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  1. Article ; 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.
    Keywords SARS-CoV-2 ; dsRNA ; Dicer ; RNA cleavage ; Host transcriptome ; Viral genome ; Science (General) ; Q1-390 ; Social sciences (General) ; H1-99
    Subject code 572
    Language English
    Publishing date 2021-06-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; 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.
    Keywords covid19
    Publisher biorxiv
    Document type Article ; Online
    DOI 10.1101/2020.04.08.031856
    Database COVID19

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  3. Article ; Online: Adaptive Variation of Buchnera Endosymbiont Density in Aphid Host Acyrthosiphon pisum Controlled by Environmental Conditions

    Fabrice Neiers / Jean-Michel Saliou / Loïc Briand / Alain Robichon

    ACS Omega, Vol 6, Iss 28, Pp 17902-

    2021  Volume 17914

    Keywords Chemistry ; QD1-999
    Language English
    Publishing date 2021-07-01T00:00:00Z
    Publisher American Chemical Society
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: A new paramutation-like example at the Delta gene of Drosophila.

    Maria Capovilla / Alain Robichon / Minoo Rassoulzadegan

    PLoS ONE, Vol 12, Iss 3, p e

    2017  Volume 0172780

    Abstract: The hereditary transmission of a phenotype independent from DNA sequence implies epigenetic effects. Paramutation is a heritable epigenetic phenomenon observed in plants and animals. To investigate paramutation in Drosophila, we used the P{ry+t7.2 = PZ} ... ...

    Abstract The hereditary transmission of a phenotype independent from DNA sequence implies epigenetic effects. Paramutation is a heritable epigenetic phenomenon observed in plants and animals. To investigate paramutation in Drosophila, we used the P{ry+t7.2 = PZ}Dl05151 P-element insertion in the Drosophila melanogaster genome that causes a dominant visible phenotype: the presence of characteristic extra-veins in the fly wings. This extra-vein phenotype presents variable expressivity and incomplete penetrance. The insert is a PZ element located 680 bp upstream from the ATG of the Delta (Dl) gene, encoding the Notch ligand involved in wing vein development, and acts as a null allele. In the G2 offspring from a cross between the heterozygous transgenic stock and wild-type flies, we observed the transmission of the extra-vein phenotype to wild-type flies without the transgene, independently of gender and across many generations. This is a "paramutation-like" example in the fly: the heritable transmission of a phenotypic change not linked to a classical genetic mutation. A "paramutagenic" allele in heterozygotes transmits the phenotype of the heterozygotes to the wild-type allele ("paramutant") in a stable manner through generations. Distinct from paramutation events so far described in Drosophila, here we deal with a dominant effect on a single gene involving variable hereditary signals.
    Keywords Medicine ; R ; Science ; Q
    Subject code 590
    Language English
    Publishing date 2017-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  5. Article ; Online: Environment exploration and colonization behavior of the pea aphid associated with the expression of the foraging gene.

    Sophie Tarès / Laury Arthaud / Marcel Amichot / Alain Robichon

    PLoS ONE, Vol 8, Iss 5, p e

    2013  Volume 65104

    Abstract: Aphids respond to specific environmental cues by producing alternative morphs, a phenomenon called polyphenism, but also by modulating their individual behavior even within the same morph. This complex plasticity allows a rapid adaptation of individuals ... ...

    Abstract Aphids respond to specific environmental cues by producing alternative morphs, a phenomenon called polyphenism, but also by modulating their individual behavior even within the same morph. This complex plasticity allows a rapid adaptation of individuals to fluctuating environmental conditions, but the underlying genetic and molecular mechanisms remain largely unknown. The foraging gene is known to be associated with behavior in various species and has been shown to mediate the behavioral shift induced by environmental changes in some insects. In this study, we investigated the function of this gene in the clonal forms of the pea aphid Acyrthosiphon pisum by identifying and cloning cDNA variants, as well as analyzing their expression levels in developmental morphs and behavioral variants. Our results indicate that the expression of foraging changes at key steps of the aphid development. This gene is also highly expressed in sedentary wingless adult morphs reared under crowded conditions, probably just before they start walking and foraging. The cGMP-dependent protein kinase (PKG) enzyme activity measured in the behavioral variants correlates with the level of foraging expression. Altogether, our results suggest that foraging could act to promote the shift from a sedentary to an exploratory behavior, being thus involved in the behavioral plasticity of the pea aphid.
    Keywords Medicine ; R ; Science ; Q
    Subject code 612
    Language English
    Publishing date 2013-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Functional Gustatory Role of Chemoreceptors in Drosophila Wings

    Hussein Raad / Jean-François Ferveur / Neil Ledger / Maria Capovilla / Alain Robichon

    Cell Reports, Vol 15, Iss 7, Pp 1442-

    2016  Volume 1454

    Abstract: Summary: Neuroanatomical evidence argues for the presence of taste sensilla in Drosophila wings; however, the taste physiology of insect wings remains hypothetical, and a comprehensive link to mechanical functions, such as flight, wing flapping, and ... ...

    Abstract Summary: Neuroanatomical evidence argues for the presence of taste sensilla in Drosophila wings; however, the taste physiology of insect wings remains hypothetical, and a comprehensive link to mechanical functions, such as flight, wing flapping, and grooming, is lacking. Our data show that the sensilla of the Drosophila anterior wing margin respond to both sweet and bitter molecules through an increase in cytosolic Ca2+ levels. Conversely, genetically modified flies presenting a wing-specific reduction in chemosensory cells show severe defects in both wing taste signaling and the exploratory guidance associated with chemodetection. In Drosophila, the chemodetection machinery includes mechanical grooming, which facilitates the contact between tastants and wing chemoreceptors, and the vibrations of flapping wings that nebulize volatile molecules as carboxylic acids. Together, these data demonstrate that the Drosophila wing chemosensory sensilla are a functional taste organ and that they may have a role in the exploration of ecological niches. : The function of Drosophila wing chemosensilla is poorly understood. GFP gene reporter assays and electrophysiology are hampered by the nano-architecture of bristles and dense chitin. Raad et al. report that the wing taste organ responds to bitter and sugar stimuli and is critical for exploration of ecological niches.
    Keywords Biology (General) ; QH301-705.5
    Subject code 590
    Language English
    Publishing date 2016-05-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; 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  Volume 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.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2014-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article ; Online: Continued neurogenesis in adult Drosophila as a mechanism for recruiting environmental cue-dependent variants.

    Selim Ben Rokia-Mille / Sylvette Tinette / Gilbert Engler / Laury Arthaud / Sophie Tares / Alain Robichon

    PLoS ONE, Vol 3, Iss 6, p e

    2008  Volume 2395

    Abstract: Background The skills used by winged insects to explore their environment are strongly dependent upon the integration of neurosensory information comprising visual, acoustic and olfactory signals. The neuronal architecture of the wing contains a vast ... ...

    Abstract Background The skills used by winged insects to explore their environment are strongly dependent upon the integration of neurosensory information comprising visual, acoustic and olfactory signals. The neuronal architecture of the wing contains a vast array of different sensors which might convey information to the brain in order to guide the trajectories during flight. In Drosophila, the wing sensory cells are either chemoreceptors or mechanoreceptors and some of these sensors have as yet unknown functions. The axons of these two functionally distinct types of neurons are entangled, generating a single nerve. This simple and accessible coincidental signaling circuitry in Drosophila constitutes an excellent model system to investigate the developmental variability in relation to natural behavioral polymorphisms. Methodology/principal findings A fluorescent marker was generated in neurons at all stages of the Drosophila life cycle using a highly efficient and controlled genetic recombination system that can be induced in dividing precursor cells (MARCM system, flybase web site). It allows fluorescent signals in axons only when the neuroblasts and/or neuronal cell precursors like SOP (sensory organ precursors) undergo division during the precedent steps. We first show that a robust neurogenesis continues in the wing after the adults emerge from the pupae followed by an extensive axonal growth. Arguments are presented to suggest that this wing neurogenesis in the newborn adult flies was influenced by genetic determinants such as the frequency dependent for gene and by environmental cues such as population density. Conclusions We demonstrate that the neuronal architecture in the adult Drosophila wing is unfinished when the flies emerge from their pupae. This unexpected developmental step might be crucial for generating non-heritable variants and phenotypic plasticity. This might therefore constitute an advantage in an unstable ecological system and explain much regarding the ability of Drosophila to robustly adapt to ...
    Keywords Medicine ; R ; Science ; Q
    Subject code 590
    Language English
    Publishing date 2008-06-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Trade-off between toxicity and signal detection orchestrated by frequency- and density-dependent genes.

    Laury Arthaud / Selim Ben Rokia-Mille / Hussein Raad / Aviv Dombrovsky / Nicolas Prevost / Maria Capovilla / Alain Robichon

    PLoS ONE, Vol 6, Iss 5, p e

    2011  Volume 19805

    Abstract: Behaviors in insects are partly highly efficient Bayesian processes that fulfill exploratory tasks ending with the colonization of new ecological niches. The foraging (for) gene in Drosophila encodes a cGMP-dependent protein kinase (PKG). It has been ... ...

    Abstract Behaviors in insects are partly highly efficient Bayesian processes that fulfill exploratory tasks ending with the colonization of new ecological niches. The foraging (for) gene in Drosophila encodes a cGMP-dependent protein kinase (PKG). It has been extensively described as a frequency-dependent gene and its transcripts are differentially expressed between individuals, reflecting the population density context. Some for transcripts, when expressed in a population at high density for many generations, concomitantly trigger strong dispersive behavior associated with foraging activity. Moreover, genotype-by-environment interaction (GEI) analysis has highlighted a dormant role of for in energetic metabolism in a food deprivation context. In our current report, we show that alleles of for encoding different cGMP-dependent kinase isoforms influence the oxidation of aldehyde groups of aromatic molecules emitted by plants via Aldh-III and a phosphorylatable adaptor. The enhanced efficiency of oxidation of aldehyde odorants into carboxyl groups by the action of for lessens their action and toxicity, which should facilitate exploration and guidance in a complex odor environment. Our present data provide evidence that optimal foraging performance requires the fast metabolism of volatile compounds emitted by plants to avoid neurosensory saturation and that the frequency-dependent genes that trigger dispersion influence these processes.
    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2011-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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