Characterization of a ballistic supermirror neutron guide

We describe the beam characteristics of the first ballistic supermirror neutron guide H113 that feeds the neutron user facility for particle physics PF1B of the Institute Laue-Langevin, Grenoble (ILL). At present, the neutron capture flux density of H113 at its 20x6cm2 exit window is 1.35x10^10/cm^2/s, and will soon be raised to above 2x10^10/cm^2/s. Beam divergence is no larger than beam divergence from a conventional Ni coated guide. A model is developed that permits rapid calculation of beam profiles and absolute event rates from such a beam. We propose a procedure that permits inter-comparability of the main features of beams emitted from ballistic or conventional neutron guides.Comment: 15 pages, 11 figures, to be submitted to Nuclear Instruments and Methods

A system in balance? ? Implications of deep vertical mixing for the nitrogen budget in the northern Red Sea, including the Gulf of Aqaba (Eilat)

International audienceWe investigated the implications of deep winter mixing for the nitrogen budget in two adjacent systems, the northern Red Sea proper, and the Gulf of Aqaba. Both are subtropical oligotrophic water bodies. The main difference is that in the gulf deep winter mixing takes place regularly, whereas the northern Red Sea proper is permanently stratified. In the Gulf of Aqaba, we observed significantly lower nitrate deficits, i.e. deviations from the Redfield ratio, than in the northern Red Sea proper. Assuming that other external inputs and losses in N or P are very similar in both systems, the higher nitrate deficit can be explained by either lower nitrogen fixation in the (stratified) northern Red Sea, which seems unlikely. An alternative explanation would be higher rates of benthic denitrification than in the gulf. By comparing the two systems we have indirect evidence that benthic denitrification was much lower in the Gulf of Aqaba due to higher oxygen concentrations. This we attributed to the occurrence of deep winter mixing, and as a consequence, the nitrate deficit was close to zero (i.e. N:P ratio close to "Redfield"). If both nitrogen fixation and benthic denitrification take place, as in the northern Red Sea proper, the result was a positive nitrate deficit (i.e. a deficit in nitrate) in the ambient water. The nitrate deficit in the northern Red Sea was observed in spite of high iron deposition from the surrounding desert. Our results strongly support the concept of nitrogen as the proximate, and phosphate as the ultimate limiting nutrient for primary production in the sea. This must not be neglected in efforts for protecting the adjacent reefs against eutrophication

Malonate Inhibits Virulence Gene Expression in Vibrio cholerae

We previously found that inhibition of the TCA cycle, either through mutations or chemical inhibition, increased toxT transcription in Vibrio cholerae. In this study, we found that the addition of malonate, an inhibitor of succinate dehydrogenase (SDH), decreased toxT transcription in V. cholerae, an observation inconsistent with the previous pattern observed. Unlike another SDH inhibitor, 2-thenoyltrifluoroacetone (TTFA), which increased toxT transcription and slightly inhibited V. cholerae growth, malonate inhibited toxT transcription in both the wild-type strain and TCA cycle mutants, suggesting malonate-mediated inhibition of virulence gene expression is independent to TCA cycle activity. Addition of malonate also inhibited ctxB and tcpA expressions but did not affect aphA, aphB, tcpP and toxR expressions. Malonate inhibited cholera toxin (CT) production in both V. cholerae classical biotype strains O395N1 and CA401, and El Tor biotype strain, N16961. Consistent with previous reports, we confirmed that these strains of V. cholerae did not utilize malonate as a primary carbon source. However, we found that the addition of malonate to the growth medium stimulated V. cholerae growth. All together, these results suggest that metabolizing malonate as a nutrient source negatively affects virulence gene expression in V. cholerae

Mortalities of Eastern and Pacific Oyster Larvae Caused by the Pathogens Vibrio coralliilyticus and Vibrio tubiashii

Vibrio tubiashii is reported to be a bacterial pathogen of larval Eastern oysters (Crassostrea virginica) and Pacific oysters (Crassostrea gigas) and has been associated with major hatchery crashes, causing shortages in seed oysters for commercial shellfish producers. Another bacterium, Vibrio coralliilyticus, a well-known coral pathogen, has recently been shown to elicit mortality in fish and shellfish. Several strains of V. coralliilyticus, such as ATCC 19105 and Pacific isolates RE22 and RE98, were misidentified as V. tubiashii until recently. We compared the mortalities caused by two V. tubiashii and four V. coralliilyticus strains in Eastern and Pacific oyster larvae. The 50% lethal dose (LD₅₀) of V. coralliilyticus in Eastern oysters (defined here as the dose required to kill 50% of the population in 6 days) ranged from 1.1 x 10⁴ to 3.0 x 10⁴ CFU/ml seawater; strains RE98 and RE22 were the most virulent. This study shows that V. coralliilyticus causes mortality in Eastern oyster larvae. Results for Pacific oysters were similar, with LD₅₀s between 1.2 x 10⁴ and 4.0 x 10⁴ CFU/ml. Vibrio tubiashii ATCC 19106 and ATCC 19109 were highly infectious toward Eastern oyster larvae but were essentially nonpathogenic toward healthy Pacific oyster larvae at dosages of ≥ 1.1 x 10⁴ CFU/ml. These data, coupled with the fact that several isolates originally thought to be V. tubiashii are actually V. coralliilyticus, suggest that V. coralliilyticus has been a more significant pathogen for larval bivalve shellfish than V. tubiashii, particularly on the U.S. West Coast, contributing to substantial hatchery-associated morbidity and mortality in recent years

An improved open-channel structure of MscL determined from FRET confocal microscopy and simulation

Mechanosensitive channels act as molecular transducers of mechanical force exerted on the membrane of living cells by opening in response to membrane bilayer deformations occurring in physiological processes such as touch, hearing, blood pressure regulation, and osmoregulation. Here, we determine the likely structure of the open state of the mechanosensitive channel of large conductance using a combination of patch clamp, fluorescence resonance energy transfer (FRET) spectroscopy, data from previous electron paramagnetic resonance experiments, and molecular and Brownian dynamics simulations. We show that structural rearrangements of the protein can be measured in similar conditions as patch clamp recordings while controlling the state of the pore in its natural lipid environment by modifying the lateral pressure distribution via the lipid bilayer. Transition to the open state is less dramatic than previously proposed, while the N terminus remains anchored at the surface of the membrane where it can either guide the tilt of or directly translate membrane tension to the conformation of the pore-lining helix. Combining FRET data obtained in physiological conditions with simulations is likely to be of great value for studying conformational changes in a range of multimeric membrane proteins

Sodium/Proton Antiporter Activity is Essential for Virulence of Yersinia pestis

We found that a strains of Yersinia pestis (KIM5) which lacked the nhaA gene was fully attenuated in a plague model. This gene produces a protein of the sodium-proton antiporter family which expel sodium ions from the bacterial cytoplasm in exchange for hydrogen ions, or protons, from the surrounding environment. A Y. pestis strain that contained the nhaA mutation showed a significant decrease in its ability to survive in both sheep’s blood and serum. Decreased growth rates were also observed when the nhaA deficient strain was tested in the artificial serum media Opti-MEM® when compared to the wild type strain. A similar growth phenotype was observed when wild type and nhaA mutant strains were tested in LB media set to mimic pH and salt conditions of blood. These observations indicate that sodium-proton antiporter activity of Y. pestis is essential for the survival of the bacterium in certain environments, such as the blood of an infected host. 2-aminopyrimidine was used to inhibit NhaA activity, and when tested in Opti-MEM®, bacterial growth rates decreased. These findings lead us to propose that sodium-proton antiporter inhibition is a novel way of treating bacterial blood-borne diseases

Identification of a novel zinc metalloprotease through a global analysis of clostridium difficile extracellular proteins

Clostridium difficile is a major cause of infectious diarrhea worldwide. Although the cell surface proteins are recognized to be important in clostridial pathogenesis, biological functions of only a few are known. Also, apart from the toxins, proteins exported by C. difficile into the extracellular milieu have been poorly studied. In order to identify novel extracellular factors of C. difficile, we analyzed bacterial culture supernatants prepared from clinical isolates, 630 and R20291, using liquid chromatography-tandem mass spectrometry. The majority of the proteins identified were non-canonical extracellular proteins. These could be largely classified into proteins associated to the cell wall (including CWPs and extracellular hydrolases), transporters and flagellar proteins. Seven unknown hypothetical proteins were also identified. One of these proteins, CD630_28300, shared sequence similarity with the anthrax lethal factor, a known zinc metallopeptidase. We demonstrated that CD630_28300 (named Zmp1) binds zinc and is able to cleave fibronectin and fibrinogen in vitro in a zinc-dependent manner. Using site-directed mutagenesis, we identified residues important in zinc binding and enzymatic activity. Furthermore, we demonstrated that Zmp1 destabilizes the fibronectin network produced by human fibroblasts. Thus, by analyzing the exoproteome of C. difficile, we identified a novel extracellular metalloprotease that may be important in key steps of clostridial pathogenesis

Roles of the Sodium-Translocating NADH:Quinone Oxidoreductase (Na⁺-NQR) on Vibrio cholerae Metabolism, Motility and Osmotic Stress Resistance

The Na⁺ translocating NADH:quinone oxidoreductase (Na⁺-NQR) is a unique respiratory enzyme catalyzing the electron transfer from NADH to quinone coupled with the translocation of sodium ions across the membrane. Typically, Vibrio spp., including Vibrio cholerae, have this enzyme but lack the proton-pumping NADH:ubiquinone oxidoreductase (Complex I). Thus, Na⁺-NQR should significantly contribute to multiple aspects of V. cholerae physiology; however, no detailed characterization of this aspect has been reported so far. In this study, we broadly investigated the effects of loss of Na⁺-NQR on V. cholerae physiology by using Phenotype Microarray (Biolog), transcriptome and metabolomics analyses. We found that the V. cholerae ΔnqrA-F mutant showed multiple defects in metabolism detected by Phenotype Microarray. Transcriptome analysis revealed that the V. cholerae ΔnqrA-F mutant up-regulates 31 genes and down-regulates 55 genes in both early and mid-growth phases. The most up-regulated genes included the cadA and cadB genes, encoding a lysine decarboxylase and a lysine/cadaverine antiporter, respectively. Increased CadAB activity was further suggested by the metabolomics analysis. The down-regulated genes include sialic acid catabolism genes. Metabolomic analysis also suggested increased reductive pathway of TCA cycle and decreased purine metabolism in the V. cholerae ΔnqrA-F mutant. Lack of Na⁺-NQR did not affect any of the Na+ pumping-related phenotypes of V. cholerae suggesting that other secondary Na⁺ pump(s) can compensate for Na⁺ pumping activity of Na⁺-NQR. Overall, our study provides important insights into the contribution of Na⁺-NQR to V. cholerae physiology

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field

MscS-like mechanosensitive channels in plants and microbes

The challenge of osmotic stress is something all living organisms must face as a result of environmental dynamics. Over the past three decades, innovative research and cooperation across disciplines have irrefutably established that cells utilize mechanically gated ion channels to release osmolytes and prevent cell lysis during hypoosmotic stress. Early electrophysiological analysis of the inner membrane of Escherichia coli identified the presence of three distinct mechanosensitive activities. The subsequent discoveries of the genes responsible for two of these activities, the mechanosensitive channels of large (MscL) and small (MscS) conductance, led to the identification of two diverse families of mechanosensitive channels. The latter of these two families, the MscS family, consists of members from bacteria, archaea, fungi, and plants. Genetic and electrophysiological analysis of these family members has provided insight into how organisms use mechanosensitive channels for osmotic regulation in response to changing environmental and developmental circumstances. Furthermore, determining the crystal structure of E. coli MscS and several homologues in several conformational states has contributed to our understanding of the gating mechanisms of these channels. Here we summarize our current knowledge of MscS homologues from all three domains of life and address their structure, proposed physiological functions, electrophysiological behaviors, and topological diversity