New tools for self-organised pattern formation

Position-dependent gene expression is a critical aspect of the development and behaviour of multicellular organisms. It requires a complex series of interactions to occur between different cell types in addition to intracellular signalling cascades. We used Escherichia coli to study the properties of an artificial signalling system at the interface between two expanding cell populations. We genetically engineered one population to produce a diffusible acyl-homoserine lactone (AHL) signal, and another population to respond to it. Our experiments demonstrate how such a signal can be used to reproducibly generate simple visible patterns with high accuracy in swimming agar. The producing and responding cassettes of two such signalling systems can be linked to produce a symmetric interface for bidirectional communication that can be used to visualise molecular logic. Intracellular feedback between these two cassettes would then create a framework for self-organised patterning of higher complexity. Adapting the experiments of Basu et al. (Basu et al., 2005) using cell motility, rather than a differential response to AHL concentrations as a way to define zones of response, we noted how the interaction of sender and receiver cell populations on a swimming plate could lead to complex pattern formation. Equipping highly motile strains such as E. coli MC1000 with AHL-mediated auto-inducing systems based on Vibrio fischeri luxI/luxR and Pseudomonas aeruginosa lasI/lasR cassettes would allow the amplification of a response to an AHL signal and its propagation. We designed and synthesised codon-optimised auto-inducing luxI/R and lasI/R cassettes as optimal gene expression is crucial for the generation of robust patterns. We still have to complete and test the entire genetic circuitry, although by modelling the system we were able to demonstrate its feasibility. © 2007 The Institution of Engineering and Technology.

Expanding adoption of drinking water treatment systems in developing countries: a case study from Tamil Nadu, India

Household-level water treatment and safe storage systems (HWTS) are simple, local, user-friendly, and low cost options to improve drinking water quality at the point of use. However, despite conclusive evidence of the health and economic benefits of HWTS, and promotion efforts in over 50 countries in the past 20 years, implementation outcomes have been slow, reaching only 5-10 million regular users. This study attempts to understand the barriers and drivers affecting HWTS implementation. Using a case study example of a biosand filter program in southern India, system dynamics modelling is shown to be a useful tool to map the inter-relationships of different critical factors and to understand the dissemination dynamics. It is found that the co-existence of expanding quickly and achieving financial sustainability appears to be difficult to achieve under the current program structure.

Robust estimation of local genetic ancestry in admixed populations using a nonparametric Bayesian approach.

We present a new haplotype-based approach for inferring local genetic ancestry of individuals in an admixed population. Most existing approaches for local ancestry estimation ignore the latent genetic relatedness between ancestral populations and treat them as independent. In this article, we exploit such information by building an inheritance model that describes both the ancestral populations and the admixed population jointly in a unified framework. Based on an assumption that the common hypothetical founder haplotypes give rise to both the ancestral and the admixed population haplotypes, we employ an infinite hidden Markov model to characterize each ancestral population and further extend it to generate the admixed population. Through an effective utilization of the population structural information under a principled nonparametric Bayesian framework, the resulting model is significantly less sensitive to the choice and the amount of training data for ancestral populations than state-of-the-art algorithms. We also improve the robustness under deviation from common modeling assumptions by incorporating population-specific scale parameters that allow variable recombination rates in different populations. Our method is applicable to an admixed population from an arbitrary number of ancestral populations and also performs competitively in terms of spurious ancestry proportions under a general multiway admixture assumption. We validate the proposed method by simulation under various admixing scenarios and present empirical analysis results from a worldwide-distributed dataset from the Human Genome Diversity Project.

Local stability results for the collective behaviors of infinite populations of pulse-coupled oscillators

In this paper, we investigate the behavior of pulse-coupled integrate-and-fire oscillators. Because the stability analysis of finite populations is intricate, we investigate stability results in the approximation of infinite populations. In addition to recovering known stability results of finite populations, we also obtain new stability results for infinite populations. In particular, under a weak coupling assumption, we solve for the continuum model a conjecture still prevailing in the finite dimensional case. © 2011 IEEE.

The dynamic response of edge clamped plates loaded by spherically expanding sand shells

The dynamic deformation of both edge clamped stainless steel sandwich panels with a pyramidal truss core and equal mass monolithic plates loaded by spherically expanding shells of dry and water saturated sand has been investigated, both experimentally and via a particle based simulation methodology. The spherically expanding sand shell is generated by detonating a sphere of explosive surrounded by a shell of either dry or water saturated synthetic sand. The measurements show that the sandwich panel and plate deflections decrease with increasing stand-off between the center of the charge and the front of the test structures. Moreover, for the same charge and sand mass, the deflections of the plates are significantly higher in the water saturated sand case compared to that of dry sand. For a given stand-off, the mid-span deflection of the sandwich panel rear faces was substantially less than that of the corresponding monolithic plate for both the dry and water saturated sand cases. The experiments were simulated via a coupled discrete-particle/ finite element scheme wherein the high velocity impacting sand is modeled by interacting particles while the plate is modeled within a Lagrangian finite element setting. The simulations are in good agreement with the measurements for the dry sand impact of both the monolithic and sandwich structures. However, the simulations underestimate the effect of stand-off in the case of the water saturated sand explosion, i.e. the deflections decrease more sharply with increasing stand-off in the experiments compared to the simulations. The simulations reveal that the momentum transmitted into the sandwich and monolithic plate structures by the sand shell is approximately the same, consistent with a small fluid-structure interaction effect. The smaller deflection of the sandwich panels is therefore primarily due to the higher bending strength of sandwich structures. © 2013 The Authors. Published by Elsevier Ltd. All rights reserved.