Enhanced cellular longevity arising from environmental fluctuations.

Cellular longevity is regulated by both genetic and environmental factors. However, the interactions of these factors in the context of aging remain largely unclear. Here, we formulate a mathematical model for dynamic glucose modulation of a core gene circuit in yeast aging, which not only guided the design of pro-longevity interventions but also revealed the theoretical principles underlying these interventions.

Phenotypic Patterning through Copy Number Adaptation to Environmental Gradients.

We recently described a paradigm for engineering bacterial adaptation using plasmids coupled to the same origin of replication. In this study, we use plasmid coupling to generate spatially separated and phenotypically distinct populations in response to heterogeneous environments. Using a custom microfluidic device, we continuously tracked engineered populations along induced gradients, enabling an in-depth analysis of the spatiotemporal dynamics of plasmid coupling.

Quantifying dynamic pro-inflammatory gene expression and heterogeneity in single macrophage cells.

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 (IFNγ) stimulation.

Enhanced cellular longevity arising from environmental fluctuations.

Cellular longevity is regulated by both genetic and environmental factors. However, the interactions of these factors in the context of aging remain largely unclear. Here, we formulate a mathematical model for dynamic glucose modulation of a core gene circuit in yeast aging, which not only guided the design of pro-longevity interventions, but also revealed the theoretical principles underlying these interventions.

Engineering longevity-design of a synthetic gene oscillator to slow cellular aging.

Synthetic biology enables the design of gene networks to confer specific biological functions, yet it remains a challenge to rationally engineer a biological trait as complex as longevity. A naturally occurring toggle switch underlies fate decisions toward either nucleolar or mitochondrial decline during the aging of yeast cells. We rewired this endogenous toggle to engineer an autonomous genetic clock that generates sustained oscillations between the nucleolar and mitochondrial aging processes in individual cells.

Statistical theory of asymmetric damage segregation in clonal cell populations.

Asymmetric damage segregation (ADS) is ubiquitous among unicellular organisms: After a mother cell divides, its two daughter cells receive sometimes slightly, sometimes strongly different fractions of damaged proteins accumulated in the mother cell. Previous studies demonstrated that ADS provides a selective advantage over symmetrically dividing cells by rejuvenating and perpetuating the population as a whole. In this work we focus on the statistical properties of damage in individual lineages and the overall damage distributions in growing populations for a variety of ADS models with different rules governing damage accumulation, segregation, and the lifetime dependence on damage.

Age-dependent aggregation of ribosomal RNA-binding proteins links deterioration in chromatin stability with challenges to proteostasis.

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 , 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.

Optimal transcriptional regulation of dynamic bacterial responses to sudden drug exposures.

Cellular responses to the presence of toxic compounds in their environment require prompt expression of the correct levels of the appropriate enzymes, which are typically regulated by transcription factors that control gene expression for the duration of the response. The characteristics of each response dictate the choice of regulatory parameters such as the affinity of the transcription factor to its binding sites and the strength of the promoters it regulates. Although much is known about the dynamics of cellular responses, we still lack a framework to understand how different regulatory strategies evolved in natural systems relate to the selective pressures acting in each particular case.

Publisher's Note: Suppression of Beneficial Mutations in Dynamic Microbial Populations [Phys. Rev. Lett. 118, 028102 (2017)].

This corrects the article DOI: 10.1103/PhysRevLett.118.

A programmable fate decision landscape underlies single-cell aging in yeast.

Chromatin instability and mitochondrial decline are conserved processes that contribute to cellular aging. Although both processes have been explored individually in the context of their distinct signaling pathways, the mechanism that determines which process dominates during aging of individual cells is unknown. We show that interactions between the chromatin silencing and mitochondrial pathways lead to an epigenetic landscape of yeast replicative aging with multiple equilibrium states that represent different types of terminal states of aging.

Genetically engineered control of phenotypic structure in microbial colonies.

Rapid advances in cellular engineering have positioned synthetic biology to address therapeutic and industrial problems, but a substantial obstacle is the myriad of unanticipated cellular responses in heterogeneous real-world environments such as the gut, solid tumours, bioreactors or soil. Complex interactions between the environment and cells often arise through non-uniform nutrient availability, which generates bidirectional coupling as cells both adjust to and modify their local environment through phenotypic differentiation. Although synthetic spatial gene expression patterns have been explored under homogeneous conditions, the mutual interaction of gene circuits, growth phenotype and the environment remains a challenge.

Flower-like patterns in multi-species bacterial colonies.

Diverse interactions among species within bacterial colonies lead to intricate spatiotemporal dynamics, which can affect their growth and survival. Here, we describe the emergence of complex structures in a colony grown from mixtures of motile and non-motile bacterial species on a soft agar surface. Time-lapse imaging shows that non-motile bacteria 'hitchhike' on the motile bacteria as the latter migrate outward.

Advances in quantitative biology methods for studying replicative aging in .

Aging is a complex, yet pervasive phenomenon in biology. As human cells steadily succumb to the deteriorating effects of aging, so too comes a host of age-related ailments such as neurodegenerative disorders, cardiovascular disease and cancer. Therefore, elucidation of the molecular networks that drive aging is of paramount importance to human health.

Rock-paper-scissors: Engineered population dynamics increase genetic stability.

Advances in synthetic biology have led to an arsenal of proof-of-principle bacterial circuits that can be leveraged for applications ranging from therapeutics to bioproduction. A unifying challenge for most applications is the presence of selective pressures that lead to high mutation rates for engineered bacteria. A common strategy is to develop cloning technologies aimed at increasing the fixation time for deleterious mutations in single cells.

Divergent Aging of Isogenic Yeast Cells Revealed through Single-Cell Phenotypic Dynamics.

Although genetic mutations that alter organisms' average lifespans have been identified in aging research, our understanding of the dynamic changes during aging remains limited. Here, we integrate single-cell imaging, microfluidics, and computational modeling to investigate phenotypic divergence and cellular heterogeneity during replicative aging of single S. cerevisiae cells.

Flavin-based metabolic cycles are integral features of growth and division in single yeast cells.

The yeast metabolic cycle (YMC) is a fascinating example of biological organization, in which cells constrain the function of specific genetic, protein and metabolic networks to precise temporal windows as they grow and divide. However, understanding the intracellular origins of the YMC remains a challenging goal, as measuring the oxygen oscillations traditionally associated with it requires the use of synchronized cultures growing in nutrient-limited chemostat environments. To address these limitations, we used custom-built microfluidic devices and time-lapse fluorescence microscopy to search for metabolic cycling in the form of endogenous flavin fluorescence in unsynchronized single yeast cells.

Microfluidics-Based Analysis of Contact-dependent Bacterial Interactions.

Bacteria in nature live in complex communities with multiple cell types and spatially-dependent interactions. Studying cells in well-mixed environments such as shaking culture tubes or flasks cannot capture these spatial dynamics, but cells growing in full-fledged biofilms are difficult to observe in real time. We present here a protocol for observing time-resolved, multi-species interactions at single-cell resolution.

Coexistence and Pattern Formation in Bacterial Mixtures with Contact-Dependent Killing.

Multistrain microbial communities often exhibit complex spatial organization that emerges because of the interplay of various cooperative and competitive interaction mechanisms. One strong competitive mechanism is contact-dependent neighbor killing enabled by the type VI secretion system. It has been previously shown that contact-dependent killing can result in bistability of bacterial mixtures so that only one strain survives and displaces the other.

Rational engineering of synthetic microbial systems: from single cells to consortia.

One promise of synthetic biology is to provide solutions for biomedical and industrial problems by rational design of added functionality in living systems. Microbes are at the forefront of this biological engineering endeavor due to their general ease of handling and their relevance in many potential applications from fermentation to therapeutics. In recent years, the field has witnessed an explosion of novel regulatory tools, from synthetic orthogonal transcription factors to posttranslational mechanisms for increased control over the behavior of synthetic circuits.

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance.

Horizontal gene transfer (HGT) plays a major role in the spread of antibiotic resistance. Of particular concern are bacteria, which recently emerged as global pathogens, with nosocomial mortality rates reaching 19-54% (Centers for Disease Control and Prevention, 2013; Joly Guillou, 2005; Talbot et al., 2006).

Multigenerational silencing dynamics control cell aging.

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.

Gene Conversion Facilitates Adaptive Evolution on Rugged Fitness Landscapes.

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.

Rapid and Scalable Preparation of Bacterial Lysates for Cell-Free Gene Expression.

Cell-free gene expression systems are emerging as an important platform for a diverse range of synthetic biology and biotechnology applications, including production of robust field-ready biosensors. Here, we combine programmed cellular autolysis with a freeze-thaw or freeze-dry cycle to create a practical, reproducible, and a labor- and cost-effective approach for rapid production of bacterial lysates for cell-free gene expression. Using this method, robust and highly active bacterial cell lysates can be produced without specialized equipment at a wide range of scales, making cell-free gene expression easily and broadly accessible.

Coupled feedback loops control the stimulus-dependent dynamics of the yeast transcription factor Msn2.

Information about environmental stimuli often can be encoded by the dynamics of signaling molecules or transcription factors. In the yeast , 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 the different dynamic responses of Msn2 to glucose limitation and osmotic stress observed 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.