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Gene conversion is a ubiquitous phenomenon that leads to the exchange of genetic information between homologous DNA regions and maintains coevolving multi-gene families in most prokaryotic and eukaryotic organisms. In this paper, we study its implications for the evolution of a single functional gene with a silenced duplicate, using two different models of evolution on rugged fitness landscapes. Our analytical and numerical results show that, by helping to circumvent valleys of low fitness, gene conversion with a passive duplicate gene can cause a significant speedup of adaptation, which depends nontrivially on the frequency of gene conversion and the structure of the landscape. We find that stochastic effects due to finite population sizes further increase the likelihood of exploiting this evolutionary pathway. A universal feature appearing in both deterministic and stochastic analysis of our models is the existence of an optimal gene conversion rate, which maximizes the speed of adaptation. Our results reveal the potential for duplicate genes to act as a "scratch paper" that frees evolution from being limited to strictly beneficial mutations in strongly selective environments. [ABSTRACT FROM AUTHOR]

Abstract: The crucial role of time-keeping has required organisms to develop sophisticated regulatory networks to ensure the reliable propagation of periodic behavior. These biological clocks have long been a focus of research; however, a clear understanding of how they maintain oscillations in the face of unpredictable environments and the inherent noise of biological systems remains elusive. Here, we review the current understanding of circadian oscillations using Drosophila melanogaster as a typical example and discuss the utility of an alternative synthetic biology approach to studying these highly intricate systems. [Copyright &y& Elsevier]

We analyze the security of encryption schemes based on chaos synchronization and active/passive decomposition. The security is quantified by the number of transmitted samples that has to be acquired in order to reconstruct the transmitted message with an accuracy that may compromise the transmitted information. The dynamics is estimated as the average of dynamics of the observed data within a small neighborhood of the time delay embedding phase space. We examine the factors that affect the choice of embedding dimension and neighborhood size by the unauthorized receiver. We show that the security can he enhanced by mixing a large randomly modulated message component with a smaller chaotic component while keeping the message modulation fine grained. This result is in contrast to the common approach to ensure security by adding a small message component to a larger chaotic component. Further, we show that even when a low dimensional chaotic map is used, then the unauthorized receiver is required to use a reconstruction embedding dimension that can be made large by using chaotic dynamics with large conditional negative Lyapunov exponent. This result allows one to avoid the common restriction to use only high dimensional chaotic dynamics to maintain security. We also suggest guidelines for the design of efficient active passive/passive decomposition schemes in order to maintain low transmission power, fast synchronization, and yet preserve security. We demonstrate our analysis using a relatively simple encryption scheme based on a one-dimensional chaotic tent map. [ABSTRACT FROM AUTHOR]

Presents a study which introduced correlation-based communication schemes, correlation delay shift keying and symmetric chaos shift keying. System description of the communication schemes; Performance analysis; Conclusion.

Macrophages must respond appropriately to pathogens and other pro-inflammatory stimuli in order to perform their roles in fighting infection. One way in which inflammatory stimuli can vary is in their dynamics--that is, the amplitude and duration of stimulus experienced by the cell. In this study, we performed long-term live cell imaging in a microfluidic device to investigate how the pro-inflammatory genes IRF1, CXCL10, and CXCL9 respond to dynamic interferon-gamma (IFN) stimulation. We found that IRF1 responds to low concentration or short duration IFN stimulation, whereas CXCL10 and CXCL9 require longer or higherconcentration stimulation to be expressed. We also investigated the heterogeneity in the expression of each gene and found that CXCL10 and CXCL9 have substantial cell-to-cell variability. In particular, the expression of CXCL10 appears to be largely stochastic with a subpopulation of nonresponding cells across all the stimulation conditions tested. We developed both deterministic and stochastic models for the expression of each gene. Our modeling analysis revealed that the heterogeneity in CXCL10 can be attributed to a slow chromatin-opening step that is on a similar timescale to that of adaptation of the upstream signal. In this way, CXCL10 expression in individual cells can remain stochastic in response to each pulse of repeated stimulation, which we also validated by experiments. Together, we conclude that pro-inflammatory genes in the same signaling pathway can respond to dynamic IFN stimulus with very different response features and that upstream signal adaptation can contribute to shaping heterogeneous gene expression. [ABSTRACT FROM AUTHOR]

Information about environmental stimuli often can be encoded by the dynamics of signaling molecules or transcription factors. In the yeast Saccharomyces cerevisiae, different types of stresses induce distinct nuclear translocation dynamics of the general stress-responsive transcription factor Msn2, but the underlying mechanisms remain unclear. Using deterministic and stochastic modeling, we reproduced in silico the different dynamic responses of Msn2 to glucose limitation and osmotic stress observed in vivo and found that a positive feedback loop on protein kinase A mediated by the AMP-activated protein kinase Snf1 is coupled with a negative feedback loop to generate the characteristic pulsatile dynamics of Msn2. The model predicted that the stimulus-specific positive feedback loop could be responsible for the difference between Msn2 dynamics induced by glucose limitation and osmotic stress. This prediction was further verified experimentally by time-lapse microscopic examinations of the snf1Δ strain. In this mutant lacking the Snf1-mediated positive feedback loop, Msn2 responds similarly to glucose limitation and osmotic stress, and its pulsatile translocation is largely abrogated. Our combined computational and experimental analysis reveals a regulatory mechanism by which cells can encode information about environmental cues into distinct signaling dynamics through stimulus-specific network architectures. [ABSTRACT FROM AUTHOR]

Chromatin instability and protein homeostasis (proteostasis) stress are two well-established hallmarks of aging, which have been considered largely independent of each other. Using microfluidics and single-cell imaging approaches, we observed that, during the replicative aging of Saccharomyces cerevisiae, a challenge to proteostasis occurs specifically in the fraction of cells with decreased stability within the ribosomal DNA (rDNA). A screen of 170 yeast RNA-binding proteins identified ribosomal RNA (rRNA)-binding proteins as the most enriched group that aggregate upon a decrease in rDNA stability induced by inhibition of a conserved lysine deacetylase Sir2. Further, loss of rDNA stability induces age-dependent aggregation of rRNA-binding proteins through aberrant overproduction of rRNAs. These aggregates contribute to age-induced proteostasis decline and limit cellular lifespan. Our findings reveal a mechanism underlying the interconnection between chromatin instability and proteostasis stress and highlight the importance of cell-to-cell variability in aging processes. [ABSTRACT FROM AUTHOR]

In this paper we develop a continuum theory of clustering in ensembles of self-propelled inelastically colliding rods with applications to collective dynamics of common gliding bacteria Myxococcus xanthus. A multiphase hydrodynamic model that couples densities of oriented and isotropic phases is described. This model is used for the analysis of an instability that leads to spontaneous formation of directionally moving dense clusters within initially dilute isotropic 'gas' of myxobacteria. Numerical simulations of this model confirm the existence of stationary dense moving clusters and also elucidate the properties of their collisions. The results are shown to be in a qualitative agreement with experiments. [ABSTRACT FROM AUTHOR]

Motivation: Many important aspects of evolutionary dynamics can only be addressed through simulations. However, accurate simulations of realistically large populations over long periods of time needed for evolution to proceed are computationally expensive. Mutants can be present in very small numbers and yet (if they are more fit than others) be the key part of the evolutionary process. This leads to significant stochasticity that needs to be accounted for. Different evolutionary events occur at very different time scales: mutations are typically much rarer than reproduction and deaths.Results: We introduce a new exact algorithm for fast fully stochastic simulations of evolutionary dynamics that include birth, death and mutation events. It produces a significant speedup compared to direct stochastic simulations in a typical case when the population size is large and the mutation rates are much smaller than birth and death rates. The algorithm performance is illustrated by several examples that include evolution on a smooth and rugged fitness landscape. We also show how this algorithm can be adapted for approximate simulations of more complex evolutionary problems and illustrate it by simulations of a stochastic competitive growth model.Contact: ltsimring@ucsd.eduSupplementary information: Supplementary data are available at Bioinformatics online. [ABSTRACT FROM PUBLISHER]

A mechanistic understanding of gene regulatory network dynamics requires quantitative single-cell data of multiple network components in response to well-defined perturbations. Recent advances in the development of fluorescent biomarkers for proteins, detection of RNA and interactions, microfluidic technology, and high-resolution imaging have set the stage for a host of new studies that elucidate the important roles of stochasticity and cell–cell variability in response to external perturbations. In this review, we briefly describe methods for high-resolution visualization and the control of gene expression, along with application of these novel methods to recent studies involving gene networks. [ABSTRACT FROM AUTHOR]

Cross-links and molecular motors play an important role in the organization of cytoskeletal filament networks. Here, we incorporate the effect of cross-links into our model of polar motor-filament organization (Aranson and Tsimring 2005 Phys. Rev. E 71 050901), through suppressing the relative sliding of filaments in the course of motor-mediated alignment. We show that this modification leads to a nontrivial macroscopic behavior, namely the oriented state exhibits a transverse instability in contrast to the isotropic instability that occurs without cross-links. This transverse instability leads to the formation of dense extended bundles of oriented filaments, similar to the recently observed structures in actomyosin. This model can be also applied to situations with two oppositely directed motor species or motors with different processing speeds. [ABSTRACT FROM AUTHOR]

The small number of reactant molecules involved in gene regulation can lead to significant fluctuations in intracellular mRNA and protein concentrations, and there have been numerous recent studies devoted to the consequences of such noise at the regulatory level. Theoretical and computational work on stochastic gene expression has tended to focus on instantaneous transcriptional and translational events, whereas the role of realistic delay times in these stochastic processes has received little attention. Here, we explore the combined effects of time delay and intrinsic noise on gene regulation. Beginning with a set of biochemical reactions, some of which are delayed, we deduce a truncated master equation for the reactive system and derive an analytical expression for the correlation function and power spectrum. We develop a generalized Gillespie algorithm that accounts for the non-Markovian properties of random biochemical events with delay and compare our analytical findings with simulations. We show how time delay in gene expression can cause a system to be oscillatory even when its deterministic counterpart exhibits no oscillations. We demonstrate how such delay-induced instabilities can compromise the ability of a negative feedback loop to reduce the deleterious effects of noise. Given the prevalence of negative feedback in gene regulation, our findings may lead to new insights related to expression variability at the whole-genome scale. [ABSTRACT FROM AUTHOR]

Presents an approach to communication with chaotic signals, which demonstrates good performance in the presence of channel distortions. How the binary information is modulated onto the pulse chain; Basic design principles for the chaotic-pulse generator and its synchronization; Discussion on the possibilities of multiuser communication using chaotic-pulse-position modulation.

Cellular aging plays an important role in many diseases, such as cancers, metabolic syndromes, and neurodegenerative disorders. There has been steady progress in identifying aging-related factors such as reactive oxygen species and genomic instability, yet an emerging challenge is to reconcile the contributions of these factors with the fact that genetically identical cells can age at significantly different rates. Such complexity requires single-cell analyses designed to unravel the interplay of aging dynamics and cell-to-cell variability. Here we use microfluidic technologies to track the replicative aging of single yeast cells and reveal that the temporal patterns of heterochromatin silencing loss regulate cellular life span. We found that cells show sporadic waves of silencing loss in the heterochromatic ribosomal DNA during the early phases of aging, followed by sustained loss of silencing preceding cell death. Isogenic cells have different lengths of the early intermittent silencing phase that largely determine their final life spans. Combining computational modeling and experimental approaches, we found that the intermittent silencing dynamics is important for longevity and is dependent on the conserved Sir2 deacetylase, whereas either sustained silencing or sustained loss of silencing shortens life span. These findings reveal that the temporal patterns of a key molecular process can directly influence cellular aging, and thus could provide guidance for the design of temporally controlled strategies to extend life span. [ABSTRACT FROM AUTHOR]

Cell membranes are dynamic structures found in all living organisms. There have been numerous constructs that model phospholipid membranes. However, unlike natural membranes, these biomimetic systems cannot sustain growth owing to an inability to replenish phospholipid-synthesizing catalysts. Here we report on the design and synthesis of artificial membranes embedded with synthetic, self-reproducing catalysts capable of perpetuating phospholipid bilayer formation. Replacing the complex biochemical pathways used in nature with an autocatalyst that also drives lipid synthesis leads to the continual formation of triazole phospholipids and membrane-bound oligotriazole catalysts from simpler starting materials. In addition to continual phospholipid synthesis and vesicle growth, the synthetic membranes are capable of remodeling their physical composition in response to changes in the environment by preferentially incorporating specific precursors. These results demonstrate that complex membranes capable of indefinite self-synthesis can emerge when supplied with simpler chemical building blocks. [ABSTRACT FROM AUTHOR]

One promise of synthetic biology is the creation of genetic circuitry that enables the execution of logical programming in living cells. Such 'wet programming' is positioned to transform a wide and diverse swathe of biotechnology ranging from therapeutics and diagnostics to water treatment strategies. Although progress in the development of a library of genetic modules continues apace, a major challenge for their integration into larger circuits is the generation of sufficiently fast and precise communication between modules. An attractive approach is to integrate engineered circuits with host processes that facilitate robust cellular signalling. In this context, recent studies have demonstrated that bacterial protein degradation can trigger a precise response to stress by overloading a limited supply of intracellular proteases. Here we use protease competition to engineer rapid and tunable coupling of genetic circuits across multiple spatial and temporal scales. We characterize coupling delay times that are more than an order of magnitude faster than standard transcription-factor-based coupling methods (less than 1 min compared with ∼20-40 min) and demonstrate tunability through manipulation of the linker between the protein and its degradation tag. We use this mechanism as a platform to couple genetic clocks at the intracellular and colony level, then synchronize the multi-colony dynamics to reduce variability in both clocks. We show how the coupled clock network can be used to encode independent environmental inputs into a single time series output, thus enabling frequency multiplexing (information transmitted on a common channel by distinct frequencies) in a genetic circuit context. Our results establish a general framework for the rapid and tunable coupling of genetic circuits through the use of native 'queueing' processes such as competitive protein degradation. [ABSTRACT FROM AUTHOR]

Many cellular stress-responsive signaling systems exhibit highly dynamic behavior with oscillatory features mediated by delayed negative feedback loops. What remains unclear is whether oscillatory behavior is the basis for a signaling code based on frequency modulation (FM) or whether the negative feedback control modules have evolved to fulfill other functional requirements. Here, we use experimentally calibrated computational models to interrogate the negative feedback loops that regulate the dynamic activity of the transcription factor NF-B. Linear stability analysis of the model shows that oscillatory frequency is a hard-wired feature of the primary negative feedback loop and not a function of the stimulus, thus arguing against an FM signaling code. Instead, our modeling studies suggest that the two feedback loops may be tuned to provide for rapid activation and inactivation capabilities for transient input signals of a wide range of durations; by minimizing late phase oscillations response durations may be fine-tuned in a graded rather than quantized manner. Further, in the presence of molecular noise the dual delayed negative feedback system minimizes stochastic excursions of the output to produce a robust NF-B response. [ABSTRACT FROM AUTHOR]

Although there has been considerable progress in the development of engineering principles for synthetic biology, a substantial challenge is the construction of robust circuits in a noisy cellular environment. Such an environment leads to considerable intercellular variability in circuit behaviour, which can hinder functionality at the colony level. Here we engineer the synchronization of thousands of oscillating colony 'biopixels' over centimetre-length scales through the use of synergistic intercellular coupling involving quorum sensing within a colony and gas-phase redox signalling between colonies. We use this platform to construct a liquid crystal display (LCD)-like macroscopic clock that can be used to sense arsenic via modulation of the oscillatory period. Given the repertoire of sensing capabilities of bacteria such as Escherichia coli, the ability to coordinate their behaviour over large length scales sets the stage for the construction of low cost genetic biosensors that are capable of detecting heavy metals and pathogens in the field. [ABSTRACT FROM AUTHOR]

Cells have evolved complex regulatory networks that reorganize gene expression patterns in response to changing environmental conditions. These changes often involve redundant mechanisms that affect various levels of gene expression. Here, we examine the consequences of enhanced mRNA degradation in the galactose utilization network of Saccharomyces cerevisiae. We observe that glucose-induced degradation of GAL1 transcripts provides a transient growth advantage to cells upon addition of glucose. We show that the advantage arises from relief of translational competition between GAL1 transcripts and those of cyclin CLN3, a translationally regulated initiator of cell division. This competition creates a translational bottleneck that balances the production of Gal1p and Cln3p and represents a posttranscriptional control mechanism that enhances the cell's ability to adapt to changes in carbon source. We present evidence that the spatial regulation of GAL1 and CLN3 transcripts is what allows growth to be maintained during fluctuations of glucose availability. Our results provide unique insights into how cells optimize energy use during growth in a dynamic environment. [ABSTRACT FROM AUTHOR]

High-throughput technologies have led to the generation of complex wiring diagrams as a postsequencing paradigm for depicting the interactions between vast and diverse cellular species. While these diagrams are useful for analyzing biological systems on a large scale, a detailed understanding of the molecular mechanisms that underlie the observed network connections is critical for the further development of systems and synthetic biology. Here, we use queueing theory to investigate how ‘waiting lines’ can lead to correlations between protein ‘customers’ that are coupled solely through a downstream set of enzymatic ‘servers’. Using the E. coli ClpXP degradation machine as a model processing system, we observe significant cross-talk between two networks that are indirectly coupled through a common set of processors. We further illustrate the implications of enzymatic queueing using a synthetic biology application, in which two independent synthetic networks demonstrate synchronized behavior when common ClpXP machinery is overburdened. Our results demonstrate that such post-translational processes can lead to dynamic connections in cellular networks and may provide a mechanistic understanding of existing but currently inexplicable links. [ABSTRACT FROM AUTHOR]

One defining goal of synthetic biology is the development of engineering-based approaches that enable the construction of gene-regulatory networks according to ‘design specifications’ generated from computational modelling. This approach provides a systematic framework for exploring how a given regulatory network generates a particular phenotypic behaviour. Several fundamental gene circuits have been developed using this approach, including toggle switches and oscillators, and these have been applied in new contexts such as triggered biofilm development and cellular population control. Here we describe an engineered genetic oscillator in Escherichia coli that is fast, robust and persistent, with tunable oscillatory periods as fast as 13 min. The oscillator was designed using a previously modelled network architecture comprising linked positive and negative feedback loops. Using a microfluidic platform tailored for single-cell microscopy, we precisely control environmental conditions and monitor oscillations in individual cells through multiple cycles. Experiments reveal remarkable robustness and persistence of oscillations in the designed circuit; almost every cell exhibited large-amplitude fluorescence oscillations throughout observation runs. The oscillatory period can be tuned by altering inducer levels, temperature and the media source. Computational modelling demonstrates that the key design principle for constructing a robust oscillator is a time delay in the negative feedback loop, which can mechanistically arise from the cascade of cellular processes involved in forming a functional transcription factor. The positive feedback loop increases the robustness of the oscillations and allows for greater tunability. Examination of our refined model suggested the existence of a simplified oscillator design without positive feedback, and we construct an oscillator strain confirming this computational prediction. [ABSTRACT FROM AUTHOR]

The structure of bacterial populations is governed by the interplay of many physical and biological factors, ranging from properties of surrounding aqueous media and substrates to cell-cell communication and gene expression in individual cells. The biomechanical interactions arising from the growth and division of individual cells in confined environments are ubiquitous, yet little work has focused on this fundamental aspect of colony formation. We analyze the spatial organization of Escherichia coil growing in a microfluidic chemostat. We find that growth and expansion of a dense colony of cells leads to a dynamical transition from an isotropic disordered phase to a nematic phase characterized by orientational alignment of rod-like cells. We develop a continuum model of collective cell dynamics based on equations for local cell density, velocity, and the tensor order parameter. We use this model and discrete element simulations to elucidate the mechanism of cell ordering and quantify the relationship between the dynamics of cell proliferation and the spatial structure of the population. [ABSTRACT FROM AUTHOR]

Natural selection dictates that cells constantly adapt to dynamically changing environments in a context-dependent manner. Gene-regulatory networks often mediate the cellular response to perturbation, and an understanding of cellular adaptation will require experimental approaches aimed at subjecting cells to a dynamic environment that mimics their natural habitat. Here we monitor the response of Saccharomyces cerevisiae metabolic gene regulation to periodic changes in the external carbon source by using a microfluidic platform that allows precise, dynamic control over environmental conditions. We show that the metabolic system acts as a low-pass filter that reliably responds to a slowly changing environment, while effectively ignoring fast fluctuations. The sensitive low-frequency response was significantly faster than in predictions arising from our computational modelling, and this discrepancy was resolved by the discovery that two key galactose transcripts possess half-lives that depend on the carbon source. Finally, to explore how induction characteristics affect frequency response, we compare two S. cerevisiae strains and show that they have the same frequency response despite having markedly different induction properties. This suggests that although certain characteristics of the complex networks may differ when probed in a static environment, the system has been optimized for a robust response to a dynamically changing environment. [ABSTRACT FROM AUTHOR]

Variable gene expression within a clonal population of cells has been implicated in a number of important processes including mutation and evolution, determination of cell fates and the development of genetic disease. Recent studies have demonstrated that a significant component of expression variability arises from extrinsic factors thought to influence multiple genes simultaneously, yet the biological origins of this extrinsic variability have received little attention. Here we combine computational modelling with fluorescence data generated from multiple promoter–gene inserts in Saccharomyces cerevisiae to identify two major sources of extrinsic variability. One unavoidable source arising from the coupling of gene expression with population dynamics leads to a ubiquitous lower limit for expression variability. A second source, which is modelled as originating from a common upstream transcription factor, exemplifies how regulatory networks can convert noise in upstream regulator expression into extrinsic noise at the output of a target gene. Our results highlight the importance of the interplay of gene regulatory networks with population heterogeneity for understanding the origins of cellular diversity. [ABSTRACT FROM AUTHOR]