332 research outputs found
Whole-Genome Sequencing-Based Characterization of 100 Listeria monocytogenes Isolates Collected from Food Processing Environments over a Four-Year Period
Listeria monocytogenes is frequently found in foods and processing facilities, where it can persist, creating concerns for the food industry. Its ability to survive under a wide range of environmental conditions enhances the potential for cross-contamination of the final food products, leading to possible outbreaks of listeriosis. In this study, whole-genome sequencing (WGS) was applied as a tool to characterize and track 100 L. monocytogenes isolates collected from three food processing environments. These WGS data from environmental and food isolates were analyzed to (i) assess the genomic diversity of L. monocytogenes, (ii) identify possible source(s) of contamination, cross-contamination routes, and persistence, (iii) detect absence/presence of antimicrobial resistance-encoding genes, (iv) assess virulence genotypes, and (v) explore in vivo pathogenicity of selected L. monocytogenes isolates carrying different virulence genotypes. The predominant L. monocytogenes sublineages (SLs) identified were SL101 (21%), SL9 (17%), SL121 (12%), and SL5 (12%). Benzalkonium chloride (BC) tolerance-encoding genes were found in 62% of these isolates, a value that increased to 73% among putative persistent subgroups. The most prevalent gene was emrC followed by bcrABC, qacH-Tn6188, and qacC. The L. monocytogenes major virulence factor inlA was truncated in 31% of the isolates, and only one environmental isolate (L. monocytogenes CFS086) harbored all major virulence factors, including Listeria pathogenicity island 4 (LIPI-4), which has been shown to confer hypervirulence. A zebrafish embryo infection model showed a low (3%) embryo survival rate for all putatively hypervirulent L. monocytogenes isolates assayed. Higher embryo survival rates were observed following infection with unknown virulence potential (20%) and putatively hypovirulent (53 to 83%) L. monocytogenes isolates showing predicted pathogenic phenotypes inferred from virulence genotypes
Wide-band optical field concentrator for low-index core propagation
We propose a novel chirped structure consisting of a low index polymer core
bounded by modulated multilayer claddings, to realize an optical field
concentrator with virtually zero propagation losses in a wide spectral range,
independent of wave polarization. In spite of the absence of the total internal
reflection mechanism, properly designed multilayer claddings ensure the
achievement of unitary transmittance in a wide spectral range, including the
widely used wavelengths for optical communications. Several cladding geometries
obtained by varying the thicknesses of the cladding layers are reported and
discussed.Comment: submitted to the Journal of the European Optical Societ
Direct photon production in d+Au collisions at sqrt(s_NN)=200 GeV
Direct photons have been measured in sqrt(s_NN)=200 GeV d+Au collisions at
midrapidity. A wide p_T range is covered by measurements of nearly-real virtual
photons (1<p_T<6 GeV/c) and real photons (5<p_T<16 GeV/c). The invariant yield
of the direct photons in d+Au collisions over the scaled p+p cross section is
consistent with unity. Theoretical calculations assuming standard cold nuclear
matter effects describe the data well for the entire p_T range. This indicates
that the large enhancement of direct photons observed in Au+Au collisions for
1.0<p_T<2.5 GeV/c is due to a source other than the initial-state nuclear
effects.Comment: 547 authors, 7 pages, 4 figures. Submitted to Phys. Rev. Lett.. Plain
text data tables for the points plotted in figures for this and previous
PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC
The uncertainty on the calorimeter energy response to jets of particles is
derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the
calorimeter response to single isolated charged hadrons is measured and
compared to the Monte Carlo simulation using proton-proton collisions at
centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009
and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter
response to specific types of particles (positively and negatively charged
pions, protons, and anti-protons) is measured and compared to the Monte Carlo
predictions. Finally, the jet energy scale uncertainty is determined by
propagating the response uncertainty for single charged and neutral particles
to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3%
for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table,
submitted to European Physical Journal
Measurement of χ c1 and χ c2 production with s√ = 7 TeV pp collisions at ATLAS
The prompt and non-prompt production cross-sections for the χ c1 and χ c2 charmonium states are measured in pp collisions at s√ = 7 TeV with the ATLAS detector at the LHC using 4.5 fb−1 of integrated luminosity. The χ c states are reconstructed through the radiative decay χ c → J/ψγ (with J/ψ → μ + μ −) where photons are reconstructed from γ → e + e − conversions. The production rate of the χ c2 state relative to the χ c1 state is measured for prompt and non-prompt χ c as a function of J/ψ transverse momentum. The prompt χ c cross-sections are combined with existing measurements of prompt J/ψ production to derive the fraction of prompt J/ψ produced in feed-down from χ c decays. The fractions of χ c1 and χ c2 produced in b-hadron decays are also measured
Supermassive Black Hole Binaries: The Search Continues
Gravitationally bound supermassive black hole binaries (SBHBs) are thought to
be a natural product of galactic mergers and growth of the large scale
structure in the universe. They however remain observationally elusive, thus
raising a question about characteristic observational signatures associated
with these systems. In this conference proceeding I discuss current theoretical
understanding and latest advances and prospects in observational searches for
SBHBs.Comment: 17 pages, 4 figures. To appear in the Proceedings of 2014 Sant Cugat
Forum on Astrophysics. Astrophysics and Space Science Proceedings, ed.
C.Sopuerta (Berlin: Springer-Verlag
Employing the Metabolic “Branch Point Effect” to Generate an All-or-None, Digital-like Response in Enzymatic Outputs and Enzyme-Based Sensors
Here, we demonstrate a strategy to convert the
graded Michaelis−Menten response typical of unregulated
enzymes into a sharp, effectively all-or-none response. We do
so using an approach analogous to the “branch point effect”, a
mechanism observed in naturally occurring metabolic networks
in which two or more enzymes compete for the same
substrate. As a model system, we used the enzymatic reaction
of glucose oxidase (GOx) and coupled it to a second,
nonsignaling reaction catalyzed by the higher affinity enzyme
hexokinase (HK) such that, at low substrate concentrations,
the second enzyme outcompetes the first, turning off the
latter’s response. Above an arbitrarily selected “threshold” substrate concentration, the nonsignaling HK enzyme saturates leading
to a “sudden” activation of the first signaling GOx enzyme and a far steeper dose−response curve than that observed for simple
Michaelis−Menten kinetics. Using the well-known GOx-based amperometric glucose sensor to validate our strategy, we have
steepen the normally graded response of this enzymatic sensor into a discrete yes/no output similar to that of a multimeric
cooperative enzyme with a Hill coefficient above 13. We have also shown that, by controlling the HK reaction we can precisely
tune the threshold target concentration at which we observe the enzyme output. Finally, we demonstrate the utility of this
strategy for achieving effective noise attenuation in enzyme logic gates. In addition to supporting the development of biosensors
with digital-like output, we envisage that the use of all-or-none enzymatic responses will also improve our ability to engineer
efficient enzyme-based catalysis reactions in synthetic biology applications
Integrated annotation and analysis of genomic features reveal new types of functional elements and large-scale epigenetic phenomena in the developing zebrafish
Zebrafish, a popular model for embryonic development and for modelling human diseases, has so far lacked a systematic functional annotation programme akin to those in other animal models. To address this, we formed the international DANIO-CODE consortium and created the first central repository to store and process zebrafish developmental functional genomic data. Our Data Coordination Center (https://danio-code.zfin.org) combines a total of 1,802 sets of unpublished and reanalysed published genomics data, which we used to improve existing annotations and show its utility in experimental design. We identified over 140,000 cis-regulatory elements in development, including novel classes with distinct features dependent on their activity in time and space. We delineated the distinction between regulatory elements active during zygotic genome activation and those active during organogenesis, identifying new aspects of how they relate to each other. Finally, we matched regulatory elements and epigenomic landscapes between zebrafish and mouse and predict functional relationships between them beyond sequence similarity, extending the utility of zebrafish developmental genomics to mammals
Astrophysics with the Laser Interferometer Space Antenna
The Laser Interferometer Space Antenna (LISA) will be a transformative experiment for gravitational wave astronomy, and, as such, it will offer unique opportunities to address many key astrophysical questions in a completely novel way. The synergy with ground-based and space-born instruments in the electromagnetic domain, by enabling multi-messenger observations, will add further to the discovery potential of LISA. The next decade is crucial to prepare the astrophysical community for LISA’s first observations. This review outlines the extensive landscape of astrophysical theory, numerical simulations, and astronomical observations that are instrumental for modeling and interpreting the upcoming LISA datastream. To this aim, the current knowledge in three main source classes for LISA is reviewed; ultra-compact stellar-mass binaries, massive black hole binaries, and extreme or interme-diate mass ratio inspirals. The relevant astrophysical processes and the established modeling techniques are summarized. Likewise, open issues and gaps in our understanding of these sources are highlighted, along with an indication of how LISA could help making progress in the different areas. New research avenues that LISA itself, or its joint exploitation with upcoming studies in the electromagnetic domain, will enable, are also illustrated. Improvements in modeling and analysis approaches, such as the combination of numerical simulations and modern data science techniques, are discussed. This review is intended to be a starting point for using LISA as a new discovery tool for understanding our Universe
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