Evolution of genomes, host shifts and the geographic spread of SARS-CoV and related coronaviruses

Severe acute respiratory syndrome (SARS) is a novel human illness caused by a previously unrecognized coronavirus (CoV) termed SARS-CoV. There are conflicting reports on the animal reservoir of SARS-CoV. Many of the groups that argue carnivores are the original reservoir of SARS-CoV use a phylogeny to support their argument. However, the phylogenies in these studies often lack outgroup and rooting criteria necessary to determine the origins of SARS-CoV. Recently, SARS-CoV has been isolated from various species of Chiroptera from China (e.g., Rhinolophus sinicus) thus leading to reconsideration of the original reservoir of SARS-CoV. We evaluated the hypothesis that SARS-CoV isolated from Chiroptera are the original zoonotic source for SARS-CoV by sampling SARS-CoV and non-SARS-CoV from diverse hosts including Chiroptera, carnivores, artiodactyls and humans. Regardless of alignment parameters, optimality criteria, or isolate sampling, the resulting phylogenies clearly show that the SARS-CoV was transmitted to small carnivores well after the epidemic of SARS in humans that began in late 2002. The SARS-CoV isolates from small carnivores in Shenzhen markets form a terminal clade that emerged recently from within the radiation of human SARS-CoV. There is evidence of subsequent exchange of SARS-CoV between humans and carnivores. In addition SARS-CoV was transmitted independently from humans to farmed pigs (Sus scrofa). The position of SARS-CoV isolates from Chiroptera are basal to the SARS-CoV clade isolated from humans and carnivores. Although sequence data indicate that Chiroptera are a good candidate for the original reservoir of SARS-CoV, the structural biology of the spike protein of SARS-CoV isolated from Chiroptera suggests that these viruses are not able to interact with the human variant of the receptor of SARS-CoV, angiotensin-converting enzyme 2 (ACE2). In SARS-CoV study, both visually and statistically, labile genomic fragments and, putative key mutations of the spike protein that may be associated with host shifts. We display host shifts and candidate mutations on trees projected in virtual globes depicting the spread of SARS-CoV. These results suggest that more sampling of coronaviruses from diverse hosts, especially Chiroptera, carnivores and primates, will be required to understand the genomic and biochemical evolution of coronaviruses, including SARS-CoV.Fil: Janies, Daniel. Ohio State University; Estados UnidosFil: Habib, Farhat. Ohio State University; Estados UnidosFil: Alexandrov, Boyan. Ohio State University; Estados UnidosFil: Hill, Andrew. University of Colorado; Estados UnidosFil: Pol, Diego. Museo Paleontológico Egidio Feruglio; Argentina. Ohio State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentin

Instability of the rhodium magnetic moment as origin of the metamagnetic phase transition in alpha-FeRh

Based on ab initio total energy calculations we show that two magnetic states of rhodium atoms together with competing ferromagnetic and antiferromagnetic exchange interactions are responsible for a temperature induced metamagnetic phase transition, which experimentally is observed for stoichiometric alpha-FeRh. A first-principle spin-based model allows to reproduce this first-order metamagnetic transition by means of Monte Carlo simulations. Further inclusion of spacial variation of exchange parameters leads to a realistic description of the experimental magneto-volume effects in alpha-FeRh.Comment: 10 pages, 13 figures, accepted for publication in Phys. Rev.

Optical properties of structurally-relaxed Si/SiO2_2 superlattices: the role of bonding at interfaces

We have constructed microscopic, structurally-relaxed atomistic models of Si/SiO$_2$ superlattices. The structural distortion and oxidation-state characteristics of the interface Si atoms are examined in detail. The role played by the interface Si suboxides in raising the band gap and producing dispersionless energy bands is established. The suboxide atoms are shown to generate an abrupt interface layer about 1.60 \AA thick. Bandstructure and optical-absorption calculations at the Fermi Golden rule level are used to demonstrate that increasing confinement leads to (a) direct bandgaps (b) a blue shift in the spectrum, and (c) an enhancement of the absorption intensity in the threshold-energy region. Some aspects of this behaviour appear not only in the symmetry direction associated with the superlattice axis, but also in the orthogonal plane directions. We conclude that, in contrast to Si/Ge, Si/SiO$_2$ superlattices show clear optical enhancement and a shift of the optical spectrum into the region useful for many opto-electronic applications.Comment: 11 pages, 10 figures (submitted to Phys. Rev. B

Interplay of Electron-Phonon Interaction and Electron Correlation in High Temperature Superconductivity

We study the electron-phonon interaction in the strongly correlated superconducting cuprates. Two types of the electron-phonon interactions are introduced in the $t-J$ model; the diagonal and off-diagonal interactions which modify the formation energy of the Zhang-Rice singlet and its transfer integral, respectively. The characteristic phonon-momentum $(\vec q)$ and electron-momentum $(\vec k)$ dependence resulted from the off-diagonal coupling can explain a variety of experiments. The vertex correction for the electron-phonon interaction is formulated in the SU(2) slave-boson theory by taking into account the collective modes in the superconducting ground states. It is shown that the vertex correction enhances the attractive potential for the d-wave paring mediated by phonon with $\vec q=(\pi(1-\delta), 0)$ around $\delta \cong 0.3$ which corresponds to the half-breathing mode of the oxygen motion.Comment: 14 pages, 13 figure

Genomic analysis of two phlebotomine sand fly vectors of Leishmania from the New and Old World.

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the kinetoplastid parasites of the genus Leishmania, the causative agents of devastating diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. No approved efficacious vaccine exists for leishmaniasis and available therapeutic drugs are either toxic and/or expensive, or the parasites are becoming resistant to the more recently developed drugs. Therefore, sand fly and/or reservoir control are currently the most effective strategies to break transmission. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two geographically widespread and important sand fly vector species: Phlebotomus papatasi, a vector of Leishmania parasites that cause cutaneous leishmaniasis, (distributed in Europe, the Middle East and North Africa) and Lutzomyia longipalpis, a vector of Leishmania parasites that cause visceral leishmaniasis (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites

Search for dark matter produced in association with a hadronically decaying vector boson in pp collisions at sqrt (s) = 13 TeV with the ATLAS detector

A search is presented for dark matter produced in association with a hadronically decaying W or Z boson using 3.2 fb−1 of pp collisions at View the MathML sources=13 TeV recorded by the ATLAS detector at the Large Hadron Collider. Events with a hadronic jet compatible with a W or Z boson and with large missing transverse momentum are analysed. The data are consistent with the Standard Model predictions and are interpreted in terms of both an effective field theory and a simplified model containing dark matter

Measurement of the cross section for isolated-photon plus jet production in pp collisions at √s=13 TeV using the ATLAS detector

The dynamics of isolated-photon production in association with a jet in proton–proton collisions at a centre-of-mass energy of 13 TeV are studied with the ATLAS detector at the LHC using a dataset with an integrated luminosity of 3.2 fb−1. Photons are required to have transverse energies above 125 GeV. Jets are identified using the anti- algorithm with radius parameter and required to have transverse momenta above 100 GeV. Measurements of isolated-photon plus jet cross sections are presented as functions of the leading-photon transverse energy, the leading-jet transverse momentum, the azimuthal angular separation between the photon and the jet, the photon–jet invariant mass and the scattering angle in the photon–jet centre-of-mass system. Tree-level plus parton-shower predictions from Sherpa and Pythia as well as next-to-leading-order QCD predictions from Jetphox and Sherpa are compared to the measurements

A search for resonances decaying into a Higgs boson and a new particle X in the XH → qqbb final state with the ATLAS detector

A search for heavy resonances decaying into a Higgs boson (H) and a new particle (X) is reported, utilizing 36.1 fb−1 of proton–proton collision data at collected during 2015 and 2016 with the ATLAS detector at the CERN Large Hadron Collider. The particle X is assumed to decay to a pair of light quarks, and the fully hadronic final state is analysed. The search considers the regime of high XH resonance masses, where the X and H bosons are both highly Lorentz-boosted and are each reconstructed using a single jet with large radius parameter. A two-dimensional phase space of XH mass versus X mass is scanned for evidence of a signal, over a range of XH resonance mass values between 1 TeV and 4 TeV, and for X particles with masses from 50 GeV to 1000 GeV. All search results are consistent with the expectations for the background due to Standard Model processes, and 95% CL upper limits are set, as a function of XH and X masses, on the production cross-section of the resonance