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  • 2015-2019  (5)
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  • 1
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    Were the May 2012 Emilia-Romagna earthquakes induced? A coupled flow-geomechanics modeling assessment (2016)
    Wiley
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    Publication Date: 2016-07-03
    Description: Seismicity induced by fluid injection and withdrawal has emerged as a central element of the scientific discussion around subsurface technologies that tap into water and energy resources. Here we present the application of coupled flow-geomechanics simulation technology to the post mortem analysis of a sequence of damaging earthquakes (Mw = 6.0 and 5.8) in May 2012 near the Cavone oil field, in Northern Italy. This sequence raised the question of whether these earthquakes might have been triggered by activities due to oil and gas production. Our analysis strongly suggests that the combined effects of fluid production and injection from the Cavone field were not a driver for the observed seismicity. More generally, our study illustrates that computational modeling of coupled flow and geomechanics permits the integration of geologic, seismotectonic, well log, fluid pressure and flow rate, and geodetic data, and provides a promising approach for assessing and managing hazards associated with induced seismicity.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    CWC22-dependent pre-mRNA splicing and eIF4A3 binding enables global deposition of exon junction complexes (2015)
    Oxford University Press
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    Publication Date: 2015-05-20
    Description: In metazoan cells, spliced mRNAs are marked by the exon junction complex (EJC), a multi-protein complex that serves as a key regulator of post-transcriptional mRNA metabolism. Deposition of EJCs on mRNA is intimately linked to the splicing process. The spliceosomal protein CWC22 directly binds the core EJC-protein eIF4A3, guides it to the spliceosome and initiates EJC assembly. In addition, CWC22 is involved in the splicing process itself, but the molecular details of its dual function remain elusive. Here we analyze the mechanisms, by which CWC22 co-regulates pre-mRNA splicing and EJC assembly. We show that the core of CWC22 is sufficient to mediate both pre-mRNA splicing and EJC assembly. Nonetheless, both processes can be functionally uncoupled with an eIF4A3-binding deficient mutant of CWC22, which impedes EJC assembly. A C-terminal domain of CWC22 strongly enhances its spliceosomal interaction and likely regulates its function. High-throughput RNA-sequencing identifies global defects of pre-mRNA splicing and downregulation of diverse gene expression pathways in CWC22-depleted cells. We propose a model, in which CWC22 represents an integral component of the spliceosome and orchestrates pre-mRNA splicing and eIF4A3 binding to achieve global assembly of exon junction complexes.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation (2015)
    Oxford University Press
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    Publication Date: 2015-01-16
    Description: The expression of almost all genes in animals is subject to post-transcriptional regulation by RNA binding proteins (RBPs) and microRNAs (miRNAs). The interactions between both RBPs and miRNAs with mRNA can be mapped on a whole-transcriptome level using experimental and computational techniques established in the past years. The combined action of RBPs and miRNAs is thought to form a post-transcriptional regulatory code. Here we present doRiNA 2.0, available at http://dorina.mdc-berlin.de . In this highly improved new version, we have completely reworked the user interface and expanded the database to improve the usability of the website. Taking into account user feedback over the past years, the input forms for both the simple and the combinatorial search function have been streamlined and combined into a single web page that will also display the search results. Especially, custom uploads is one of the key new features in doRiNA 2.0. To enable the inclusion of doRiNA into third-party analysis pipelines, all operations are accessible via a REST API. Alternatively, local installations can be queried using a Python API. Both the web application and the APIs are available under an OSI-approved Open Source license that allows research and commercial access and re-use.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Specific identification and quantification of circular RNAs from sequencing data (2016)
    Oxford University Press
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    Publication Date: 2016-03-26
    Description: Motivation: Circular RNAs (circRNAs) are a poorly characterized class of molecules that have been identified decades ago. Emerging high-throughput sequencing methods as well as first reports on confirmed functions have sparked new interest in this RNA species. However, the computational detection and quantification tools are still limited. Results: We developed the software tandem, DCC and CircTest . DCC uses output from the STAR read mapper to systematically detect back-splice junctions in next-generation sequencing data. DCC applies a series of filters and integrates data across replicate sets to arrive at a precise list of circRNA candidates. We assessed the detection performance of DCC on a newly generated mouse brain data set and publicly available sequencing data. Our software achieves a much higher precision than state-of-the-art competitors at similar sensitivity levels. Moreover, DCC estimates circRNA versus host gene expression from counting junction and non-junction reads. These read counts are finally used to test for host gene-independence of circRNA expression across different experimental conditions by our R package CircTest . We demonstrate the benefits of this approach on previously reported age-dependent circRNAs in the fruit fly. Availability and implementation: The source code of DCC and CircTest is licensed under the GNU General Public Licence (GPL) version 3 and available from https://github.com/dieterich-lab/ [DCC or CircTest]. Contact: christoph.dieterich@age.mpg.de 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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  • 5
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    Summer hydrographic changes in the Baltic Sea, Kattegat and Skagerrak projected in an ensemble of climate scenarios downscaled with a coupled regional ocean–sea ice–atmosphere model (2019)
    Springer
    Details
    Publication Date: 2019-08-01
    Print ISSN: 0930-7575
    Electronic ISSN: 1432-0894
    Topics: Geosciences , Physics
    Published by Springer
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