Transcriptional Termination Modulated by Nucleotides Outside the Characterized Gene End Sequence of Respiratory Syncytial Virus

AbstractThe genes of respiratory syncytial (RS) virus are transcribed sequentially by the viral RNA polymerase from a single 3′-proximal promoter. Polyadenylation and termination are directed by a sequence at the end of each gene, after which the polymerase crosses an intergenic region and reinitiates at the start sequence of the next gene. The 10 viral genes have different gene end sequences and different termination efficiencies, which allow for regulation of gene expression, since termination of each gene is required for initiation of the downstream gene. RNA sequences within the previously characterized 13 nucleotide gene end, including a conserved sequence 3′-UCAAU-5′ and a tract of U residues, are important for termination. In this study, two additional sequence elements outside of the 13 nucleotide gene end were found to modulate termination efficiency: the A residue upstream of the 3′-UCAAU-5′ sequence, and the first nucleotide of the intergenic region when it follows a U4 tract

Role of plant relatedness in plant–soil feedback dynamics of sympatric Asclepias species

Plants affect associated biotic and abiotic edaphic factors, with reciprocal feedbacks from soil characteristics affecting plants. These two-way interactions between plants and soils are collectively known as plant–soil feedbacks (PSFs). The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of PSFs, although the strength and direction of feedbacks among sympatric congeners are not well-understood. We examined plant–soil feedback responses of Asclepias syriaca, a common clonal milkweed species, with several sympatric congeners across a gradient of increasing phylogenetic distances (A. tuberosa, A. viridis, A. sullivantii, and A. verticillata, respectively). Plant–soil feedbacks were measured through productivity and colonization by arbuscular mycorrhizal (AM) fungi. Asclepias syriaca produced less biomass in soils conditioned by the most phylogenetically distant species (A. verticillata), relative to conspecific-conditioned soils. Similarly, arbuscular mycorrhizal (AM) fungal colonization of A. syriaca roots was reduced when grown in soils conditioned by A. verticillata, compared with colonization in plants grown in soil conditioned by any of the other three Asclepias species, indicating mycorrhizal associations are a potential mechanism of observed positive PSFs. This display of differences between the most phylogenetically distant, but not close or intermediate, paring(s) suggests a potential phylogenetic threshold, although other exogenous factors cannot be ruled out. Overall, these results highlight the potential role of phylogenetic distance in influencing positive PSFs through mutualists. The role of phylogenetic relatedness and evolutionary histories have recently emerged as a potential driver of plant–soil feedbacks (PSFs), although the strength and direction of feedbacks among sympatric congeners are not well-understood. Congeneric, sympatric milkweeds typically generated positive PSFs in terms of productivity and AM fungal colonization, suggesting the low likelihood of coexistence among tested pairs, with a strength of feedback increasing as the phylogenetic distance increases

The Photophysics of the Carrier of Extended Red Emission

Interstellar dust contains a component which reveals its presence by emitting a broad, unstructured band of light in the 540 to 950 nm wavelength range, referred to as Extended Red Emission (ERE). The presence of interstellar dust and ultraviolet photons are two necessary conditions for ERE to occur. This is the basis for suggestions which attribute ERE to an interstellar dust component capable of photoluminescence. In this study, we have collected all published ERE observations with absolute-calibrated spectra for interstellar environments, where the density of ultraviolet photons can be estimated reliably. In each case, we determined the band-integrated ERE intensity, the wavelength of peak emission in the ERE band, and the efficiency with which absorbed ultraviolet photons are contributing to the ERE. The data show that radiation is not only driving the ERE, as expected for a photoluminescence process, but is modifying the ERE carrier as manifested by a systematic increase in the ERE band's peak wavelength and a general decrease in the photon conversion efficiency with increasing densities of the prevailing exciting radiation. The overall spectral characteristics of the ERE and the observed high quantum efficiency of the ERE process are currently best matched by the recently proposed silicon nanoparticle (SNP) model. Using the experimentally established fact that ionization of semiconductor nanoparticles quenches their photoluminescence, we proceeded to test the SNP model by developing a quantitative model for the excitation and ionization equilibrium of SNPs under interstellar conditions for a wide range of radiation field densities.Comment: 42 p., incl. 8 fig. Accepted for publication by Ap

Climate Affects Plant-Soil Feedback of Native and Invasive Grasses: Negative Feedbacks in Stable but Not in Variable Environments

This work is licensed under a Creative Commons Attribution 4.0 International License.The plant-soil feedback framework allows researchers to target the interaction of plants and root-associated microbes and to determine its interplay on plant-plant interactions. Plant-soil feedbacks in terrestrial ecology are well-documented, but the strength and direction of feedbacks as influenced by abiotic environmental factors, such as temperature and soil moisture, has not been fully explored. In our study, we examined plant-soil feedback responses of both cool- and warm-season native and non-native grasses to elevated temperatures (ambient and +5°C) and soil moisture (100 and 75% field capacity). In a previous experiment, grasses were grown under temperature and soil moisture conditions similar to our current study. The resultant trained soil communities served as the inoculum sources for our current experiment. We found that consistent training and experimental temperatures resulted in negative PSF, where plants produced greater biomass in soils conditioned by heterospecifics. However, the direction of PSF was reversed when training and experimental conditions were mismatched. That is, when training and experimental temperatures mirrored one another, negative PSF occurred, suggesting coexistence between the two species is likely under these conditions. However, when only training or testing temperatures were elevated, positive PSF were detected, favoring the non-native species. These alterations in plant-soil feedbacks were relatively consistent across pairings of warm- and cool-season grasses. Overall, our results indicate inconsistent year-to-year environmental conditions, such as extreme temperatures, may undermine the stabilizing forces of negative PSF and favor of non-native grasses

Evaluation of striped bass stocks in Virginia : monitoring and tagging studies, 2004-2008 Annual report 1 September 2004 - 31 August 2005

This report presents the results of striped bass (Marone saxatilis) tagging and monitoring activities in Virginia during the period 1 September 2004 through 31 August 2005. It includes an assessment of the biological characteristics of striped bass taken from the 2005 spring spawning run, estimates of annual survival based on annual spring tagging, and the results of the fall 2004 directed mortality study that is a collaborative effort with the Maryland Department of Natural Resources. The information contained in this report is required by the Atlantic States Marine Fisheries Commission and is used to implement a coordinated management plan for striped bass in Virginia, and along the eastern seaboar

Course-based Science Research Promotes Learning in Diverse Students at Diverse Institutions

Course-based research experiences (CREs) are powerful strategies for spreading learning and improving persistence for all students, both science majors and nonscience majors. Here we address the crucial components of CREs (context, discovery, ownership, iteration, communication, presentation) found across a broad range of such courses at a variety of academic institutions. We also address how the design of a CRE should vary according to the background of student participants; no single CRE format is perfect. We provide a framework for implementing CREs across multiple institutional types and several disciplines throughout the typical four years of undergraduate work, designed to a variety of student backgrounds. Our experiences implementing CREs also provide guidance on overcoming barriers to their implementation

Nucleon Generalized Parton Distributions from Full Lattice QCD

We present a comprehensive study of the lowest moments of nucleon generalized parton distributions in N_f=2+1 lattice QCD using domain wall valence quarks and improved staggered sea quarks. Our investigation includes helicity dependent and independent generalized parton distributions for pion masses as low as 350 MeV and volumes as large as (3.5 fm)^3, for a lattice spacing of 0.124 fm. We use perturbative renormalization at one-loop level with an improvement based on the non-perturbative renormalization factor for the axial vector current, and only connected diagrams are included in the isosinglet channel.Comment: 40 pages, 49 figures; Revised chiral extrapolations in sections A-K, main conclusions unchange

Recently integrated Alu elements and human genomic diversity

A comprehensive analysis of two Alu Y lineage subfamilies was undertaken to assess Alu-associated genomic diversity and identify new Alu insertion polymorphisms for the study of human population genetics. Recently integrated Alu elements (283) from the Yg6 and Yi6 subfamilies were analyzed by polymerase chain reaction (PCR), and 25 of the loci analyzed were polymorphic for insertion presence/absence within the genomes of a diverse array of human populations. These newly identified Alu insertion polymorphisms will be useful tools for the study of human genomic diversity. Our screening of the Alu insertion loci also resulted in the recovery of several young Alu elements that resided at orthologous positions in nonhuman primate genomes. Sequence analysis demonstrated these young Alu insertions were the products of gene conversion events of older, preexisting Alu elements or independent parallel forward insertions of older Alu elements in the same short genomic region. The level of gene conversion between Alu elements suggests that it may have an influence on the single nucleotide polymorphism within Alu elements in the genome. We have also identified two genomic deletions associated with the retroposition and insertion of Alu Y lineage elements into the human genome. This type of Alu retroposition-mediated genomic deletion is a novel source of lineage-specific evolution within primate genomes

Infrared Spectroscopic Study of a Selection of AGB and Post-AGB Stars

We present here near-infrared spectroscopy in the H and K bands of a selection of nearly 80 stars that belong to various AGB types, namely S type, M type and SR type. This sample also includes 16 Post-AGB (PAGB) stars. From these spectra, we seek correlations between the equivalent widths of some important spectral signatures and the infrared colors that are indicative of mass loss. Repeated spectroscopic observations were made on some PAGB stars to look for spectral variations. We also analyse archival SPITZER mid-infrared spectra on a few PAGB stars to identify spectral features due to PAH molecules providing confirmation of the advanced stage of their evolution. Further, we model the SEDs of the stars (compiled from archival data) and compare circumstellar dust parameters and mass loss rates in different types. Our near-infrared spectra show that in the case of M and S type stars, the equivalent widths of the CO(3-0) band are moderately correlated with infrared colors, suggesting a possible relationship with mass loss processes. A few PAGB stars revealed short term variability in their spectra, indicating episodic mass loss: the cooler stars showed in CO first overtone bands and the hotter ones showed in HI Brackett lines. Our spectra on IRAS 19399+2312 suggest that it is a transition object. From the SPITZER spectra, there seems to be a dependence between the spectral type of the PAGB stars and the strength of the PAH features. Modelling of SEDs showed among the M and PAGB stars that the higher the mass loss rates, the higher the [K-12] colour in our sample.Comment: 14 pages; accepted in MNRAS, 200

Extended view on the dust shells around two carbon stars

Stars on the asymptotic giant branch (AGB) lose considerable amounts of matter through their dust-driven stellar winds. A number of such sources have been imaged by Herschel/PACS, revealing a diverse sample of different morphological types. Among them are a few examples which show geometrically thin, spherically symmetric shells which can be used to probe the mass loss history of their host stars. We aim to determine the physical properties of the dust envelope around the two carbon stars U Hya and W Ori. With the much-improved spatial constraints from the new far-infrared maps, our primary goal is to measure the dust masses contained in the shells and see how they fit the proposed scenarios of shell formation. We calculated the radiative transfer of the circumstellar dust envelope using the 1D code More of DUSTY (MoD). Adopting a parametrised density profile, we obtained a best-fit model in terms of the photometric and spectroscopic data, as well as a radial intensity profile based on Herschel/PACS data. For the case of U Hya, we also computed a grid of circumstellar envelopes by means of a stationary wind code and compare the results of the two modelling approaches. The Herschel/PACS maps show U Hya surrounded by a detached shell of $114''\ (0.12\,\mathrm{pc})$ in radius, confirming the observations from previous space missions. The dust masses calculated for the shell by the two approaches are consistent with respect to the adopted dust grain properties. In addition, around W Ori, we detect for the first time a weak spherically symmetric structure with a radius of $92''\ (0.17\,\mathrm{pc})$and a dust mass of$(3.5\pm0.3)\times10^{-6}\,\mathrm{M_\odot}$