Biology subjects

Durand, K.

Publications and source records attributed to Durand, K..

7 recordsLinked to original sources

bioRxiv2025

A characterization of piARNs, their biogenesis and their targets in Spodoptera frugiperda (Lepidoptera, Noctuidae)

PIWI-interacting RNAs (piRNAs) and PIWI proteins were initially described as involved in gametogenesis and preservation of genome integrity through the control of transposable elements (TE). Expressed also in the soma and able to regulate protein coding gene expression, they are involved in multiple biological pathways including host-pathogens interaction, sex determination, reproductive isolation. Spodoptera frugiperda is a major invasive insect pest species consisting of two strains with different host-plant ranges. In this paper, we characterized proteins and genomic regions involved in their biogenesis as well as TE and gene transcripts regulated by piRNAs. By phylogenetic analysis, we identified two new Piwi genes conserved in the genus Spodoptera, compared to the Lepidopteran model Bombyx mori, one more than in Drosophila. One of them, more expressed in gonads then soma could be a functional homolog of Drosophila PIWI or replace AGO3. A pool of 11 sRNA-Seq libraries was used to annotate piRNA clusters with Shortstack in the genomes of the two strains of Spodoptera frugiperda. Identification of TE targeted by piRNAs revealed that active transposons differ between the two strains of S. frugiperda despite of a similar TE content, as putative cause or consequence of reproductive isolation. GO analysis of genes targeted by piRNAs shows that some are involved in protein translation initiation. A piRNA cluster in the Masc gene suggests that sex determination is regulated by piRNAs in Spodoptera frugiperda. Our analysis supports that piRNAs have additional roles than silencing of transposable elements and contributes to functional annotation of the two strains genomes of Spodoptera frugiperda.

genomics↗

bioRxiv2024

Predicting Tumor Mutational Burden from UHF-Dielectrophoresis Crossover Frequency

Tumor Mutational Burden (TMB) has emerged as a crucial biomarker to guide patient eligibility for immunotherapy. However, whole exome sequencing, the gold-standard method for TMB measurement, remains limited in accessibility due to its high costs, operational complexity, and lengthy processing times. To address these limitations, we investigated whether Ultra-High-Frequency (UHF) technology could serve as a novel approach to assess TMB by analyzing the crossover frequencies or electromagnetic signature (EMS) of cancer cells on a lab-on-a-chip biosensor, integrating microfluidics and dielectrophoresis. In a panel of 12 cancer cell lines with varying TMB levels, we observed that EMS showed an upward shift correlating with higher TMB, particularly in solid tumor cell lines. This finding suggests a potential relationship between TMB and EMS. To further explore this hypothesis, we artificially increased mutation levels by treating cells with the highly mutagenic compound N-ethyl-N-nitrosourea (ENU). Results showed that EMS captured significant TMB variations in ENU-treated cells with enhanced proliferative capacity compared to their parental counterparts. These results underscore the importance of matched control samples for reliable EMS measurements. Altogether, our findings highlight the potential of EMS to detect TMB variations associated with proliferative activity, a key hallmark of cancer cells, thereby enabling a more precise stratification of cancer cells. HighlightsO_LIWe propose a new biosensor to improve patient stratification for ICI eligibility C_LIO_LIHigh frequency fields and dielectric spectroscopy can estimate TMB in cancer cells C_LIO_LISignificant changes in UHF-DEP signatures correlate with varying TMB levels C_LIO_LIUHF-DEP provides a cheap, rapid and label-free method to predict ICI response C_LIO_LIOffers an innovative and complementary marker to conventional diagnostic approaches C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=92 SRC="FIGDIR/small/622085v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@703983org.highwire.dtl.DTLVardef@1cfdf46org.highwire.dtl.DTLVardef@4b9285org.highwire.dtl.DTLVardef@1809255_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

Olfactory-to-visual facilitation in the infant brain declines gradually from 4 to 12 months

During infant development, intersensory facilitation declines gradually as unisensory perception improves. However, this developmental trade-off has been mainly investigated using audiovisual stimulations. Here, fifty 4- to 12-month-old infants were tested to determine whether the facilitating effect of their mothers body odor on neural face categorization, as previously observed at 4 months, decreases with age. In a baseline odor context, results revealed a face-selective electroencephalographic (EEG) response that increases and changes qualitatively between 4 and 12 months, marking improved face categorization. At the same time, the benefit of adding maternal odor fades gradually with age, indicating an inverse relation with the strength of the sole visual response, and generalizing to olfactory-visual interactions previous evidence from the audiovisual domain.

neuroscience↗

bioRxiv2023

Analysis of the worldwide diversity of Xanthomonas hortorum pv. carotae, the agent of bacterial blight of carrot, reveals two distinct populations.

Xanthomonas hortorum pv. carotae is a pathogen responsible for the bacterial blight of carrot. While it infects carrot fields worldwide, its diversity remains unknown. Here, we validated by PCR the identification as X. hortorum pv. carotae of most of the strains isolated from carrot symptoms. We study their diversity by sequencing seven housekeeping genes. The analysis confirmed the identity of most of the strains previously identified as X. hortorum pv. carotae and highlighted the presence of two clusters inside the pathovar carotae. The 18 non-X. hortorum pv. carotae have been identified as Xanthomonas from other species. As the X. hortorum pv. carotae strains clustered only in two groups by this analysis, a new MLVA scheme was developed. It allowed to validate the subclusteration in two groups and observe diversity among them. At the same times based on this study and data from the literature, we proposed the strain CFBP 7900 as the neopathotype strain of the pathovar. The strain should replacement the holopathotype strain CFBP 4997, as it is no longer available in international collection.

pathology↗

bioRxiv2022

Host-plant adaptation as a driver of incipient speciation in the fall armyworm (Spodoptera frugiperda)

BackgroundDivergent selection on host-plants is one of the main evolutionary forces driving ecological speciation in phytophagous insects. The ecological speciation might be challenging in the presence of gene flow and assortative mating because the direction of divergence is not necessarily the same between ecological selection (through host-plant adaptation) and assortative mating. The fall armyworm (FAW), a major lepidopteran pest species, is composed of two sympatric strains, corn and rice strains, named after two of their preferred host-plants. These two strains have been hypothesized to undergo incipient speciation, based on (i) several lines of evidence encompassing both pre- and post-zygotic reproductive isolation, and (ii) the presence of a substantial level of genetic differentiation. Even though the status of these two strains has been established a long time ago, it is still yet to be found whether these two strains indeed exhibit a marked level of genetic differentiation from a large number of genomic loci. Here, we analyzed whole genome sequences from 56 FAW individuals either collected from pasture grasses (a part of the favored host range of the rice strain) or corn to assess the role of host-plant adaptation in incipient speciation. ResultsPrincipal component analysis of whole genome data shows that the pattern of divergence in the fall armyworm is predominantly explained by the genetic differentiation associated with host-plants. The level of genetic differentiation between corn and rice strains is particularly marked in the Z chromosome. We identified one autosomal locus and two Z chromosome loci targeted by selective sweeps specific to rice strain and corn strain, respectively. The autosomal locus has both increased DXY and FST while the Z chromosome loci had decreased DXY and increased FST. ConclusionThese results show that the FAW population structure is dominated by the genetic differentiation between corn and rice strains. This differentiation involves divergent selection targeting at least three loci, which include a locus potentially causing reproductive isolation. Taken together, these results suggest the evolutionary scenario that host-plant speciation is a driver of incipient speciation in the fall armyworm.

evolutionary biology↗

bioRxiv2022

Two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France

Of American origin, a wide diversity of Xylella fastidiosa strains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspecies multiplex (ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 x 10-7 substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Cote dAzur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations.

microbiology↗

bioRxiv2021

Smell what you hardly see: Odors assist categorization in the human visual cortex

Visual categorization is the brain ability to rapidly and automatically respond to widely variable visual inputs in a category-selective manner (i.e., distinct responses between categories and similar responses within categories). Whether category-selective neural responses are purely visual or can be influenced by other sensory modalities remains unclear. Here, we test whether odors modulate visual categorization, expecting that odors facilitate the neural categorization of congruent visual objects, especially when the visual category is ambiguous. Scalp electroencephalogram (EEG) was recorded while natural images depicting various objects were displayed in rapid 12-Hz streams (i.e., 12 images / second) and variable exemplars of a target category (either human faces, cars, or facelike objects in dedicated sequences) were interleaved every 9th stimulus to tag category-selective responses at 12/9 = 1.33 Hz in the EEG frequency spectrum. During visual stimulation, participants (N = 26) were implicitly exposed to odor contexts (either body, gasoline or baseline odors) and performed an orthogonal cross-detection task. We identify clear category-selective responses to every category over the occipito-temporal cortex, with the largest response for human faces and the lowest for facelike objects. Critically, body odor boosts the response to the ambiguous facelike objects (i.e., either perceived as nonface objects or faces) over the right hemisphere, especially for participants reporting their presence post-stimulation. By contrast, odors do not significantly modulate other category-selective responses, nor the general visual response recorded at 12 Hz, revealing a specific influence on the categorization of congruent ambiguous stimuli. Overall, these findings support the view that the brain actively uses cues from the different senses to readily categorize visual inputs, and that olfaction, which is generally considered as poorly functional in humans, is well placed to disambiguate visual information.

neuroscience↗