Identifying regulation with adversarial surrogates.

Homeostasis, the ability to maintain a relatively constant internal environment in the face of perturbations, is a hallmark of biological systems. It is believed that this constancy is achieved through multiple internal regulation and control processes. Given observations of a system, or even a detailed model of one, it is both valuable and extremely challenging to extract the control objectives of the homeostatic mechanisms. In this work, we develop a robust data-driven method to identify these objectives, namely to understand: "what does the system care about?". We propose an algorithm, Identifying Regulation with Adversarial Surrogates (IRAS), that receives an array of temporal measurements of the system and outputs a candidate for the control objective, expressed as a combination of observed variables. IRAS is an iterative algorithm consisting of two competing players. The first player, realized by an artificial deep neural network, aims to minimize a measure of invariance we refer to as the coefficient of regulation. The second player aims to render the task of the first player more difficult by forcing it to extract information about the temporal structure of the data, which is absent from similar "surrogate" data. We test the algorithm on four synthetic and one natural data set, demonstrating excellent empirical results. Interestingly, our approach can also be used to extract conserved quantities, e.g., energy and momentum, in purely physical systems, as we demonstrate empirically.

Scale free topology as an effective feedback system.

Biological networks are often heterogeneous in their connectivity pattern, with degree distributions featuring a heavy tail of highly connected hubs. The implications of this heterogeneity on dynamical properties are a topic of much interest. Here we show that interpreting topology as a feedback circuit can provide novel insights on dynamics. Based on the observation that in finite networks a small number of hubs have a disproportionate effect on the entire system, we construct an approximation by lumping these nodes into a single effective hub, which acts as a feedback loop with the rest of the nodes. We use this approximation to study dynamics of networks with scale-free degree distributions, focusing on their probability of convergence to fixed points. We find that the approximation preserves convergence statistics over a wide range of settings. Our mapping provides a parametrization of scale free topology which is predictive at the ensemble level and also retains properties of individual realizations. Specifically, outgoing hubs have an organizing role that can drive the network to convergence, in analogy to suppression of chaos by an external drive. In contrast, incoming hubs have no such property, resulting in a marked difference between the behavior of networks with outgoing vs. incoming scale free degree distribution. Combining feedback analysis with mean field theory predicts a transition between convergent and divergent dynamics which is corroborated by numerical simulations. Furthermore, they highlight the effect of a handful of outlying hubs, rather than of the connectivity distribution law as a whole, on network dynamics.

Individuality and slow dynamics in bacterial growth homeostasis.

Microbial growth and division are fundamental processes relevant to many areas of life science. Of particular interest are homeostasis mechanisms, which buffer growth and division from accumulating fluctuations over multiple cycles. These mechanisms operate within single cells, possibly extending over several division cycles. However, all experimental studies to date have relied on measurements pooled from many distinct cells. Here, we disentangle long-term measured traces of individual cells from one another, revealing subtle differences between temporal and pooled statistics. By analyzing correlations along up to hundreds of generations, we find that the parameter describing effective cell size homeostasis strength varies significantly among cells. At the same time, we find an invariant cell size, which acts as an attractor to all individual traces, albeit with different effective attractive forces. Despite the common attractor, each cell maintains a distinct average size over its finite lifetime with suppressed temporal fluctuations around it, and equilibration to the global average size is surprisingly slow ([Formula: see text] cell cycles). To show a possible source of variable homeostasis strength, we construct a mathematical model relying on intracellular interactions, which integrates measured properties of cell size with those of highly expressed proteins. Effective homeostasis strength is then influenced by interactions and by noise levels and generally varies among cells. A predictable and measurable consequence of variable homeostasis strength appears as distinct oscillatory patterns in cell size and protein content over many generations. We discuss implications of our results to understanding mechanisms controlling division in single cells and their characteristic timescales.

Coexistence and cooperation in structured habitats.

BACKGROUND: Natural habitats are typically structured, imposing constraints on inhabiting populations and their interactions. Which conditions are important for coexistence of diverse communities, and how cooperative interaction stabilizes in such populations, have been important ecological and evolutionary questions. RESULTS: We investigate a minimal ecological framework of microbial population dynamics that exhibits crucial features to show coexistence: Populations repeatedly undergo cycles of separation into compartmentalized habitats and mixing with new resources. The characteristic time-scale is longer than that typical of individual growth. Using analytic approximations, averaging techniques and phase-plane methods of dynamical systems, we provide a framework for analyzing various types of microbial interactions. Population composition and population size are both dynamic variables of the model; they are found to be decoupled both in terms of time-scale and parameter dependence. We present specific results for two examples of cooperative interaction by public goods: collective antibiotics resistance, and enhanced iron-availability by pyoverdine. We find stable coexistence to be a likely outcome. CONCLUSIONS: The two simple features of a long mixing time-scale and spatial compartmentalization are enough to enable coexisting strains. In particular, costly social traits are often stabilized in such an environment-and thus cooperation established.

Cooperative stochastic binding and unbinding explain synaptic size dynamics and statistics.

Synapses are dynamic molecular assemblies whose sizes fluctuate significantly over time-scales of hours and days. In the current study, we examined the possibility that the spontaneous microscopic dynamics exhibited by synaptic molecules can explain the macroscopic size fluctuations of individual synapses and the statistical properties of synaptic populations. We present a mesoscopic model, which ties the two levels. Its basic premise is that synaptic size fluctuations reflect cooperative assimilation and removal of molecules at a patch of postsynaptic membrane. The introduction of cooperativity to both assimilation and removal in a stochastic biophysical model of these processes, gives rise to features qualitatively similar to those measured experimentally: nanoclusters of synaptic scaffolds, fluctuations in synaptic sizes, skewed, stable size distributions and their scaling in response to perturbations. Our model thus points to the potentially fundamental role of cooperativity in dictating synaptic remodeling dynamics and offers a conceptual understanding of these dynamics in terms of central microscopic features and processes.

Synaptic size dynamics as an effectively stochastic process.

Long-term, repeated measurements of individual synaptic properties have revealed that synapses can undergo significant directed and spontaneous changes over time scales of minutes to weeks. These changes are presumably driven by a large number of activity-dependent and independent molecular processes, yet how these processes integrate to determine the totality of synaptic size remains unknown. Here we propose, as an alternative to detailed, mechanistic descriptions, a statistical approach to synaptic size dynamics. The basic premise of this approach is that the integrated outcome of the myriad of processes that drive synaptic size dynamics are effectively described as a combination of multiplicative and additive processes, both of which are stochastic and taken from distributions parametrically affected by physiological signals. We show that this seemingly simple model, known in probability theory as the Kesten process, can generate rich dynamics which are qualitatively similar to the dynamics of individual glutamatergic synapses recorded in long-term time-lapse experiments in ex-vivo cortical networks. Moreover, we show that this stochastic model, which is insensitive to many of its underlying details, quantitatively captures the distributions of synaptic sizes measured in these experiments, the long-term stability of such distributions and their scaling in response to pharmacological manipulations. Finally, we show that the average kinetics of new postsynaptic density formation measured in such experiments is also faithfully captured by the same model. The model thus provides a useful framework for characterizing synapse size dynamics at steady state, during initial formation of such steady states, and during their convergence to new steady states following perturbations. These findings show the strength of a simple low dimensional statistical model to quantitatively describe synapse size dynamics as the integrated result of many underlying complex processes.

Single-cell protein dynamics reproduce universal fluctuations in cell populations.

Protein variability in single cells has been studied extensively in populations, but little is known about temporal protein fluctuations in a single cell over extended times. We present here traces of protein copy number measured in individual bacteria over multiple generations and investigate their statistical properties, comparing them to previously measured population snapshots. We find that temporal fluctuations in individual cells exhibit the same properties as those previously observed in populations. Scaled fluctuations around the mean of each trace exhibit the universal distribution shape measured in populations under a wide range of conditions and in two distinct microorganisms; the mean and variance of the traces over time obey the same quadratic relation. Analyzing the individual protein traces reveals that within a cell cycle protein content increases exponentially, with a rate that varies from cycle to cycle. This leads to a compact description of the trace as a 3-variable stochastic process -exponential rate, cell cycle duration and value at the cycle start- sampled once a cycle. This description is sufficient to reproduce both universal statistical properties of the protein fluctuations. Our results show that the protein distribution shape is insensitive to sub-cycle intracellular microscopic details and reflects global cellular properties that fluctuate between generations.

Coexistence of productive and non-productive populations by fluctuation-driven spatio-temporal patterns.

Cooperative interactions, their stability and evolution, provide an interesting context in which to study the interface between cellular and population levels of organization. Here we study a public goods model relevant to microorganism populations actively extracting a growth resource from their environment. Cells can display one of two phenotypes - a productive phenotype that extracts the resources at a cost, and a non-productive phenotype that only consumes the same resource. Both proliferate and are free to move by diffusion; growth rate and diffusion coefficient depend only weakly phenotype. We analyze the continuous differential equation model as well as simulate stochastically the full dynamics. We find that the two sub-populations, which cannot coexist in a well-mixed environment, develop spatio-temporal patterns that enable long-term coexistence in the shared environment. These patterns are purely fluctuation-driven, as the corresponding continuous spatial system does not display Turing instability. The average stability of coexistence patterns derives from a dynamic mechanism in which the producing sub-population equilibrates with the environmental resource and holds it close to an extinction transition of the other sub-population, causing it to constantly hover around this transition. Thus the ecological interactions support a mechanism reminiscent of self-organized criticality; power-law distributions and long-range correlations are found. The results are discussed in the context of general pattern formation and critical behavior in ecology as well as in an experimental context.

Minimal Surviving Inoculum in Collective Antibiotic Resistance.

A common strategy used by bacteria to resist antibiotics is enzymatic degradation or modification. This reduces the antibiotic threat in the environment and is therefore potentially a collective mechanism that also enhances the survival of nearby cells. Collective resistance is of clinical significance, yet a quantitative understanding at the population level is still incomplete. Here, we develop a general theoretical framework of collective resistance by antibiotic degradation. Our modeling study reveals that population survival crucially depends on the ratio of timescales of two processes: the rates of population death and antibiotic removal. However, it is insensitive to molecular, biological, and kinetic details of the underlying processes that give rise to these timescales. Another important aspect of antibiotic degradation is the degree of cooperativity, related to the permeability of the cell wall to antibiotics and enzymes. These observations motivate a coarse-grained, phenomenological model, with two compound parameters representing the population's race to survival and single-cell effective resistance. We propose a simple experimental assay to measure the dose-dependent minimal surviving inoculum and apply it to Escherichia coli expressing several types of ß-lactamase. Experimental data analyzed within the theoretical framework corroborate it with good agreement. Our simple model may serve as a reference for more complex situations, such as heterogeneous bacterial communities. IMPORTANCE Collective resistance occurs when bacteria work together to decrease the concentration of antibiotics in their environment, for example, by actively breaking down or modifying them. This can help bacteria survive by reducing the effective antibiotic concentration below their threshold for growth. In this study, we used mathematical modeling to examine the factors that influence collective resistance and to develop a framework to understand the minimum population size needed to survive a given initial antibiotic concentration. Our work helps to identify generic mechanism-independent parameters that can be derived from population data and identifies combinations of parameters that play a role in collective resistance. Specifically, it highlights the relative timescales involved in the survival of populations that inactivate antibiotics, as well as the levels of cooperation versus privatization. The results of this study contribute to our understanding of population-level effects on antibiotic resistance and may inform the design of antibiotic therapies.

Universal protein fluctuations in populations of microorganisms.

The copy number of any protein fluctuates among cells in a population; characterizing and understanding these fluctuations is a fundamental problem in biophysics. We show here that protein distributions measured under a broad range of biological realizations collapse to a single non-gaussian curve under scaling by the first two moments. Moreover, in all experiments the variance is found to depend quadratically on the mean, showing that a single degree of freedom determines the entire distribution. Our results imply that protein fluctuations do not reflect any specific molecular or cellular mechanism, and suggest that some buffering process masks these details and induces universality.

Adaptive response by state-dependent inactivation.

Many membrane channels and receptors exhibit adaptive, or desensitized, response to a strong sustained input stimulus. A key mechanism that underlies this response is the slow, activity-dependent removal of responding molecules to a pool which is unavailable to respond immediately to the input. This mechanism is implemented in different ways in various biological systems and has traditionally been studied separately for each. Here we highlight the common aspects of this principle, shared by many biological systems, and suggest a unifying theoretical framework. We study theoretically a class of models which describes the general mechanism and allows us to distinguish its universal from system-specific features. We show that under general conditions, regardless of the details of kinetics, molecule availability encodes an averaging over past activity and feeds back multiplicatively on the system output. The kinetics of recovery from unavailability determines the effective memory kernel inside the feedback branch, giving rise to a variety of system-specific forms of adaptive response-precise or input-dependent, exponential or power-law-as special cases of the same model.

A leader cell triggers end of lag phase in populations of Pseudomonas fluorescens.

The relationship between the number of cells colonizing a new environment and time for resumption of growth is a subject of long-standing interest. In microbiology this is known as the "inoculum effect." Its mechanistic basis is unclear with possible explanations ranging from the independent actions of individual cells, to collective actions of populations of cells. Here, we use a millifluidic droplet device in which the growth dynamics of hundreds of populations founded by controlled numbers of Pseudomonas fluorescens cells, ranging from a single cell, to one thousand cells, were followed in real time. Our data show that lag phase decreases with inoculum size. The decrease of average lag time and its variance across droplets, as well as lag time distribution shapes, follow predictions of extreme value theory, where the inoculum lag time is determined by the minimum value sampled from the single-cell distribution. Our experimental results show that exit from lag phase depends on strong interactions among cells, consistent with a "leader cell" triggering end of lag phase for the entire population.

Cancer progression as a learning process.

Drug resistance and metastasis-the major complications in cancer-both entail adaptation of cancer cells to stress, whether a drug or a lethal new environment. Intriguingly, these adaptive processes share similar features that cannot be explained by a pure Darwinian scheme, including dormancy, increased heterogeneity, and stress-induced plasticity. Here, we propose that learning theory offers a framework to explain these features and may shed light on these two intricate processes. In this framework, learning is performed at the single-cell level, by stress-driven exploratory trial-and-error. Such a process is not contingent on pre-existing pathways but on a random search for a state that diminishes the stress. We review underlying mechanisms that may support this search, and show by using a learning model that such exploratory learning is feasible in a high-dimensional system as the cell. At the population level, we view the tissue as a network of exploring agents that communicate, restraining cancer formation in health. In this view, disease results from the breakdown of homeostasis between cellular exploratory drive and tissue homeostasis.

Multiple timescales in bacterial growth homeostasis.

In balanced exponential growth, bacteria maintain many properties statistically stable for a long time: cell size, cell cycle time, and more. As these are strongly coupled variables, it is not a-priori obvious which are directly regulated and which are stabilized through interactions. Here, we address this problem by separating timescales in bacterial single-cell dynamics. Disentangling homeostatic set points from fluctuations around them reveals that some variables, such as growth-rate, cell size and cycle time, are "sloppy" with highly volatile set points. Quantifying the relative contribution of environmental and internal sources, we find that sloppiness is primarily driven by the environment. Other variables such as fold-change define "stiff" combinations of coupled variables with robust set points. These results are manifested geometrically as a control manifold in the space of variables: set points span a wide range of values within the manifold, whereas out-of-manifold deviations are constrained. Our work offers a generalizable data-driven approach for identifying control variables in a multidimensional system.

Dynamic modeling of cooperative protein secretion in microorganism populations.

Interactions between microorganisms can have a crucial effect on their population dynamics. Typically, interactions are mediated through the environment by molecules and proteins that are products of cell metabolism and physiology; they therefore reflect the internal dynamics of the single cell. In this work we aim to integrate single-cell properties of gene expression that affect indirect interactions between microorganisms under challenging conditions, into a quantitative model of population dynamics. Specifically we address the problem of a microbial population secreting a protein that can actively extract a growth-limiting resource, such as a simple sugar or iron, from the environment. The genes coding for the protein can undergo random epigenetic transitions between active and silenced states, and can be repressed by the product of their reaction. We model cooperative and competitive interactions between protein producing and non-producing phenotypes by nonlinear dynamical systems and analyze them both in terms of asymptotic states and of transient dynamics. Our model shows that phenotypic transitions allow a stable coexistence of the two phenotypes, and enables us to make predictions regarding the conditions required for such coexistence and the typical timescales of transient dynamics. It also shows how repression by the reaction product induces a feedback at the population-environment level that can result in limit cycle dynamics. The relation of these results to experiments are discussed.

Local and global features of genetic networks supporting a phenotypic switch.

Phenotypic switches are associated with alterations in the cell's gene expression profile and are vital to many aspects of biology. Previous studies have identified local motifs of the genetic regulatory network that could underlie such switches. Recent advancements allowed the study of networks at the global, many-gene, level; however, the relationship between the local and global scales in giving rise to phenotypic switches remains elusive. In this work, we studied the epithelial-mesenchymal transition (EMT) using a gene regulatory network model. This model supports two clusters of stable steady-states identified with the epithelial and mesenchymal phenotypes, and a range of intermediate less stable hybrid states, whose importance in cancer has been recently highlighted. Using an array of network perturbations and quantifying the resulting landscape, we investigated how features of the network at different levels give rise to these landscape properties. We found that local connectivity patterns affect the landscape in a mostly incremental manner; in particular, a specific previously identified double-negative feedback motif is not required when embedded in the full network, because the landscape is maintained at a global level. Nevertheless, despite the distributed nature of the switch, it is possible to find combinations of a few local changes that disrupt it. At the level of network architecture, we identified a crucial role for peripheral genes that act as incoming signals to the network in creating clusters of states. Such incoming signals are a signature of modularity and are expected to appear also in other biological networks. Hybrid states between epithelial and mesenchymal arise in the model due to barriers in the interaction between genes, causing hysteresis at all connections. Our results suggest emergent switches can neither be pinpointed to local motifs, nor do they arise as typical properties of random network ensembles. Rather, they arise through an interplay between the nature of local interactions, and the core-periphery structure induced by the modularity of the cell.

Visual detection of time-varying signals: Opposing biases and their timescales.

Human visual perception is a complex, dynamic and fluctuating process. In addition to the incoming visual stimulus, it is affected by many other factors including temporal context, both external and internal to the observer. In this study we investigate the dynamic properties of psychophysical responses to a continuous stream of visual near-threshold detection tasks. We manipulate the incoming signals to have temporal structures with various characteristic timescales. Responses of human observers to these signals are analyzed using tools that highlight their dynamical features as well. Our experiments show two opposing biases that shape perceptual decision making simultaneously: positive recency, biasing towards repeated response; and adaptation, entailing an increased probability of changed response. While both these effects have been reported in previous work, our results shed new light on the timescales involved in these effects, and on their interplay with varying inputs. We find that positive recency is a short-term bias, inversely correlated with response time, suggesting it can be compensated by afterthought. Adaptation, in contrast, reflects trends over longer times possibly including multiple previous trials. Our entire dataset, which includes different input signal temporal structures, is consistent with a simple model with the two biases characterized by a fixed parameter set. These results suggest that perceptual biases are inherent features which are not flexible to tune to input signals.

Stable memory with unstable synapses.

What is the physiological basis of long-term memory? The prevailing view in Neuroscience attributes changes in synaptic efficacy to memory acquisition, implying that stable memories correspond to stable connectivity patterns. However, an increasing body of experimental evidence points to significant, activity-independent fluctuations in synaptic strengths. How memories can survive these fluctuations and the accompanying stabilizing homeostatic mechanisms is a fundamental open question. Here we explore the possibility of memory storage within a global component of network connectivity, while individual connections fluctuate. We find that homeostatic stabilization of fluctuations differentially affects different aspects of network connectivity. Specifically, memories stored as time-varying attractors of neural dynamics are more resilient to erosion than fixed-points. Such dynamic attractors can be learned by biologically plausible learning-rules and support associative retrieval. Our results suggest a link between the properties of learning-rules and those of network-level memory representations, and point at experimentally measurable signatures.

Genome-wide transcriptional plasticity underlies cellular adaptation to novel challenge.

Cells adjust their transcriptional state to accommodate environmental and genetic perturbations. An open question is to what extent transcriptional response to perturbations has been specifically selected along evolution. To test the possibility that transcriptional reprogramming does not need to be 'pre-designed' to lead to an adaptive metabolic state on physiological timescales, we confronted yeast cells with a novel challenge they had not previously encountered. We rewired the genome by recruiting an essential gene, HIS3, from the histidine biosynthesis pathway to a foreign regulatory system, the GAL network responsible for galactose utilization. Switching medium to glucose in a chemostat caused repression of the essential gene and presented the cells with a severe challenge to which they adapted over approximately 10 generations. Using genome-wide expression arrays, we show here that a global transcriptional reprogramming (>1200 genes) underlies the adaptation. A large fraction of the responding genes is nonreproducible in repeated experiments. These results show that a nonspecific transcriptional response reflecting the natural plasticity of the regulatory network supports adaptation of cells to novel challenges.

Synaptic Tenacity or Lack Thereof: Spontaneous Remodeling of Synapses.

Synaptic plasticity - the directed modulation of synaptic connections by specific activity histories or physiological signals - is believed to be a major mechanism for the modification of neuronal network function. This belief, however, has a 'flip side': the supposition that synapses do not change spontaneously in manners unrelated to such signals. Contrary to this supposition, recent studies reveal that synapses do change spontaneously, and to a fairly large extent. Here we review experimental results on spontaneous synaptic remodeling, its relative contributions to total synaptic remodeling, its statistical characteristics, and its physiological importance. We also address challenges it poses and avenues it opens for future experimental and theoretical research.