Phylogenetic relationships among Oryza species revealed by AFLP markers

The genus Oryza to which cultivated rice belongs has 22 wild species. Seventy-seven accessions of 23 Oryza species, five related genera, and three outgroup taxa were fingerprinted using amplified fragment length polymorphism (AFLP). A total of 1191 polymorphic markers were obtained using five AFLP primer combinations. AFLP data were analyzed to study species relationships using different clustering algorithms, and the resulting phenograms were tested for stability and robustness. The findings suggest a common ancestry to the genus Oryza. Moreover, the results demonstrate that: (1) evolution in Oryza has followed a polyphyletic path wherein multiple lineages underwent independent divergence after separation early in the evolution from a common ancestor/pool of related taxa; (2) newly assigned genomes, GG for O. meyeriana and HHJJ for O. ridleyi complexes, are among the most diverged in the genus; (3) CCDD tetraploids have a relatively ancient origin among the Officinalis complex; (4) O. malampuzhaensis, O. indandamanica, O. alta, and O. grandiglumis are diverged enough to deserve species status; (5) O. officinalis and O. eichingeri (CC) are putative progenitors of O. minuta/O. malampuzhaensis and tetraploid O. punctata, respectively, (6) O. brachyantha is most diverged species in the genus. AFLP is reliable molecular technique and provides one of the most informative approaches to ascertain genetic relationships in Oryza, which may also be true for other related species/organisms

The plasma virome in longitudinal samples from pregnant patients

INTRODUCTION: Nucleic acid from viruses is common in peripheral blood, even in asymptomatic individuals. How physiologic changes of pregnancy impact host-virus dynamics for acute, chronic, and latent viral infections is not well described. Previously we found higher viral diversity in the vagina during pregnancy associated with preterm birth (PTB) and Black race. We hypothesized that higher diversity and viral copy numbers in the plasma would show similar trends. METHODS: To test this hypothesis, we evaluated longitudinally collected plasma samples from 23 pregnant patients (11 term and 12 preterm) using metagenomic sequencing with ViroCap enrichment to enhance virus detection. Sequence data were analyzed with the ViroMatch pipeline. RESULTS: We detected nucleic acid from at least 1 virus in at least 1 sample from 87% (20/23) of the maternal subjects. The viruses represented 5 families: DISCUSSION: These results emphasize the importance of longitudinal sampling and diverse cohorts in studies of virome dynamics during pregnancy

Local density of states and scanning tunneling currents in graphene

We present exact analytical calculations of scanning tunneling currents in locally disordered graphene using a multimode description of the microscope tip. Analytical expressions for the local density of states (LDOS) are given for energies beyond the Dirac cone approximation. We show that the LDOS at the $A$ and $B$ sublattices of graphene are out of phase by $\pi$ implying that the averaged LDOS, as one moves away from the impurity, shows no trace of the $2q_F$ (with $q_F$ the Fermi momentum) Friedel modulation. This means that a STM experiment lacking atomic resolution at the sublattice level will not be able of detecting the presence of the Friedel oscillations [this seems to be the case in the experiments reported in Phys. Rev. Lett. {\bf 101}, 206802 (2008)]. The momentum maps of the LDOS for different types of impurities are given. In the case of the vacancy, $2q_F$ features are seen in these maps. In all momentum space maps, $K$ and $K+K^\prime$ features are seen. The $K+K^\prime$ features are different from what is seen around zero momentum. An interpretation for these features is given. The calculations reported here are valid for chemical substitution impurities, such as boron and nitrogen atoms, as well as for vacancies. It is shown that the density of states close to the impurity is very sensitive to type of disorder: diagonal, non-diagonal, or vacancies. In the case of weakly coupled (to the carbon atoms) impurities, the local density of states presents strong resonances at finite energies, which leads to steps in the scanning tunneling currents and to suppression of the Fano factor.Comment: 21 pages. Figures 6 and 7 are correctly displayed in this new versio

A case of persistent human pegivirus infection in two separate pregnancies of a woman

Human pegivirus (HPgV) is best known for persistent, presumably non-pathogenic, infection and a propensity to co-infect with human immunodeficiency virus or hepatitis C virus. However, unique attributes, such as the increased risk of malignancy or immune modulation, have been recently recognized for HPgV. We have identified a unique case of a woman with high levels HPgV infection in two pregnancies, which occurred 4 years apart and without evidence of human immunodeficiency virus or hepatitis C virus infection. The second pregnancy was complicated by congenital heart disease. A high level of HPgV infection was detected in the maternal blood from different trimesters by RT-PCR and identified as HPgV type 1 genotype 2 in both pregnancies. In the second pregnancy, the decidua and intervillous tissue of the placenta were positive for HPgV by PCR but not the chorion or cord blood (from both pregnancies), suggesting no vertical transmission despite high levels of viremia. The HPgV genome sequence was remarkably conserved over the 4 years. Using VirScan, sera antibodies for HPgV were detected in the first trimester of both pregnancies. We observed the same anti-HPgV antibodies against the non-structural NS5 protein in both pregnancies, suggesting a similar non-E2 protein humoral immune response over time. To the best of our knowledge, this is the first report of persistent HPgV infection involving placental tissues with no clear indication of vertical transmission. Our results reveal a more elaborate viral-host interaction than previously reported, expand our knowledge about tropism, and opens avenues for exploring the replication sites of this virus

Resonant Visible Light Modulation with Graphene

Fast modulation and switching of light at visible and near-infrared (vis-NIR) frequencies is of utmost importance for optical signal processing and sensing technologies. No fundamental limit appears to prevent us from designing wavelength-sized devices capable of controlling the light phase and intensity at gigaherts (and even terahertz) speeds in those spectral ranges. However, this problem remains largely unsolved, despite recent advances in the use of quantum wells and phase-change materials for that purpose. Here, we explore an alternative solution based upon the remarkable electro-optical properties of graphene. In particular, we predict unity-order changes in the transmission and absorption of vis-NIR light produced upon electrical doping of graphene sheets coupled to realistically engineered optical cavities. The light intensity is enhanced at the graphene plane, and so is its absorption, which can be switched and modulated via Pauli blocking through varying the level of doping. Specifically, we explore dielectric planar cavities operating under either tunneling or Fabry-Perot resonant transmission conditions, as well as Mie modes in silicon nanospheres and lattice resonances in metal particle arrays. Our simulations reveal absolute variations in transmission exceeding 90% as well as an extinction ratio >15 dB with small insertion losses using feasible material parameters, thus supporting the application of graphene in fast electro-optics at vis-NIR frequencies.Comment: 17 pages, 13 figures, 54 reference

Emergence of Superlattice Dirac Points in Graphene on Hexagonal Boron Nitride

The Schr\"odinger equation dictates that the propagation of nearly free electrons through a weak periodic potential results in the opening of band gaps near points of the reciprocal lattice known as Brillouin zone boundaries. However, in the case of massless Dirac fermions, it has been predicted that the chirality of the charge carriers prevents the opening of a band gap and instead new Dirac points appear in the electronic structure of the material. Graphene on hexagonal boron nitride (hBN) exhibits a rotation dependent Moir\'e pattern. In this letter, we show experimentally and theoretically that this Moir\'e pattern acts as a weak periodic potential and thereby leads to the emergence of a new set of Dirac points at an energy determined by its wavelength. The new massless Dirac fermions generated at these superlattice Dirac points are characterized by a significantly reduced Fermi velocity. The local density of states near these Dirac cones exhibits hexagonal modulations indicating an anisotropic Fermi velocity.Comment: 16 pages, 6 figure

Egg retention and dispersal activity in the parasitoid wasp, Trichogramma principium

Effects of egg retention on movement and dispersal activity of Trichogramma principium (Hymenoptera, Trichogrammatidae) females were investigated under laboratory conditions. Individual females were observed during one minute in the absence of hosts. Movement activity and dispersal rate were estimated by the length of the track and by the distance from the start point, respectively. Before the test, all wasps during 2 – 4 days were presented with a possibility to parasitize a factitious laboratory host, Sitotroga cerealella Oliv. (Lepidoptera, Gelechiidae). Wasps that had parasitized before the test show significant reduction of spontaneous walking activity and dispersal rate when compared with females that refused to parasitize the non-preferred host (i.e. manifested egg retention). This effect cannot be considered as a direct arrestment reaction to the host because during the test period, no hosts were provided. Thus, egg retention results not only in temporal spread, but also in more intensive spatial dispersal of a group of simultaneously emerged females

Electronic properties of bilayer and multilayer graphene

We study the effects of site dilution disorder on the electronic properties in graphene multilayers, in particular the bilayer and the infinite stack. The simplicity of the model allows for an easy implementation of the coherent potential approximation and some analytical results. Within the model we compute the self-energies, the density of states and the spectral functions. Moreover, we obtain the frequency and temperature dependence of the conductivity as well as the DC conductivity. The c-axis response is unconventional in the sense that impurities increase the response for low enough doping. We also study the problem of impurities in the biased graphene bilayer.Comment: 36 pages, 42 figures, references adde

Parapharyngeal space hemangiopericytoma treated with surgery and postoperative radiation- a case report

Hemangiopericytoma (HPC) is a rare tumor of uncertain malignant potential arising from mesenchymal cells with pericytic differentiation. It accounts for 3-5% of soft tissue sarcomas and 1% of vascular tumors. It usually presents in 5th to 6th decade of life. Most common sites are limbs, pelvis and head and neck. About 20% of all hemangiopericytomas are seen in head and neck, mostly in adults. Usually it presents in orbit, nasal cavity, oral cavity, jaw, parotid gland, parapharyngeal space, masticator space and jugular foramen. Long term follow up is important because of imprecise nature of the histological criteria for prediction of biologic behavior

Plasmon-phonon coupling in large-area graphene dot and antidot arrays

Nanostructured graphene on SiO2 substrates pave the way for enhanced light-matter interactions and explorations of strong plasmon-phonon hybridization in the mid-infrared regime. Unprecedented large-area graphene nanodot and antidot optical arrays are fabricated by nanosphere lithography, with structural control down to the sub-100 nanometer regime. The interaction between graphene plasmon modes and the substrate phonons is experimentally demonstrated and structural control is used to map out the hybridization of plasmons and phonons, showing coupling energies of the order 20 meV. Our findings are further supported by theoretical calculations and numerical simulations.Comment: 7 pages including 6 figures. Supporting information is available upon request to author