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  • 1
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    BioPlat: a software for human cancer biomarker discovery (2014)
    Oxford University Press
    Details
    Publication Date: 2014-06-17
    Description: : Development of effective tools such as oligo-microarrays and next-generation sequencing methods for monitoring gene expression on a large scale has resulted in the discovery of gene signatures with prognostic/predictive value in various malignant neoplastic diseases. However, with the exponential growth of gene expression databases, biologists are faced with the challenge of extracting useful information from these repositories. Here, we present a software package, BioPlat (Biomarkers Platform), which allows biologists to identify novel prognostic and predictive cancer biomarkers based on the data mining of gene expression signatures and gene expression profiling databases. BioPlat has been designed as an easy-to-use and flexible desktop software application, which provides a set of analytical tools related to data extraction, preprocessing, filtering, gene expression signature calculation, in silico validation, feature selection and annotation that leverage the integration and reuse of gene expression signatures in the context of follow-up data. Availability and implementation: BioPlat is a platform-independent software implemented in Java and supported on GNU/Linux and MS Windows, which is freely available for download at http://www.cancergenomics.net . Contact: mcabba@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Mouse model reveals the role of SOX7 in the development of congenital diaphragmatic hernia associated with recurrent deletions of 8p23.1 (2012)
    Oxford University Press
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    Publication Date: 2012-08-28
    Description: Recurrent microdeletions of 8p23.1 that include GATA4 and SOX7 confer a high risk of both congenital diaphragmatic hernia (CDH) and cardiac defects. Although GATA4-deficient mice have both CDH and cardiac defects, no humans with cardiac defects attributed to GATA4 mutations have been reported to have CDH. We were also unable to identify deleterious GATA4 sequence changes in a CDH cohort. This suggested that haploinsufficiency of another 8p23.1 gene may contribute, along with GATA4 , to the development of CDH. To determine if haploinsufficiency of SOX7 —another transcription factor encoding gene—contributes to the development of CDH, we generated mice with a deletion of the second exon of Sox7 . A portion of these Sox7 ex2/+ mice developed retrosternal diaphragmatic hernias located in the anterior muscular portion of the diaphragm. Anterior CDH is also seen in Gata4 +/– mice and has been described in association with 8p23.1 deletions in humans. Immunohistochemistry revealed that SOX7 is expressed in the vascular endothelial cells of the developing diaphragm and may be weakly expressed in some diaphragmatic muscle cells. Sox7 ex2/ex2 embryos die prior to diaphragm development with dilated pericardial sacs and failure of yolk sac remodeling suggestive of cardiovascular failure. Similar to our experience screening GATA4 , no clearly deleterious SOX7 sequence changes were identified in our CDH cohort. We conclude that haploinsufficiency of Sox7 or Gata4 is sufficient to produce anterior CDH in mice and that haploinsufficiency of SOX7 and GATA4 may each contribute to the development of CDH in individuals with 8p23.1 deletions.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    Rescue of severely affected dystrophin/utrophin-deficient mice through scAAV-U7snRNA-mediated exon skipping (2012)
    Oxford University Press
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    Publication Date: 2012-05-11
    Description: Duchenne muscular dystrophy (DMD) is a severe neuromuscular disorder caused by mutations in the dystrophin gene that result in the absence of functional protein. Antisense-mediated exon skipping is one of the most promising approaches for the treatment of DMD and recent clinical trials have demonstrated encouraging results. However, antisense oligonucleotide-mediated exon skipping for DMD still faces major hurdles such as extremely low efficacy in the cardiac muscle, poor cellular uptake and relatively rapid clearance from circulation, which means that repeated administrations are required to achieve some therapeutic efficacy. To overcome these limitations, we previously proposed the use of small nuclear RNAs (snRNAs), especially U7snRNA to shuttle the antisense sequences after vectorization into adeno-associated virus (AAV) vectors. In this study, we report for the first time the efficiency of the AAV-mediated exon skipping approach in the utrophin/dystrophin double-knockout (dKO) mouse which is a very severe and progressive mouse model of DMD. Following a single intravenous injection of scAAV9-U7ex23 in dKO mice, near-normal levels of dystrophin expression were restored in all muscles examined, including the heart. This resulted in a considerable improvement of their muscle function and dystrophic pathology as well as a remarkable extension of the dKO mice lifespan. These findings suggest great potential for AAV-U7 in systemic treatment of the DMD phenotype.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 4
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    GReEn: a tool for efficient compression of genome resequencing data (2012)
    Oxford University Press
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    Publication Date: 2012-02-28
    Description: Research in the genomic sciences is confronted with the volume of sequencing and resequencing data increasing at a higher pace than that of data storage and communication resources, shifting a significant part of research budgets from the sequencing component of a project to the computational one. Hence, being able to efficiently store sequencing and resequencing data is a problem of paramount importance. In this article, we describe GReEn (Genome Resequencing Encoding), a tool for compressing genome resequencing data using a reference genome sequence. It overcomes some drawbacks of the recently proposed tool GRS, namely, the possibility of compressing sequences that cannot be handled by GRS, faster running times and compression gains of over 100-fold for some sequences. This tool is freely available for non-commercial use at ftp://ftp.ieeta.pt/~ap/codecs/GReEn1.tar.gz .
    Keywords: Computational Methods, Genomics, Miscellaneous/other
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Solar radiation measurements compared to simulations at the BSRN Izaña station. Mineral dust radiative forcing and efficiency study (2013)
    Wiley
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    Publication Date: 2013-12-07
    Description: [1]  This paper presents a comparative study of shortwave downward radiation (SDR) measurements and simulations, obtained with the radiative transfer model (RTM) LibRadtran, at the Baseline Surface Radiation Network (BSRN) site of Izaña Atmospheric Observatory (IZA, Spain). The analysis is based on cloud-free days between March 2009 and August 2012 (386 days), including aerosol-free and Saharan mostly pure mineral dust conditions and comparing the day-to-day, annual and inter-annual variability.The observed agreement between simulations and measurements is excellent: the variance of daily measurements overall agrees within 99% with the variance of daily simulations and the mean bias (simulations - measurements) is -0.30 ± 0.24 MJm -2 (-1.1 ± 0.9%) for global, -0.16 ± 0.34 MJm -2 (-0.4 ± 0.9%) for direct and +0.02 ± 0.25 MJm -2 (+0.9 ± 9.2%) for diffuse SDR. Furthermore, the diurnally averaged aerosol radiative forcing ( Δ DF) and radiative forcing efficiency ( ΔDF eff ) due to Saharan mostly pure mineral dust events has been computed at Izaña Observatory. The mean Δ DF values are -7 ± 1, -96 ± 5 and 44 ± 2 Wm -2 for global, direct and diffuse BSRN SDR,respectively (mean aerosol optical depth, AOD, at 500 nm of 0.18 ± 0.01), while the mean ΔDF eff values are -59 ± 6, -495 ± 11 and 230 ± 8 Wm -2 per unit of AOD at 500 nm for global, direct and diffuse BSRN SDR, respectively. These values highlight the importance of scattering processes for mineral dust aerosols: the ratio between Δ DF and the corresponding SDR without aerosols is ~ 2.5% for diffuse SDR versus 0.2% for direct SDR. This illustrates the significant potential of mineral dust particles to cool the Earth-atmosphere system.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    Organization of the human mitochondrial transcription initiation complex (2014)
    Oxford University Press
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    Publication Date: 2014-04-03
    Description: Initiation of transcription in human mitochondria involves two factors, TFAM and TFB2M, in addition to the mitochondrial RNA polymerase, POLRMT. We have investigated the organization of the human mitochondrial transcription initiation complex on the light-strand promoter (LSP) through solution X-ray scattering, electron microscopy (EM) and biochemical studies. Our EM results demonstrate a compact organization of the initiation complex, suggesting that protein–protein interactions might help mediate initiation. We demonstrate that, in the absence of DNA, only POLRMT and TFAM form a stable interaction, albeit one with low affinity. This is consistent with the expected transient nature of the interactions necessary for initiation and implies that the promoter DNA acts as a scaffold that enables formation of the full initiation complex. Docking of known crystal structures into our EM maps results in a model for transcriptional initiation that strongly correlates with new and existing biochemical observations. Our results reveal the organization of TFAM, POLRMT and TFB2M around the LSP and represent the first structural characterization of the entire mitochondrial transcriptional initiation complex.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Low-resolution optical spectra of ultracool dwarfs with OSIRIS/GTC (2014)
    Oxford University Press
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    Publication Date: 2014-12-11
    Description: We present the results of low-resolution optical spectroscopy with OSIRIS/GTC (Optical System for Imaging and Low Resolution Integrated Spectroscopy/Gran Telescopio Canarias) for a sample of ultracool dwarfs. For a subsample of seven objects, based on 2 Micron Sky Survey (2MASS) NIR photometric colours, a ‘photometric’ spectral type is determined and compared to the results of the optical spectroscopy. For the stars, showing Hα line in emission, equivalent widths were measured, and the ratio of Hα to bolometric luminosity were calculated. We find that two dwarfs show the presence of magnetic activity over long periods, LP 326-21 – quasi-constant-like, and 2MASS J17071830+6439331 – variable.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Decoupled crust-mantle accommodation of Africa-Eurasia convergence in the NW Moroccan margin (2011)
    Wiley
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    Publication Date: 2011-08-16
    Description: The extent of the area accommodating convergence between the African and Iberian plates, how this convergence is partitioned between crust and mantle, and the role of the plate boundary in accommodating deformation are not well-understood subjects. We calculate the structure of the lithosphere derived from its density distribution along a profile running from the Tagus Abyssal Plain to the Sahara Platform and crossing the Gorringe Bank, the NW Moroccan margin, and the Atlas Mountains. The model is based on the integration of gravity, geoid, elevation, and heat flow data and on the crustal structure across the NW Moroccan margin derived from reflection and wide-angle seismic data. The resulting mantle density anomalies suggest important variations of the lithosphere-asthenosphere boundary (LAB) topography, indicating prominent lithospheric mantle thickening beneath the margin (LAB 〉 200 km depth) followed by thinning beneath the Atlas Mountains (LAB ∼90 km depth). At crustal levels the Iberia-Africa convergence is sparsely accommodated in a ∼950 km wide area and localized in the Atlas and Gorringe regions, with an inferred shortening of ∼50 km. In contrast, mantle thickening accommodates a 400 km wide region, thus advocating for a decoupled crustal-mantle mechanical response. A combination of mantle underthrusting due to oblique convergence, together with a viscous dripping fed by lateral mantle dragging, can explain the imaged lithospheric structure. The model is consistent with crustal shortening estimates and with the accommodation of part of the Iberia-Africa convergence farther NW of the Gorringe Bank and/or off the strike of the profile.
    Print ISSN: 0148-0227
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
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    Uncovering multiple Wolf-Rayet star clusters and the ionized ISM in Mrk 178: the closest metal-poor Wolf-Rayet H II galaxy (2013)
    Oxford University Press
    Details
    Publication Date: 2013-06-18
    Description: New integral field spectroscopy (IFS) has been obtained for the nearby metal-poor Wolf–Rayet (WR) galaxy Mrk 178 to examine the spatial correlation between its WR stars and the neighbouring ionized interstellar medium (ISM). The strength of the broad WR features and its low metallicity make Mrk 178 an intriguing object. We have detected the blue and red WR bumps in different locations across the field of view (~300 pc  x 230 pc) in Mrk 178. The study of the WR content has been extended, for the first time, beyond its brightest star-forming knot uncovering new WR star clusters. Using Large/Small Magellanic Cloud-template WR stars, we empirically estimate a minimum of ~20 WR stars within the region sampled. Maps of the spatial distribution of the emission lines and of the physical–chemical properties of the ionized ISM have been created and analysed. Here, we refine the statistical methodology by Pérez-Montero et al. (2011) to probe the presence of variations in the ISM properties. An error-weighted mean of 12+log(O/H) = 7.72 ± 0.01 is taken as the representative oxygen abundance for Mrk 178. A localized N and He enrichment, spatially correlated with WR stars, is suggested by this analysis. Nebular He ii 4686 emission is shown to be spatially extended reaching well beyond the location of the WR stars. This spatial offset between WRs and He ii emission can be explained based on the mechanical energy input into the ISM by the WR star winds, and does not rule out WR stars as the He ii ionization source. We study systematic aperture effects on the detection and measurement of the WR features, using Sloan Digital Sky Survey spectra combined with the power of IFS. In this regard, the importance of targeting low metallicity nearby systems is discussed.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Simultaneous Purifying Selection on the Ancestral MC1R Allele and Positive Selection on the Melanoma-Risk Allele V60L in South Europeans (2013)
    Oxford University Press
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    Publication Date: 2013-11-27
    Description: In humans, the geographical apportionment of the coding diversity of the pigmentary locus melanocortin-1 receptor ( MC1R ) is, unusually, higher in Eurasians than in Africans. This atypical observation has been interpreted as the result of purifying selection due to functional constraint on MC1R in high UV-B radiation environments. By analyzing 3,142 human MC1R alleles from different regions of Spain in the context of additional haplotypic information from the 1000 Genomes (1000G) Project data, we show that purifying selection is also strong in southern Europe, but not so in northern Europe. Furthermore, we show that purifying and positive selection act simultaneously on MC1R . Thus, at least in Spain, regions at opposite ends of the incident UV-B radiation distribution show significantly different frequencies for the melanoma-risk allele V60L (a mutation also associated to red hair and fair skin and even blonde hair), with higher frequency of V60L at those regions of lower incident UV-B radiation. Besides, using the 1000G south European data, we show that the V60L haplogroup is also characterized by an extended haplotype homozygosity (EHH) pattern indicative of positive selection. We, thus, provide evidence for an adaptive value of human skin depigmentation in Europe and illustrate how an adaptive process can simultaneously help to maintain a disease-risk allele. In addition, our data support the hypothesis proposed by Jablonski and Chaplin (Human skin pigmentation as an adaptation to UVB radiation. Proc Natl Acad Sci U S A . 2010;107:8962–8968), which posits that habitation of middle latitudes involved the evolution of partially depigmented phenotypes that are still capable of suitable tanning.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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