58 research outputs found
Assessing the impact of silicon nanowires on bacterial transformation and viability of Escherichia coli
We investigated the biomaterial interface between the bacteria Escherichia coli DH5α and silicon nanowire patterned surfaces. We optimised the engineering of silicon nanowire coated surfaces using metal-assisted chemical etching. Using a combination of focussed ion beam scanning electron microscopy, and cell viability and transformation assays, we found that with increasing interfacing force, cell viability decreases, as a result of increasing cell rupture. However, despite this aggressive interfacing regime, a proportion of the bacterial cell population remains viable. We found that the silicon nanowires neither resulted in complete loss of cell viability nor partial membrane disruption and corresponding DNA plasmid transformation. Critically, assay choice was observed to be important, as a reduction-based metabolic reagent was found to yield false-positive results on the silicon nanowire substrate. We discuss the implications of these results for the future design and assessment of bacteria–nanostructure interfacing experiments
A model for improving microbial biofuel production using a synthetic feedback loop
Cells use feedback to implement a diverse range of regulatory functions. Building synthetic feedback control systems may yield insight into the roles that feedback can play in regulation since it can be introduced independently of native regulation, and alternative control architectures can be compared. We propose a model for microbial biofuel production where a synthetic control system is used to increase cell viability and biofuel yields. Although microbes can be engineered to produce biofuels, the fuels are often toxic to cell growth, creating a negative feedback loop that limits biofuel production. These toxic effects may be mitigated by expressing efflux pumps that export biofuel from the cell. We developed a model for cell growth and biofuel production and used it to compare several genetic control strategies for their ability to improve biofuel yields. We show that controlling efflux pump expression directly with a biofuel-responsive promoter is a straightforward way of improving biofuel production. In addition, a feed forward loop controller is shown to be versatile at dealing with uncertainty in biofuel production rates
Regulation of signal duration and the statistical dynamics of kinase activation by scaffold proteins
Scaffolding proteins that direct the assembly of multiple kinases into a
spatially localized signaling complex are often essential for the maintenance
of an appropriate biological response. Although scaffolds are widely believed
to have dramatic effects on the dynamics of signal propagation, the mechanisms
that underlie these consequences are not well understood. Here, Monte Carlo
simulations of a model kinase cascade are used to investigate how the temporal
characteristics of signaling cascades can be influenced by the presence of
scaffold proteins. Specifically, we examine the effects of spatially localizing
kinase components on a scaffold on signaling dynamics. The simulations indicate
that a major effect that scaffolds exert on the dynamics of cell signaling is
to control how the activation of protein kinases is distributed over time.
Scaffolds can influence the timing of kinase activation by allowing for kinases
to become activated over a broad range of times, thus allowing for signaling at
both early and late times. Scaffold concentrations that result in optimal
signal amplitude also result in the broadest distributions of times over which
kinases are activated. These calculations provide insights into one mechanism
that describes how the duration of a signal can potentially be regulated in a
scaffold mediated protein kinase cascade. Our results illustrate another
complexity in the broad array of control properties that emerge from the
physical effects of spatially localizing components of kinase cascades on
scaffold proteins.Comment: 12 pages, 6 figure
Synthetic human cell fate regulation by protein-driven RNA switches
Understanding how to control cell fate is crucial in biology, medical science and engineering. In this study, we introduce a method that uses an intracellular protein as a trigger for regulating human cell fate. The ON/OFF translational switches, composed of an intracellular protein L7Ae and its binding RNA motif, regulate the expression of a desired target protein and control two distinct apoptosis pathways in target human cells. Combined use of the switches demonstrates that a specific protein can simultaneously repress and activate the translation of two different mRNAs: one protein achieves both up- and downregulation of two different proteins/pathways. A genome-encoded protein fused to L7Ae controlled apoptosis in both directions (death or survival) depending on its cellular expression. The method has potential for curing cellular defects or improving the intracellular production of useful molecules by bypassing or rewiring intrinsic signal networks
Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity
Synthetic biology: Understanding biological design from synthetic circuits
An important aim of synthetic biology is to uncover the design principles of natural biological systems through the rational design of gene and protein circuits. Here, we highlight how the process of engineering biological systems — from synthetic promoters to the control of cell–cell interactions — has contributed to our understanding of how endogenous systems are put together and function. Synthetic biological devices allow us to grasp intuitively the ranges of behaviour generated by simple biological circuits, such as linear cascades and interlocking feedback loops, as well as to exert control over natural processes, such as gene expression and population dynamics
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