Implications of Rewiring Bacterial Quorum Sensing

Bacteria employ quorum sensing, a form of cell-cell communication, to sense changes in population density and regulate gene expression accordingly. This work investigated the rewiring of one quorum-sensing module, the lux circuit from the marine bacterium Vibrio fischeri. Steady-state experiments demonstrate that rewiring the network architecture of this module can yield graded, threshold, and bistable gene expression as predicted by a mathematical model. The experiments also show that the native lux operon is most consistent with a threshold, as opposed to a bistable, response. Each of the rewired networks yielded functional population sensors at biologically relevant conditions, suggesting that this operon is particularly robust. These findings (i) permit prediction of the behaviors of quorum-sensing operons in bacterial pathogens and (ii) facilitate forward engineering of synthetic gene circuits

On the origins of approximations for stochastic chemical kinetics

This paper considers the derivation of approximations for stochastic chemical kinetics governed by the discrete master equation. Here, the concepts of (1) partitioning on the basis of fast and slow reactions as opposed to fast and slow species and (2) conditional probability densities are used to derive approximate, partitioned master equations, which are Markovian in nature, from the original master equation. Under different conditions dictated by relaxation time arguments, such approximations give rise to both the equilibrium and hybrid (deterministic or Langevin equations coupled with discrete stochastic simulation) approximations previously reported. In addition, the derivation points out several weaknesses in previous justifications of both the hybrid and equilibrium systems and demonstrates the connection between the original and approximate master equations. Two simple examples illustrate situations in which these two approximate methods are applicable and demonstrate the two methods' efficiencies

Synthetic Gene Circuits: Design with Directed Evolution

Synthetic circuits offer great promise for generating insights into nature's underlying design principles or forward engineering novel biotechnology applications. However, construction of these circuits is not straightforward. Synthetic circuits generally consist of components optimized to function in their natural context, not in the context of the synthetic circuit. Combining mathematical modeling with directed evolution offers one promising means for addressing this problem. Modeling identifies mutational targets and limits the evolutionary search space for directed evolution, which alters circuit performance without the need for detailed biophysical information. This review examines strategies for integrating modeling and directed evolution and discusses the utility and limitations of available methods

Stochastic simulation of catalytic surface reactions in the fast diffusion limit

The master equation of a lattice gas reaction tracks the probability of visiting all spatial configurations. The large number of unique spatial configurations on a lattice renders master equation simulations infeasible for even small lattices. In this work, a reduced master equation is derived for the probability distribution of the coverages in the infinite diffusion limit. This derivation justifies the widely used assumption that the adlayer is in equilibrium for the current coverages and temperature when all reactants are highly mobile. Given the reduced master equation, two novel and efficient simulation methods of lattice gas reactions in the infinite diffusion limit are derived. The first method involves solving the reduced master equation directly for small lattices, which is intractable in configuration space. The second method involves reducing the master equation further in the large lattice limit to a set of differential equations that tracks only the species coverages. Solution of the reduced master equation and differential equations requires information that can be obtained through short, diffusion-only kinetic Monte Carlo simulation runs at each coverage. These simulations need to be run only once because the data can be stored and used for simulations with any set of kinetic parameters, gas-phase concentrations, and initial conditions. An idealized CO oxidation reaction mechanism with strong lateral interactions is used as an example system for demonstrating the reduced master equation and deterministic simulation techniques

Two classes of quasi-steady-state model reductions for stochastic kinetics

The quasi-steady-state approximation (QSSA) is a model reduction technique used to remove highly reactive species from deterministic models of reaction mechanisms. In many reaction networks the highly reactive intermediates (QSSA species) have populations small enough to require a stochastic representation. In this work we apply singular perturbation analysis to remove the QSSA species from the chemical master equation for two classes of problems. The first class occurs in reaction networks where all the species have small populations and the QSSA species sample zero the majority of the time. The perturbation analysis provides a reduced master equation in which the highly reactive species can sample only zero, and are effectively removed from the model. The reduced master equation can be sampled with the Gillespie algorithm. This first stochastic QSSA reduction is applied to several example reaction mechanisms (including Michaelis-Menten kinetics) [Biochem. Z. 49, 333 (1913)]. A general framework for applying the first QSSA reduction technique to new reaction mechanisms is derived. The second class of QSSA model reductions is derived for reaction networks where non-QSSA species have large populations and QSSA species numbers are small and stochastic. We derive this second QSSA reduction from a combination of singular perturbation analysis and the Omega expansion. In some cases the reduced mechanisms and reaction rates from these two stochastic QSSA models and the classical deterministic QSSA reduction are equivalent; however, this is not usually the case

THE EVOLUTION OF THE DESIGN AND CONSTRUCTION OF MASONRY BUILDINGS IN THE UK

The paper gives a brief history of the use of masonry, mainly clay brickwork and stonework, for historic buildings in the UK. The development of a modern Code of Practice is described, leading to BS 5628: Parts 1 (1978), 2 (1985) and 3 (1985). The development and use of reinforced masonry is covered, as is the need for sensible rules to ensure that correct materials and workmanship are used. The development of new materials and methods is mentioned. The result of the European Union succeeding in changing National European Codes of Practice into Eurocodes has made a profound difference for designers and the Eurocodes are described. Finally the future use of masonry in the UK is discussed

Victims of Substantiated Child Abuse: Missouri’s New Reasonably Ascertainable Creditors

A recent decision from the Supreme Court of Missouri, In re Austin, held that victims of substantiated child abuse are reasonably ascertainable creditors. The practical effect of Austin is to afford victims of substantiated child abuse an extra six months to file claims against the estate of his or her abuser. While this decision is a small victory for victims of sexual abuse, the facts in Austin raise controversial questions about whether the unique circumstances surrounding claims of childhood sexual abuse warrant an exception to the one-year claim bar against a decedent’s estate. This Note begins with an exploration of the unique factual circumstances that gave rise to the court’s determination that victims of child abuse are reasonably ascertainable creditors. The Note goes on to discuss the constitutionality of creditor claim bars and the evolution of the reasonably ascertainable creditor in Missouri. Next, this Note provides an analysis of the Supreme Court of Missouri’s reasoning in Austin and – finally – explores possible extensions of Austin while weighing the policy considerations associated with a broad extension of the court’s holding to future claims of child abuse against decedents’ estates

A relational-exploratory study : how attitudes towards deafness affect quality of behavioral health services provided to the deaf/deaf/hard of hearing client

This study utilized a relational-exploratory design in an attempt to develop a clearer understanding of how attitudes towards deafness are related to potential quality of services rendered. It was hypothesized that amount of contact or level of knowledge of deafness might affect attitudes. It was inferred that attitudes that are more positive would result in more appropriate services, and attitudes that are more negative would result in less appropriate services. The sample was compromised of students at the undergraduate and graduate level as well as experienced clinicians recruited from a community mental health center in rural New Hampshire (N=86). Participants either completed an online survey or filled out a hard copy survey. The Attitudes Towards Deafness Scale was the instrument utilized to measure attitudes of subjects. Demographic and additional questions designed by the researcher were incorporated into the survey. The purpose of additional questions was to attempt to substantiate amount of knowledge of deafness and level of contact in order to correlate results of the attitude survey. Results of the data analysis showed significant difference in the attitude score between those who had served a deaf person and those who had not. Additionally, results also showed a significant difference between those who had received training and those who had not