Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation

Background Outer membrane proteins (OMPs) of Pasteurella multocida have various functions related to virulence and pathogenesis and represent important targets for vaccine development. Various bioinformatic algorithms can predict outer membrane localization and discriminate OMPs by structure or function. The designation of a confident prediction framework by integrating different predictors followed by consensus prediction, results integration and manual confirmation will improve the prediction of the outer membrane proteome. Results In the present study, we used 10 different predictors classified into three groups (subcellular localization, transmembrane β-barrel protein and lipoprotein predictors) to identify putative OMPs from two available P. multocida genomes: those of avian strain Pm70 and porcine non-toxigenic strain 3480. Predicted proteins in each group were filtered by optimized criteria for consensus prediction: at least two positive predictions for the subcellular localization predictors, three for the transmembrane β-barrel protein predictors and one for the lipoprotein predictors. The consensus predicted proteins were integrated from each group into a single list of proteins. We further incorporated a manual confirmation step including a public database search against PubMed and sequence analyses, e.g. sequence and structural homology, conserved motifs/domains, functional prediction, and protein-protein interactions to enhance the confidence of prediction. As a result, we were able to confidently predict 98 putative OMPs from the avian strain genome and 107 OMPs from the porcine strain genome with 83% overlap between the two genomes. Conclusions The bioinformatic framework developed in this study has increased the number of putative OMPs identified in P. multocida and allowed these OMPs to be identified with a higher degree of confidence. Our approach can be applied to investigate the outer membrane proteomes of other Gram-negative bacteria

Skyrme-force time-dependent Hartree-Fock calculations with axial symmetry

We discuss axially symmetric time-dependent Hartree-Fock calculations using a finite-range modification of the Skyrme energy functional. The finite-difference forms of the coordinate-space time-dependent Hartree-Fock equations, the method of time evolution, and other numerical aspects are presented. Detailed results for (^84)Kr-induced deep-inelastic collisions with (^208)Pb at E_(lab) = 494 MeV and with (^209)Bi at E_(lab) = 600 MeV and 714 MeV are compared with experiment. [NUCLEAR REACTIONS (^84)Kr + (^208)Pb at E_lab = 494 MeV and (^84)Kr + (^209)Bi at E_1ab=600 and 714 MeV, in the time-dependent Hartree-Fock approximation. Strongy damped collisions. Details of Skyrme force calculations with axial symmetry.

Elucidating the role of DEPTOR in Alzheimer's disease

This article has been made available through the Brunel Open Access Publishing Fund.The mammalian or mechanistic target of rapamycin (mTOR) is a Ser/Thr protein kinase that, in response to nutrient stimulation, regulates cellular growth, proliferation, survival, protein synthesis and gene transcription. It has also been implicated in Alzheimer's disease (AD) with neuronal cells and hippocampal slices of AD transgenic mice experiencing dysregulated mTOR and synaptic plasticity in response to treatment with the toxic amyloid β (Aβ1-42) peptide, which has been implicated in AD. DEP domain-containing mTOR-interacting protein (DEPTOR) is a protein which can bind to mTOR and cause its inhibition, and functions as a regulatory protein of mTOR to control its activity. The inhibition of mTOR has been shown to have a neuroprotective effect; in an animal model, it was shown to protect against Aβ-induced neurotoxicity. In the present study, to investigate to role of DEPTOR in a model of AD, we neuronally differentiated the SH-SY5Y cell line and examined the effects of treatment with an Aβ42 peptide, thus mimicking plaque formation. This resulted in a significant increase in mTOR and a significant decrease in DEPTOR expression compared to the unstimulated controls. Moreover, to the best of our knowledge, we demonstrate for the first time a reduction in the protein level of DEPTOR in the precentral gyrus, postcentral gyrus and occipital lobe of a brain with AD compared to a normal control, as well as a significant reduction in DEPTOR expression in samples from late-onset AD (LOAD) compared to early-onset familial AD (EOFAD). The reduction in DEPTOR expression in cases of AD compared to healthy controls can lead to an augmentation of mTOR signalling, leading to Aβ accumulation, which in turn leads to a further reduction in DEPTOR expression. This results in the accumulation of amyloid plaque, shifting the balance from neuroprotection to neurodegeneration

Geological evaluation of Nimbus vidicon photography, Chesapeake Bay-Blue Ridge

Geological evaluation of Nimbus vidicon photography of Chesapeake Bay to Blue Ridge are

Are There Magnetars in High Mass X-ray Binaries? The Case of SuperGiant Fast X-Ray Transients

In this paper we survey the theory of wind accretion in high mass X-ray binaries hosting a magnetic neutron star and a supergiant companion. We concentrate on the different types of interaction between the inflowing wind matter and the neutron star magnetosphere that are relevant when accretion of matter onto the neutron star surface is largely inhibited; these include the inhibition through the centrifugal and magnetic barriers. Expanding on earlier work, we calculate the expected luminosity for each regime and derive the conditions under which transition from one regime to another can take place. We show that very large luminosity swings (~10^4 or more on time scales as short as hours) can result from transitions across different regimes. The activity displayed by supergiant fast X-ray transients, a recently discovered class of high mass X-ray binaries in our galaxy, has often been interpreted in terms of direct accretion onto a neutron star immersed in an extremely clumpy stellar wind. We show here that the transitions across the magnetic and/or centrifugal barriers can explain the variability properties of these sources as a results of relatively modest variations in the stellar wind velocity and/or density. According to this interpretation we expect that supergiant fast X-ray transients which display very large luminosity swings and host a slowly spinning neutron star are characterized by magnetar-like fields, irrespective of whether the magnetic or the centrifugal barrier applies. Supergiant fast X-ray transients might thus provide a new opportunity to detect and study magnetars in binary systems.Comment: Accepted for publication in ApJ. 16 pages, 6 figure

Commensurability oscillations due to pinned and drifting orbits in a two-dimensional lateral surface superlattice

We have simulated conduction in a two-dimensional electron gas subject to a weak two-dimensional periodic potential, $V_x \cos(2\pi x/a) + V_y \cos(2\pi y/a)$. The usual commensurability oscillations in $\rho_{xx}(B)$ are seen with $V_x$ alone. An increase of $V_y$ suppresses these oscillations, rather than introducing the additional oscillations in $\rho_{yy}(B)$ expected from previous perturbation theories. We show that this behavior arises from drift of the guiding center of cyclotron motion along contours of an effective potential. Periodic modulation in the magnetic field can be treated in the same way.Comment: 3 pages text, 4 eps figures, revte

Stellar and Molecular Gas Kinematics of NGC1097: Inflow Driven by a Nuclear Spiral

We present spatially resolved distributions and kinematics of the stars and molecular gas in the central 320pc of NGC1097. The stellar continuum confirms the previously reported 3-arm spiral pattern extending into the central 100pc. The stellar kinematics and the gas distribution imply this is a shadowing effect due to extinction by gas and dust in the molecular spiral arms. The molecular gas kinematics show a strong residual (i.e. non-circular) velocity, which is manifested as a 2-arm kinematic spiral. Linear models indicate that this is the line-of-sight velocity pattern expected for a density wave in gas that generates a 3-arm spiral morphology. We estimate the inflow rate along the arms. Using hydrodynamical models of nuclear spirals, we show that when deriving the accretion rate into the central region, outflow in the disk plane between the arms has to be taken into account. For NGC1097, despite the inflow rate along the arms being ~1.2Msun/yr, the net gas accretion rate to the central few tens of parsecs is much smaller. The numerical models indicate that the inflow rate could be as little as ~0.06Msun/yr. This is sufficient to generate recurring starbursts, similar in scale to that observed, every 20-150Myr. The nuclear spiral represents a mechanism that can feed gas into the central parsecs of the galaxy, with the gas flow sustainable for timescales of a Gigayear.Comment: accepted by Ap

FliPer: Checking the reliability of global seismic parameters from automatic pipelines

Our understanding of stars through asteroseismic data analysis is limited by our ability to take advantage of the huge amount of observed stars provided by space missions such as CoRoT, Kepler, K2, and soon TESS and PLATO. Global seismic pipelines provide global stellar parameters such as mass and radius using the mean seismic parameters, as well as the effective temperature. These pipelines are commonly used automatically on thousands of stars observed by K2 for 3 months (and soon TESS for at least around 1 month). However, pipelines are not immune from misidentifying noise peaks and stellar oscillations. Therefore, new validation techniques are required to assess the quality of these results. We present a new metric called FliPer (Flicker in Power), which takes into account the average variability at all measured time scales. The proper calibration of FliPer enables us to obtain good estimations of global stellar parameters such as surface gravity that are robust against the influence of noise peaks and hence are an excellent way to find faults in asteroseismic pipelines.Comment: 4 pages, 3 figures, Proceedings for SF2A 2017 (Paris

Radio Observations of GRB Host Galaxies

We present 5.5 and 9.0 GHz observations of a sample of seventeen GRB host galaxies at 0.5<z<1.4, using the radio continuum to explore their star formation properties in the context of the small but growing sample of galaxies with similar observations. Four sources are detected, one of those (GRB 100418A) likely due to lingering afterglow emission. We suggest that the previously-reported radio afterglow of GRB 100621A may instead be due to host galaxy flux. We see no strong evidence for redshift evolution in the typical star formation rate of GRB hosts, but note that the fraction of `dark' bursts with detections is higher than would be expected given constraints on the more typical long GRB population. We also determine the average radio-derived star formation rates of core collapse supernovae at comparable redshift, and show that these are still well below the limits obtained for GRB hosts, and show evidence for a rise in typical star formation rate with redshift in supernova hosts.Comment: 15 pages, MNRAS accepte