Publications

2020
Lin J, Amir A. Disentangling intrinsic and extrinsic gene expression noise in growing cells. [Internet]. 2020. bioRxivAbstract
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. 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 protein number and the translation burst parameter.
Guo Y, Amir A. Stability of gene regulatory networks. [Internet]. 2020. arXivAbstract
Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) 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. Here, we explore factors affecting the stability of this system by coupling the dynamics of mRNAs and protein concentrations in a growing cell. We find that it is possible for protein concentrations to become unstable if the regulation strengths or system size becomes too large, and that other global structural features of the networks can dramatically enhance the stability of the system. In particular, given the same number of proteins, TFs, number of interactions, and regulation strengths, a network that resembles a bipartite graph with a lower fraction of interactions that target TFs has a higher chance of being stable. By scrambling the E. coli. transcription network, we find that the randomized network with the same number of regulatory interactions is much more likely to be unstable than the real network. These findings suggest that constraints imposed by system stability could have played a role in shaping the existing regulatory network during the evolutionary process. We also find that contrary to what one might expect from random matrix theory and what has been argued in the literature, the degradation rate of mRNA does not affect whether the system is stable.
Ash B, Amir A, Bar-Sinai Y, Oreg Y, Imry Y. Thermal conductance of one-dimensional disordered harmonic chains. Physical Review B [Internet]. 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 [Internet]. 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 [Internet]. 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 [Internet]. 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 [Internet]. 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.
Lin J, Manhart M, Amir A. Evolution of microbial growth traits under serial dilution. Genetics [Internet]. 2020;215 (2). Publisher's VersionAbstract
Selection of mutants in a microbial population depends on multiple cellular traits. In serial-dilution evolution experiments, three key traits are the lag time when transitioning from starvation to growth, the exponential growth rate, and the yield (number of cells per unit resource). Here we investigate how these traits evolve in laboratory evolution experiments using a minimal model of population dynamics, where the only interaction between cells is competition for a single limiting resource. We find that the fixation probability of a beneficial mutation depends on a linear combination of its growth rate and lag time relative to its immediate ancestor, even under clonal interference. The relative selective pressure on growth rate and lag time is set by the dilution factor; a larger dilution factor favors the adaptation of growth rate over the adaptation of lag time. The model shows that yield, however, is under no direct selection. We also show how the adaptation speeds of growth and lag depend on experimental parameters and the underlying supply of mutations. Finally, we investigate the evolution of covariation between these traits across populations, which reveals that the population growth rate and lag time can evolve a nonzero correlation even if mutations have uncorrelated effects on the two traits. Altogether these results provide useful guidance to future experiments on microbial evolution.
Ho P-Y, Martins BMC, Amir A. A Mechanistic Model of the Regulation of Division Timing by the Circadian Clock in Cyanobacteria. Biophysical Journal [Internet]. 2020;118 (12) :2905-2913. Publisher's VersionAbstract
The cyanobacterium Synechococcus elongatus possesses a circadian clock in the form of a group of proteins whose concentrations and phosphorylation states oscillate with daily periodicity under constant conditions. The circadian clock regulates the cell cycle such that the timing of the cell divisions is biased toward certain times during the circadian period, but the mechanism underlying this phenomenon remains unclear. Here, we propose a mechanism in which a protein limiting for division accumulates at a rate proportional to the cell volume growth and is modulated by the clock. This “modulated rate” model, in which the clock signal is integrated over time to affect division timing, differs fundamentally from the previously proposed “gating” concept, in which the clock is assumed to suppress divisions during a specific time window. We found that although both models can capture the single-cell statistics of division timing in S. elongatus, only the modulated rate model robustly places divisions away from darkness during changes in the environment. Moreover, within the framework of the modulated rate model, existing experiments on S. elongatus are consistent with the simple mechanism that division timing is regulated by the accumulation of a division limiting protein in a phase with genes whose activity peaks at dusk.
Levien E, Kondev J, Amir A. The interplay of phenotypic variability and fitness in finite microbial populations. Journal of the Royal Society Interface [Internet]. 2020;17 (166). Publisher's VersionAbstract

In isogenic microbial populations, phenotypic variability is generated by a combination of stochastic mechanisms, such as gene expression, and deterministic factors, such as asymmetric segregation of cell volume. Here we address the question: how does phenotypic variability of a microbial population affect its fitness? While this question has previously been studied for exponentially growing populations, the situation when the population size is kept fixed has received much less attention, despite its relevance to many natural scenarios. We show that the outcome of competition between multiple microbial species can be determined from the distribution of phenotypes in the culture using a generalization of the well-known Euler–Lotka equation, which relates the steady-state distribution of phenotypes to the population growth rate. We derive a generalization of the Euler–Lotka equation for finite cultures, which relates the distribution of phenotypes among cells in the culture to the exponential growth rate. Our analysis reveals that in order to predict fitness from phenotypes, it is important to understand how distributions of phenotypes obtained from different subsets of the genealogical history of a population are related. To this end, we derive a mapping between the various ways of sampling phenotypes in a finite population and show how to obtain the equivalent distributions from an exponentially growing culture. Finally, we use this mapping to show that species with higher growth rates in exponential growth conditions will have a competitive advantage in the finite culture.

2019
Dieterle P, Min J, Irimia D, Amir A. Dynamics of diffusive cell signaling relays. [Internet]. 2019. bioRxivAbstract
Cells can communicate with each other by emitting diffusible signaling molecules into the surrounding environment. However, simple diffusion is slow. Even small molecules take hours to diffuse millimeters away from their source, making it difficult for thousands of cells to coordinate their activity over millimeters, as happens routinely during development and immune response. Moreover, simple diffusion creates shallow, Gaussian-tailed concentration profiles. Attempting to move up or down such shallow gradients - to chemotax - is a difficult task for cells, as they see only small spatial and temporal concentration changes. Here, we demonstrate that cells 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, can propagate fast-traveling diffusive waves that give rise to steep chemical gradients. Our methods are general and capture the effects of dimensionality, cell density, signaling molecule degradation, pulsed emission, and cellular chemotaxis on the diffusive wave dynamics. We show that system dimensionality - the size and shape of the extracellular medium and the distribution of the cells within it - can have a particularly dramatic effect on wave initiation and asymptotic propagation, and that these dynamics are insensitive to the details of cellular activation. As an example, we show that neutrophil swarming experiments exhibit dynamical signatures consistent with the proposed signaling motif. Interpreted in the context of these experiments, our results provide insight into the utility of signaling relays in immune response.
Fai TG, Mohapatra L, Kar P, Kondev J, Amir A. Length regulation of multiple flagella that self-assemble from a shared pool of components. eLife. 2019;8.Abstract
The single-celled green algae Chlamydomonas reinhardtii with its two flagella - microtubule-based structures of equal and constant lengths - is the canonical model organism for studying size control of organelles. Experiments have identified motor-driven transport of tubulin to the flagella tips as a key component of their length control. Here we consider a class of models whose key assumption is that proteins responsible for the intraflagellar transport (IFT) of tubulin are present in limiting amounts. We show that the limiting-pool assumption is insufficient to describe the results of severing experiments, in which a flagellum is regenerated after it has been severed. Next, we consider an extension of the limiting-pool model that incorporates proteins that depolymerize microtubules. We show that this 'active disassembly' model of flagellar length control explains in quantitative detail the results of severing experiments and use it to make predictions that can be tested in experiments.
Guo Y, Vucelja M, Amir A. Stochastic tunneling across fitness valleys can give rise to a logarithmic long-term fitness trajectory. Science Advances [Internet]. 2019;5 (7). Publisher's VersionAbstract
Adaptation, where a population evolves increasing fitness in a fixed environment, is typically thought of as a hill-climbing process on a fitness landscape. With a finite genome, such a process eventually leads the population to a fitness peak, at which point fitness can no longer increase through individual beneficial mutations. Instead, the ruggedness of typical landscapes due to epistasis between genes or DNA sites suggests that the accumulation of multiple mutations (via a process known as stochastic tunneling) can allow a population to continue increasing in fitness. However, it is not clear how such a phenomenon would affect long-term fitness evolution. By using a spin-glass type model for the fitness function that takes into account microscopic epistasis, we find that hopping between metastable states can mechanistically and robustly give rise to a slow, logarithmic average fitness trajectory.
Wong F, Garner EC, Amir A. Mechanics and dynamics of translocating MreB filaments on curved membranes. eLife [Internet]. 2019;8 :e40472. Publisher's VersionAbstract

MreB is an actin homolog that is essential for coordinating the cell wall synthesis required for the rod shape of many bacteria. Previously we have shown that filaments of MreB bind to the curved membranes of bacteria and translocate in directions determined by principal membrane curvatures to create and reinforce the rod shape (Hussain et al., 2018). Here, in order to understand how MreB filament dynamics affects their cellular distribution, we model how MreB filaments bind and translocate on membranes with different geometries. We find that it is both energetically favorable and robust for filaments to bind and orient along directions of largest membrane curvature. Furthermore, significant localization to different membrane regions results from processive MreB motion in various geometries. These results demonstrate that the in vivo localization of MreB observed in many different experiments, including those examining negative Gaussian curvature, can arise from translocation dynamics alone.

Paul N, Amir A. Quantum Diffusion in the Strong Tunneling Regime. Physical Review B [Internet]. 2019;100 (2). Publisher's VersionAbstract
We study the spread of a quantum-mechanical wave packet in a noisy environment, modeled using a tight-binding Hamiltonian. Despite the coherent dynamics, the fluctuating environment may give rise to diffusive behavior. When correlations between different level-crossing events can be neglected, we use the solution of the Landau-Zener problem to find how the diffusion constant depends on the noise. We also show that when an electric field or external disordered potential is applied to the system, the diffusion constant is suppressed with no drift term arising. The results are relevant to various quantum systems, including exciton diffusion in photosynthesis and electronic transport in solid-state physics.
Wong F, Amir A. Mechanics and Dynamics of Bacterial Cell Lysis. Biophysical Journal [Internet]. 2019;116 (12) :2378-2389. Publisher's VersionAbstract
Membrane lysis, or rupture, is a cell death pathway in bacteria frequently caused by cell wall-targeting antibiotics. Although previous studies have clarified the biochemical mechanisms of antibiotic action, a physical understanding of the processes leading to lysis remains lacking. Here, we analyze the dynamics of membrane bulging and lysis in Escherichia coli, in which the formation of an initial, partially subtended spherical bulge (“bulging”) after cell wall digestion occurs on a characteristic timescale of 1 s and the growth of the bulge (“swelling”) occurs on a slower characteristic timescale of 100 s. We show that bulging can be energetically favorable due to the relaxation of the entropic and stretching energies of the inner membrane, cell wall, and outer membrane and that the experimentally observed timescales are consistent with model predictions. We then show that swelling is mediated by the enlargement of wall defects, after which cell lysis is consistent with both the inner and outer membranes exceeding characteristic estimates of the yield areal strains of biological membranes. These results contrast biological membrane physics and the physics of thin, rigid shells. They also have implications for cellular morphogenesis and antibiotic discovery across different species of bacteria.
Lin J, Min J, Amir A. Optimal segregation of proteins: phase transitions and symmetry breaking. Physical Review Letters [Internet]. 2019;122 :068101. Publisher's VersionAbstract

Asymmetric segregation of key proteins at cell division—be it a beneficial or deleterious protein—is ubiquitous in unicellular organisms and often considered as an evolved trait to increase fitness in a stressed environment. Here, we provide a general framework to describe the evolutionary origin of this asymmetric segregation. We compute the population fitness as a function of the protein segregation asymmetry a, and show that the value of a which optimizes the population growth manifests a phase transition between symmetric and asymmetric partitioning phases. Surprisingly, the nature of phase transition is different for the case of beneficial proteins as opposed to deleterious proteins: a smooth (second order) transition from purely symmetric to asymmetric segregation is found in the former, while a sharp transition occurs in the latter. Our study elucidates the optimization problem faced by evolution in the context of protein segregation, and motivates further investigation of asymmetric protein segregation in biological systems.

    2018
    Lin J, Amir A. Homeostasis of protein and mRNA concentrations in growing cells. Nature Communications [Internet]. 2018;9 (4496). Publisher's VersionAbstract

    Many experiments show that the numbers of mRNA and protein are proportional to the cell volume in growing cells. However, models of stochastic gene expression often assume constant transcription rate per gene and constant translation rate per mRNA, which are incompatible with these experiments. Here, we construct a minimal gene expression model to fill this gap. Assuming ribosomes and RNA polymerases are limiting in gene expression, we show that the numbers of proteins and mRNAs both grow exponentially during the cell cycle and that the concentrations of all mRNAs and proteins achieve cellular homeostasis; the competition between genes for the RNA polymerases makes the transcription rate independent of the genome number. Furthermore, by extending the model to situations in which DNA (mRNA) can be saturated by RNA polymerases (ribosomes) and becomes limiting, we predict a transition from exponential to linear growth of cell volume as the protein-to-DNA ratio increases.

    Amir A, Balaban NQ. Learning from Noise: How Observing Stochasticity May Aid Microbiology. Trends in Microbiology [Internet]. 2018;26 :374-385. Publisher's VersionAbstract
    For many decades, the wedding of quantitative data with mathematical modeling has been fruitful, leading to important biological insights. Here, we review some of the ongoing efforts to gain insights into problems in microbiology – and, in particular, cell-cycle progression and its regulation – through observation and quantitative analysis of the natural fluctuations in the system. We first illustrate this idea by reviewing a classic example in microbiology – the Luria–Delbrück experiment – and discussing how, in that case, useful information was obtained by looking beyond the mean outcome of the experiment, but instead paying attention to the variability between replicates of the experiment. We then switch gears to the contemporary problem of cell cycle progression and discuss in more detail how insights into cell size regulation and, when relevant, coupling between the cell cycle and the circadian clock, can be gained by studying the natural fluctuations in the system and their statistical properties. We end with a more general discussion of how (in this context) the correct level of phenomenological model should be chosen, as well as some of the pitfalls associated with this type of analysis. Throughout this review the emphasis is not on providing details of the experimental setups or technical details of the models used, but rather, in fleshing out the conceptual structure of this particular approach to the problem. For this reason, we choose to illustrate the framework on a rather broad range of problems, and on organisms from all domains of life, to emphasize the commonality of the ideas and analysis used (as well as their differences).
    Amir A, Oreg Y, Imry Y. Thermal conductivity in 1d: disorder-induced transition from anomalous to normal scaling. Europhysics Letters [Internet]. 2018;124 (1). Publisher's VersionAbstract
    It is well known that the contribution of harmonic phonons to the thermal conductivity of 1D systems diverges with the harmonic chain length L (explicitly, increases with L as a power-law with a positive power). Furthermore, within various one-dimensional models containing disorder it was shown that this divergence persists, with the thermal conductivity scaling as √L under certain boundary conditions, where L is the length of the harmonic chain. Here we show that when the chain is weakly coupled to the heat reservoirs and there is strong disorder this scaling can be violated. We find a weaker power-law dependence on L, and show that for sufficiently strong disorder the thermal conductivity stops being anomalous -- despite both density-of-states and the diverging localization length scaling anomalously. Surprisingly, in this strong disorder regime two anomalously scaling quantities cancel each other to recover Fourier's law of heat transport.

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