Systems biology of proteins expressed during the Moniliophthora perniciosa necrotrophic phase : S01P12

The fungus Moniliophthora perniciosa, the etiologic agent of witches' broom disease of cacao (Theobroma cacao L.) has a hemibiotrophic life cycle, with a biotrophic and a necrotrophic phase. The biotrophic phase, initiating the disease, is characterized by a monokaryotic mycelium, while the necrotrophic phase is characterized by a dikaryotic mycelium leading to plant necrosis. During the culture of M. perniciosa on bran-based solid medium, six different developmental phases were observed according to the dikaryotic mycelium color or the organ produced: white, yellow, pink, dark pink, primordium and basidiomata. A proteomic analysis of the different M. perniciosa development stages associated to mass spectrometry allowed the identification of about 250 differentially expressed proteins. In this study, using such differentially expressed proteins, we developed a systems biology analysis to identify physical protein-protein interaction (PPPI) networks related to the fungus development focusing on basidiocarp formation. First, orthologous protein sequences of M. perniciosa were obtained in N. crassa using the BLASTX tool. The data mining screening and PPPI network design associated with fungal development was performed using the Cytoscape software, version 2.5.0. These data were downloaded from the STRING 8.3 database. The interactome networks obtained from this first screening were analyzed with the Molecular Complex Detection software, a Cytoscape plugin, in order to evaluate potential subgraphs that were used further for network expansion. Gene ontology clustering analysis was performed using the Biological Network Gene Ontology software. Moreover, an analysis of centrality was performed using the software Centiscape 1.2.1.; several hub-bottlenecks, hub and bottlenecks proteins, as well as proteins involved in biological processes important for the M. perniciosa development were identified. The main biological processes encountered were anatomy and morphology, reproduction, oxidative stress, cell wall biosynthesis, pigmentation, development and cell differentiation. The identification of proteins involved in the formation of basidiomata, as well as the knowledge about their interactions, may contribute to the future development of witches' broom control strategies. To our knowledge, this is the first system biology analysis of proteins involved in the M. perniciosa life cycle. Supported by: CAPES, CIRAD, BNB, PRONEM/FAPESB. (Texte intégral

MUMAL: multivariate analysis in shotgun proteomics using machine learning techniques.

BACKGROUND: The shotgun strategy (liquid chromatography coupled with tandem mass spectrometry) is widely applied for identification of proteins in complex mixtures. This method gives rise to thousands of spectra in a single run, which are interpreted by computational tools. Such tools normally use a protein database from which peptide sequences are extracted for matching with experimentally derived mass spectral data. After the database search, the correctness of obtained peptide-spectrum matches (PSMs) needs to be evaluated also by algorithms, as a manual curation of these huge datasets would be impractical. The target-decoy database strategy is largely used to perform spectrum evaluation. Nonetheless, this method has been applied without considering sensitivity, i.e., only error estimation is taken into account. A recently proposed method termed MUDE treats the target-decoy analysis as an optimization problem, where sensitivity is maximized. This method demonstrates a significant increase in the retrieved number of PSMs for a fixed error rate. However, the MUDE model is constructed in such a way that linear decision boundaries are established to separate correct from incorrect PSMs. Besides, the described heuristic for solving the optimization problem has to be executed many times to achieve a significant augmentation in sensitivity. RESULTS: Here, we propose a new method, termed MUMAL, for PSM assessment that is based on machine learning techniques. Our method can establish nonlinear decision boundaries, leading to a higher chance to retrieve more true positives. Furthermore, we need few iterations to achieve high sensitivities, strikingly shortening the running time of the whole process. Experiments show that our method achieves a considerably higher number of PSMs compared with standard tools such as MUDE, PeptideProphet, and typical target-decoy approaches. CONCLUSION: Our approach not only enhances the computational performance, and thus the turn around time of MS-based experiments in proteomics, but also improves the information content with benefits of a higher proteome coverage. This improvement, for instance, increases the chance to identify important drug targets or biomarkers for drug development or molecular diagnostics

Consistency analysis of a nonbirefringent Lorentz-violating planar model

In this work analyze the physical consistency of a nonbirefringent Lorentz-violating planar model via the analysis of the pole structure of its Feynman propagators. The nonbirefringent planar model, obtained from the dimensional reduction of the CPT-even gauge sector of the standard model extension, is composed of a gauge and a scalar fields, being affected by Lorentz-violating (LIV) coefficients encoded in the symmetric tensor $\kappa_{\mu\nu}$. The propagator of the gauge field is explicitly evaluated and expressed in terms of linear independent symmetric tensors, presenting only one physical mode. The same holds for the scalar propagator. A consistency analysis is performed based on the poles of the propagators. The isotropic parity-even sector is stable, causal and unitary mode for $0\leq\kappa_{00}<1$. On the other hand, the anisotropic sector is stable and unitary but in general noncausal. Finally, it is shown that this planar model interacting with a $\lambda|\varphi|^{4}-$Higgs field supports compactlike vortex configurations.Comment: 11 pages, revtex style, final revised versio

Stationary solutions for the parity-even sector of the CPT-even and Lorentz-covariance-violating term of the standard model extension

In this work, we focus on some properties of the parity-even sector of the CPT-even electrodynamics of the standard model extension. We analyze how the six non-birefringent terms belonging to this sector modify the static and stationary classical solutions of the usual Maxwell theory. We observe that the parity-even terms do not couple the electric and magnetic sectors (at least in the stationary regime). The Green's method is used to obtain solutions for the field strengths E and B at first order in the Lorentz- covariance-violating parameters. Explicit solutions are attained for point-like and spatially extended sources, for which a dipolar expansion is achieved. Finally, it is presented an Earth-based experiment that can lead (in principle) to an upper bound on the anisotropic coefficients as stringent as $(\widetilde{\kappa}_{e-}) ^{ij}<2.9\times10^{-20}.$Comment: 8 pages, revtex style, revised published version, to appear in EPJC (2009

On the influence of a Coulomb-like potential induced by the Lorentz symmetry breaking effects on the Harmonic Oscillator

In this work, we obtain bound states for a nonrelativistic spin-half neutral particle under the influence of a Coulomb-like potential induced by the Lorentz symmetry breaking effects. We present a new possible scenario of studying the Lorentz symmetry breaking effects on a nonrelativistic quantum system defined by a fixed space-like vector field parallel to the radial direction interacting with a uniform magnetic field along the z-axis. Furthermore, we also discuss the influence of a Coulomb-like potential induced by Lorentz symmetry violation effects on the two-dimensional harmonic oscillator.Comment: 14 pages, no figure, this work has been accepted for publication in The European Physical Journal Plu

Measurement of the top quark-pair production cross section with ATLAS in pp collisions at \sqrt{s}=7\TeV

A measurement of the production cross-section for top quark pairs(\ttbar) in $pp$ collisions at \sqrt{s}=7 \TeV is presented using data recorded with the ATLAS detector at the Large Hadron Collider. Events are selected in two different topologies: single lepton (electron $e$ or muon $\mu$) with large missing transverse energy and at least four jets, and dilepton ($ee$, $\mu\mu$ or $e\mu$) with large missing transverse energy and at least two jets. In a data sample of 2.9 pb-1, 37 candidate events are observed in the single-lepton topology and 9 events in the dilepton topology. The corresponding expected backgrounds from non-\ttbar Standard Model processes are estimated using data-driven methods and determined to be $12.2 \pm 3.9$ events and $2.5 \pm 0.6$ events, respectively. The kinematic properties of the selected events are consistent with SM \ttbar production. The inclusive top quark pair production cross-section is measured to be \sigmattbar=145 \pm 31 ^{+42}_{-27} pb where the first uncertainty is statistical and the second systematic. The measurement agrees with perturbative QCD calculations.Comment: 30 pages plus author list (50 pages total), 9 figures, 11 tables, CERN-PH number and final journal adde

Inclusive search for same-sign dilepton signatures in pp collisions at root s=7 TeV with the ATLAS detector

An inclusive search is presented for new physics in events with two isolated leptons (e or mu) having the same electric charge. The data are selected from events collected from p p collisions at root s = 7 TeV by the ATLAS detector and correspond to an integrated luminosity of 34 pb(-1). The spectra in dilepton invariant mass, missing transverse momentum and jet multiplicity are presented and compared to Standard Model predictions. In this event sample, no evidence is found for contributions beyond those of the Standard Model. Limits are set on the cross-section in a fiducial region for new sources of same-sign high-mass dilepton events in the ee, e mu and mu mu channels. Four models predicting same-sign dilepton signals are constrained: two descriptions of Majorana neutrinos, a cascade topology similar to supersymmetry or universal extra dimensions, and fourth generation d-type quarks. Assuming a new physics scale of 1 TeV, Majorana neutrinos produced by an effective operator V with masses below 460 GeV are excluded at 95% confidence level. A lower limit of 290 GeV is set at 95% confidence level on the mass of fourth generation d-type quarks

Standalone vertex finding in the ATLAS muon spectrometer

A dedicated reconstruction algorithm to find decay vertices in the ATLAS muon spectrometer is presented. The algorithm searches the region just upstream of or inside the muon spectrometer volume for multi-particle vertices that originate from the decay of particles with long decay paths. The performance of the algorithm is evaluated using both a sample of simulated Higgs boson events, in which the Higgs boson decays to long-lived neutral particles that in turn decay to bbar b final states, and pp collision data at √s = 7 TeV collected with the ATLAS detector at the LHC during 2011

Measurement of inclusive two-particle angular correlations in pp collisions with the ATLAS detector at the LHC

We present a measurement of two-particle angular correlations in proton- proton collisions at s√=900 GeV and 7 TeV. The collision events were collected during 2009 and 2010 with the ATLAS detector at the Large Hadron Collider using a single-arm minimum bias trigger. Correlations are measured for charged particles produced in the kinematic range of transverse momentum p T  > 100 MeV and pseudorapidity |η| < 2.5. A complex structure in pseudorapidity and azimuth is observed at both collision energies. Results are compared to pythia 8 and herwig++ as well as to the AMBT2B, DW and Perugia 2011 tunes of pythia 6. The data are not satisfactorily described by any of these models

Bacterial and microeukaryotic plankton communities in a semi-intensive aquaculture system of sea bass (Dicentrarchus labrax): a seasonal survey

The importance of microbial diversity and their role in the maintenance of fish health in aquaculture systems has been increasingly recognized in recent years. However, there is still a major knowledge gap regarding the ecology, composition and dynamics of microbial plankton assemblages during fish production. In this study, we aimed to investigate the seasonal dynamics and potential interactions of bacterial and microeukaryotic plankton communities in a semi-intensive aquaculture for European sea bass (Dicentrarchus labrax) cultured together with low density of gilthead sea bream (Sparus aurata) over a one-year period (January/2014 – November/2014). While the most abundant bacterial classes were Gammaproteobacteria, Flavobacteriia and Alphaproteobacteria; microeukaryotic communities were dominated by Ochrophyta, Chlorophyta and Ciliophora groups. Temperature and salinity were identified as significant drivers of the overall microbial community composition, which varied congruently along the seasons. However, while the dominant (more abundant) groups of bacteria occurred in the warmest months, the dominant groups of microeukaryotes occurred in the coldest months. There was also an inverse relationship between abundances of grazers and bacterial operational taxonomic units (OTUs). Overall, besides the potential effects of the abiotic parameters on the microbial plankton communities, the correlation between bacteria and microeukaryotic populations observed here may be an indication of trophic and/or metabolic interdependence between these two domains. Future studies should focus on the underlying mechanisms of this interdependence for a better understand of the impact of microeukaryotic communities on aquaculture bacterioplankton structure and function. In addition, this knowledge could be of interest in the development of microbial management strategies for aquaculture systems.publishe