three universality classes (Gumbel, Weibull and Fréchet). Here, we rederive these known results following a mathematically non-rigorous yet highly transparent renormalization-group-inspired approach that captures both of these universal results following a nearly identical procedure.
Barber F, Amir A, Murray AW. Cell-size regulation in budding yeast does not depend on linear accumulation of Whi5. PNAS. 2020. Publisher's VersionAbstract
Cells must couple cell-cycle progress to their growth rate to restrict the spread of cell sizes present throughout a population. Linear, rather than exponential, accumulation of Whi5, was proposed to provide this coordination by causing a higher Whi5 concentration in cells born at a smaller size. We tested this model using the inducible GAL1 promoter to make the Whi5 concentration independent of cell size. At an expression level that equalizes the mean cell size with that of wild-type cells, the size distributions of cells with galactose-induced Whi5 expression and wild-type cells are indistinguishable. Fluorescence microscopy confirms that the endogenous and GAL1 promoters produce different relationships between Whi5 concentration and cell volume without diminishing size control in the G1 phase. We also expressed Cln3 from the GAL1 promoter, finding that the spread in cell sizes for an asynchronous population is unaffected by this perturbation. Our findings indicate that size control in budding yeast does not fundamentally originate from the linear accumulation of Whi5, contradicting a previous claim and demonstrating the need for further models of cell-cycle regulation to explain how cell size controls passage through Start.
Lin J, Amir A. From single-cell variability to population growth. Physical Review E. 2020;101 (1) :012401. Publisher's VersionAbstract
Single-cell experiments have revealed cell-to-cell variability in generation times and growth rates for genetically identical cells. Theoretical models relating the fluctuating generation times of single cells to the population growth rate are usually based on the assumption that the generation times of mother and daughter cells are uncorrelated. This assumption, however, is inconsistent with the exponential growth of cell volume in time observed for many cell types. Here we develop a more general and biologically relevant model in which cells grow exponentially and generation times are correlated in a manner which controls cell size. In addition to the fluctuating generation times, we also allow the single-cell growth rates to fluctuate and account for their correlations across the lineage tree. Surprisingly, we find that the population growth rate only depends on the distribution of single-cell growth rates and their correlations.

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