Showing papers by "James J. Collins published in 2000"

Construction of a genetic toggle switch in Escherichia coli

Abstract: It has been proposed' that gene-regulatory circuits with virtually any desired property can be constructed from networks of simple regulatory elements. These properties, which include multistability and oscillations, have been found in specialized gene circuits such as the bacteriophage lambda switch and the Cyanobacteria circadian oscillator. However, these behaviours have not been demonstrated in networks of non-specialized regulatory components. Here we present the construction of a genetic toggle switch-a synthetic, bistable gene-regulatory network-in Escherichia coli and provide a simple theory that predicts the conditions necessary for bistability. The toggle is constructed from any two repressible promoters arranged in a mutually inhibitory network. It is flipped between stable states using transient chemical or thermal induction and exhibits a nearly ideal switching threshold. As a practical device, the toggle switch forms a synthetic, addressable cellular memory unit and has implications for biotechnology, biocomputing and gene therapy.

Noise-based switches and amplifiers for gene expression.

Abstract: The regulation of cellular function is often controlled at the level of gene transcription. Such genetic regulation usually consists of interacting networks, whereby gene products from a single network can act to control their own expression or the production of protein in another network. Engineered control of cellular function through the design and manipulation of such networks lies within the constraints of current technology. Here we develop a model describing the regulation of gene expression and elucidate the effects of noise on the formulation. We consider a single network derived from bacteriophage λ and construct a two-parameter deterministic model describing the temporal evolution of the concentration of λ repressor protein. Bistability in the steady-state protein concentration arises naturally, and we show how the bistable regime is enhanced with the addition of the first operator site in the promotor region. We then show how additive and multiplicative external noise can be used to regulate expression. In the additive case, we demonstrate the utility of such control through the construction of a protein switch, whereby protein production is turned “on” and “off” by using short noise pulses. In the multiplicative case, we show that small deviations in the transcription rate can lead to large fluctuations in the production of protein, and we describe how these fluctuations can be used to amplify protein production significantly. These results suggest that an external noise source could be used as a switch and/or amplifier for gene expression. Such a development could have important implications for gene therapy.

Neutralizing noise in gene networks.

Abstract: Noise is inherent in gene expression, and can lead to sizeable fluctuations in the concentrations of expressed RNA and proteins. But many biological processes, such as circadian rhythms, are predictable and must be robust to internal noise. New simulations and studies of synthetic gene networks indicate that negative feedback may counteract noise.

Mortality surveillance and occupational hazards: the Solutia mortality experience 1980-94

Abstract: Objectives—Several investigators argue that company wide mortalities for recent workers allow early identification of potential workplace hazards. Mortalities for recent workers were compared with published studies of workers with specific exposures in the same company to find whether mortality surveillance results could be used to identify previously unknown health eVects from workplace hazards. Methods—Relative risks for causes of death in published substance specific studies at the plants were compared with the relative risks in the mortality surveillance of workers 20 or more years after first being employed. Results—As reported by other companies, low mortalities were found among workers in the mortality surveillance. The mortality surveillance reports often found no increased risk of disease at plants in which substance specific studies had found no eVects. However, disease specific relative risks were not found by the mortality surveillance predictions of relative risks in the substance specific studies with increased risk. Conclusion—Mortality surveillance is of limited use for identifying health eVects from past workplace exposures to specific materials. The healthy worker and survivor eVects, the failure to identify subsets of workers exposed to potentially toxic substances, the typically long induction period between exposure and disease, and the inability of recent mortality levels to reflect historical conditions all may make it diYcult to use mortality surveillance to identify workplace hazards. Combining mortality surveillance with studies of workers with potentially toxic exposures helps identify occupational hazards. (Occup Environ Med 2000;57:710‐717)

Stochastic regulation of gene expression

Abstract: We analyze the effect of additive noise on a previously proposed biochemical model describing the genetic regulation of the production of protein. The steady-state mean value of protein concentration is obtained through the equilibrium solution of the Fokker-Planck equation. In this way it is shown how external noise can serve as a type of control on the overall protein concentration. We demonstrate the utility of such control through the construction of a protein switch, whereby protein production is abruptly altered using short pulses in the magnitude of the external noise source.

A framework for addressing health issues in or near a manufacturing facility.

Abstract: Clustering of health events in or around industrial facilities sometimes leads to worker and community concerns that plant management or local health professionals must address. We provide an eight-step process to deal with these concerns systematically. We emphasize the use of good scientific practices with managerial oversight for effective worker and community communication. This process is directed to plant management and the local health professional and emphasizes the practical aspects of the investigation.

Suppressing arrhythmias in cardiac models with overdrive pacing

Abstract: Recent findings indicate that fibrillating cardiac tissue arises from spiral wave chaos. Here we show that spiral wave chaos can be suppressed in a cardiac model by pacing the system with low-amplitude, high-frequency current pulses. This overdrive pacing technique is analyzed using a one-dimensional chain and a two-dimensional lattice of coupled, excitable elements with the kinetics described by the Luo-Rudy action potential model (1991). When two-dimensional media were excited with frequencies from 1:1 synchronization region, we found that spiral wave chaos could be suppressed in a limited number of cases. However, when used in conjunction with calcium channel blockers, high-frequency pacing suppressed spiral wave chaos in all episodes. These findings suggest that low-amplitude overdrive pacing in combination with class IV antiarrhythmic drugs, inhibitors of calcium channels, may be useful for eliminating fibrillation in cardiac tissue.