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  • Oxford University Press  (10)
  • International Union of Crystallography (IUCr)  (4)
  • American Geophysical Union  (2)
  • Copernicus  (1)
  • 1
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    Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-27
    Description: Motivation: With the advent of meta-‘omics’ data, the use of metabolic networks for the functional analysis of microbial communities became possible. However, while network-based methods are widely developed for single organisms, their application to bacterial communities is currently limited. Results: Herein, we provide a novel, context-specific reconstruction procedure based on metaproteomic and taxonomic data. Without previous knowledge of a high-quality, genome-scale metabolic networks for each different member in a bacterial community, we propose a meta-network approach, where the expression levels and taxonomic assignments of proteins are used as the most relevant clues for inferring an active set of reactions. Our approach was applied to draft the context-specific metabolic networks of two different naphthalene-enriched communities derived from an anthropogenically influenced, polyaromatic hydrocarbon contaminated soil, with (CN2) or without (CN1) bio-stimulation. We were able to capture the overall functional differences between the two conditions at the metabolic level and predict an important activity for the fluorobenzoate degradation pathway in CN1 and for geraniol metabolism in CN2. Experimental validation was conducted, and good agreement with our computational predictions was observed. We also hypothesize different pathway organizations at the organismal level, which is relevant to disentangle the role of each member in the communities. The approach presented here can be easily transferred to the analysis of genomic, transcriptomic and metabolomic data. Contact: fplanes@ceit.es or mferrer@icp.csic.es 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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    Improving initial conditions for cosmological N-body simulations (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-29
    Description: In cosmological N -body simulations, the representation of dark matter as discrete ‘macroparticles’ suppresses the growth of structure, such that simulations no longer reproduce linear theory on small scales near k Nyquist . Marcos et al. demonstrate that this is due to sparse sampling of modes near k Nyquist and that the often-assumed continuum growing modes are not proper growing modes of the particle system. We develop initial conditions (ICs) that respect the particle linear theory growing modes and then rescale the mode amplitudes to account for growth suppression. These ICs also allow us to take advantage of our very accurate N -body code abacus to implement second-order Lagrangian perturbation theory (2LPT) in configuration space. The combination of 2LPT and rescaling improves the accuracy of the late-time power spectra, halo mass functions, and halo clustering. In particular, we achieve 1 per cent accuracy in the power spectrum down to k Nyquist , versus k Nyquist /4 without rescaling or k Nyquist /13 without 2LPT, relative to an oversampled reference simulation. We anticipate that our 2LPT will be useful for large simulations where fast Fourier transforms are expensive and that rescaling will be useful for suites of medium-resolution simulations used in cosmic emulators and galaxy survey mock catalogues. Code to generate ICs is available at https://github.com/lgarrison/zeldovich-PLT .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinsons disease revealed by deep sequencing analysis (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-27
    Description: Motivation: Most computational tools for small non-coding RNAs (sRNA) sequencing data analysis focus in microRNAs (miRNAs), overlooking other types of sRNAs that show multi-mapping hits. Here, we have developed a pipeline to non-redundantly quantify all types of sRNAs, and extract patterns of expression in biologically defined groups. We have used our tool to characterize and profile sRNAs in post-mortem brain samples of control individuals and Parkinson’s disease (PD) cases at early-premotor and late-symptomatic stages. Results: Clusters of co-expressed sRNAs mapping onto tRNAs significantly separated premotor and motor cases from controls. A similar result was obtained using a matrix of miRNAs slightly varying in sequence (isomiRs). The present framework revealed sRNA alterations at premotor stages of PD, which might reflect initial pathogenic perturbations. This tool may be useful to discover sRNA expression patterns linked to different biological conditions. Availability and Implementation: The full code is available at http://github.com/lpantano/seqbuster . Contact: lpantano@hsph.harvard.edu or eulalia.marti@crg.eu 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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  • 4
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    Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-02
    Description: As the use of RNA-seq has popularized, there is an increasing consciousness of the importance of experimental design, bias removal, accurate quantification and control of false positives for proper data analysis. We introduce the NOISeq R-package for quality control and analysis of count data. We show how the available diagnostic tools can be used to monitor quality issues, make pre-processing decisions and improve analysis. We demonstrate that the non-parametric NOISeqBIO efficiently controls false discoveries in experiments with biological replication and outperforms state-of-the-art methods. NOISeq is a comprehensive resource that meets current needs for robust data-aware analysis of RNA-seq differential expression.
    Keywords: Transcriptome Mapping - Monitoring Gene Expression
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Impaired mitochondrial oxidative phosphorylation in the peroxisomal disease X-linked adrenoleukodystrophy (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-26
    Description: X-linked adrenoleukodystrophy (X-ALD) is an inherited metabolic disorder of the nervous system characterized by axonopathy in spinal cords and/or cerebral demyelination, adrenal insufficiency and accumulation of very long-chain fatty acids (VLCFAs) in plasma and tissues. The disease is caused by malfunction of the ABCD1 gene, which encodes a peroxisomal transporter of VLCFAs or VLCFA-CoA. In the mouse, Abcd1 loss causes late onset axonal degeneration in the spinal cord, associated with locomotor disability resembling the most common phenotype in patients, adrenomyeloneuropathy. We have formerly shown that an excess of the VLCFA C26:0 induces oxidative damage, which underlies the axonal degeneration exhibited by the Abcd1 – mice. In the present study, we sought to investigate the noxious effects of C26:0 on mitochondria function. Our data indicate that in X-ALD patients' fibroblasts, excess of C26:0 generates mtDNA oxidation and specifically impairs oxidative phosphorylation (OXPHOS) triggering mitochondrial ROS production from electron transport chain complexes. This correlates with impaired complex V phosphorylative activity, as visualized by high-resolution respirometry on spinal cord slices of Abcd1 – mice. Further, we identified a marked oxidation of key OXPHOS system subunits in Abcd1 – mouse spinal cords at presymptomatic stages. Altogether, our results illustrate some of the mechanistic intricacies by which the excess of a fatty acid targeted to peroxisomes activates a deleterious process of oxidative damage to mitochondria, leading to a multifaceted dysfunction of this organelle. These findings may be of relevance for patient management while unveiling novel therapeutic targets for X-ALD.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
    Electronic Resource
    Electronic Resource
    An Algorithm for Automatic Mosaic Spread Analysis of a Protein Crystal (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 31 (1998), S. 523-532 
    Details
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The present paper describes the program MOSAICITY which assembles tools developed for the mosaic spread analysis of protein crystals. This analysis, performed in an automatic and nonparametric way, combines wavelet filters and morphological treatment in order to localize reflections in a diffraction pattern. The reflection intensities, rescaled according to incidence-beam intensity and corrected for the background, are measured using a fine rotation angle slicing. A Gaussian profile fitting is performed. The angular width can be corrected for the Lorentz factor, beam divergence and energy resolution in order to obtain an estimate of the mosaic spread of the crystal. For this last stage, a new analytical expression for the φ extent of the reflection range has been derived.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0021889897015045
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  • 7
    Electronic Resource
    Electronic Resource
    D2AM, a Beamline with a High-Intensity Point-Focusing Fixed-Exit Monochromator for Multiwavelength Anomalous Diffraction Experiments (1998)
    Chester : International Union of Crystallography (IUCr)
    Journal of synchrotron radiation 5 (1998), S. 1346-1356 
    Details
    ISSN: 1600-5775
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: D2AM is a french CRG beamline installed at the ESRF (European Synchrotron Radiation Facility) in Grenoble, with half of the time dedicated to biological macromolecule crystallography and half to materials science studies (diffraction, wide-angle and small-angle scattering). It is constructed at the front-end BM02 of the ESRF storage ring, using the X-ray beam from a 0.8 T bending magnet. D2AM entered into routine operation at the end of 1994, and is used either for single-wavelength or for multiwavelength anomalous diffraction studies. The beam is monochromated by an Si[111] two-crystal monochromator with a resolution of about 2 × 10−4. The first crystal is water cooled. The X-ray photon energy covers the range between 6.5 keV (λ ∼ 1.9 Å) and 17 keV (λ ∼ 0.7 Å), a domain of energy with many K or L absorption edges of heavy atoms of interest for biological macromolecules studies and in materials science. The X-ray beam is focused in the vertical plane by two long curved mirrors and in the horizontal plane by the second crystal of the monochromator which is given an adjustable sagittal curvature. A spot size of 0.3 × 0.1 mm (FWHM) is measured at the sample position. Both mirrors are cut out of a 6"-diameter 1.1 m-long Si single crystal, polished and coated with a 400 Å Pt thin film. The rugosity is better than 4 Å r.m.s. and the longitudinal slope error is better than 5 × 10−6 rad r.m.s. The first mirror is water cooled, the second is not. The beam intensity on the sample is about 1011 photon s−1 on a 0.3 × 0.3 mm focus area at 100 mA in the storage ring of the ESRF. The harmonic rejection ratio obtained with the two mirrors is better than 10−5 for λ/3. The combined optical system, mirror/monochromating-crystals/mirror, used on D2AM constitutes altogether a high-intensity point-focusing fixed-exit monochromator, which has the additional property that the energy resolution is not dependent on the beam divergence in use. Its stability and resolution are perfectly adapted to multiwavelength anomalous diffraction studies. The alignment of the mirrors and the monochromator is fully automated, taking 5 min, with the exception of the adjustment of the sagittal focusing. During multiwavelength diffraction experiments the wavelength is changed by a fast single monochromator rotation. Neither realignment of the mirrors nor readjustment of the beam focusing are necessary. The stability and reproducibility of the selected X-ray photon energy is better than 0.5 eV.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0909049598004257
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  • 8
    Electronic Resource
    Electronic Resource
    Data Compression for Diffraction Patterns (1998)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 54 (1998), S. 184-199 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Efficient coding (lossless) and compression (lossy) of diffraction patterns is important in protein crystallography experiments because of storage and transmission limitations. The goal is to reduce the bit-rate significantly while keeping diffraction peak intensity distortion at an acceptable level. This paper presents an overview of coding and compression techniques more or less adapted to such problems. A large part of this study is dedicated to time-frequency-transform based compression algorithms and some of their extensions. Wavelet based software has been developed and tested. Results are compared with the discrete cosine transform (DCT) and other classical algorithms. These tools seem attractive and very promising for analyzing and compressing signals with singularities and transient phenomena such as diffraction peaks. Tests were performed on a standard protein crystallography data set coming from the CCD detector of D2AM beamline at the European Synchrotron Radiation Facility at Grenoble. These were compressed with DCT and wavelet-based algorithms. It appears that alterations of the result of the processing of restored images remain very weak for compression rates up to 10. These preliminary results indicate that the proposed wavelet method is a good standard technique for efficient compression of diffraction patterns.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444997007257
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  • 9
    Electronic Resource
    Electronic Resource
    Automated data processing on beamline FIP (BM30A) at ESRF (2001)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1752-1753 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Automation of protein crystallography synchrotron beamlines is becoming necessary to face challenging structural genomics projects. In this context, a program has been developed that processes diffraction frames using popular software but analyzes statistics and makes choices the way crystallographers usually do. This program includes the classical peak search, indexing, integration, scaling and anomalous signal analysis. The result, comparable with that obtained by standard users, is rapidly available, providing the required information for a more efficient use of the beam time.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444901013385
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  • 10
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    Globally aligned photomosaic of the Lucky Strike hydrothermal vent field (Mid-Atlantic Ridge, 37°18.5′N) : release of georeferenced data, mosaic construction, and viewing software (2010)
    American Geophysical Union
    Details
    Publication Date: 2022-05-25
    Description: Author Posting. © American Geophysical Union, 2008. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Geochemistry Geophysics Geosystems 9 (2008): Q12009, doi:10.1029/2008GC002204.
    Description: We present a georeferenced photomosaic of the Lucky Strike hydrothermal vent field (Mid-Atlantic Ridge, 37°18′N). The photomosaic was generated from digital photographs acquired using the ARGO II seafloor imaging system during the 1996 LUSTRE cruise, which surveyed a ∼1 km2 zone and provided a coverage of ∼20% of the seafloor. The photomosaic has a pixel resolution of 15 mm and encloses the areas with known active hydrothermal venting. The final mosaic is generated after an optimization that includes the automatic detection of the same benthic features across different images (feature-matching), followed by a global alignment of images based on the vehicle navigation. We also provide software to construct mosaics from large sets of images for which georeferencing information exists (location, attitude, and altitude per image), to visualize them, and to extract data. Georeferencing information can be provided by the raw navigation data (collected during the survey) or result from the optimization obtained from image matching. Mosaics based solely on navigation can be readily generated by any user but the optimization and global alignment of the mosaic requires a case-by-case approach for which no universally software is available. The Lucky Strike photomosaics (optimized and navigated-only) are publicly available through the Marine Geoscience Data System (MGDS, http://www.marine-geo.org). The mosaic-generating and viewing software is available through the Computer Vision and Robotics Group Web page at the University of Girona (http://eia.udg.es/∼rafa/mosaicviewer.html).
    Description: This work has been supported by the EU Marie Curie RTNs MOMARNet (OD, RG, JE, LN, JF, NG) and FREESUBNet (RG, NG, XC), the Spanish Ministry of Science and Innovation (grant CTM2007–64751; RG, JE), CNRS and ANR (grant ANR NT05–3_42212, JE), ICREA (LN), and by the Generalitat de Catalunya (JE, RG). JF has been funded by MICINN under FPI grant BES-2006-12733 and NG has been supported by MICINN under the ‘‘Ramon y Cajal’’ program.
    Keywords: Mid-ocean ridge ; Photomosaic ; MoMAR ; Lucky Strike ; Hydrothermal field
    Repository Name: Woods Hole Open Access Server
    Type: Article
    Format: application/pdf
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