Short interspersed repetitive elements (SINEs) from the cichlid fish, Oreochromis niloticus, and their chromosomal localization by fluorescent in situ hybridization

In the present study, we describe the cloning and characterization of a new SINE-like element from O. niloticus (ROn-2) and show the distribution of this SINE and a previously isolated SINE, ROn-1, in the chromosomes of O. niloticus. The ROn-2 element is 359 base pairs (bp) in length, contains short direct terminal repeats, a tRNA-related region similar to tRNA Val and tRNA Arg, a tRNA-unrelated region, and a poly-A tail. Analysis of the chromosomal distribution of ROn-1 and ROn-2 by fluorescent in situ hybridization showed that both SINE sequences are present in all chromosomes of tilapia, and organized in small clusters. The only exception was a large cluster of ROn-1 repeats found in the middle of the long arm of chromosome 1. In view of our data we discuss the hypothesis that the absence of large clusters of SINE sequences and the structural composition of these sequences may explain the absence of base-specific fluorochrome bands in the chromosomes of tilapia.

Cytogenetic characterization of the silverside fish Odontesthes regia (Humboldt, 1833) (Teleostei: Atheriniformes: Atherinopsidae) from Iquique, Chile

This paper describes the karyotype of Odontesthes regia by means of Giemsa staining, C-banding, to reveal the distribution of the constitutive heterochromatin, and by Ag-staining and fluorescent in situ hybridization (FISH), to locate ribosomal genes (rDNA). The chromosome diploid modal count in the species was 2n = 48. The karyotype is composed of one submetacentric pair (pair 1), 16 subtelocentric pairs (pairs 2 to 17), and 7 acrocentric pairs (pairs 18 to 24). With the exception of pair 1 it was not possible to classify the homologous chromosomes accurately because differences in chromosome size were too slight between adjacent pairs. The distribution of C-banded heterochromatin allowed for a more accurate matching of the majority of chromosomes of the subtelocentric series. Silver staining of metaphase spreads allowed for the identification of Nucleolus Organizer Regions (Ag-NOR) on pair 1. FISH experiments showed that 18S rDNA sequences were located, as expected, in the same chromosome pair identified as the Ag-NOR-bearing one.

Phylogenetic systematics of dart-poison frogs and their relatives (Amphibia: Athesphatanura: Dendrobatidae)

The known diversity of dart-poison frog species has grown from 70 in the 1960s to 247 at present, with no sign that the discovery of new species will wane in the foreseeable future. Although this growth in knowledge of the diversity of this group has been accompanied by detailed investigations of many aspects of the biology of dendrobatids, their phylogenetic relationships remain poorly understood. This study was designed to test hypotheses of dendrobatid diversification by combining new and prior genotypic and phenotypic evidence in a total evidence analysis. DNA sequences were sampled for five mitochondrial and six nuclear loci (approximately 6,100 base pairs [bp]; x=3,740 bp per terminal; total dataset composed of approximately 1.55 million bp), and 174 phenotypic characters were scored from adult and larval morphology, alkaloid profiles, and behavior. These data were combined with relevant published DNA sequences. Ingroup sampling targeted several previously unsampled species, including Aromobates nocturnus, which was hypothesized previously to be the sister of all other dendrobatids. Undescribed and problematic species were sampled from multiple localities when possible. The final dataset consisted of 414 terminals: 367 ingroup terminals of 156 species and 47 outgroup terminals of 46 species. Direct optimization parsimony analysis of the equally weighted evidence resulted in 25,872 optimal trees. Forty nodes collapse in the strict consensus, with all conflict restricted to conspecific terminals. Dendrobatids were recovered as monophyletic, and their sister group consisted of Crossodactylus, Hylodes, and Megaelosia, recognized herein as Hylodidae. Among outgroup taxa, Centrolenidae was found to be the sister group of all athesphatanurans except Hylidae, Leptodactyidae was polyphyletic, Thoropa was nested within Cycloramphidae, and Ceratophryinae was paraphyletic with respect to Telmatobiinae. Among dendrobatids, the monophyly and content of Mannophryne and Phyllobates were corroborated. Aromobates nocturnus and Colostethus saltuensis were found to be nested within Nephelobates, and Minyobates was paraphyletic and nested within Dendrobates. Colostethus was shown to be rampantly nonmonophyletic, with most species falling into two unrelated cis- and trans-Andean clades. A morphologically and behaviorally diverse clade of median lingual process-possessing species was discovered. In light of these findings and the growth in knowledge of the diversity of this large clade over the past 40 years, we propose a new, monophyletic taxonomy for dendrobatids, recognizing the inclusive clade as a superfamily (Dendrobatoidea) composed of two families (one of which is new), six subfamilies (three new), and 16 genera (four new). Although poisonous frogs did not form a monophyletic group, the three poisonous lineages are all confined to the revised family Dendrobatidae, in keeping with the traditional application of this name. We also propose changes to achieve a monophyletic higher-level taxonomy for the athesphatanuran outgroup taxa. Analysis of character evolution revealed multiple origins of phytotelm-breeding, parental provisioning of nutritive oocytes for larval consumption (larval oophagy), and endotrophy. Available evidence indicates that transport of tadpoles on the dorsum of parent nurse frogs-a dendrobatid synapomorphy-is carried out primitively by male nurse frogs, with three independent origins of female transport and five independent origins of biparental transport. Reproductive amplexus is optimally explained as having been lost in the most recent common ancestor of Dendrobatoidea, with cephalic amplexus arising independently three times. © American Museum of Natural History 2006.

Search for a light charged Higgs boson in top quark decays in pp collisions at √s = 7 TeV

Results are presented on a search for a light charged Higgs boson that can be produced in the decay of the top quark t → H +b and which, in turn, decays into τ +ν t. The analysed data correspond to an integrated luminosity of about 2 fb -1 recorded in protonproton collisions at √s = 7 TeV by the CMS experiment at the LHC. The search is sensitive to the decays of the top quark pairs tt̄ → H ±W ∓bb̄ and tt̄ → H ±H ∓bb̄. Various final states have been studied separately, all requiring presence of a τ lepton from H + decays, missing transverse energy, and multiple jets. Upper limits on the branching fraction B(t → H +b) in the range of 2-4% are established for charged Higgs boson masses between 80 and 160 GeV, under the assumption that B(H + → τ +ν τ) = 1.

Search for stopped long-lived particles produced in pp collisions at √s = 7 TeV

A search has been performed for long-lived particles that have stopped in the CMS detector, during 7TeV proton-proton operations of the CERN LHC. The existence of such particles could be inferred from observation of their decays when there were no protonproton collisions in the CMS detector, namely during gaps between LHC beam crossings. Using a data set in which CMS recorded an integrated luminosity of 4.0 fb -1, and a search interval corresponding to 246 hours of trigger live time, 12 events are observed, with a mean background prediction of 8:6 ± 2:4 events. Limits are presented at 95% confidence level on long-lived gluino and stop production, over 13 orders of magnitude of particle lifetime. Assuming the cloud model of R-hadron interactions, a gluino with mass below 640 GeV and a stop with mass below 340 GeV are excluded, for lifetimes between 10 μs and 1000 s.

Search for resonant t̄t production in lepton+jets events in pp collisions at √s=7 TeV

A model-independent search for the production of heavy resonances decaying into top-antitop quark pairs is presented. The search is based on events containing one lepton (muon or electron) and at least two jets selected from data samples corresponding to an integrated luminosity of 4.4-5.0 fb -1 collected in pp collisions at √s =7 TeV. Results are presented from the combination of two dedicated searches optimized for boosted production and production at threshold. No excess of events is observed over the expected yield from the standard model processes. Topcolor Z′ bosons with narrow (wide) width are excluded at 95% confidence level for masses below 1.49 (2.04) TeV and an upper limit of 0.3 (1.3) pb or lower is set on the production cross section times branching fraction for resonance masses above 1 TeV. Kaluza-Klein excitations of a gluon with masses below 1.82 TeV (at 95% confidence level) in the Randall-Sundrum model are also excluded, and an upper limit of 0.7 pb or lower is set on the production cross section times branching fraction for resonance masses above 1 TeV.[Figure not available: See fulltext.] © 2012 CERN for the benefit of the CMS collaboration.

Measurement of the single-top-quark t-channel cross section in pp collisions at √s=7 TeV

A measurement of the single-top-quark t-channel production cross section in pp collisions at √s=7 TeV with the CMS detector at the LHC is presented. Two different and complementary approaches have been followed. The first approach exploits the distributions of the pseudorapidity of the recoil jet and reconstructed top-quark mass using background estimates determined from control samples in data. The second approach is based on multivariate analysis techniques that probe the compatibility of the candidate events with the signal. Data have been collected for the muon and electron final states, corresponding to integrated luminosities of 1.17 and 1.56 fb-1, respectively. The single-top-quark production cross section in the t-channel is measured to be 67.2±6.1 pb, in agreement with the approximate next-to-next-to-leading- order standard model prediction. Using the standard model electroweak couplings, the CKM matrix element |V tb| is measured to be 1.020 ± 0.046 (meas.) ± 0.017 (theor.). © 2012 CERN for the benefit of the CMS collaboration.

Search for third-generation leptoquarks and scalar bottom quarks in pp collisions at √s=7Tev

Results are presented from a search for third-generation leptoquarks and scalar bottom quarks in a sample of proton-proton collisions at √s=7Tev collected by the CMS experiment at the LHC, corresponding to an integrated luminosity of 4.7 fb-1. A scenario where the new particles are pair produced and each decays to a b quark plus a tau neutrino or neutralino is considered. The number of observed events is found to be in agreement with the standard model prediction. Upper limits are set at 95% confidence level on the production cross sections. Leptoquarks with masses below ~450 GeV are excluded. Upper limits in the mass plane of the scalar quark and neutralino are set such that scalar bottom quark masses up to 410 GeV are excluded for neutralino masses of 50 GeV. © 2012 CERN for the benefit of CMS collaboration.

Measurement of the top-quark mass in t̄t events with lepton+jets final states in pp collisions at √s =7 TeV

The mass of the top quark is measured using a sample of t̄t candidate events with one electron or muon and at least four jets in the final state, collected by CMS in pp collisions at √s =7 TeV at the LHC. A total of 5174 candidate events is selected from data corresponding to an integrated luminosity of 5.0 fb-1. For each event the mass is reconstructed from a kinematic fit of the decay products to a t̄t hypothesis. The top-quark mass is determined simultaneously with the jet energy scale (JES), constrained by the known mass of the W boson in q̄q decays, to be 173.49 ± 0.43 (stat. + JES) ±0.98 (syst.) GeV. © 2012 CERN for the benefit of the CMS collaboration.

A search for a doubly-charged Higgs boson in pp collisions at √s=7 TeV

A search for a doubly-charged Higgs boson in pp collisions at √s=7 TeV is presented. The data correspond to an integrated luminosity of 4. 9 fb-1, collected by the CMS experiment at the LHC. The search is performed using events with three or more isolated charged leptons of any flavor, giving sensitivity to the decays of pair-produced triplet components Φ++Φ--, and Φ++Φ- from associated production. No excess is observed compared to the background prediction, and upper limits at the 95 % confidence level are set on the Φ++ production cross section, under specific assumptions on its branching fractions. Lower bounds on the Φ++ mass are reported, providing significantly more stringent constraints than previously published limits. © 2012 CERN for the benefit of the CMS collaboration.

Forward-backward asymmetry of Drell-Yan lepton pairs in pp collisions at s=7TeV

A measurement of the forward-backward asymmetry (AFB) of Drell-Yan lepton pairs in pp collisions at s=7TeV is presented. The data sample, collected with the CMS detector, corresponds to an integrated luminosity of 5fb-1. The asymmetry is measured as a function of dilepton mass and rapidity in the dielectron and dimuon channels. Combined results from the two channels are presented, and are compared with the standard model predictions. The AFB measurement in the dimuon channel and the combination of the two channels are the first such results obtained at a hadron collider. The measured asymmetries are consistent with the standard model predictions. © 2012 CERN.

Observation of long-range, near-side angular correlations in pPb collisions at the LHC

Results on two-particle angular correlations for charged particles emitted in pPb collisions at a nucleon-nucleon center-of-mass energy of 5.02 TeV are presented. The analysis uses two million collisions collected with the CMS detector at the LHC. The correlations are studied over a broad range of pseudorapidity, η, and full azimuth, φ, as a function of charged particle multiplicity and particle transverse momentum, pT. In high-multiplicity events, a long-range (2<|δη|<4), near-side (δφ≈0) structure emerges in the two-particle δη-δφ correlation functions. This is the first observation of such correlations in proton-nucleus collisions, resembling the ridge-like correlations seen in high-multiplicity pp collisions at s=7 TeV and in AA collisions over a broad range of center-of-mass energies. The correlation strength exhibits a pronounced maximum in the range of pT=1-1.5 GeV/c and an approximately linear increase with charged particle multiplicity for high-multiplicity events. These observations are qualitatively similar to those in pp collisions when selecting the same observed particle multiplicity, while the overall strength of the correlations is significantly larger in pPb collisions. © 2012 CERN.

Observation of a diffractive contribution to dijet production in proton-proton collisions at √s=7 TeV

The cross section for dijet production in proton-proton collisions at √s=7 TeV is presented as a function of a variable that approximates the fractional momentum loss of the scattered proton in single-diffractive events. The analysis is based on an integrated luminosity of 2.7 nb-1 collected with the CMS detector at the LHC at low instantaneous luminosities, and uses events with jet transverse momentum of at least 20 GeV. The dijet cross section results are compared to the predictions of diffractive and nondiffractive models. The low- data show a significant contribution from diffractive dijet production, observed for the first time at the LHC. The associated rapidity gap survival probability is estimated. © 2013 CERN. Published by the American Physical Society.

Evidence for associated production of a single top quark and W Boson in pp collisions at √s=7 TeV

Evidence is presented for the associated production of a single top quark and W boson in pp collisions at √s=7 TeV with the CMS experiment at the LHC. The analyzed data correspond to an integrated luminosity of 4.9 fb -1. The measurement is performed using events with two leptons and a jet originated from a b quark. A multivariate analysis based on kinematic properties is utilized to separate the tt̄ background from the signal. The observed signal has a significance of 4.0σ and corresponds to a cross section of 16-4+5 pb, in agreement with the standard model expectation of 15.6±0.4-1.2+1.0 pb. © 2013 CERN, for the CMS Collaboration Published by the American Physical Society under the terms of the http://creativecommons.org/licenses/by/3.0/ Creative Commons Attribution 3.0 License. Further distribution of this work must maintain attribution to the author(s) and the published article's title, journal citation, and DOI.

Measurement of the azimuthal anisotropy of neutral pions in Pb-Pb collisions at √sNN=2.76 TeV

First measurements of the azimuthal anisotropy of neutral pions produced in Pb-Pb collisions at a center-of-mass energy of √sNN=2.76 TeV are presented. The amplitudes of the second Fourier component (v2) of the π0 azimuthal distributions are extracted using an event-plane technique. The values of v2 are studied as a function of the neutral pion transverse momentum (pT) for different classes of collision centrality in the kinematic range 1.6