186 research outputs found

    Monte Carlo of Trapped Ultracold Neutrons in the UCNτ Trap

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    In the UCNτ experiment, ultracold neutrons (UCN) are confined by magnetic fields and the Earth’s gravitational field. Field-trapping mitigates the problem of UCN loss on material surfaces, which caused the largest correction in prior neutron experiments using material bottles. However, the neutron dynamics in field traps differ qualitatively from those in material bottles. In the latter case, neutrons bounce off material surfaces with significant diffusivity and the population quickly reaches a static spatial distribution with a density gradient induced by the gravitational potential. In contrast, the field-confined UCN—whose dynamics can be described by Hamiltonian mechanics—do not exhibit the stochastic behaviors typical of an ideal gas model as observed in material bottles. In this report, we will describe our efforts to simulate UCN trapping in the UCNτ magneto-gravitational trap. We compare the simulation output to the experimental results to determine the parameters of the neutron detector and the input neutron distribution. The tuned model is then used to understand the phase space evolution of neutrons observed in the UCNτ experiment. We will discuss the implications of chaotic dynamics on controlling the systematic effects, such as spectral cleaning and microphonic heating, for a successful UCN lifetime experiment to reach a 0.01% level of precision

    Dual inhibition of DNA polymerase PolC and protein tyrosine phosphatase CpsB uncovers a novel antibiotic target

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    Increasing antibiotic resistance is making the identification of novel antimicrobial targets critical. Recently, we discovered an inhibitor of protein tyrosine phosphatase CpsB, fascioquinol E (FQE), which unexpectedly inhibited the growth of Gram-positive pathogens. CpsB is a member of the polymerase and histidinol phosphate phosphatase (PHP) domain family. Another member of this family found in a variety of Gram-positive pathogens is DNA polymerase PolC. We purified the PHP domain from PolC (PolC(PHP)), and showed that this competes away FQE inhibition of CpsB phosphatase activity. Furthermore, we showed that this domain hydrolyses the 5'-p-nitrophenyl ester of thymidine-5'-monophosphate (pNP-TMP), which has been used as a measure of exonuclease activity. Finally, we showed that FQE not only inhibits the phosphatase activity of CpsB, but also ability of PolC(PHP) to catalyse the hydrolysis of pNP-TMP. This suggests that PolC may be the essential target of FQE, and that the PHP domain may represent an as yet untapped target for the development of novel antibiotics.Alistair J. Standish, Angela A. Salim, Robert J. Capon, Renato Moron

    Unusual Regulation of a Leaderless Operon Involved in the Catabolism of Dimethylsulfoniopropionate in Rhodobacter sphaeroides

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    Rhodobacter sphaeroides strain 2.4.1 is a widely studied bacterium that has recently been shown to cleave the abundant marine anti-stress molecule dimethylsulfoniopropionate (DMSP) into acrylate plus gaseous dimethyl sulfide. It does so by using a lyase encoded by dddL, the promoter-distal gene of a three-gene operon, acuR-acuI-dddL. Transcription of the operon was enhanced when cells were pre-grown with the substrate DMSP, but this induction is indirect, and requires the conversion of DMSP to the product acrylate, the bona fide co-inducer. This regulation is mediated by the product of the promoter-proximal gene acuR, a transcriptional regulator in the TetR family. AcuR represses the operon in the absence of acrylate, but this is relieved by the presence of the co-inducer. Another unusual regulatory feature is that the acuR-acuI-dddL mRNA transcript is leaderless, such that acuR lacks a Shine-Dalgarno ribosomal binding site and 5′-UTR, and is translated at a lower level compared to the downstream genes. This regulatory unit may be quite widespread in bacteria, since several other taxonomically diverse lineages have adjacent acuR-like and acuI-like genes; these operons also have no 5′ leader sequences or ribosomal binding sites and their predicted cis-acting regulatory sequences resemble those of R. sphaeroides acuR-acuI-dddL

    Local and regional components of aerosol in a heavily trafficked street canyon in central London derived from PMF and cluster analysis of single-particle ATOFMS spectra.

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    Positive matrix factorization (PMF) has been applied to single particle ATOFMS spectra collected on a six lane heavily trafficked road in central London (Marylebone Road), which well represents an urban street canyon. PMF analysis successfully extracted 11 factors from mass spectra of about 700,000 particles as a complement to information on particle types (from K-means cluster analysis). The factors were associated with specific sources and represent the contribution of different traffic related components (i.e., lubricating oils, fresh elemental carbon, organonitrogen and aromatic compounds), secondary aerosol locally produced (i.e., nitrate, oxidized organic aerosol and oxidized organonitrogen compounds), urban background together with regional transport (aged elemental carbon and ammonium) and fresh sea spray. An important result from this study is the evidence that rapid chemical processes occur in the street canyon with production of secondary particles from road traffic emissions. These locally generated particles, together with aging processes, dramatically affected aerosol composition producing internally mixed particles. These processes may become important with stagnant air conditions and in countries where gasoline vehicles are predominant and need to be considered when quantifying the impact of traffic emissions.This is the author accepted manuscript. The final version is available via ACS at http://pubs.acs.org/doi/abs/10.1021/es506249z

    Finding the Needles in the Metagenome Haystack

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    In the collective genomes (the metagenome) of the microorganisms inhabiting the Earth’s diverse environments is written the history of life on this planet. New molecular tools developed and used for the past 15 years by microbial ecologists are facilitating the extraction, cloning, screening, and sequencing of these genomes. This approach allows microbial ecologists to access and study the full range of microbial diversity, regardless of our ability to culture organisms, and provides an unprecedented access to the breadth of natural products that these genomes encode. However, there is no way that the mere collection of sequences, no matter how expansive, can provide full coverage of the complex world of microbial metagenomes within the foreseeable future. Furthermore, although it is possible to fish out highly informative and useful genes from the sea of gene diversity in the environment, this can be a highly tedious and inefficient procedure. Microbial ecologists must be clever in their pursuit of ecologically relevant, valuable, and niche-defining genomic information within the vast haystack of microbial diversity. In this report, we seek to describe advances and prospects that will help microbial ecologists glean more knowledge from investigations into metagenomes. These include technological advances in sequencing and cloning methodologies, as well as improvements in annotation and comparative sequence analysis. More significant, however, will be ways to focus in on various subsets of the metagenome that may be of particular relevance, either by limiting the target community under study or improving the focus or speed of screening procedures. Lastly, given the cost and infrastructure necessary for large metagenome projects, and the almost inexhaustible amount of data they can produce, trends toward broader use of metagenome data across the research community coupled with the needed investment in bioinformatics infrastructure devoted to metagenomics will no doubt further increase the value of metagenomic studies in various environments

    Living with diabetes: rationale, study design and baseline characteristics for an Australian prospective cohort study

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    Background: Diabetes mellitus is a major global public health threat. In Australia, as elsewhere, it is responsible for a sizeable portion of the overall burden of disease, and significant costs. The psychological and social impact of diabetes on individuals with the disease can be severe, and if not adequately addressed, can lead to the worsening of the overall disease picture. The Living With Diabetes Study aims to contribute to a holistic understanding of the psychological and social aspects of diabetes mellitus
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