Genome Evolution of Wolbachia Strain wPip from the Culex pipiens Group

The obligate intracellular bacterium Wolbachia pipientis strain wPip induces cytoplasmic incompatibility (CI), patterns of crossing sterility, in the Culex pipiens group of mosquitoes. The complete sequence is presented of the 1.48-Mbp genome of wPip which encodes 1386 coding sequences (CDSs), representing the first genome sequence of a B-supergroup Wolbachia. Comparisons were made with the smaller genomes of Wolbachia strains wMel of Drosophila melanogaster, an A-supergroup Wolbachia that is also a CI inducer, and wBm, a mutualist of Brugia malayi nematodes that belongs to the D-supergroup of Wolbachia. Despite extensive gene order rearrangement, a core set of Wolbachia genes shared between the 3 genomes can be identified and contrasts with a flexible gene pool where rapid evolution has taken place. There are much more extensive prophage and ankyrin repeat encoding (ANK) gene components of the wPip genome compared with wMel and wBm, and both are likely to be of considerable importance in wPip biology. Five WO-B–like prophage regions are present and contain some genes that are identical or highly similar in multiple prophage copies, whereas other genes are unique, and it is likely that extensive recombination, duplication, and insertion have occurred between copies. A much larger number of genes encode ankyrin repeat (ANK) proteins in wPip, with 60 present compared with 23 in wMel, many of which are within or close to the prophage regions. It is likely that this pattern is partly a result of expansions in the wPip lineage, due for example to gene duplication, but their presence is in some cases more ancient. The wPip genome underlines the considerable evolutionary flexibility of Wolbachia, providing clear evidence for the rapid evolution of ANK-encoding genes and of prophage regions. This host–Wolbachia system, with its complex patterns of sterility induced between populations, now provides an excellent model for unraveling the molecular systems underlying host reproductive manipulation

Centrality dependence of charged hadron production in deuteron+gold and nucleon+gold collisions at sqrt(s_NN)=200 GeV

We present transverse momentum (p_T) spectra of charged hadrons measured in deuteron-gold and nucleon-gold collisions at \sqrts = 200 GeV for four centrality classes. Nucleon-gold collisions were selected by tagging events in which a spectator nucleon was observed in one of two forward rapidity detectors. The spectra and yields were investigated as a function of the number of binary nucleon-nucleon collisions, \nu, suffered by deuteron nucleons. A comparison of charged particle yields to those in p+p collisions show that the yield per nucleon-nucleon collision saturates with \nu for high momentum particles. We also present the charged hadron to neutral pion ratios as a function of p_T.Comment: 330 authors, 15 pages text, 16 figures, 3 tables. Submitted to Phys. Rev. Lett. v2 has minor changes to reflect revisions during review process. 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

Jet Structure from Dihadron Correlations in d+Au collisions at sqrt(s_NN) = 200 GeV

Dihadron correlations at high transverse momentum in d+Au collisions at sqrt(s_NN) = 200 GeV at midrapidity are measured by the PHENIX experiment at the Relativistic Heavy Ion Collider (RHIC). From these correlations we extract several structural characteristics of jets; the root-mean-squared (RMS) transverse momentum of fragmenting hadrons with respect to the jet sqrt(), the mean sine-squared angle between the scattered partons , and the number of particles produced within the dijet that are associated with a high-p_T particle (dN/dx_E distributions). We observe that the fragmentation characteristics of jets in d+Au collisions are very similar to those in p+p collisions and that there is also little dependence on the centrality of the d+Au collision. This is consistent with the nuclear medium having little influence on the fragmentation process. Furthermore, there is no statistically significant increase in the value of from p+p to d+Au collisions. This constrains the amount of multiple scattering that partons undergo in the cold nuclear medium before and after a hard-collision.Comment: 330 authors, 30 pages text, RevTeX4, 42 figures, 20 tables. Submitted to Physical Review C. 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

Inclusive cross section and double helicity asymmetry for pi^0 production in p+p collisions at sqrt(s) = 62.4 GeV

The PHENIX experiment presents results from the RHIC 2006 run with polarized proton collisions at sqrt(s) = 62.4 GeV for inclusive pi^0 production at mid-rapidity. Unpolarized cross section results are measured for transverse momenta p_T = 0.5 to 7 GeV/c. Next-to-leading order perturbative quantum chromodynamics calculations are compared with the data, and while the calculations are consistent with the measurements, next-to-leading logarithmic corrections improve the agreement. Double helicity asymmetries A_LL are presented for p_T = 1 to 4 GeV/c and probe the higher range of Bjorken_x of the gluon (x_g) with better statistical precision than our previous measurements at sqrt(s)=200 GeV. These measurements are sensitive to the gluon polarization in the proton for 0.06 < x_g < 0.4.Comment: 387 authors from 63 institutions, 10 pages, 6 figures, 1 table. Submitted to Physical Review D. 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

Medium modification of jet fragmentation in Au+Au collisions at sqrt(s_NN)=200 GeV measured in direct photon-hadron correlations

The jet fragmentation function is measured with direct photon-hadron correlations in p+p and Au+Au collisions at sqrt(s_NN)=200 GeV. The p_T of the photon is an excellent approximation to the initial p_T of the jet and the ratio z_T=p_T^h/p_T^\gamma is used as a proxy for the jet fragmentation function. A statistical subtraction is used to extract the direct photon-hadron yields in Au+Au collisions while a photon isolation cut is applied in p+p. I_ AA, the ratio of jet fragment yield in Au+Au to that in p+p, indicates modification of the jet fragmentation function. Suppression, most likely due to energy loss in the medium, is seen at high z_T. The fragment yield at low z_T is enhanced at large angles. Such a trend is expected from redistribution of the lost energy into increased production of low-momentum particles.Comment: 562 authors, 70 insitutions, 8 pages, and 3 figures. Submitted to Phys. Rev. Lett. v2 has minor changes to improve clarity. 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

Breast cancer prognosis predicted by nuclear receptor-coregulator networks

Although molecular signatures based on transcript expression in breast cancer samples have provided new insights into breast cancer classification and prognosis, there are acknowledged limitations in current signatures. To provide rational, pathway-based signatures of disrupted physiology in cancer tissues that may be relevant to prognosis, this study has directly quantitated changed gene expression, between normal breast and cancer tissue, as a basis for signature development. The nuclear receptor (NR) family of transcription factors, and their coregulators, are fundamental regulators of every aspect of metazoan life, and were rigorously quantified in normal breast tissues and ERα positive and ERα negative breast cancers. Coregulator expression was highly correlated with that of selected NR in normal breast, particularly from postmenopausal women. These associations were markedly decreased in breast cancer, and the expression of the majority of coregulators was down-regulated in cancer tissues compared with normal. While in cancer the loss of NR-coregulator associations observed in normal breast was common, a small number of NR (Rev-ERBβ, GR, NOR1, LRH-1 and PGR) acquired new associations with coregulators in cancer tissues. Elevated expression of these NR in cancers was associated with poorer outcome in large clinical cohorts, as well as suggesting the activation of ERα -related, but ERα-independent, pathways in ERα negative cancers. In addition, the combined expression of small numbers of NR and coregulators in breast cancer was identified as a signature predicting outcome in ERα negative breast cancer patients, not linked to proliferation and with predictive power superior to existing signatures containing many more genes. These findings highlight the power of predictive signatures derived from the quantitative determination of altered gene expression between normal breast and breast cancers. Taken together, the findings of this study identify networks of NR-coregulator associations active in normal breast but disrupted in breast cancer, and moreover provide evidence that signatures based on NR networks disrupted in cancer can provide important prognostic information in breast cancer patients

Double Helicity Asymmetry in Inclusive Mid-Rapidity neutral pion Production for Polarized p+p Collisions at sqrt(s)=200 GeV

We present a measurement of the double longitudinal spin asymmetry in inclusive pi^0 production in polarized proton-proton collisions at sqrt(s)=200 GeV. The data were taken at the Relativistic Heavy Ion Collider with average beam polarizations of 26%. The measurements are the first of a program to study the longitudinal spin structure of the proton, using strongly interacting probes, at collider energies. The asymmetry is presented for transverse momenta 1-5 GeV/c at mid-rapidity, where next-to-leading order perturbative quantum chromodynamic (NLO pQCD) calculations describe the unpolarized cross section well. The observed asymmetry is small and is compared with a NLO pQCD calculation with a range of polarized gluon distributions.Comment: 326 authors, 6 pages text, RevTeX, 3 figures, 1 table. To be submitted to PRL. 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

Cross sections and double-helicity asymmetries of midrapidity inclusive charged hadrons in p+p collisions at sqrt(s)=62.4 GeV

Unpolarized cross sections and double-helicity asymmetries of single-inclusive positive and negative charged hadrons at midrapidity from p+p collisions at sqrt(s)=62.4 GeV are presented. The PHENIX measurements for 1.0 < p_T < 4.5 GeV/c are consistent with perturbative QCD calculations at next-to-leading order in the strong coupling constant, alpha_s. Resummed pQCD calculations including terms with next-to-leading-log accuracy, yielding reduced theoretical uncertainties, also agree with the data. The double-helicity asymmetry, sensitive at leading order to the gluon polarization in a momentum-fraction range of 0.05 ~< x_gluon ~< 0.2, is consistent with recent global parameterizations disfavoring large gluon polarization.Comment: PHENIX Collaboration. 447 authors, 12 pages, 5 figures, 5 tables. Submitted to Physical Review

Upsilon (1S+2S+3S) production in d+Au and p+p collisions at sqrt(s_NN)=200 GeV and cold-nuclear matter effects

The three Upsilon states, Upsilon(1S+2S+3S), are measured in d+Au and p+p collisions at sqrt(s_NN)=200 GeV and rapidities 1.2<|y|<2.2 by the PHENIX experiment at the Relativistic Heavy-Ion Collider. Cross sections for the inclusive Upsilon(1S+2S+3S) production are obtained. The inclusive yields per binary collision for d+Au collisions relative to those in p+p collisions (R_dAu) are found to be 0.62 +/- 0.26 (stat) +/- 0.13 (syst) in the gold-going direction and 0.91 +/- 0.33 (stat) +/- 0.16 (syst) in the deuteron-going direction. The measured results are compared to a nuclear-shadowing model, EPS09 [JHEP 04, 065 (2009)], combined with a final-state breakup cross section, sigma_br, and compared to lower energy p+A results. We also compare the results to the PHENIX J/psi results [Phys. Rev. Lett. 107, 142301 (2011)]. The rapidity dependence of the observed Upsilon suppression is consistent with lower energy p+A measurements.Comment: 495 authors, 11 pages, 9 figures, 5 tables. Submitted to Phys. Rev. C. 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