ALBERT

Description: Motivation: Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) detects genome-wide DNA–protein interactions and chromatin modifications, returning enriched regions (ERs), usually associated with a significance score. Moderately significant interactions can correspond to true, weak interactions, or to false positives; replicates of a ChIP-seq experiment can provide co-localised evidence to decide between the two cases. We designed a general methodological framework to rigorously combine the evidence of ERs in ChIP-seq replicates, with the option to set a significance threshold on the repeated evidence and a minimum number of samples bearing this evidence. Results : We applied our method to Myc transcription factor ChIP-seq datasets in K562 cells available in the ENCODE project. Using replicates, we could extend up to 3 times the ER number with respect to single-sample analysis with equivalent significance threshold. We validated the ‘rescued’ ERs by checking for the overlap with open chromatin regions and for the enrichment of the motif that Myc binds with strongest affinity; we compared our results with alternative methods (IDR and jMOSAiCS), obtaining more validated peaks than the former and less peaks than latter, but with a better validation. Availability and implementation : An implementation of the proposed method and its source code under GPLv3 license are freely available at http://www.bioinformatics.deib.polimi.it/MSPC/ and http://mspc.codeplex.com/ , respectively. Contact : marco.morelli@iit.it Supplementary information: Supplementary Material are available at Bioinformatics online.

Description: Motivation: Cellular mRNA levels originate from the combined action of multiple regulatory processes, which can be recapitulated by the rates of pre-mRNA synthesis, pre-mRNA processing and mRNA degradation. Recent experimental and computational advances set the basis to study these intertwined levels of regulation. Nevertheless, software for the comprehensive quantification of RNA dynamics is still lacking. Results: INSPEcT is an R package for the integrative analysis of RNA- and 4sU-seq data to study the dynamics of transcriptional regulation. INSPEcT provides gene-level quantification of these rates, and a modeling framework to identify which of these regulatory processes are most likely to explain the observed mRNA and pre-mRNA concentrations. Software performance is tested on a synthetic dataset, instrumental to guide the choice of the modeling parameters and the experimental design. Availability and implementation: INSPEcT is submitted to Bioconductor and is currently available as Supplementary Additional File S1 . Contact: mattia.pelizzola@iit.it Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: The effect of bioaugmentation with Sphingobium sp. AM strain on different soils microbiomes, pristine soil (PS), chronically contaminated soil (IPK) and recently contaminated soil (Phe) and their implications in bioremediation efficiency was studied by focusing on the ecology that drives bacterial communities in response to inoculation. AM strain draft genome codifies genes for metabolism of aromatic and aliphatic hydrocarbons. In Phe, the inoculation improved the elimination of phenanthrene during the whole treatment, whereas in IPK no improvement of degradation of any PAH was observed. Through the pyrosequencing analysis, we observed that inoculation managed to increase the richness and diversity in both contaminated microbiomes, therefore, independently of PAH degradation improvement, we observed clues of inoculant establishment, suggesting it may use other resources to survive. On the other hand, the inoculation did not influence the bacterial community of PS. On both contaminated microbiomes, incubation conditions produced a sharp increase on Actinomycetales and Sphingomonadales orders, while inoculation caused a relative decline of Actinomycetales. Inoculation of most diverse microbiomes, PS and Phe, produced a coupled increase of Sphingomonadales , Burkholderiales and Rhizobiales orders, although it may exist a synergy between those genera; our results suggest that this would not be directly related to PAH degradation.

Description: We investigated the properties of the stellar populations in the discs of a sample of 10 spiral galaxies. Our analysis focused on the galaxy region where the disc contributes more than 95 per cent of total surface brightness in order to minimize the contamination of the bulge and bar. The luminosity-weighted age and metallicity were obtained by fitting the galaxy spectra with a linear combination of stellar population synthesis models, while the total overabundance of α-elements over iron was derived by measuring the line-strength indices. Most of the sample discs display a bimodal age distribution and they are characterized by a total [α/Fe] enhancement ranging from solar and supersolar. We interpreted the age bimodality as due to the simultaneous presence of both a young (Age ≤ 4 Gyr) and an old (Age 〉 4 Gyr) stellar population. The old stellar component usually dominates the disc surface brightness and its light contribution is almost constant within the observed radial range. For this reason, no age gradient is observed in half of the sample galaxies. The old component is slightly more metal poor than the young one. The metallicity gradient is negative and slightly positive in the old and young components, respectively. These results are in agreement with an inside-out scenario of disc formation and suggest a reduced impact of the radial migration on the stellar populations of the disc. The young component could be the result of a second burst of star formation in gas captured from the environment.

Description: SUMMARY We present a new 3-D transversely isotropic shear wave velocity model of the European and Mediterranean upper mantle obtained by analysis of surface waves. Data used are fundamental-mode Rayleigh and Love group velocity measurements in the period range 35–170 s, taken on seismograms recorded by European stations for regional earthquakes. The tomographic inversion to map the 3-D earth structure is split into two steps. First, we regionalize the group velocity dispersion measurements, obtaining distinct geographical group velocity maps at different periods; then, each local dispersion curve is inverted separately to find the shear wave velocity structure at depth. The inversion benefits from using a priori information from a 3-D global mantle model (S20RTS) and a new detailed European crustal model (EPcrust) to constrain the shallower layers. The inversion scheme follows a non-linear iterative algorithm by which Rayleigh and Love group slowness are inverted simultaneously for the best-fitting isotropic Voigt shear wave speed and radial anisotropy parameter ( v SH − v SV ) . Final merging of the v S profiles results in a new higher resolution 3-D model of European upper mantle. We find that Western Europe and Mediterranean Sea are mainly characterized by relatively low velocities, strongly contrasting with the fast roots of the Eastern European Craton. Many regional scale structures are also evident in the model, thus providing insights into the complex geodynamic framework of the European continent. Most prominent are the low-velocity West Mediterranean spreading basins and European Cenozoic rift system, and seismically fast features connected to subduction of Adria microplate, Hellenic Arc and Calabrian Arc. Radial anisotropy does not vary very significantly with respect to the PREM profile, as available data only resolve lateral variations to a limited degree due to trade-off with velocity. EPmantle has the potential to provide a reliable seismological reference for the upper-mantle structure in the broad European region.

Description: Plant artificial micro-RNAs (amiRs) have been engineered to target viral genomes and induce their degradation. However, the exceptional evolutionary plasticity of RNA viruses threatens the durability of the resistance conferred by these amiRs. It has recently been shown that viral populations not experiencing strong selective pressure from an antiviral amiR may already contain enough genetic variability in the target sequence to escape plant resistance in an almost deterministic manner. Furthermore, it has also been shown that viral populations exposed to subinhibitory concentrations of the antiviral amiR speed up this process. In this article, we have characterized the molecular evolutionary dynamics of an amiR target sequence in a viral genome under both conditions. The use of Illumina ultradeep sequencing has allowed us to identify virus sequence variants at frequencies as low as 2 x 10 –6 and to track their variation in time before and after the viral population was able of successfully infecting plants fully resistant to the ancestral virus. We found that every site in the amiR-target sequence of the viral genome presented variation and that the variant that eventually broke resistance was sampled among the many coexisting ones. In this system, viral evolution in fully susceptible plants results from an equilibrium between mutation and genetic drift, whereas evolution in partially resistant plants originates from more complex dynamics involving mutation, selection, and drift.

Description: Small kinematically decoupled stellar discs with scalelengths of a few tens of parsec are known to reside in the centre of galaxies. Different mechanisms have been proposed to explain how they form, including gas dissipation and merging of globular clusters. Using archival Hubble Space Telescope imaging and ground-based integral-field spectroscopy, we investigated the structure and stellar populations of the nuclear stellar disc hosted in the interacting SB0 galaxy NGC 1023. The stars of the nuclear disc are remarkably younger and more metal rich with respect to the host bulge. These findings support a scenario in which the nuclear disc is the end result of star formation in metal enriched gas piled up in the galaxy centre. The gas can be of either internal or external origin, i.e. from either the main disc of NGC 1023 or the nearby satellite galaxy NGC 1023A. The dissipationless formation of the nuclear disc from already formed stars, through the migration and accretion of star clusters into the galactic centre, is rejected.

Description: Approximately 20 per cent of early-type galaxies host small nuclear stellar discs that are tens to a few hundred parsecs in size. Such discs are expected to be easily disrupted during major galactic encounters, hence their age serve to constrain their assembly history. We use VIsible MultiObject Spectrograph integral-field spectroscopic observations for the intermediate-mass E0 galaxy NGC 4458 and age-date its nuclear disc via high-resolution fitting of various model spectra. We find that the nuclear disc is at least 6 Gyr old. A clue to gain narrow limits to the stellar age is our knowledge of the nuclear disc contribution to the central surface brightness. The presence of an old nuclear disc, or the absence of disruptive encounters since z  ~ 0.6, for a small galaxy such as NGC 4458 which belongs to the Virgo cluster, may be consistent with a hierarchical picture for galaxy formation where the smallest galaxies assembles earlier and the crowded galactic environments reduce the incidence of galaxy mergers. On the other hand, NGC 4458 displays little or no bulk rotation except for a central kpc-scale kinematically decoupled core. Slow rotation and decoupled core are usually explained in terms of mergers. The presence and age of the nuclear disc constraint these mergers to have happened at high redshift.

Description: SUMMARY The structure of the Earth’s upper mantle near convergent plate margins, such as along the Nubia–Eurasia collision zone in the Mediterranean, involves strong seismic wave speed contrasts associated with subducting lithospheric slabs and opening backarc basins. In this environment, seismic wave propagation is strongly influenced by heterogeneity, and requires appropriate modelling practice. Although accurate numerical methods are often used to model seismic traveltimes in the crust, only approximate techniques have been used for the mantle, on the assumption that speed contrasts are weaker. We devise, optimize, and test a method aimed at recovering strongly heterogeneous mantle structures using a finite-difference scheme to calculate first-arrival traveltimes and trace seismic rays with high accuracy even in the presence of strong gradients. We adapt this forward scheme—successfully used in local-scale tomography—to spherical geometry through source-specific Earth flattening approximations, and we split calculations in meshes with different step size to model optimally the crust (with a 2 km step) and the mantle (6 km step). We then use an iterative non-linear inversion approach, starting from a simple 1-D prior model. We test the ability of this procedure to reconstruct sample structures, devised to be illustrative for the Mediterranean region, using synthetic data calculated on the real distribution of sources and stations reported by the Bulletins of the International Seismological Centre (ISC). Besides regular checkerboard patterns, we also reconstruct a more representative model. Different strategies are used and compared in linear and non-linear inversion. We find that a linear approach, by which rays are only traced once in the background model, may result in an illusory fit to data. Realistic upper-mantle structures strongly deflect seismic rays, and correct paths can only be found after a few iterations. Although linear inversion seems able to identify the main features quite well, we verify how non-linear inversion and 3-D ray tracing significantly improve the results, especially when we attempt to reconstruct a realistic structure. We also apply the finite-difference, non-linear, traveltime tomography to data from the ISC to retrieve upper-mantle structure in the Central Mediterranean. We verify that the non-linear inversion is able to reveal sharpened velocity contrasts and thinner bodies than linear inversion. Clear differentiation found in the non-linear result, between signatures of northern and southern Dinarides—showing lithosphere subducting only beneath the southern sector—is more coherent with the regional geodynamic framework. Such improvements due to non-linear mantle tomography may contribute to the general picture of slab detachment and small-scale mantle convection in the Mediterranean region, and therefore, significantly impact on geodynamic implications of resulting models.