Chinmaya Gupta

Engineered temperature compensation in a synthetic genetic clock

Significance Synthetic gene circuits are often fragile, as perturbations to cellular conditions frequently alter their behavior. This lack of robustness limits the utility of engineered gene circuits and hinders advances in synthetic biology. Here, we demonstrate that environmental sensitivity can be reduced by simultaneously engineering circuits at the protein and network levels. Specifically, we designed and constructed a synthetic genetic clock that exhibits temperature compensation—the clock’s period does not depend on temperature. This feature is nontrivial since biochemical reactions speed up with increasing temperature. To accomplish this goal, we engineered thermal-inducibility into the clock’s regulatory structure. Computational modeling predicted and experiments confirmed that this thermal-inducibility results in a clock with a stable period across a large range of temperatures. Synthetic biology promises to revolutionize biotechnology by providing the means to reengineer and reprogram cellular regulatory mechanisms. However, synthetic gene circuits are often unreliable, as changes to environmental conditions can fundamentally alter a circuit’s behavior. One way to improve robustness is to use intrinsic properties of transcription factors within the circuit to buffer against intra- and extracellular variability. Here, we describe the design and construction of a synthetic gene oscillator in Escherichia coli that maintains a constant period over a range of temperatures. We started with a previously described synthetic dual-feedback oscillator with a temperature-dependent period. Computational modeling predicted and subsequent experiments confirmed that a single amino acid mutation to the core transcriptional repressor of the circuit results in temperature compensation. Specifically, we used a temperature-sensitive lactose repressor mutant that loses the ability to repress its target promoter at high temperatures. In the oscillator, this thermoinduction of the repressor leads to an increase in period at high temperatures that compensates for the decrease in period due to Arrhenius scaling of the reaction rates. The result is a transcriptional oscillator with a nearly constant period of 48 min for temperatures ranging from 30 °C to 41 °C. In contrast, in the absence of the mutation the period of the oscillator drops from 60 to 30 min over the same temperature range. This work demonstrates that synthetic gene circuits can be engineered to be robust to extracellular conditions through protein-level modifications.

Extreme value theory and return time statistics for dispersing billiard maps and flows, Lozi maps and Lorenz-like maps

In this paper we establish extreme value statistics for observations on a class of hyperbolic systems: planar dispersing billiard maps and flows, Lozi maps and Lorenz-like maps. In particular we show that for time series arising from Hölder observations on these systems the successive maxima of the time series are distributed according to the corresponding extreme value distributions for independent identically distributed processes. These results imply an exponential law for the hitting and return time statistics of these dynamical systems.

Extreme-value distributions for some classes of non-uniformly partially hyperbolic dynamical systems

In this note, we obtain verifiable sufficient conditions for the extreme value distribution for a certain class of skew product extensions of non-uniformly hyperbolic base maps. We show that these conditions, formulated in terms of the decay of correlations on the product system and the measure of rapidly returning points on the base, lead to a distribution for the maximum of

Transcriptional Delay Stabilizes Bistable Gene Networks

\Phi(p) = -\log(d(p, p_0))

Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations

that is of the first type. In particular, we establish the Type I distribution for

A Borel–Cantelli lemma for nonuniformly expanding dynamical systems

S^1

Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors

extensions of piecewise

Effects of cell cycle noise on excitable gene circuits

C^2

Timing and Variability of Galactose Metabolic Gene Activation Depend on the Rate of Environmental Change

uniformly expanding maps of the interval, non-uniformly expanding maps of the interval modeled by a Young Tower, and a skew product extension of a uniformly expanding map with a curve of neutral points.

Biomarker signature discovery from mass spectrometry data

Transcriptional delay can significantly impact the dynamics of gene networks. Here we examine how such delay affects bistable systems. We investigate several stochastic models of bistable gene networks and find that increasing delay dramatically increases the mean residence times near stable states. To explain this, we introduce a non-Markovian, analytically tractable reduced model. The model shows that stabilization is the consequence of an increased number of failed transitions between stable states. Each of the bistable systems that we simulate behaves in this manner.