Publications

2022
Hachmo O, Amir A. Conditional Probability as Found in Nature: Facilitated Diffusion. 2022. arXivAbstract
Transcription Factors (TFs) are proteins that regulate gene expression. The regulation mechanism is via the binding of a TF to a specific part of the gene associated with it, the TF's target. The target of a specific TF corresponds to a vanishingly small part of the entire DNA, where at the same time the search must end in a matter of tens of seconds at most for its biological purpose to be fulfilled - this makes the search a problem of high interest. Facilitated Diffusion is a mechanism used in nature for a robust and efficient search process. This mechanism combines 1D diffusion along the DNA and "excursions" of diffusion in 3D that help the TF to quickly arrive at distant parts of the DNA. In this paper we provide a derivation concerning this mechanism that links this search process to fundamental concepts in probability theory (conditional probability).
Jafarpour F, Levien E, Amir A. Evolutionary dynamics in non-Markovian models of microbial populations. 2022. bioRxivAbstract

In the past decade, great strides have been made to quantify the dynamics of single-cell growth and division in microbes. In order to make sense of the evolutionary history of these organisms, we must understand how features of single-cell growth and division influence evolutionary dynamics. This requires us to connect processes on the single-cell scale to population dynamics. Here, we consider a model of microbial growth in finite populations which explicitly incorporates the single- cell dynamics. We study the behavior of a mutant population in such a model and ask: can the evolutionary dynamics be coarse-grained so that the forces of natural selection and genetic drift can be expressed in terms of the long-term fitness? We show that it is in fact not possible, as there is no way to define a single fitness parameter (or reproductive rate) that defines the fate of an organism even in a constant environment. This is due to fluctuations in the population averaged division rate. As a result, various details of the single-cell dynamics affect the fate of a new mutant independently from how they affect the long-term growth rate of the mutant population. In particular, we show that in the case of neutral mutations, variability in generation times increases the rate of genetic drift, and in the case of beneficial mutations, variability decreases its fixation probability. Furthermore, we explain the source of the persistent division rate fluctuations and provide analytic solutions for the fixation probability as a multi-species generalization of the Euler-Lotka equation.

Pastrana CL, Qiu L, Armon S, Gerland U, Amir A. Pressure-induced Shape-shifting of Helical Bacteria. 2022. arXivAbstract
Many bacterial species are helical in form, including the widespread pathogen H. pylori. Motivated by recent experiments on H. pylori showing that cell wall synthesis is not uniform, we investigate the possible formation of helical cell shape induced by elastic heterogeneity. We show, experimentally and theoretically, that helical morphogenesis can be produced by pressurizing an elastic cylindrical vessel with helical reinforced lines. The properties of the pressurized helix are highly dependent on the initial helical angle of the reinforced region. We find that steep angles result in crooked helices with, surprisingly, reduced end-to-end distance upon pressurization. This work helps to explain the possible mechanisms for the generation of helical cell morphologies and may inspire the design of novel pressure-controlled helical actuators.
Vertti-Quintero N, Levien E, Poggi L, Amir A, Richard G-F, Baroud CN. Single-cell microfluidic analysis unravels individual cellular fates during Double-Strand Break Repair. 2022. bioRxivAbstract
Trinucleotide repeat expansions are responsible for two dozen human disorders. Contracting expanded repeats by Double-Strand Break Repair (DSBR) might be a therapeutic approach. Given the complexity of manipulating human cells, recent assays were made to quantify DSBR efficacy in yeast, using a fluorescent reporter. In this study DSBR is characterized with an interdisciplinary approach, linking large population dynamics and individual cells. Time-resolved molecular measurements of changes in the population are first confronted to a coupled differential equation model to obtain repair processes rates. Comparisons with measurements in microfluidic devices, where the progeny of 80-150 individual cells are followed, show good agreement between individual trajectories and mathematical and molecular results. Further analysis of individual progenies shows the heterogeneity of individual cell contributions to global repair efficacy. Three different categories of repair are identified: high-efficacy error-free, low-efficacy error-free and low-efficacy error-prone. These categories depend on the type of endonuclease used and on the target sequence.
Dieterle PB, Zheng J, Garner E, Amir A. Universal catastrophe time distributions of dynamically unstable polymers. Physical Review E. 2022;105 (6). Publisher’s VersionAbstract
Dynamic instability -- the growth, catastrophe, and shrinkage of quasi-one-dimensional filaments -- has been observed in multiple biopolymers. Scientists have long understood the catastrophic cessation of growth and subsequent depolymerization as arising from the interplay of hydrolysis and polymerization at the tip of the polymer. Here, we show that for a broad class of catastrophe models, the expected catastrophe time distribution is exponential. We show that the distribution shape is insensitive to noise, but that depletion of monomers from a finite pool can dramatically change the distribution shape by reducing the polymerization rate. We derive a form for this finite-pool catastrophe time distribution and show that finite-pool effects can be important even when the depletion of monomers does not greatly alter the polymerization rate.
Guo Y, Amir A. The effect of weak clonal interference on average fitness trajectories in the presence of macroscopic epistasis. Genetics. 2022. Publisher’s VersionAbstract
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).
Qiu L, Hutchinson JW, Amir A. Bending Instability of Rod-shaped Bacteria. Physical Review Letters. 2022;128 (5). Publisher's VersionAbstract
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.
Zareei A, Pan D, Amir A. Temporal Evolution of Flow in Pore-Networks: From Homogenization to Instability. Physical Review Letters. 2022;128 (23). Publisher's VersionAbstract
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. Coupling between DNA replication, segregation, and the onset of constriction in Escherichia coli. Cell Report. 2022;38 (12). Publisher’s VersionAbstract
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.
2021
Levien E, Min J, Kondev J, Amir A. Non-genetic variability in microbial populations: survival strategy or nuisance?. Rep. Prog. Phys. 2021;84. Publisher's VersionAbstract
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 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.
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.
Kar P, Tiruvadi-Krishnan S, Männik J, Männik J, Amir A. Distinguishing different modes of growth using single-cell data. eLife. 2021. Publisher's VersionAbstract
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.
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.

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