Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli.

The translational GTPase BipA regulates the expression of virulence and pathogenicity factors in several eubacteria. BipA-dependent expression of virulence factors occurs under starvation conditions, such as encountered during infection of a host. Under these conditions, BipA associates with the small ribosomal subunit. BipA also has a second function to promote the efficiency of late steps in biogenesis of large ribosomal subunits at low temperatures, presumably while bound to the ribosome. During starvation, the cellular concentration of stress alarmone guanosine-3', 5'-bis pyrophosphate (ppGpp) is increased. This increase allows ppGpp to bind to BipA and switch its binding specificity from ribosomes to small ribosomal subunits. A conformational change of BipA upon ppGpp binding could explain the ppGpp regulation of the binding specificity of BipA. Here, we present the structures of the full-length BipA from Escherichia coli in apo, GDP-, and ppGpp-bound forms. The crystal structure and small-angle x-ray scattering data of the protein with bound nucleotides, together with a thermodynamic analysis of the binding of GDP and of ppGpp to BipA, indicate that the ppGpp-bound form of BipA adopts the structure of the GDP form. This suggests furthermore, that the switch in binding preference only occurs when both ppGpp and the small ribosomal subunit are present. This molecular mechanism would allow BipA to interact with both the ribosome and the small ribosomal subunit during stress response

Composition for component-based modeling

We propose a framework for component-based modeling using an abstract layered model for components. A component is the superposition of two models: a behavior model and an interaction model. Interaction models describe architectural constraints induced by connectors between components. We propose and analyze general requirements for component composition that motivated and guided the development of the framework. We define an associative and commutative composition operator on components encompassing heterogeneous interaction. As a particular instance of the proposed framework, we consider components where behavior models are transition systems and interaction models are described by priority relations on interactions. This leads to a concept of "flexible" composition different from usual composition in that it preserves deadlock-freedom and is appropriate for correctness by construction. Nevertheless, flexible composition is a partial operation. Product systems should be interaction safe in the sense that they do not violate constraints of the interaction model. We propose results ensuring correctness by construction of a system from properties of its interaction model and of its components. The properties considered include global deadlock-freedom, individual deadlock-freedom of components, and interaction safety. © 2004 Elsevier B.V. All rights reserved

Priority Systems

Projet POP_ARTWe present a framework for the incremental construction of deadlock-free systems meeting given safety properties. The framework borrows concepts and basic results from the controller synthesis paradigm by considering a step in the construction process as a controller synthesis problem. We show that priorities are expressive enough to represent restrictions induced by deadlock-free controllers preserving safety properties. We define a correspondence between such restrictions and priorities and provide compositionality results about the preservation of this correspondence by operations on safety properties and priorities. Finally, we provide an example illustrating an application of the results

The status of shark and ray fishery resources in the Gulf of California: applied research to improve management and conservation

Seasonal surveys were conducted during 1998–1999 in Baja California, Baja California Sur, Sonora, and Sinaloa to determine the extent and activities of artisanal elasmobranch fisheries in the Gulf of California. One hundred and forty–seven fishing sites, or camps, were documented, the majority of which (n = 83) were located in Baja California Sur. Among camps with adequate fisheries information, the great majority (85.7%) targeted elasmobranchs during some part of the year. Most small, demersal sharks and rays were landed in mixed species fisheries that also targeted demersal teleosts, but large sharks were usually targeted in directed drift gillnet or, to a lesser extent, surface longline fisheries. Artisanal fishermen were highly opportunistic, and temporally switched targets depending on the local productivity of teleost, invertebrate, and elasmobranch fishery resources. Major fisheries for small sharks ( 1.5 m, “tiburón”) were minor components of artisanal elasmobranch fisheries in Sonora and Sinaloa, but were commonly targeted during summer and early autumn in Baja California and Baja California Sur. The pelagic thresher shark (Alopias pelagicus) and silky shark (Carcharhinus falciformis) were most commonly landed in Baja California, whereas a diverse assemblage of pelagic and large coastal sharks was noted among Baja California Sur landings. Rays dominated summer landings in Baja California and Sinaloa, when elevated catch rates of the shovelnose guitarfish (Rhinobatos productus, 13.2 individuals/vessel/trip) and golden cownose ray (Rhinoptera steindachneri, 11.1 individuals/vesse/trip) primarily supported the respective fisheries. The Sonoran artisanal elasmobranch fishery was the most expansive recorded during this study, and rays (especially R. productus) dominated spring and summer landings in this state. Seasonal catch rates of small demersal sharks and rays were considerably greater in Sonora than in other surveyed states. Many tiburón populations (e.g., C. leucas, C. limbatus, C. obscurus, Galeocerdo cuvier) have likely been overfished, possibly shifting effort towards coastal populations of cazón and rays. Management recommendations, including conducting demographic analyses using available life history data, determining and protecting nursery areas, and enacting seasonal closures in areas of elasmobranch aggregation (e.g., reproduction, feeding), are proposed. Without effective, enforceable management to sustain or rebuild targeted elasmobranch populations in the Gulf of California, collapse of many fisheries is a likely outcome. (PDF contains 243 pages

Transcription-translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits.

In prokaryotes, RNA polymerase and ribosomes can bind concurrently to the same RNA transcript, leading to the functional coupling of transcription and translation. The interactions between RNA polymerase and ribosomes are crucial for the coordination of transcription with translation. Here, we report that RNA polymerase directly binds ribosomes and isolated large and small ribosomal subunits. RNA polymerase and ribosomes form a one-to-one complex with a micromolar dissociation constant. The formation of the complex is modulated by the conformational and functional states of RNA polymerase and the ribosome. The binding interface on the large ribosomal subunit is buried by the small subunit during protein synthesis, whereas that on the small subunit remains solvent-accessible. The RNA polymerase binding site on the ribosome includes that of the isolated small ribosomal subunit. This direct interaction between RNA polymerase and ribosomes may contribute to the coupling of transcription to translation

On the construction of live timed systems

We present a method that allows to guarantee liveness by construction of a class of timed systems. The method is based on the use of a set of structural properties which can be checked locallyat low cost. We provide sufficient conditions for liveness preservation byparallel composition and prioritychoice operators. The latter allow to restrict a system's behavior according to a given priorityorder on its actions. We present several examples illustrating the use of the results, in particular for the construction of live controllers. © Springer-Verlag Berlin Heidelberg 2000

Universal sign control of coupling in tight-binding lattices

We present a method of locally inverting the sign of the coupling term in tight-binding systems, by means of inserting a judiciously designed ancillary site and eigenmode matching of the resulting vertex triplet. Our technique can be universally applied to all lattice configurations, as long as the individual sites can be detuned. We experimentally verify this method in laser-written photonic lattices and confirm both the magnitude and the sign of the coupling by interferometric measurements. Based on these findings, we demonstrate how such universal sign-flipped coupling links can be embedded into extended lattice structures to impose a Z2-gauge transformation. This opens a new avenue for investigations on topological effects arising from magnetic fields with aperiodic flux patterns or in disordered systems

Perceptions about Probiotic Yogurt for Health and Nutrition in the Context of HIV/AIDS in Mwanza, Tanzania

Recently, the food and malnutrition issues have taken centre stage within the arena of HIV/AIDS epidemic, with several calls being made for context-specific health and nutrition interventions to deal with the emerging food insecurity and malnutrition issues in settings with high burdens of HIV/AIDS. The use of probiotics as nutritional supplements in HIV/AIDS-affected and resource-poor settings has also been advocated. This paper presents the results of a qualitative study on community knowledge and perceptions about probiotics and their potential impact on people's everyday life in the context of the HIV/AIDS epidemic. In-depth interviews (n=26) were conducted with residents in Mwanza, Tanzania. The results showed that people living with HIV/AIDS, who were using probiotic yogurt produced through a joint partnership of Western Heads East, Tanzania Medical Research Institute and the Tukwamune Women's Group, reported perceived beneficial effects, such as gain in weight and improved health and well-being. Yet, these beneficial effects might be resulting in growing misconceptions about probiotic yogurt being ‘medicine’ for the treatment of HIV/AIDS; this is leading some people living with HIV/AIDS to abandon taking their antiretroviral medications based on the view that the probiotic yogurt is making them feel much better. The findings illustrate the potential challenges with regard to the introduction of nutritional food supplements into new contexts plagued by malnutrition and infectious diseases. Public-health education and awareness programmes are needed when introducing novel foods into such contexts