Horizontal gene transfer and diverse functional constrains within a common replication-partitioning system in Alphaproteobacteria: the repABC operon

<p>Abstract</p> <p>Background</p> <p>The <it>repABC </it>plasmid family, which is extensively present within <it>Alphaproteobacteria</it>, and some secondary chromosomes of the <it>Rhizobiales </it>have the particular feature that all the elements involved in replication and partitioning reside within one transcriptional unit, the <it>repABC </it>operon. Given the functional interactions among the elements of the <it>repABC </it>operon, and the fact that they all reside in the same operon, a common evolutionary history would be expected if the entire operon had been horizontally transferred. Here, we tested whether there is a common evolutionary history within the <it>repABC </it>operon. We further examined different incompatibility groups in terms of their differentiation and degree of adaptation to their host.</p> <p>Results</p> <p>We did not find a single evolutionary history within the <it>repABC </it>operon. Each protein had a particular phylogeny, horizontal gene transfer events of the individual genes within the operon were detected, and different functional constraints were found within and between the Rep proteins. When different <it>repABC </it>operons coexisted in the same genome, they were well differentiated from one another. Finally, we found different levels of adaptation to the host genome within and between <it>repABC </it>operons coexisting in the same species.</p> <p>Conclusion</p> <p>Horizontal gene transfer with conservation of the <it>repABC </it>operon structure provides a highly dynamic operon in which each member of this operon has its own evolutionary dynamics. In addition, it seems that different incompatibility groups present in the same species have different degrees of adaptation to their host genomes, in proportion to the amount of time the incompatibility group has coexisted with the host genome.</p

Rapid evolutionary change of common bean (Phaseolus vulgaris L) plastome, and the genomic diversification of legume chloroplasts

<p>Abstract</p> <p>Background</p> <p>Fabaceae (legumes) is one of the largest families of flowering plants, and some members are important crops. In contrast to what we know about their great diversity or economic importance, our knowledge at the genomic level of chloroplast genomes (cpDNAs or plastomes) for these crops is limited.</p> <p>Results</p> <p>We sequenced the complete genome of the common bean (<it>Phaseolus vulgari</it>s cv. Negro Jamapa) chloroplast. The plastome of <it>P. vulgaris </it>is a 150,285 bp circular molecule. It has gene content similar to that of other legume plastomes, but contains two pseudogenes, <it>rpl</it>33 and <it>rps</it>16. A distinct inversion occurred at the junction points of <it>trn</it>H-GUG/<it>rpl</it>14 and <it>rps</it>19/<it>rps</it>8, as in adzuki bean <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>. These two pseudogenes and the inversion were confirmed in 10 varieties representing the two domestication centers of the bean. Genomic comparative analysis indicated that inversions generally occur in legume plastomes and the magnitude and localization of insertions/deletions (indels) also vary. The analysis of repeat sequences demonstrated that patterns and sequences of tandem repeats had an important impact on sequence diversification between legume plastomes and tandem repeats did not belong to dispersed repeats. Interestingly, <it>P. vulgaris </it>plastome had higher evolutionary rates of change on both genomic and gene levels than <it>G. max</it>, which could be the consequence of pressure from both mutation and natural selection.</p> <p>Conclusion</p> <p>Legume chloroplast genomes are widely diversified in gene content, gene order, indel structure, abundance and localization of repetitive sequences, intracellular sequence exchange and evolutionary rates. The <it>P. vulgaris </it>plastome is a rapidly evolving genome.</p

Diagnostic ability of multifocal electroretinogram in early multiple sclerosis using a new signal analysis method

Purpose To determine if a novel analysis method will increase the diagnostic value of the multifocal electroretinogram (mfERG) in diagnosing early-stage multiple sclerosis (MS). Methods We studied the mfERG signals of OD (Oculus Dexter) eyes of fifteen patients diagnosed with early-stage MS (in all cases &lt; 12 months) and without a history of optic neuritis (ON) (F: M = 11:4), and those of six controls (F:M = 3:3). We obtained values of amplitude and latency of N1 and P1 waves, and a method to assess normalized root-mean-square error (FNRMSE) between model signals and mfERG recordings was used. Responses of each eye were analysed at a global level, and by rings, quadrants and hemispheres. AUC (area under the ROC curve) is used as discriminant factor. Results The standard method of analysis obtains further discrimination between controls and MS in ring R3 (AUC = 0.82), analysing N1 waves amplitudes. In all of the retina analysis regions, FNRMSE value shows a greater discriminating power than the standard method. The highest AUC value (AUC = 0.91) was in the superior temporal quadrant. Conclusion By analysing mfERG recordings and contrasting them with those of healthy controls it is possible to detect early-stage MS in patients without a previous history of ON

Charged-particle multiplicities in pp interactions at root s=900 GeV measured with the ATLAS detector at the LHC

The first measurements from proton-proton collisions recorded with the ATLAS detector at the LHC are presented. Data were collected in December 2009 using a minimum-bias trigger during collisions at a centre-of-mass energy of 900 GeV. The charged-particle multiplicity, its dependence on transverse momentum and pseudorapidity, and the relationship between mean transverse momentum and charged-particle multiplicity are measured for events with at least one charged particle in the kinematic range |eta|500 MeV. The measurements are compared to Monte Carlo models of proton-proton collisions and to results from other experiments at the same centre-of-mass energy. The charged-particle multiplicity per event and unit of pseudorapidity at eta = 0 is measured to be 1.333 +/- 0.003 (stat.) +/- 0.040 (syst.), which is 5-15% higher than the Monte Carlo models predict

Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

The inclusive and dijet production cross-sections have been measured for jets containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The measurements use data corresponding to an integrated luminosity of 34 pb(-1). The b-jets are identified using either a lifetime-based method, where secondary decay vertices of b-hadrons in jets are reconstructed using information from the tracking detectors, or a muon-based method where the presence of a muon is used to identify semileptonic decays of b-hadrons inside jets. The inclusive b-jet cross-section is measured as a function of transverse momentum in the range 20 -dijet cross-section is measured as a function of the dijet invariant mass in the range 110 < m(jj) < 760 GeV, the azimuthal angle difference between the two jets and the angular variable chi in two dijet mass regions. The results are compared with next-to-leading-order QCD predictions. Good agreement is observed between the measured cross-sections and the predictions obtained using POWHEG + Pythia. MC@NLO + Herwig shows good agreement with the measured b (b) over bar -dijet cross-section. However, it does not reproduce the measured inclusive cross-section well, particularly for central b-jets with large transverse momenta

Properties of jets measured from tracks in proton-proton collisions at center-of-mass energy sqrt(s) = 7 TeV with the ATLAS detector

Jets are identified and their properties studied in center-of-mass energy sqrt(s) = 7 TeV proton-proton collisions at the Large Hadron Collider using charged particles measured by the ATLAS inner detector. Events are selected using a minimum bias trigger, allowing jets at very low transverse momentum to be observed and their characteristics in the transition to high-momentum fully perturbative jets to be studied. Jets are reconstructed using the anti-k(t) algorithm applied to charged particles with two radius parameter choices, 0.4 and 0.6. An inclusive charged jet transverse momentum cross section measurement from 4 GeV to 100 GeV is shown for four ranges in rapidity extending to 1.9 and corrected to charged particle-level truth jets. The transverse momenta and longitudinal momentum fractions of charged particles within jets are measured, along with the charged particle multiplicity and the particle density as a function of radial distance from the jet axis. Comparison of the data with the theoretical models implemented in existing tunings of Monte Carlo event generators indicates reasonable overall agreement between data and Monte Carlo. These comparisons are sensitive to Monte Carlo parton showering, hadronization, and soft physics models

Measurement of the top quark pair production cross section in pp collisions at sqrt(s) = 7 TeV in dilepton final states with ATLAS

A measurement of the production cross section of top quark pairs (t (t) over bar) in proton-proton collisions at a center-of-mass energy of 7 TeV recorded with the ATLAS detector at the Large Hadron Collider is reported. Candidate events are selected in the dilepton topology with large missing transverse energy and at least two jets. Using a data sample corresponding to an integrated luminosity of 35 pb(-1), a t (t) over bar production cross section sigma(t (t) over bar) = 177 +/- 20(stat.) +/- 14(syst.) +/- 7(lum.) pb is measured for an assumed top quark mass of m(t) = 172.5 GeV. A second measurement requiring at least one jet identified as coming from a b quark yields a comparable result, demonstrating that the dilepton final states are consistent with being accompanied by b-quark jets. These measurements are in good agreement with Standard Model predictions

Search for anomaly-mediated supersymmetry breaking with the ATLAS detector based on a disappearing-track signature in pp collisions at √(s) = 7 TeV

In models of anomaly-mediated supersymmetry breaking (AMSB), the lightest chargino is predicted to have a lifetime long enough to be detected in collider experiments. This letter explores AMSB scenarios in pp collisions at root s = 7 TeV by attempting to identify decaying charginos which result in tracks that appear to have few associated hits in the outer region of the tracking system. The search was based on data corresponding to an integrated luminosity of 1.02 fb(-1) collected with the ATLAS detector in 2011. The p(T) spectrum of candidate tracks is found to be consistent with the expectation from Standard Model background processes and constraints on the lifetime and the production cross section were obtained. In the minimal AMSB framework with m(3/2) 0, a chargino having mass below 92 GeV and a lifetime between 0.5 ns and 2 ns is excluded at 95 % confidence level