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  • 1
    Electronic Resource
    Electronic Resource
    Fine structural observations of the pecten oculi capillaries of the chicken (1973)
    Springer
    Cell & tissue research 146 (1973), S. 473-489 
    Details
    ISSN: 1432-0878
    Keywords: Pecten oculi ; Chicken ; Capillaries ; Transmission and scanning electron microscopy ; Freeze-etching
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Description / Table of Contents: Zusammenfassung Der Pecten oculi des Haushuhns wurde licht-, scanning- und transmissions-elektronenmikroskopisch sowie mit der Gefrierätz-Technik unter besonderer Berücksichtigung seiner Kapillarstruktur untersucht. Die Kapillaren bilden ausgedehnte anastomosierende Netze. Ihre Endothelzellen besitzen sowohl apikal (luminal) als auch basal längsorientierte Mikrofalten. Es wird angenommen, daß die Ausbildung der apikalen endothelialen Oberflächendifferenzierung haemodynamisch bedingt ist. Hierbei wird gleichzeitig ausreichend Platz für membrangebundene Fermente geschaffen, die für aktive energie-verbrauchende transzelluläre Transportprozesse benötigt werden. Die Gefrierätzbefunde lassen unterschiedlich strukturierte Membranoberflächen an den Mikrofalten erkennen, die im Zusammenhang mit Transportfunktionen der Kapillarendothelzellen des Pectenoculi diskutiert werden. Vermutlich spielt der Pecten eine wichtige Rolle für die Ernährung von Retina und Glaskörper.
    Notes: Summary The pecten oculi of the domestic chicken was examined with light, scanning and transmission electron microscopy and with freeze-etching techniques. Particular attention has been given to the capillary structure. The capillaries form an extensive anastomotic network. Their endothelial cells have apical (luminal), as well as basal, longitudinally oriented microfolds. It is assumed that the formation of apical differentiations of the endothelial surface is due to haemodynamic influences. Thus, sufficient surface area for membrane bound enzymes is achieved. These enzymes are necessary for active transcellular transport processes that require energy. In freeze-etched material, two different structures of the membrane surface of microfolds can be recognized. These results are discussed in relation to transport functions through capillary endothelial cells of the pecten. It is assumed that the pecten plays an important role in the nourishment of the retina and vitreous body.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02347177
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    Paper (German National Licenses)
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  • 2
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    Global profiling of miRNAs and the hairpin precursors: insights into miRNA processing and novel miRNA discovery (2013)
    Oxford University Press
    Details
    Publication Date: 2013-04-02
    Description: MicroRNAs (miRNAs) constitute an important class of small regulatory RNAs that are derived from distinct hairpin precursors (pre-miRNAs). In contrast to mature miRNAs, which have been characterized in numerous genome-wide studies of different organisms, research on global profiling of pre-miRNAs is limited. Here, using massive parallel sequencing, we have performed global characterization of both mouse mature and precursor miRNAs. In total, 87 369 704 and 252 003 sequencing reads derived from 887 mature and 281 precursor miRNAs were obtained, respectively. Our analysis revealed new aspects of miRNA/pre-miRNA processing and modification, including eight Ago2-cleaved pre-miRNAs, eight new instances of miRNA editing and exclusively 5' tailed mirtrons. Furthermore, based on the sequences of both mature and precursor miRNAs, we developed a miRNA discovery pipeline, miRGrep, which does not rely on the availability of genome reference sequences. In addition to 239 known mouse pre-miRNAs, miRGrep predicted 41 novel ones with high confidence. Similar as known ones, the mature miRNAs derived from most of these novel loci showed both reduced abundance following Dicer knockdown and the binding with Argonaute2. Evaluation on data sets obtained from Caenorhabditis elegans and Caenorhabditis sp.11 demonstrated that miRGrep could be widely used for miRNA discovery in metazoans, especially in those without genome reference sequences.
    Keywords: Computational Methods
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications (2014)
    Oxford University Press
    Details
    Publication Date: 2014-11-07
    Description: Motivation: The identification of active transcriptional regulatory elements is crucial to understand regulatory networks driving cellular processes such as cell development and the onset of diseases. It has recently been shown that chromatin structure information, such as DNase I hypersensitivity (DHS) or histone modifications, significantly improves cell-specific predictions of transcription factor binding sites. However, no method has so far successfully combined both DHS and histone modification data to perform active binding site prediction. Results: We propose here a method based on hidden Markov models to integrate DHS and histone modifications occupancy for the detection of open chromatin regions and active binding sites. We have created a framework that includes treatment of genomic signals, model training and genome-wide application. In a comparative analysis, our method obtained a good trade-off between sensitivity versus specificity and superior area under the curve statistics than competing methods. Moreover, our technique does not require further training or sequence information to generate binding location predictions. Therefore, the method can be easily applied on new cell types and allow flexible downstream analysis such as de novo motif finding. Availability and implementation: Our framework is available as part of the Regulatory Genomics Toolbox. The software information and all benchmarking data are available at http://costalab.org/wp/dh-hmm . Contact: ivan.costa@rwth-aachen.de or eduardo.gusmao@rwth-aachen.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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  • 4
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    Were the May 2012 Emilia-Romagna earthquakes induced? A coupled flow-geomechanics modeling assessment (2016)
    Wiley
    Details
    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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  • 5
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    CWC22-dependent pre-mRNA splicing and eIF4A3 binding enables global deposition of exon junction complexes (2015)
    Oxford University Press
    Details
    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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  • 6
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    Fine structural observations of the pecten oculi capillaries of the chicken (1973)
    Springer
    Details
    Publication Date: 1973-12-01
    Print ISSN: 0302-766X
    Electronic ISSN: 1432-0878
    Topics: Biology , Medicine
    Published by Springer
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  • 7
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    DoRiNA 2.0--upgrading the doRiNA database of RNA interactions in post-transcriptional regulation (2015)
    Oxford University Press
    Details
    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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  • 8
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    Specific identification and quantification of circular RNAs from sequencing data (2016)
    Oxford University Press
    Details
    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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  • 9
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    ACCUSA2: multi-purpose SNV calling enhanced by probabilistic integration of quality scores (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-06
    Description: : Direct comparisons of assembled short-read stacks are one way to identify single-nucleotide variants. Single-nucleotide variant detection is especially challenging across samples with different read depths (e.g. RNA-Seq) and high-background levels (e.g. selection experiments). We present ACCUSA2 to identify variant positions where nucleotide frequency spectra differ between two samples. To this end, ACCUSA2 integrates quality scores for base calling and read mapping into a common framework. Our benchmarks demonstrate that ACCUSA2 is superior to a state-of-the-art SNV caller in situations of diverging read depths and reliably detects subtle differences among sample nucleotide frequency spectra. Additionally, we show that ACCUSA2 is fast and robust against base quality score deviations. Availability: ACCUSA2 is available free of charge to academic users and may be obtained from https://bbc.mdc-berlin.de/software . Contact: christoph.dieterich@mdc-berlin.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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  • 10
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    Conserved miRNAs Are Candidate Post-Transcriptional Regulators of Developmental Arrest in Free-Living and Parasitic Nematodes (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-05
    Description: Animal development is complex yet surprisingly robust. Animals may develop alternative phenotypes conditional on environmental changes. Under unfavorable conditions, Caenorhabditis elegans larvae enter the dauer stage, a developmentally arrested, long-lived, and stress-resistant state. Dauer larvae of free-living nematodes and infective larvae of parasitic nematodes share many traits including a conserved endocrine signaling module (DA/DAF-12), which is essential for the formation of dauer and infective larvae. We speculated that conserved post-transcriptional regulatory mechanism might also be involved in executing the dauer and infective larvae fate. We used an unbiased sequencing strategy to characterize the microRNA (miRNA) gene complement in C. elegans , Pristionchus pacificus , and Strongyloides ratti. Our study raised the number of described miRNA genes to 257 for C. elegans , tripled the known gene set for P. pacificus to 362 miRNAs, and is the first to describe miRNAs in a Strongyloides parasite. Moreover, we found a limited core set of 24 conserved miRNA families in all three species. Interestingly, our estimated expression fold changes between dauer versus nondauer stages and infective larvae versus free-living stages reveal that despite the speed of miRNA gene set evolution in nematodes, homologous gene families with conserved "dauer-infective" expression signatures are present. These findings suggest that common post-transcriptional regulatory mechanisms are at work and that the same miRNA families play important roles in developmental arrest and long-term survival in free-living and parasitic nematodes.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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