11,066 research outputs found
Design of a bistable switch to control cellular uptake
International audienceBistable switches are widely used in synthetic biology to trigger cellular functions in response to environmental signals. All bistable switches developed so far, however, control the expression of target genes without access to other layers of the cellular machinery. Here, we propose a bistable switch to control the rate at which cells take up a metabolite from the environment. An uptake switch provides a new interface to command metabolic activity from the extracellular space and has great potential as a building block in more complex circuits that coordinate pathway activity across cell cultures, allocate metabolic tasks among different strains or require cell-to-cell communication with metabolic signals. Inspired by uptake systems found in nature, we propose to couple metabolite import and utilization with a genetic circuit under feedback regulation. Using mathematical models and analysis, we determined the circuit architectures that produce bistability and obtained their design space for bistability in terms of experimentally tuneable parameters. We found an activation–repression architecture to be the most robust switch because it displays bistability for the largest range of design parameters and requires little fine-tuning of the promoters' response curves. Our analytic results are based on on–off approximations of promoter activity and are in excellent qualitative agreement with simulations of more realistic models. With further analysis and simulation, we established conditions to maximize the parameter design space and to produce bimodal phenotypes via hysteresis and cell-to-cell variability. Our results highlight how mathematical analysis can drive the discovery of new circuits for synthetic biology, as the proposed circuit has all the hallmarks of a toggle switch and stands as a promising design to control metabolic phenotypes across cell cultures
Synthetic biology: advancing biological frontiers by building synthetic systems
Advances in synthetic biology are contributing
to diverse research areas, from basic biology to
biomanufacturing and disease therapy. We discuss the
theoretical foundation, applications, and potential of
this emerging field
Coupled Reversible and Irreversible Bistable Switches Underlying TGF-\beta-induced Epithelial to Mesenchymal Transition
Epithelial to mesenchymal transition (EMT) plays important roles in embryonic
development, tissue regeneration and cancer metastasis. While several feedback
loops have been shown to regulate EMT, it remains elusive how they coordinately
modulate EMT response to TGF-\beta treatment. We construct a mathematical model
for the core regulatory network controlling TGF-\beta-induced EMT. Through
deterministic analyses and stochastic simulations, we show that EMT is a
sequential two-step program that an epithelial cell first transits to partial
EMT then to the mesenchymal state, depending on the strength and duration of
TGF-\beta stimulation. Mechanistically the system is governed by coupled
reversible and irreversible bistable switches. The SNAIL1/miR-34 double
negative feedback loop is responsible for the reversible switch and regulates
the initiation of EMT, while the ZEB/miR-200 feedback loop is accountable for
the irreversible switch and controls the establishment of the mesenchymal
state. Furthermore, an autocrine TGF-\beta/miR-200 feedback loop makes the
second switch irreversible, modulating the maintenance of EMT. Such coupled
bistable switches are robust to parameter variation and molecular noise. We
provide a mechanistic explanation on multiple experimental observations. The
model makes several explicit predictions on hysteretic dynamic behaviors,
system response to pulsed stimulation and various perturbations, which can be
straightforwardly tested.Comment: 32 pages, 8 figures, accepted by Biophysical Journa
Design, modeling and synthesis of an in vitro transcription rate regulatory circuit
This paper describes the design, modeling and realization of a synthetic in vitro circuit that aims at regulating the rate of mRNA transcription. Two DNA templates are designed to interact through their transcripts, creating negative feedback loops that will equate their transcription rates at steady state. A mathematical model is developed for this circuit, consisting of a set of ODEs derived from the mass action laws and Michaelis-Menten kinetics involving all the present chemical species. The DNA strands were accordingly designed, following thermodynamics principles and minimizing unwanted interactions. Preliminary experimental results show that the circuit is performing the expected task, by matching at steady state the transcription rates of the two DNA templates
Noise control and utility: From regulatory network to spatial patterning
Stochasticity (or noise) at cellular and molecular levels has been observed
extensively as a universal feature for living systems. However, how living
systems deal with noise while performing desirable biological functions remains
a major mystery. Regulatory network configurations, such as their topology and
timescale, are shown to be critical in attenuating noise, and noise is also
found to facilitate cell fate decision. Here we review major recent findings on
noise attenuation through regulatory control, the benefit of noise via
noise-induced cellular plasticity during developmental patterning, and
summarize key principles underlying noise control
Designer Gene Networks: Towards Fundamental Cellular Control
The engineered control of cellular function through the design of synthetic
genetic networks is becoming plausible. Here we show how a naturally occurring
network can be used as a parts list for artificial network design, and how
model formulation leads to computational and analytical approaches relevant to
nonlinear dynamics and statistical physics.Comment: 35 pages, 8 figure
Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks
The gene regulatory network (GRN) is the central decision‐making module of the cell. We have developed a theory called Buffered Qualitative Stability (BQS) based on the hypothesis that GRNs are organised so that they remain robust in the face of unpredictable environmental and evolutionary changes. BQS makes strong and diverse predictions about the network features that allow stable responses under arbitrary perturbations, including the random addition of new connections. We show that the GRNs of E. coli, M. tuberculosis, P. aeruginosa, yeast, mouse, and human all verify the predictions of BQS. BQS explains many of the small- and large‐scale properties of GRNs, provides conditions for evolvable robustness, and highlights general features of transcriptional response. BQS is severely compromised in a human cancer cell line, suggesting that loss of BQS might underlie the phenotypic plasticity of cancer cells, and highlighting a possible sequence of GRN alterations concomitant with cancer initiation. DOI: http://dx.doi.org/10.7554/eLife.02863.00
Theory on the Dynamics of Oscillatory Loops in the Transcription Factor Networks
We develop a detailed theoretical framework for various types of
transcription factor gene oscillators. We further demonstrate that one can
build genetic-oscillators which are tunable and robust against perturbations in
the critical control parameters by coupling two or more independent
Goodwin-Griffith oscillators through either -OR- or -AND- type logic. Most of
the coupled oscillators constructed in the literature so far seem to be of -OR-
type. When there are transient perturbations in one of the -OR- type
coupled-oscillators, then the overall period of the system remains constant
(period-buffering) whereas in case of -AND- type coupling the overall period of
the system moves towards the perturbed oscillator. Though there is a
period-buffering, the amplitudes of oscillators coupled through -OR- type logic
are more sensitive to perturbations in the parameters associated with the
promoter state dynamics than -AND- type. Further analysis shows that the period
of -AND- type coupled dual-feedback oscillators can be tuned without conceding
on the amplitudes. Using these results we derive the basic design principles
governing the robust and tunable synthetic gene oscillators without
compromising on their amplitudes.Comment: 37 pages, 13 figures, 2 table
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