Transcriptome sequencing in an ecologically important tree species: assembly, annotation, and marker discovery

<p>Abstract</p> <p>Background</p> <p>Massively parallel sequencing of cDNA is now an efficient route for generating enormous sequence collections that represent expressed genes. This approach provides a valuable starting point for characterizing functional genetic variation in non-model organisms, especially where whole genome sequencing efforts are currently cost and time prohibitive. The large and complex genomes of pines (<it>Pinus </it>spp.) have hindered the development of genomic resources, despite the ecological and economical importance of the group. While most genomic studies have focused on a single species (<it>P. taeda</it>), genomic level resources for other pines are insufficiently developed to facilitate ecological genomic research. Lodgepole pine (<it>P. contorta</it>) is an ecologically important foundation species of montane forest ecosystems and exhibits substantial adaptive variation across its range in western North America. Here we describe a sequencing study of expressed genes from <it>P. contorta</it>, including their assembly and annotation, and their potential for molecular marker development to support population and association genetic studies.</p> <p>Results</p> <p>We obtained 586,732 sequencing reads from a 454 GS XLR70 Titanium pyrosequencer (mean length: 306 base pairs). A combination of reference-based and <it>de novo </it>assemblies yielded 63,657 contigs, with 239,793 reads remaining as singletons. Based on sequence similarity with known proteins, these sequences represent approximately 17,000 unique genes, many of which are well covered by contig sequences. This sequence collection also included a surprisingly large number of retrotransposon sequences, suggesting that they are highly transcriptionally active in the tissues we sampled. We located and characterized thousands of simple sequence repeats and single nucleotide polymorphisms as potential molecular markers in our assembled and annotated sequences. High quality PCR primers were designed for a substantial number of the SSR loci, and a large number of these were amplified successfully in initial screening.</p> <p>Conclusions</p> <p>This sequence collection represents a major genomic resource for <it>P. contorta</it>, and the large number of genetic markers characterized should contribute to future research in this and other pines. Our results illustrate the utility of next generation sequencing as a basis for marker development and population genomics in non-model species.</p

A TRLFS study on the complexation of Cm(III) and Eu(III) with 4-t-butyl-6,6´-bis-(5,6-diethyl-1,2,4-tiazin-3-yl)-2,2´-bipyridine in a water / 2-propanol mixture

The complexation of Cm(III) and Eu(III) with 4-t-butyl-6,6´-bis-(5,6-diethyl-1,2,4-tiazin-3-yl)-2,2´-bipyridine(t-Bu-C2-BTBP) in water / 2-propanol solution is studies.JRC.E-Institute for Transuranium Elements (Karlsruhe

Body Mass Index and Nationality (Argentine vs. Spanish) Moderate the Relationship Between Internalization of the Thin Ideal and Body Dissatisfaction: A Conditional Mediation Model

It is believed that Women’s exposure to Western sociocultural pressures to attain a “thin-ideal” results in the internalization of a desire to be thin that consequently leads to body dissatisfaction (BD). It is also well documented that body mass index (BMI; kg/m2) correlates with BD. We tested for the first time a conditional mediation model where thin-ideal Awareness predicted BD through Internalization of the thin ideal and the path from Internalization to BD was hypothesized to be moderated by BMI and Nationality (Argentine vs. Spanish). The model was tested with a sample of 499 young women (age = 18 to 29) from Argentina (n = 290) and Spain (n = 209). Awareness and internalization were measured with the SATAQ-4 (Schaefer et al., 2015) and BD was measured with the BSQ (Cooper et al., 1987). The model was analyzed using PROCESSv3.1 (Hayes, 2018). As hypothesized, thin-ideal awareness predicted BD through internalization and the path from internalization to BD was moderated by BMI and nationality. Specifically, internalization predicted BD at all level of BMI and in both samples, but the relationship between internalization and BD increased with BMI and was also stronger among Spaniards than Argentines. We argue that the findings are congruent with theories that predict that economic development and modernization contribute to normative female BD through internalization of the thin ideal and that upward social comparisons or cognitive discrepancy between self-perceived body image and the sociocultural thin ideal interacts synergistically with thin-ideal internalization to increase BD

The Ursinus Weekly, October 9, 1975

\u2779 elects Delli-Bovi; Jill Leauber fills vacancy • Ursinus hosts family fete • Danforth Foundation offers fellowships • Dept. addition • From the cluttered desk of the U.S.G.A. President • Correction • Editorial: The Fact, after or before • Focus: Dr. Parsons • Overview: Intro. Philosophy • Lions in another Bowl? • The Throwaway children • U.S.G.A. Carnival • Phila. singers open season • Aerosmith: Bedlam • Opportunity for women • Reflections: A letter home • AFC forecast • George McGinnis: $3 million man • Field hockey report • Lebanon Valley crushes Ursinushttps://digitalcommons.ursinus.edu/weekly/1042/thumbnail.jp

Measurements of differential cross sections of Z/gamma*+jets+X events in proton anti-proton collisions at sqrt{s}=1.96 TeV

We present cross section measurements for Z/gamma*+jets+X production, differential in the transverse momenta of the three leading jets. The data sample was collected with the D0 detector at the Fermilab Tevatron proton anti-proton collider at a center-of-mass energy of 1.96 TeV and corresponds to an integrated luminosity of 1 fb-1. Leading and next-to-leading order perturbative QCD predictions are compared with the measurements, and agreement is found within the theoretical and experimental uncertainties. We also make comparisons with the predictions of four event generators. Two parton-shower-based generators show significant shape and normalization differences with respect to the data. In contrast, two generators combining tree-level matrix elements with a parton shower give a reasonable description of the the shapes observed in data, but the predicted normalizations show significant differences with respect to the data, reflecting large scale uncertainties. For specific choices of scales, the normalizations for either generator can be made to agree with the measurements.Comment: Published in PLB. 11 pages, 3 figure

Measurement of the B0_s semileptonic branching ratio to an orbitally excited D_s** state, Br(B0_s -> Ds1(2536) mu nu)

In a data sample of approximately 1.3 fb-1 collected with the D0 detector between 2002 and 2006, the orbitally excited charm state D_s1(2536) has been observed with a measured mass of 2535.7 +/- 0.6 (stat) +/- 0.5 (syst) MeV via the decay mode B0_s -> D_s1(2536) mu nu X. A first measurement is made of the branching ratio product Br(b(bar) -> D_s1(2536) mu nu X).Br(D_s1(2536)->D* K0_S). Assuming that D_s1(2536) production in semileptonic decay is entirely from B0_s, an extraction of the semileptonic branching ratio Br(B0_s -> D_s1(2536) mu nu X) is made.Comment: 7 pages, 2 figures, LaTeX, version with minor changes as accepted by Phys. Rev. Let

Measurement of the t-channel single top quark production cross section

The D0 collaboration reports direct evidence for electroweak production of single top quarks through the t-channel exchange of a virtual W boson. This is the first analysis to isolate an individual single top quark production channel. We select events containing an isolated electron or muon, missing transverse energy, and two, three or four jets from 2.3 fb^-1 of ppbar collisions at the Fermilab Tevatron Collider. One or two of the jets are identified as containing a b hadron. We combine three multivariate techniques optimized for the t-channel process to measure the t- and s-channel cross sections simultaneously. We measure cross sections of 3.14 +0.94 -0.80 pb for the t-channel and 1.05 +-0.81 pb for the s-channel. The measured t-channel result is found to have a significance of 4.8 standard deviations and is consistent with the standard model prediction.Comment: 7 pages, 6 figure

Measurement of trilinear gauge boson couplings from WW + WZ to lnu jj events in pp-bar collisions at sqrt{s}=1.96 TeV

We present a direct measurement of trilinear gauge boson couplings at gammaWW and ZWW vertices in WW and WZ events produced in pp-bar collisions at sqrt{s}=1.96 TeV. We consider events with one electron or muon, missing transverse energy, and at least two jets. The data were collected using the D0 detector and correspond to 1.1/fb of integrated luminosity. Considering two different relations between the couplings at the gammaWW and ZWW vertices, we measure these couplings at 68% C.L. to be kappa_{gamma}=1.07^{+0.26}_{-0.29}, lambda =0.00^{+0.06}_{-0.06} and g_{1}^{Z}=1.04^{+0.09}_{-0.09} in a scenario respecting SU(2)_L x U(1)_Y gauge symmetry and kappa =1.04^{+0.11}_{-0.11} and lambda=0.00^{+0.06}_{-0.06} in an "equal couplings" scenario.Comment: 14 pages, 7 figures, published in Phys. Rev. D, updated to published versio

Measurement of the W boson mass

We present a measurement of the W boson mass in W -> ev decays using 1 fb^-1 of data collected with the D0 detector during Run II of the Fermilab Tevatron collider. With a sample of 499830 W -> ev candidate events, we measure M_W = 80.401 +- 0.043 GeV. This is the most precise measurement from a single experiment.Comment: As published in PR

Search for charged massive long-lived particles with the D0 detector

We search for charged massive long-lived particles using 1.1 fb$^{-1}$ of data collected by the D0 detector at the Fermilab Tevatron $p\bar{p}$ Collider. Time-of-flight information is used to search for pair produced long-lived tau sleptons, gaugino-like charginos, and higgsino-like charginos. We find no evidence of a signal and set 95% C.L. cross section upper limits for staus, which vary from 0.31pb to 0.04pb for stau masses between 60 GeV and 300 GeV. We also set lower mass limits of 206 GeV (171 GeV) for pair produced charged gauginos (higgsinos).Comment: To be submitted to Phys. Rev. Letters, V2: updated the figures and references, V3: final version submitted to PRL and changes in title and abstracts from "stable" to "long-lived