ALBERT

Description: DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging owing to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of cytosine–guanine dinucleotide islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared with adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development.

Description: Extensive and multi-dimensional data sets generated from recent cancer omics profiling projects have presented new challenges and opportunities for unraveling the complexity of cancer genome landscapes. In particular, distinguishing the unique complement of genes that drive tumorigenesis in each patient from a sea of passenger mutations is necessary for translating the full benefit of cancer genome sequencing into the clinic. We address this need by presenting a data integration framework (OncoIMPACT) to nominate patient-specific driver genes based on their phenotypic impact. Extensive in silico and in vitro validation helped establish OncoIMPACT's robustness, improved precision over competing approaches and verifiable patient and cell line specific predictions (2/2 and 6/7 true positives and negatives, respectively). In particular, we computationally predicted and experimentally validated the gene TRIM24 as a putative novel amplified driver in a melanoma patient. Applying OncoIMPACT to more than 1000 tumor samples, we generated patient-specific driver gene lists in five different cancer types to identify modes of synergistic action. We also provide the first demonstration that computationally derived driver mutation signatures can be overall superior to single gene and gene expression based signatures in enabling patient stratification and prognostication. Source code and executables for OncoIMPACT are freely available from http://sourceforge.net/projects/oncoimpact .

Description: Detecting allelic biases from high-throughput sequencing data requires an approach that maximises sensitivity while minimizing false positives. Here, we present Allelome.PRO, an automated user-friendly bioinformatics pipeline, which uses high-throughput sequencing data from reciprocal crosses of two genetically distinct mouse strains to detect allele-specific expression and chromatin modifications. Allelome.PRO extends approaches used in previous studies that exclusively analyzed imprinted expression to give a complete picture of the ‘allelome’ by automatically categorising the allelic expression of all genes in a given cell type into imprinted, strain-biased, biallelic or non-informative. Allelome.PRO offers increased sensitivity to analyze lowly expressed transcripts, together with a robust false discovery rate empirically calculated from variation in the sequencing data. We used RNA-seq data from mouse embryonic fibroblasts from F1 reciprocal crosses to determine a biologically relevant allelic ratio cutoff, and define for the first time an entire allelome. Furthermore, we show that Allelome.PRO detects differential enrichment of H3K4me3 over promoters from ChIP-seq data validating the RNA-seq results. This approach can be easily extended to analyze histone marks of active enhancers, or transcription factor binding sites and therefore provides a powerful tool to identify candidate cis regulatory elements genome wide.

Description: The terrestrial reference frame is a cornerstone for modern geodesy and its applications for a wide range of Earth sciences. The underlying assumption for establishing a terrestrial reference frame is that the motion of the solid Earth's figure centre relative to the mass centre of the Earth system on a multidecadal timescale is linear. However, past international terrestrial reference frames (ITRFs) showed unexpected accelerated motion in their translation parameters. Based on this underlying assumption, the inconsistency of relative origin motions of the ITRFs has been attributed to data reduction imperfection. We investigated the impact of surface mass loading from atmosphere, ocean, snow, soil moisture, ice sheet, glacier and sea level from 1983 to 2008 on the geocentre variations. The resultant geocentre time-series display notable trend acceleration from 1998 onward, in particular in the z -component. This effect is primarily driven by the hydrological mass redistribution in the continents (soil moisture, snow, ice sheet and glacier). The acceleration is statistically significant at the 99 per cent confidence level as determined using the Mann–Kendall test, and it is highly correlated with the satellite laser ranging determined translation series. Our study, based on independent geophysical and hydrological models, demonstrates that, in addition to systematic errors from analysis procedures, the observed non-linearity of the Earth-system behaviour at interannual timescales is physically driven and is able to explain 42 per cent of the disparity between the origins of ITRF2000 and ITRF2005, as well as the high level of consistency between the ITRF2005 and ITRF2008 origins.

Description: Sensitive instruments like strainmeters and tiltmeters are necessary for measuring slowly varying low amplitude Earth deformations. Nonetheless, laser and fibre interferometers are particularly suitable for interrogating such instruments due to their extreme precision and accuracy. In this paper, a practical design of a simple pendulum borehole tiltmeter based on laser fibre interferometric displacement sensors is presented. A prototype instrument has been constructed using welded borosilicate with a pendulum length of 0.85 m resulting in a main resonance frequency of 0.6 Hz. By implementing three coplanar extrinsic fibre Fabry-Perot interferometric probes and appropriate signal filtering, our instrument provides tilt measurements that are insensitive to parasitic deformations caused by temperature and pressure variations. This prototype has been installed in an underground facility (Rustrel, France) where results show accurate measurements of Earth strains derived from Earth and ocean tides, local hydrologic effects, as well as local and remote earthquakes. The large dynamic range and the high sensitivity of this tiltmeter render it an invaluable tool for numerous geophysical applications such as transient fault motion, volcanic strain and reservoir monitoring.

Description: We review the theory of the Earth's elastic and gravitational response to a surface disk load. The solutions for displacement of the surface and the geoid are developed using expansions of Legendre polynomials, their derivatives and the load Love numbers. We provide a matlab  function called diskload that computes the solutions for both uncompensated and compensated disk loads. In order to numerically implement the Legendre expansions, it is necessary to choose a harmonic degree, n max , at which to truncate the series used to construct the solutions. We present a rule of thumb (ROT) for choosing an appropriate value of n max , describe the consequences of truncating the expansions prematurely and provide a means to judiciously violate the ROT when that becomes a practical necessity.

Description: In autumn 2012, the new release 05 (RL05) of monthly geopotencial spherical harmonics Stokes coefficients (SC) from Gravity Recovery and Climate Experiment (GRACE) mission was published. This release reduces the noise in high degree and order SC, but they still need to be filtered. One of the most common filtering processing is the combination of decorrelation and Gaussian filters. Both of them are parameters dependent and must be tuned by the users. Previous studies have analyzed the parameters choice for the RL05 GRACE data for oceanic applications, and for RL04 data for global application. This study updates the latter for RL05 data extending the statistics analysis. The choice of the parameters of the decorrelation filter has been optimized to: (1) balance the noise reduction and the geophysical signal attenuation produced by the filtering process; (2) minimize the differences between GRACE and model-based data and (3) maximize the ratio of variability between continents and oceans. The Gaussian filter has been optimized following the latter criteria. Besides, an anisotropic filter, the fan filter, has been analyzed as an alternative to the Gauss filter, producing better statistics.

Description: RNA-seq is a sensitive and accurate technique to compare steady-state levels of RNA between different cellular states. However, as it does not provide an account of transcriptional activity per se , other technologies are needed to more precisely determine acute transcriptional responses. Here, we have developed an easy, sensitive and accurate novel computational method, iRNA-seq , for genome-wide assessment of transcriptional activity based on analysis of intron coverage from total RNA-seq data. Comparison of the results derived from iRNA-seq analyses with parallel results derived using current methods for genome-wide determination of transcriptional activity, i.e. global run-on (GRO)-seq and RNA polymerase II (RNAPII) ChIP-seq, demonstrate that iRNA-seq provides similar results in terms of number of regulated genes and their fold change. However, unlike the current methods that are all very labor-intensive and demanding in terms of sample material and technologies, iRNA-seq is cheap and easy and requires very little sample material. In conclusion, iRNA-seq offers an attractive novel alternative to current methods for determination of changes in transcriptional activity at a genome-wide level.

Description: In the present work we illustrate a new local inversion algorithm to retrieve the Moho depth from GOCE (Gravity field and steady-state Ocean Circulation Explorer) gravity field. In details the proposed procedure can be divided into two main steps: the first one consists in recognizing and isolating the different geological provinces in the study area by exploiting information coming from the GOCE global gravity field model. Once the main geological provinces are defined, a function relating the crust density of each province with depth is built and used to reduce the data. The gravitational effects of sediments, topography, bathymetry and upper mantle are also removed. In the second step the residual gravitational field is inverted to retrieve the Moho depth and some information on the crustal density. In particular, the clustering of geological province is performed by means of an automatic Bayesian classification algorithm while the inversion of GOCE residual field is performed by adapting the global algorithm developed in the framework of the GEMMA project to the local scale. The procedure, based on an iterative Wiener filter, allows to compute the Moho depth considering lateral as well as radial variations of crustal density. The algorithm has been applied to the fifth release of GOCE time-wise global gravity field model to infer information on the crustal structure in the Western Balkan area, that is, the region laying between Bulgaria and the Adriatic Sea. This region is one of the most complex and active, from the tectonic point of view, in the whole Europe and it is characterized by the presence of the Alpine-Himalayan orogenic belt, formed by the collision between the African and Eurasian plates, and by the opening of the Pannonian Basin. Results show a good agreement between the obtained geological provinces with the actual knowledge on the region. The resulting Moho depth ranges between about 20 km beneath the Adriatic Sea and 45 km in the Dinarides. Comparisons with available seismic data show differences smaller than 1 km (standard deviation).

Description: The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates’ recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins , implemented in Python and C and supported on Linux and Mac OS X.