The coevolution of toxin and antitoxin genes drives the dynamics of bacterial addiction complexes and intragenomic conflict

Bacterial genomes commonly contain ‘addiction’ gene complexes that code for both a toxin and a corresponding antitoxin. As long as both genes are expressed, cells carrying the complex can remain healthy. However, loss of the complex (including segregational loss in daughter cells) can entail death of the cell. We develop a theoretical model to explore a number of evolutionary puzzles posed by toxin–antitoxin (TA) population biology. We first extend earlier results demonstrating that TA complexes can spread on plasmids, as an adaptation to plasmid competition in spatially structured environments, and highlight the role of kin selection. We then considered the emergence of TA complexes on plasmids from previously unlinked toxin and antitoxin genes. We find that one of these traits must offer at least initially a direct advantage in some but not all environments encountered by the evolving plasmid population. Finally, our study predicts non-transitive ‘rock-paper-scissors’ dynamics to be a feature of intragenomic conflict mediated by TA complexes. Intragenomic conflict could be sufficient to select deleterious genes on chromosomes and helps to explain the previously perplexing observation that many TA genes are found on bacterial chromosomes

Surface Roughness Dominated Pinning Mechanism of Magnetic Vortices in Soft Ferromagnetic Films

Although pinning of domain walls in ferromagnets is ubiquitous, the absence of an appropriate characterization tool has limited the ability to correlate the physical and magnetic microstructures of ferromagnetic films with specific pinning mechanisms. Here, we show that the pinning of a magnetic vortex, the simplest possible domain structure in soft ferromagnets, is strongly correlated with surface roughness, and we make a quantitative comparison of the pinning energy and spatial range in films of various thickness. The results demonstrate that thickness fluctuations on the lateral length scale of the vortex core diameter, i.e. an effective roughness at a specific length scale, provides the dominant pinning mechanism. We argue that this mechanism will be important in virtually any soft ferromagnetic film.Comment: 4 figure

Contamination in complex healthcare trials:the falls in care homes (FinCH) study experience

BACKGROUND: Trials are at risk of contamination bias which can occur when participants in the control group are inadvertently exposed to the intervention. This is a particular risk in rehabilitation studies where it is easy for trial interventions to be either intentionally or inadvertently adopted in control settings. The Falls in Care Homes (FinCH) trial is used in this paper as an example of a large randomised controlled trial of a complex intervention to explore the potential risks of contamination bias. We outline the FinCH trial design, present the potential risks from contamination bias, and the strategies used in the design of the trial to minimise or mitigate against this. The FinCH trial was a multi-centre randomised controlled trial, with embedded process evaluation, which evaluated whether systematic training in the use of the Guide to Action Tool for Care Homes reduced falls in care home residents. Data were collected from a number of sources to explore contamination in the FinCH trial. Where specific procedures were adopted to reduce risk of, or mitigate against, contamination, this was recorded. Data were collected from study e-mails, meetings with clinicians, research assistant and clinician network communications, and an embedded process evaluation in six intervention care homes. During the FinCH trial, there were six new falls prevention initiatives implemented outside the study which could have contaminated our intervention and findings. Methods used to minimise contamination were: cluster randomisation at the level of care home; engagement with the clinical community to highlight the risks of early adoption; establishing local collaborators in each site familiar with the local context; signing agreements with NHS falls specialists that they would maintain confidentiality regarding details of the intervention; opening additional research sites; and by raising awareness about the importance of contamination in research among participants. CONCLUSION: Complex rehabilitation trials are at risk of contamination bias. The potential for contamination bias in studies can be minimized by strengthening collaboration and dialogue with the clinical community. Researchers should recognise that clinicians may contaminate a study through lack of research expertise

Some Results On Convex Greedy Embedding Conjecture for 3-Connected Planar Graphs

A greedy embedding of a graph $G = (V,E)$ into a metric space $(X,d)$ is a function $x : V(G) \to X$ such that in the embedding for every pair of non-adjacent vertices $x(s), x(t)$ there exists another vertex $x(u)$ adjacent to $x(s)$ which is closer to $x(t)$ than $x(s)$. This notion of greedy embedding was defined by Papadimitriou and Ratajczak (Theor. Comput. Sci. 2005), where authors conjectured that every 3-connected planar graph has a greedy embedding (possibly planar and convex) in the Euclidean plane. Recently, greedy embedding conjecture has been proved by Leighton and Moitra (FOCS 2008). However, their algorithm do not result in a drawing that is planar and convex for all 3-connected planar graph in the Euclidean plane. In this work we consider the planar convex greedy embedding conjecture and make some progress. We derive a new characterization of planar convex greedy embedding that given a 3-connected planar graph $G = (V,E)$, an embedding x: V \to \bbbr^2 of $G$ is a planar convex greedy embedding if and only if, in the embedding $x$, weight of the maximum weight spanning tree ($T$) and weight of the minimum weight spanning tree (\func{MST}) satisfies \WT(T)/\WT(\func{MST}) \leq (\card{V}-1)^{1 - \delta}, for some $0 < \delta \leq 1$.Comment: 19 pages, A short version of this paper has been accepted for presentation in FCT 2009 - 17th International Symposium on Fundamentals of Computation Theor

Birth and growth of cavitation bubbles within water under tension confined in a simple synthetic tree

Water under tension, as can be found in several systems including tree vessels, is metastable. Cavitation can spontaneously occur, nucleating a bubble. We investigate the dynamics of spon- taneous or triggered cavitation inside water filled microcavities of a hydrogel. Results show that a stable bubble is created in only a microsecond timescale, after transient oscillations. Then, a diffusion driven expansion leads to filling of the cavity. Analysis reveals that the nucleation of a bubble releases a tension of several tens of MPa, and a simple model captures the different time scales of the expansion process

Information Arbitrage in Bipartite Heat Engines

Heat engines and information engines have each historically served as motivating examples for the development of thermodynamics. While these two types of systems are typically thought of as two separate kinds of machines, recent empirical studies of specific systems have hinted at possible connections between the two. Inspired by molecular machines in the cellular environment, which in many cases have separate components in contact with distinct sources of fluctuations, we study bipartite heat engines. We show that a bipartite heat engine can only produce net output work by acting as an information engine. Conversely, information engines can only extract more work than the work consumed to power them if they have access to different sources of fluctuations, i.e., act as heat engines. We illustrate these findings first through an analogy to economics and a cyclically controlled 2D ideal gas. We then explore two analytically tractable model systems in more detail: a Brownian-gyrator heat engine which we show can be reinterpreted as a feedback-cooling information engine, and a quantum-dot information engine which can be reinterpreted as a thermoelectric heat engine. Our results suggest design principles for both heat engines and information engines at the nanoscale, and ultimately imply constraints on how free-energy transduction is carried out in biological molecular machines.Comment: 20 pages, 5 figure