Activation of the Listeria monocytogenes Virulence Program by a Reducing Environment.

Upon entry into the host cell cytosol, the facultative intracellular pathogen Listeria monocytogenes coordinates the expression of numerous essential virulence factors by allosteric binding of glutathione (GSH) to the Crp-Fnr family transcriptional regulator PrfA. Here, we report that robust virulence gene expression can be recapitulated by growing bacteria in a synthetic medium containing GSH or other chemical reducing agents. Bacteria grown under these conditions were 45-fold more virulent in an acute murine infection model and conferred greater immunity to a subsequent lethal challenge than bacteria grown in conventional media. During cultivation in vitro, PrfA activation was completely dependent on the intracellular levels of GSH, as a glutathione synthase mutant (ΔgshF) was activated by exogenous GSH but not reducing agents. PrfA activation was repressed in a synthetic medium supplemented with oligopeptides, but the repression was relieved by stimulation of the stringent response. These data suggest that cytosolic L. monocytogenes interprets a combination of metabolic and redox cues as a signal to initiate robust virulence gene expression in vivoIMPORTANCE Intracellular pathogens are responsible for much of the worldwide morbidity and mortality from infectious diseases. These pathogens have evolved various strategies to proliferate within individual cells of the host and avoid the host immune response. Through cellular invasion or the use of specialized secretion machinery, all intracellular pathogens must access the host cell cytosol to establish their replicative niches. Determining how these pathogens sense and respond to the intracellular compartment to establish a successful infection is critical to our basic understanding of the pathogenesis of each organism and for the rational design of therapeutic interventions. Listeria monocytogenes is a model intracellular pathogen with robust in vitro and in vivo infection models. Studies of the host-sensing and downstream signaling mechanisms evolved by L. monocytogenes often describe themes of pathogenesis that are broadly applicable to less tractable pathogens. Here, we describe how bacteria use external redox states as a cue to activate virulence

Embedding a Native State into a Random Heteropolymer Model: The Dynamic Approach

We study a random heteropolymer model with Langevin dynamics, in the supersymmetric formulation. Employing a procedure similar to one that has been used in static calculations, we construct an ensemble in which the affinity of the system for a native state is controlled by a "selection temperature" T0. In the limit of high T0, the model reduces to a random heteropolymer, while for T0-->0 the system is forced into the native state. Within the Gaussian variational approach that we employed previously for the random heteropolymer, we explore the phases of the system for large and small T0. For large T0, the system exhibits a (dynamical) spin glass phase, like that found for the random heteropolymer, below a temperature Tg. For small T0, we find an ordered phase, characterized by a nonzero overlap with the native state, below a temperature Tn \propto 1/T0 > Tg. However, the random-globule phase remains locally stable below Tn, down to the dynamical glass transition at Tg. Thus, in this model, folding is rapid for temperatures between Tg and Tn, but below Tg the system can get trapped in conformations uncorrelated with the native state. At a lower temperature, the ordered phase can also undergo a dynamical glass transition, splitting into substates separated by large barriers.Comment: 19 pages, revtex, 6 figure

Radiobiological experiments with plant seeds aboard the biosatellite Cosmos 1887

The effects of spaceflight factors on the seeds of Arabidopsis thaliana and Crepis capillaris were studied. The seeds were located inside the satellite in an open space, protected with aluminum foil and also exposed without the foil cover. When the seeds were in open space without any protection, their viability was found to be suppressed; the survival rate and fertility of plants grown from these seeds were also diminished. An increase in the frequency of chromosome aberrations (CA) and in the number of multiple injuries was registered in this case. Experiments with the aluminum foil shielding showed a decrease in the suppression of the seeds' viability, but mutational changes were found to be even more increased, while the survival rate and fertility of the plants decreased. An increase in the thickness of shielding resulted in a decrease in the effects up to the level of the control, except for the effects connected with CA and fertility of the plants. Analysis of the results shows that these impairments can be ascribed to the action of single heavy charged particles (HCP). The seeds can thus be regarded as an integral biological 'dosimeter' which allows estimation of the total effects of radiation, ecological and biological factors

Optimization and evaluation of a coarse-grained model of protein motion using X-ray crystal data

Simple coarse-grained models, such as the Gaussian Network Model, have been shown to capture some of the features of equilibrium protein dynamics. We extend this model by using atomic contacts to define residue interactions and introducing more than one interaction parameter between residues. We use B-factors from 98 ultra-high resolution X-ray crystal structures to optimize the interaction parameters. The average correlation between GNM fluctuation predictions and the B-factors is 0.64 for the data set, consistent with a previous large-scale study. By separating residue interactions into covalent and noncovalent, we achieve an average correlation of 0.74, and addition of ligands and cofactors further improves the correlation to 0.75. However, further separating the noncovalent interactions into nonpolar, polar, and mixed yields no significant improvement. The addition of simple chemical information results in better prediction quality without increasing the size of the coarse-grained model.Comment: 18 pages, 4 figures, 1 supplemental file (cnm_si.tex

Spin-Glass Model for Inverse Freezing

We analyze the Blume-Emery-Griffiths model with disordered magnetic interaction displaying the inverse freezing phenomenon. The behaviour of this spin-1 model in crystal field is studied throughout the phase diagram and the transition and spinodal lines for the model are computed using the Full Replica Symmetry Breaking Ansatz that always yelds a thermodynamically stable phase. We compare the results both with the quenched disordered model with Ising spins on lattice gas - where no reentrance takes place - and with the model with generalized spin variables recently introduced by Schupper and Shnerb [Phys. Rev. Lett. 93, 037202 (2004)]. The simplest version of all these models, known as Ghatak-Sherrington model, turns out to hold all the general features characterizing an inverse transition to an amorphous phase, including the right thermodynamic behavior.Comment: 6 pages, 4 figures, to appear in the Proceeding for the X International Workshop on Disordered Systems (2006), Molveno, Ital

Fabrication of crystals from single metal atoms

YesMetal nanocrystals offer new concepts for the design of nanodevices with a range of potential applications. Currently the formation of metal nanocrystals cannot be controlled at the level of individual atoms. Here we describe a new general method for the fabrication of multi-heteroatom-doped graphitic matrices decorated with very small, ångström-sized, three-dimensional (3D)-metal crystals of defined size. We irradiate boron-rich precious-metal-encapsulated self-spreading polymer micelles with electrons and produce, in real time, a doped graphitic support on which individual osmium atoms hop and migrate to form 3D-nanocrystals, as small as 15 Å in diameter, within 1 h. Crystal growth can be observed, quantified and controlled in real time. We also synthesize the first examples of mixed ruthenium–osmium 3D-nanocrystals. This technology not only allows the production of ångström-sized homo- and hetero-crystals, but also provides new experimental insight into the dynamics of nanocrystals and pathways for their assembly from single atoms.We thank the Leverhulme Trust (Early Career Fellowship No. ECF-2013-414 to NPEB), the University of Warwick (Grant No. RDF 2013-14 to NPEB), the Swiss National Science Foundation (Grant No. PA00P2_145308 to NPEB and PBNEP2_142949 to APB), the ERC (Grant No. 247450 to PJS), EPSRC (EP/G004897/1 to RKOR, and EP/F034210/1 to PJS) and Science City (AWM/ERDF) for support. We thank the Wellcome Trust (Grant No. 055663/Z/98/Z) for funding the Electron Microscopy Facility, School of Life Sciences, University of Warwick. We also thank COST Action CM1105 for stimulating discussions, Thomas Wilks for supplying the micelle image for Figure 1, and the Australian Synchrotron and the University of Monash for allocation of time on the SAXS/ WAXS beamline and funding. The 2000FX Gatan Orius digital TEM camera used in this research was funded by Science City: Creating and Characterizing Next Generation Advanced Materials, with support from Advantage West Midlands and part funded by the European Regional Development Fund

The landscape of gifted and talented education in England and Wales: How are teachers implementing policy?

This is an Author's Accepted Manuscript of an article published in Research Papers in Education, 27(2), 167-186, 2012, copyright Taylor & Francis, available online at: http://www.tandfonline.com/10.1080/02671522.2010.509514.This paper explores the evidence relating to how primary schools are responding to the ‘gifted and talented’ initiative in England and Wales. A questionnaire survey which invited both closed and open-ended responses was carried out with a national sample of primary schools. The survey indicated an increasing proportion of coordinators, compared with a survey carried out in 1996, were identifying their gifted and talented children as well as having associated school policies. However, the survey also highlighted a number of issues which need addressing if the initiative is to achieve its objective of providing the best possible educational opportunities for children. For example, it was found that a significant number of practitioners were not aware of the existence of the National Quality Standards for gifted and talented education, provided by the UK government in 2007, and the subject-specific criteria provided by the UK’s Curriculum Authority for identification and provision have been largely ignored. The process of identifying children to be placed on the ‘gifted and talented’ register seems haphazard and based on pragmatic reasons. Analysis of teachers’ responses also revealed a range of views and theoretical positioning held by them, which have implications for classroom practice. As the ‘gifted and talented’ initiative in the UK is entering a second decade, and yet more significant changes in policy are introduced, pertinent questions need to be raised and given consideration

Clinical, methodology, and patient/carer expert advice in pediatric drug development by conect4children.

Many medicines are used "off-label" in children outside the terms of the license. Feasible pediatric clinical trials are a challenge to design. Conect4children (c4c) is an Innovative Medicines Initiative project to set up a pan-European pediatric clinical trial network aiming to facilitate the development of new medicines for children. To optimize pediatric trial development by promoting innovative trial design, c4c set up a European multidisciplinary advice service, including the voice of young patients and families, tailored to industry and academia. A network of experts was established to provide multidisciplinary advice to trial sponsors. Experts were selected to join clinical and innovative methodology expert groups. A patient and public involvement (PPI) database, to include the expert opinion of patients and parents/carers was formed. A stepwise process was developed: (1) sponsors contact c4c, (2) scoping interview takes place, (3) ad hoc advice group formed, (5) advice meeting held, and (6) advice report provided. Feedback on the process was collected. Twenty-four clinical and innovative methodology expert groups (>400 experts) and a PPI database of 135 registrants were established. As of September 30, 2022, 36 advice requests were received, with 25 requests completed. Clinical and methodology experts and PPI representatives participated in several advice requests. Sponsors appreciated the advice quality and the multidisciplinary experts from different countries, including experts not known before. Experts and PPI participants were generally satisfied with the process. The c4c project has shown successful proof of concept for a service that presents a new framework to plan innovative and feasible pediatric trials

The Energy Landscape, Folding Pathways and the Kinetics of a Knotted Protein

The folding pathway and rate coefficients of the folding of a knotted protein are calculated for a potential energy function with minimal energetic frustration. A kinetic transition network is constructed using the discrete path sampling approach, and the resulting potential energy surface is visualized by constructing disconnectivity graphs. Owing to topological constraints, the low-lying portion of the landscape consists of three distinct regions, corresponding to the native knotted state and to configurations where either the N- or C-terminus is not yet folded into the knot. The fastest folding pathways from denatured states exhibit early formation of the N-terminus portion of the knot and a rate-determining step where the C-terminus is incorporated. The low-lying minima with the N-terminus knotted and the C-terminus free therefore constitute an off-pathway intermediate for this model. The insertion of both the N- and C-termini into the knot occur late in the folding process, creating large energy barriers that are the rate limiting steps in the folding process. When compared to other protein folding proteins of a similar length, this system folds over six orders of magnitude more slowly.Comment: 19 page