Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus.

BACKGROUND: Pseudorabies virus (PRV) is an alphaherpesviruses whose native host is pig. PRV infection mainly causes signs of central nervous system disorder in young pigs, and respiratory system diseases in the adult. RESULTS: In this report, we have analyzed native host (piglets) gene expression changes in response to acute pseudorabies virus infection of the brain and lung using a printed human oligonucleotide gene set from Illumina. A total of 210 and 1130 out of 23,000 transcript probes displayed differential expression respectively in the brain and lung in piglets after PRV infection (p-value < 0.01), with most genes displaying up-regulation. Biological process and pathways analysis showed that most of the up-regulated genes are involved in cell differentiation, neurodegenerative disorders, the nervous system and immune responses in the infected brain whereas apoptosis, cell cycle control, and the mTOR signaling pathway genes were prevalent in the infected lung. Additionally, a number of differentially expressed genes were found to map in or close to quantitative trait loci for resistance/susceptibility to pseudorabies virus in piglets. CONCLUSION: This is the first comprehensive analysis of the global transcriptional response of the native host to acute alphaherpesvirus infection. The differentially regulated genes reported here are likely to be of interest for the further study and understanding of host viral gene interactions.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Global transcriptional response of pig brain and lung to natural infection by Pseudorabies virus

<p>Abstract</p> <p>Background</p> <p>Pseudorabies virus (PRV) is an alphaherpesviruses whose native host is pig. PRV infection mainly causes signs of central nervous system disorder in young pigs, and respiratory system diseases in the adult.</p> <p>Results</p> <p>In this report, we have analyzed native host (piglets) gene expression changes in response to acute pseudorabies virus infection of the brain and lung using a printed human oligonucleotide gene set from Illumina. A total of 210 and 1130 out of 23,000 transcript probes displayed differential expression respectively in the brain and lung in piglets after PRV infection (p-value < 0.01), with most genes displaying up-regulation. Biological process and pathways analysis showed that most of the up-regulated genes are involved in cell differentiation, neurodegenerative disorders, the nervous system and immune responses in the infected brain whereas apoptosis, cell cycle control, and the mTOR signaling pathway genes were prevalent in the infected lung. Additionally, a number of differentially expressed genes were found to map in or close to quantitative trait loci for resistance/susceptibility to pseudorabies virus in piglets.</p> <p>Conclusion</p> <p>This is the first comprehensive analysis of the global transcriptional response of the native host to acute alphaherpesvirus infection. The differentially regulated genes reported here are likely to be of interest for the further study and understanding of host viral gene interactions.</p

Subhalo abundance matching and assembly bias in the EAGLE simulation

Subhalo abundance matching (SHAM) is a widely used method to connect galaxies with dark matter structures in numerical simulations. SHAM predictions agree remarkably well with observations, yet they still lack strong theoretical support. We examine the performance, implementation, and assumptions of SHAM using the ‘Evolution and Assembly of Galaxies and their Environment’ (EAGLE) project simulations. We find that Vrelax, the highest value of the circular velocity attained by a subhalo while it satisfies a relaxation criterion, is the subhalo property that correlates most strongly with galaxy stellar mass (Mstar). Using this parameter in SHAM, we retrieve the real-space clustering of EAGLE to within our statistical uncertainties on scales greater than 2 Mpc for galaxies with 8.77 < log 10(Mstar[M⊙]) < 10.77. Conversely, clustering is overestimated by 30 per cent on scales below 2 Mpc for galaxies with 8.77 < log 10(Mstar[M⊙]) < 9.77 because SHAM slightly overpredicts the fraction of satellites in massive haloes compared to EAGLE. The agreement is even better in redshift space, where the clustering is recovered to within our statistical uncertainties for all masses and separations. Additionally, we analyse the dependence of galaxy clustering on properties other than halo mass, i.e. the assembly bias. We demonstrate assembly bias alters the clustering in EAGLE by 20  per cent and Vrelax captures its effect to within 15  per cent. We trace small differences in the clustering to the failure of SHAM as typically implemented, i.e. the Mstar assigned to a subhalo does not depend on (i) its host halo mass, (ii) whether it is a central or a satellite. In EAGLE, we find that these assumptions are not completely satisfied

The EAGLE simulations of galaxy formation: the importance of the hydrodynamics scheme

We present results from a subset of simulations from the "Evolution and Assembly of GaLaxies and their Environments" (EAGLE) suite in which the formulation of the hydrodynamics scheme is varied. We compare simulations that use the same subgrid models without re-calibration of the parameters but employing the standard GADGET flavour of smoothed particle hydrodynamics (SPH) instead of the more recent state-of-the-art ANARCHY formulation of SPH that was used in the fiducial EAGLE runs. We find that the properties of most galaxies, including their masses and sizes, are not significantly affected by the details of the hydrodynamics solver. However, the star formation rates of the most massive objects are affected by the lack of phase mixing due to spurious surface tension in the simulation using standard SPH. This affects the efficiency with which AGN activity can quench star formation in these galaxies and it also leads to differences in the intragroup medium that affect the X-ray emission from these objects. The differences that can be attributed to the hydrodynamics solver are, however, likely to be less important at lower resolution. We also find that the use of a time step limiter is important for achieving the feedback efficiency required to match observations of the low-mass end of the galaxy stellar mass function

Colours and luminosities of z=0.1 simulated galaxies in the EAGLE simulations

We calculate the colours and luminosities of redshift z = 0.1 galaxies from the EAGLE simulation suite using the GALAXEV population synthesis models. We take into account obscuration by dust in birth clouds and diffuse ISM using a two-component screen model, following the prescription of Charlot and Fall. We compare models in which the dust optical depth is constant to models where it depends on gas metallicity, gas fraction and orientation. The colours of EAGLE galaxies for the more sophisticated models are in broad agreement with those of observed galaxies. In particular, EAGLE produces a red sequence of passive galaxies and a blue cloud of star forming galaxies, with approximately the correct fraction of galaxies in each population and with g-r colours within 0.1 magnitudes of those observed. Luminosity functions from UV to NIR wavelengths differ from observations at a level comparable to systematic shifts resulting from a choice between Petrosian and Kron photometric apertures. Despite the generally good agreement there are clear discrepancies with observations. The blue cloud of EAGLE galaxies extends to somewhat higher luminosities than in the data, consistent with the modest underestimate of the passive fraction in massive EAGLE galaxies. There is also a moderate excess of bright blue galaxies compared to observations. The overall level of agreement with the observed colour distribution suggests that EAGLE galaxies at z = 0.1 have ages, metallicities and levels of obscuration that are comparable to those of observed galaxies

The masses and density profiles of halos in a LCDM galaxy formation simulation

We investigate the internal structure and density profiles of halos of mass $10^{10}-10^{14}~M_\odot$ in the Evolution and Assembly of Galaxies and their Environment (EAGLE) simulations. These follow the formation of galaxies in a $\Lambda$CDM Universe and include a treatment of the baryon physics thought to be relevant. The EAGLE simulations reproduce the observed present-day galaxy stellar mass function, as well as many other properties of the galaxy population as a function of time. We find significant differences between the masses of halos in the EAGLE simulations and in simulations that follow only the dark matter component. Nevertheless, halos are well described by the Navarro-Frenk-White (NFW) density profile at radii larger than ~5% of the virial radius but, closer to the centre, the presence of stars can produce cuspier profiles. Central enhancements in the total mass profile are most important in halos of mass $10^{12}-10^{13}M_\odot$, where the stellar fraction peaks. Over the radial range where they are well resolved, the resulting galaxy rotation curves are in very good agreement with observational data for galaxies with stellar mass $M_*<5\times10^{10}M_\odot$. We present an empirical fitting function that describes the total mass profiles and show that its parameters are strongly correlated with halo mass

The impact of angular momentum on black hole accretion rates in simulations of galaxy formation

Feedback from energy liberated by gas accretion onto black holes (BHs) is an attractive mechanism to explain the exponential cut-off at the massive end of the galaxy stellar mass function (SMF). Semi-analytic models of galaxy formation in which this form of feedback is assumed to suppress cooling in haloes where the gas cooling time is large compared to the dynamical time do indeed achieve a good match to the observed SMF. Furthermore, hydrodynamic simulations of individual halos in which gas is assumed to accrete onto the central BH at the Bondi rate have shown that a self-regulating regime is established in which the BH grows just enough to liberate an amount of energy comparable to the thermal energy of the halo. However, this process is efficient at suppressing the growth not only of massive galaxies but also of galaxies like the Milky Way, leading to disagreement with the observed SMF. The Bondi accretion rate, however, is inappropriate when the accreting material has angular momentum. We present an improved accretion model that takes into account the circularisation and subsequent viscous transport of infalling material and include it as a "subgrid" model in hydrodynamic simulations of the evolution of halos with a wide range of masses. The resulting accretion rates are generally low in low mass (\lsim 10^{11.5} \msun) halos, but show outbursts of Eddington-limited accretion during galaxy mergers. During outbursts these objects strongly resemble quasars. In higher mass haloes, gas accretion occurs continuously, typically at $~10$ % of the Eddington rate, which is conducive to the formation of radio jets. The resulting dependence of the accretion behaviour on halo mass induces a break in the relation between galaxy stellar mass and halo mass in these simulations that matches observations

Molecular hydrogen abundances of galaxies in the EAGLE simulations

We investigate the abundance of galactic molecular hydrogen (H$_2$) in the "Evolution and Assembly of GaLaxies and their Environments" (EAGLE) cosmological hydrodynamic simulations. We assign H$_2$ masses to gas particles in the simulations in post-processing using two different prescriptions that depend on the local dust-to-gas ratio and the interstellar radiation field. Both result in H$_2$ galaxy mass functions that agree well with observations in the local and high-redshift Universe. The simulations reproduce the observed scaling relations between the mass of H$_2$ and the stellar mass, star formation rate and stellar surface density. Towards high edshifts, galaxies in the simulations display larger H$_2$ mass fractions, and correspondingly lower H$_2$ depletion timescales, also in good agreement with observations. The comoving mass density of H$_2$ in units of the critical density, $\Omega_{\rm H_2}$, peaks at $z\approx 1.2-1.5$, later than the predicted peak of the cosmic star formation rate activity, at $z\approx 2$. This difference stems from the decrease in gas metallicity and increase in interstellar radiation field with redshift, both of which hamper H$_2$ formation. We find that the cosmic H$_2$ budget is dominated by galaxies with $M_{\rm H_2}>10^9\,\rm M_{\odot}$, star formation rates $>10\,\rm M_{\odot}\,\rm yr^{-1}$ and stellar masses $M_{\rm stellar}>10^{10}\,\rm M_{\odot}$, which are readily observable in the optical and near-IR. The match between the H$_2$ properties of galaxies that emerge in the simulations and observations is remarkable, particularly since H$_2$ observations were not used to adjust parameters in EAGLE