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  1. Book ; Online ; Thesis: Organic or conventional?

    Grehl, Claudius [Verfasser] / Glaser, Bruno [Gutachter] / Bäumlein, Helmut [Gutachter]

    developing a method for food fraud detection based on DNA methylation patterns

    2022  

    Author's details Claudius Grehl ; Gutachter: Bruno Glaser, Helmut Bäumlein
    Keywords Landwirtschaft, Veterinärmedizin ; Agriculture, Veterinary Science
    Subject code sg630
    Language English
    Publisher Universitäts- und Landesbibliothek Sachsen-Anhalt
    Publishing place Halle (Saale)
    Document type Book ; Online ; Thesis
    Database Digital theses on the web

    Full text online

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  2. Article: Detection of SARS-CoV-2 Derived Small RNAs and Changes in Circulating Small RNAs Associated with COVID-19

    Grehl, Claudius / Schultheiß, Christoph / Hoffmann, Katrin / Binder, Mascha / Altmann, Thomas / Grosse, Ivo / Kuhlmann, Markus

    Viruses. 2021 Aug. 11, v. 13, no. 8

    2021  

    Abstract: Cleavage of double-stranded RNA is described as an evolutionary conserved host defense mechanism against viral infection. Small RNAs are the product and triggers of post transcriptional gene silencing events. Up until now, the relevance of this mechanism ...

    Abstract Cleavage of double-stranded RNA is described as an evolutionary conserved host defense mechanism against viral infection. Small RNAs are the product and triggers of post transcriptional gene silencing events. Up until now, the relevance of this mechanism for SARS-CoV-2-directed immune responses remains elusive. Herein, we used high throughput sequencing to profile the plasma of active and convalescent COVID-19 patients for the presence of small circulating RNAs. The existence of SARS-CoV-2 derived small RNAs in plasma samples of mild and severe COVID-19 cases is described. Clusters of high siRNA abundance were discovered, homologous to the nsp2 3′-end and nsp4 virus sequence. Four virus-derived small RNA sequences have the size of human miRNAs, and a target search revealed candidate genes associated with ageusia and long COVID symptoms. These virus-derived small RNAs were detectable also after recovery from the disease. The additional analysis of circulating human miRNAs revealed differentially abundant miRNAs, discriminating mild from severe cases. A total of 29 miRNAs were reduced or absent in severe cases. Several of these are associated with JAK-STAT response and cytokine storm.
    Keywords COVID-19 infection ; Severe acute respiratory syndrome coronavirus 2 ; cytokines ; double-stranded RNA ; genes ; humans ; microRNA ; transcription (genetics) ; viruses
    Language English
    Dates of publication 2021-0811
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2516098-9
    ISSN 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13081593
    Database NAL-Catalogue (AGRICOLA)

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  3. Article: Performance of Mapping Approaches for Whole-Genome Bisulfite Sequencing Data in Crop Plants.

    Grehl, Claudius / Wagner, Marc / Lemnian, Ioana / Glaser, Bruno / Grosse, Ivo

    Frontiers in plant science

    2020  Volume 11, Page(s) 176

    Abstract: DNA methylation is involved in many different biological processes in the development and well-being of crop plants such as transposon activation, heterosis, environment-dependent transcriptome plasticity, aging, and many diseases. Whole-genome bisulfite ...

    Abstract DNA methylation is involved in many different biological processes in the development and well-being of crop plants such as transposon activation, heterosis, environment-dependent transcriptome plasticity, aging, and many diseases. Whole-genome bisulfite sequencing is an excellent technology for detecting and quantifying DNA methylation patterns in a wide variety of species, but optimized data analysis pipelines exist only for a small number of species and are missing for many important crop plants. This is especially important as most existing benchmark studies have been performed on mammals with hardly any repetitive elements and without CHG and CHH methylation. Pipelines for the analysis of whole-genome bisulfite sequencing data usually consists of four steps: read trimming, read mapping, quantification of methylation levels, and prediction of differentially methylated regions (DMRs). Here we focus on read mapping, which is challenging because un-methylated cytosines are transformed to uracil during bisulfite treatment and to thymine during the subsequent polymerase chain reaction, and read mappers must be capable of dealing with this cytosine/thymine polymorphism. Several read mappers have been developed over the last years, with different strengths and weaknesses, but their performances have not been critically evaluated. Here, we compare eight read mappers: Bismark, BismarkBwt2, BSMAP, BS-Seeker2, Bwameth, GEM3, Segemehl, and GSNAP to assess the impact of the read-mapping results on the prediction of DMRs. We used simulated data generated from the genomes of
    Language English
    Publishing date 2020-02-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2711035-7
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2020.00176
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Detection of SARS-CoV-2 Derived Small RNAs and Changes in Circulating Small RNAs Associated with COVID-19.

    Grehl, Claudius / Schultheiß, Christoph / Hoffmann, Katrin / Binder, Mascha / Altmann, Thomas / Grosse, Ivo / Kuhlmann, Markus

    Viruses

    2021  Volume 13, Issue 8

    Abstract: Cleavage of double-stranded RNA is described as an evolutionary conserved host defense mechanism against viral infection. Small RNAs are the product and triggers of post transcriptional gene silencing events. Up until now, the relevance of this mechanism ...

    Abstract Cleavage of double-stranded RNA is described as an evolutionary conserved host defense mechanism against viral infection. Small RNAs are the product and triggers of post transcriptional gene silencing events. Up until now, the relevance of this mechanism for SARS-CoV-2-directed immune responses remains elusive. Herein, we used high throughput sequencing to profile the plasma of active and convalescent COVID-19 patients for the presence of small circulating RNAs. The existence of SARS-CoV-2 derived small RNAs in plasma samples of mild and severe COVID-19 cases is described. Clusters of high siRNA abundance were discovered, homologous to the nsp2 3'-end and nsp4 virus sequence. Four virus-derived small RNA sequences have the size of human miRNAs, and a target search revealed candidate genes associated with ageusia and long COVID symptoms. These virus-derived small RNAs were detectable also after recovery from the disease. The additional analysis of circulating human miRNAs revealed differentially abundant miRNAs, discriminating mild from severe cases. A total of 29 miRNAs were reduced or absent in severe cases. Several of these are associated with JAK-STAT response and cytokine storm.
    MeSH term(s) COVID-19/blood ; COVID-19/complications ; COVID-19/genetics ; COVID-19/virology ; Cell-Free Nucleic Acids/blood ; Female ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; MicroRNAs/blood ; MicroRNAs/genetics ; RNA, Viral/blood ; RNA, Viral/genetics ; SARS-CoV-2/genetics ; Severity of Illness Index ; Viral Nonstructural Proteins/genetics
    Chemical Substances Cell-Free Nucleic Acids ; MicroRNAs ; RNA, Viral ; Viral Nonstructural Proteins ; nsp2 protein, SARS-CoV-2
    Language English
    Publishing date 2021-08-11
    Publishing country Switzerland
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2516098-9
    ISSN 1999-4915 ; 1999-4915
    ISSN (online) 1999-4915
    ISSN 1999-4915
    DOI 10.3390/v13081593
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: How to Design a Whole-Genome Bisulfite Sequencing Experiment

    Claudius Grehl / Markus Kuhlmann / Claude Becker / Bruno Glaser / Ivo Grosse

    Epigenomes, Vol 2, Iss 4, p

    2018  Volume 21

    Abstract: Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation. Methyl groups can be covalently bound to the carbon-5 of cytosines or the carbon-6 of ... ...

    Abstract Aside from post-translational histone modifications and small RNA populations, the epigenome of an organism is defined by the level and spectrum of DNA methylation. Methyl groups can be covalently bound to the carbon-5 of cytosines or the carbon-6 of adenine bases. DNA methylation can be found in both prokaryotes and eukaryotes. In the latter, dynamic variation is shown across species, along development, and by cell type. DNA methylation usually leads to a lower binding affinity of DNA-interacting proteins and often results in a lower expression rate of the subsequent genome region, a process also referred to as transcriptional gene silencing. We give an overview of the current state of research facilitating the planning and implementation of whole-genome bisulfite-sequencing (WGBS) experiments. We refrain from discussing alternative methods for DNA methylation analysis, such as reduced representation bisulfite sequencing (rrBS) and methylated DNA immunoprecipitation sequencing (MeDIPSeq), which have value in specific experimental contexts but are generally disadvantageous compared to WGBS.
    Keywords WGBS ; coverage ; library ; DNA methylation ; 5mC ; epigenome ; epigenetics ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2018-12-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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  6. Article: Phenolic Compounds as Unambiguous Chemical Markers for the Identification of Keystone Plant Species in the Bale Mountains, Ethiopia.

    Lemma, Bruk / Grehl, Claudius / Zech, Michael / Mekonnen, Betelhem / Zech, Wolfgang / Nemomissa, Sileshi / Bekele, Tamrat / Glaser, Bruno

    Plants (Basel, Switzerland)

    2019  Volume 8, Issue 7

    Abstract: ...

    Abstract :
    Language English
    Publishing date 2019-07-16
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants8070228
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article: Phenolic Compounds as Unambiguous Chemical Markers for the Identification of Keystone Plant Species in the Bale Mountains, Ethiopia

    Lemma, Bruk / Grehl, Claudius / Zech, Michael / Mekonnen, Betelhem / Zech, Wolfgang / Nemomissa, Sileshi / Bekele, Tamrat / Glaser, Bruno

    Plants. 2019 July 16, v. 8, no. 7

    2019  

    Abstract: Despite the fact that the vegetation pattern and history of the Bale Mountains in Ethiopia were reconstructed using pollen, little is known about the former extent of Erica species. The main objective of the present study is to identify unambiguous ... ...

    Abstract Despite the fact that the vegetation pattern and history of the Bale Mountains in Ethiopia were reconstructed using pollen, little is known about the former extent of Erica species. The main objective of the present study is to identify unambiguous chemical proxies from plant-derived phenolic compounds to characterize Erica and other keystone species. Mild alkaline CuO oxidation has been used to extract sixteen phenolic compounds. After removal of undesired impurities, individual phenols were separated by gas chromatography and were detected by mass spectrometry. While conventional phenol ratios such as syringyl vs. vanillyl and cinnamyl vs. vanillyl and hierarchical cluster analysis of phenols failed for unambiguous Erica identification, the relative abundance of coumaryl phenols (>0.20) and benzoic acids (0.05—0.12) can be used as a proxy to distinguish Erica from other plant species. Moreover, a Random Forest decision tree based on syringyl phenols, benzoic acids (>0.06), coumaryl phenols (<0.21), hydroxybenzoic acids, and vanillyl phenols (>0.3) could be established for unambiguous Erica identification. In conclusion, serious caution should be given before interpreting this calibration study in paleovegetation reconstruction in respect of degradation and underground inputs of soil organic matter.
    Keywords Erica ; cluster analysis ; cupric oxide ; gas chromatography ; hydroxybenzoic acids ; keystone species ; mass spectrometry ; mountains ; oxidation ; phenol ; pollen ; soil organic matter ; vegetation ; Ethiopia
    Language English
    Dates of publication 2019-0716
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants8070228
    Database NAL-Catalogue (AGRICOLA)

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