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  1. AU="Claude Pasquier"
  2. AU="Guomin Zhang"
  3. AU=van der Donk Lieve E H
  4. AU="Reynaerts, Audrey"
  5. AU="Alberts, Susan C"
  6. AU="Kosicki, Jakub Z"
  7. AU=Eifling Michael
  8. AU="Xing, Xinxin"
  9. AU="Baigun, Claudio"
  10. AU="Abu-Hamad, Ghassan"
  11. AU="Mulla, Zuber D"
  12. AU="Schröder, H"
  13. AU=Ruiz Michael Anthony
  14. AU="Kemmoku, Haruka"
  15. AU="Meseguer, M"
  16. AU="Pillaye, Jayshree"
  17. AU="Andrew Pettitt"
  18. AU="Malawski, M"
  19. AU=Marhofer P
  20. AU=Mandel H G
  21. AU="Duffy, Richard"
  22. AU=Kaseb Hatem AU=Kaseb Hatem
  23. AU=Kong Tak?kwan AU=Kong Tak?kwan
  24. AU=Nagaraja Sridevi
  25. AU="Bu, Yingzi"
  26. AU=Seddighi Hamed AU=Seddighi Hamed
  27. AU="De Keyser, Johan"
  28. AU="Zhenqiang Bi"
  29. AU=Wang Jun
  30. AU=Zhang Fuping
  31. AU="Shatilov, D N"

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  1. Artikel ; Online: Computational search of hybrid human/SARS-CoV-2 dsRNA reveals unique viral sequences that diverge from those of other coronavirus strains

    Claude Pasquier / Alain Robichon

    Heliyon, Vol 7, Iss 6, Pp e07284- (2021)

    2021  

    Abstract: The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral ... ...

    Abstract The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral infection as an accessory function. However, recent publications highlight the existence of abundant viral small interference and micro RNAs (VsiRNAs and VmiRNAs) in both cell-line and whole organism based experiments, indicating a contribution of these molecules in host responses and/or viral replication. We explore the theoretical possibility that RNAi triggered by SARS-CoV-2 might degrade some host transcripts in the opposite direction, although this hypothesis seems counterintuitive. The SARS-CoV-2 genome was therefore computationally searched for exact intrapairing within the viral RNA and exact hybrid pairing with the human transcriptome over a minimum of 20 bases in length. Minimal segments of 20-base lengths of SARS-CoV-2 RNA were found based on the theoretical matching with existing complementary strands in the human host transcriptome. Few human genes potentially annealing with SARS-CoV-2 RNA, including mitochondrial deubiquitinase USP30, the subunit of ubiquitin protein ligase complex FBXO21 and two long noncoding RNAs, were retrieved. The hypothesis that viral-originated RNAi might mediate degradation of host transcriptome messages was corroborated by published high throughput sequencing of RNA from infected tissues and cultured cells, clinical observation and phylogenetic comparative analysis, indicating a strong specificity of these SARS-CoV-2 hybrid pairing sequences for human genomes.
    Schlagwörter SARS-CoV-2 ; dsRNA ; Dicer ; RNA cleavage ; Host transcriptome ; Viral genome ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Thema/Rubrik (Code) 572
    Sprache Englisch
    Erscheinungsdatum 2021-06-01T00:00:00Z
    Verlag Elsevier
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  2. Artikel ; Online: SARS-CoV-2 might manipulate against its host the immunity RNAi/Dicer/Ago system Does mitochondria collapse upon COVID-19 infection?

    Claude Pasquier / Alain Robichon

    Abstract: AbstractThe role of the RNAi/Dicer/Ago system to degrade RNA viruses has been elusive, which prompt authors to think that interferon (IFN) synthesis is essential, relegating the dsRNAs as accessory function. We investigate SARS-CoV-2 genome responsible ... ...

    Abstract AbstractThe role of the RNAi/Dicer/Ago system to degrade RNA viruses has been elusive, which prompt authors to think that interferon (IFN) synthesis is essential, relegating the dsRNAs as accessory function. We investigate SARS-CoV-2 genome responsible of the new deadly COVID-19 pandemic for the theoretical possibilities to engage intra pairing within the viral RNA and also hybrid pairing with human transcriptome. Segmental pieces of RNAs that originate from SARS-CoV-2 were computationally searched as a potential source of one strand, the complementary strand being from the host transcriptome. We therefore considered perfect complementarity of host RNA with any piece of SARS-CoV-2 RNA as a collection of theoretical siRNAs potentially Dicer substrates. Few human genes seems targeted by SARS-CoV-2 RNA, among them mitochondrial deubiquitinase USP30 and a subunit of ubiquitin protein ligase complex FBXO21 could explain premature death of infected cell by the collapse of mitochondria.
    Schlagwörter covid19
    Verlag biorxiv
    Dokumenttyp Artikel ; Online
    DOI 10.1101/2020.04.08.031856
    Datenquelle COVID19

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  3. Artikel ; Online: Prediction of miRNA-disease Associations using an Evolutionary Tuned Latent Semantic Analysis

    Denis Pallez / Julien Gardès / Claude Pasquier

    Scientific Reports, Vol 7, Iss 1, Pp 1-

    2017  Band 13

    Abstract: Abstract MicroRNAs, small non-coding elements implied in gene regulation, are very interesting biomarkers for various diseases such as cancers. They represent potential prodigious biotechnologies for early diagnosis and gene therapies. However, ... ...

    Abstract Abstract MicroRNAs, small non-coding elements implied in gene regulation, are very interesting biomarkers for various diseases such as cancers. They represent potential prodigious biotechnologies for early diagnosis and gene therapies. However, experimental verification of microRNA-disease associations are time-consuming and costly, so that computational modeling is a proper solution. Previously, we designed MiRAI, a predictive method based on distributional semantics, to identify new associations between microRNA molecules and human diseases. Our preliminary results showed very good prediction scores compared to other available methods. However, MiRAI performances depend on numerous parameters that cannot be tuned manually. In this study, a parallel evolutionary algorithm is proposed for finding an optimal configuration of our predictive method. The automatically parametrized version of MiRAI achieved excellent performance. It highlighted new miRNA-disease associations, especially the potential implication of mir-188 and mir-795 in various diseases. In addition, our method allowed to detect several putative false associations contained in the reference database.
    Schlagwörter Medicine ; R ; Science ; Q
    Thema/Rubrik (Code) 006
    Sprache Englisch
    Erscheinungsdatum 2017-09-01T00:00:00Z
    Verlag Nature Publishing Group
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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  4. Artikel ; Online: Environmentally selected aphid variants in clonality context display differential patterns of methylation in the genome.

    Claude Pasquier / Mathilde Clément / Aviv Dombrovsky / Stéphanie Penaud / Martine Da Rocha / Corinne Rancurel / Neil Ledger / Maria Capovilla / Alain Robichon

    PLoS ONE, Vol 9, Iss 12, p e

    2014  Band 115022

    Abstract: Heritability of acquired phenotypic traits is an adaptive evolutionary process that appears more complex than the basic allele selection guided by environmental pressure. In insects, the trans-generational transmission of epigenetic marks in clonal and/ ... ...

    Abstract Heritability of acquired phenotypic traits is an adaptive evolutionary process that appears more complex than the basic allele selection guided by environmental pressure. In insects, the trans-generational transmission of epigenetic marks in clonal and/or sexual species is poorly documented. Aphids were used as a model to explore this feature because their asexual phase generates a stochastic and/or environment-oriented repertoire of variants. The a priori unchanged genome in clonal individuals prompts us to hypothesize whether covalent methyl DNA marks might be associated to the phenotypic variability and fitness selection. The full differential transcriptome between two environmentally selected clonal variants that originated from the same founder mother was mapped on the entire genomic scaffolds, in parallel with the methyl cytosine distribution. Data suggest that the assortments of heavily methylated DNA sites are distinct in these two clonal phenotypes. This might constitute an epigenetic mechanism that confers the robust adaptation of insect species to various environments involving clonal reproduction.
    Schlagwörter Medicine ; R ; Science ; Q
    Sprache Englisch
    Erscheinungsdatum 2014-01-01T00:00:00Z
    Verlag Public Library of Science (PLoS)
    Dokumenttyp Artikel ; Online
    Datenquelle BASE - Bielefeld Academic Search Engine (Lebenswissenschaftliche Auswahl)

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