Exploitation of NHERF proteins by Diarrheagenic Escherichia coli

Enteropathogenic (EPEC) and enterohaemorrhagic (EHEC) Escherichia coli cause severe disease with symptoms ranging from mild diarrhoea to haemolytic uremic syndrome. During infection of the gut, these bacteria provoke attaching and effacing lesions (A/E lesions), characterised by intimate bacterial attachment and effacement of microvilli from the surface of enterocytes. A type III secretion system (T3SS), encoded by the locus of enterocyte effacement (LEE), allows EPEC and EHEC to inject more than twenty effector proteins into the host cell cytoplasm and to manipulate a large number of cellular processes. The non-LEE encoded effector proteins EspI and NleH1 are involved in inhibition of vesicular transport and apoptosis, respectively. The effector protein Map induces filopodia formation by activating the Rho GTPase Cdc42. Persistence of filopodia on the host cell surface depends on the interaction of Map with Na+/H+ Exchanger Regulatory Factor 1 (NHERF1) and activation of RhoA. NHERF proteins are PDZ domain-containing proteins involved in addressing, recycling and regulating numerous proteins such as ion channels in epithelial cells. Using a PDZ proteomic array and biochemical interaction assays, we confirmed that Map and EspI interact with both NHERF1 and NHERF2 through their C-terminal PDZ binding motifs. In addition, we identified NleH1 as a new binding partner of NHERF2. Employing a newly generated HeLa-NHERF2 stable cell line, we found that overexpression of NHERF2 in HeLa cells affected distribution and function of these three effectors: the transit of EspI from the bacterial attachment site to the Golgi apparatus was accelerated; Map-dependent filopodia during EPEC infection were stabilised and NleH1-mediated inhibition of apoptosis was reduced. The investigation of NHERF recruitment by diarrhoeagenic E. coli showed that EPEC, EHEC and Citrobacter rodentium, the mouse model for EPEC and EHEC, recruited NHERF1 and NHERF2 at the site of bacterial adherence. We revealed that both EPEC and EHEC could recruit NHERF2 by a mechanism which required the T3SS translocated intimin receptor (Tir), but did not involve Tir-induced actin polymerisation pathways. Furthermore, EPEC recruited NHERF2 by a T3SS-independent mechanism which, in contrast to the T3SS-dependent pathway, relied on the NHERF2 ezrin-binding domain (EBD). This work demonstrates that NHERF proteins are recruited by several diarrhoeagenic Escherichia coli and are able to modulate function of at least three effector proteins from A/E pathogens. The data strongly points to a model in which NHERFs act as central hubs regulating the temporal and spatial localisation and function of effector proteins in the host cell and indicates that they might play an essential role in the process of intestinal epithelium colonisation by these pathogens

Randomness, information encoding, and shape replication in various models of DNA-inspired self-assembly

Self-assembly is the process by which simple, unorganized components autonomously combine to form larger, more complex structures. Researchers are turning to self-assembly technology for the design of ever smaller, more complex, and precise nanoscale devices, and as an emerging fundamental tool for nanotechnology. We introduce the robust random number generation problem, the problem of encoding a target string of bits in the form of a bit string pad, and the problem of shape replication in various models of tile-based self-assembly. Also included are preliminary results in each of these directions with discussion of possible future work directions

Optimal Staged Self-Assembly of General Shapes

We analyze the number of tile types $t$, bins $b$, and stages necessary to assemble $n \times n$ squares and scaled shapes in the staged tile assembly model. For $n \times n$ squares, we prove $\mathcal{O}(\frac{\log{n} - tb - t\log t}{b^2} + \frac{\log \log b}{\log t})$ stages suffice and $\Omega(\frac{\log{n} - tb - t\log t}{b^2})$ are necessary for almost all $n$. For shapes $S$ with Kolmogorov complexity $K(S)$, we prove $\mathcal{O}(\frac{K(S) - tb - t\log t}{b^2} + \frac{\log \log b}{\log t})$ stages suffice and $\Omega(\frac{K(S) - tb - t\log t}{b^2})$ are necessary to assemble a scaled version of $S$, for almost all $S$. We obtain similarly tight bounds when the more powerful flexible glues are permitted.Comment: Abstract version appeared in ESA 201

Continuous data assimilation with blurred-in-time measurements of the surface quasi-geostrophic equation

An intrinsic property of almost any physical measuring device is that it makes observations which are slightly blurred in time. We consider a nudging-based approach for data assimilation that constructs an approximate solution based on a feedback control mechanism that is designed to account for observations that have been blurred by a moving time average. Analysis of this nudging model in the context of the subcritical surface quasi-geostrophic equation shows, provided the time-averaging window is sufficiently small and the resolution of the observations sufficiently fine, that the approximating solution converges exponentially fast to the observed solution over time. In particular, we demonstrate that observational data with a small blur in time possess no significant obstructions to data assimilation provided that the nudging properly takes the time averaging into account. Two key ingredients in our analysis are additional boundedness properties for the relevant interpolant observation operators and a non-local Gronwall inequality.Comment: 44 page