Biology subjects

Robert, C.

Publications and source records attributed to Robert, C..

30 records · Page 2Linked to original sources

bioRxiv2023

Soil chemical and microbial gradients determine accumulation of root exuded secondary metabolites and plant-soil feedbacks in the field

IntroductionHarnessing positive plant-soil feedbacks via crop rotations is a promising strategy for sustainable agriculture. Plants can influence soil properties including microbes by exuding specialized metabolites. However, the effects are often context dependent and variable. If and how local soil heterogeneity may explain this variation is unknown. Benzoxazinoids are specialized metabolites that are released in high quantities by cereals such as wheat and maize. Benzoxazinoids can alter rhizosphere microbiota and the performance of plants subsequently growing in the exposed soils and are thus an excellent model to study agriculturally relevant plant-soil feedbacks in the field, and to assess how soil factors affect their outcome. Materials & methodsTo understand the importance of local variation in soil properties on benzoxazinoid-mediated plant-soil feedbacks, we conditioned plots with wild-type maize and benzoxazinoid-deficient bx1 mutant plants in a grid pattern across an arable field. We then grew winter wheat across the entire field in the following season. We determined accumulation of benzoxazinoids, root-associated microbial communities, abiotic soil properties and wheat performance in each plot. We also determined benzoxazinoid conversion dynamics in a labelling experiment under controlled conditions, and then assessed associations between soil chemical variation and benzoxazinoid-mediated plant-soil feedbacks. ResultsAcross the field, we detected a marked gradient in soil chemical and microbial community composition. This gradient resulted in significant differences in benzoxazinoid accumulation. These differences were explained by differential benzoxazinoid degradation rather than exudation. Benzoxazinoid exudation modulated alpha diversity of root and rhizosphere bacteria and fungi during maize growth, but not during subsequent wheat growth, while the chemical fingerprint of benzoxazinoid accumulation persisted. Averaged across the field, we detected no significant feedback effects of benzoxazinoid conditioning on wheat performance and defence, apart from a transient decrease in biomass during vegetative growth. Closer analysis however, revealed pronounced feedback effects along the chemical and microbial gradient of the field, with effects gradually changing from negative to positive along the gradient. ConclusionOverall, this study revealed that plant-soil feedbacks differ in strength and direction within a field, and that this variation can be explained by standing chemical and microbial gradients, which strongly affect benzoxazinoid accumulation in the soil. Understanding within-field soil heterogeneity is crucial for the future exploitation of plant-soil feedbacks in sustainable precision agriculture.

plant biology↗

bioRxiv2022

Neural, physiological and behavioral correlates of empathy for pain in Tourette syndrome

Persons with Tourette syndrome show altered social behaviors, such as echophenomena and increased personal distress in emotional situations. These symptoms may reflect an overactive mirror neuron system, causing both increased automatic imitation and a stronger tendency to share others emotions. To test this, we measured the individual level of echophenomena with a video protocol and experimentally induced empathy for pain in 21 participants with Tourette syndrome and 25 matched controls. In the empathy for pain paradigm, pictures of hands and feet in painful or neutral situations were presented, while we measured participants EEG and skin conductance response. Changes in somatosensory mu suppression during the observation of the pictures and pain ratings were compared between groups and correlations were calculated with the occurrence of echophenomena, self-reported empathy and clinical measures. Our Tourette syndrome sample showed significantly more echophenomena than controls, but the groups showed no behavioral differences in empathic abilities. However, controls, but not patients with Tourette syndrome, showed the predicted increased mu suppression when watching painful compared to neutral actions. While echophenomena were present in all persons with Tourette syndrome, the hypothesis of an overactive mirror neuron system in Tourette syndrome could not be substantiated. On the contrary, the Tourette syndrome group showed a noticeable lack of mu attenuation in response to pain stimuli. In conclusion, we found a first hint of altered processing of others emotional states in a brain region associated with the mirror neuron system.

neuroscience↗

bioRxiv2022

Analysis of Skin Cancers from Xeroderma Pigmentosum Patients Reveals Heterogeneous UV-Induced Mutational Profiles Shaped by DNA Repair

Xeroderma pigmentosum (XP) is a genetic disorder caused by mutations in genes of the Nucleotide Excision Repair (NER) pathway (groups A-G) or in Translesion Synthesis (TLS) DNA polymerase {eta} (V). XP is associated with an increased skin cancer risk, reaching, for some groups, several thousand-fold compared to the general population. Here, we analyzed 38 skin cancer genomes from five XP groups. We found that the activity of NER determines heterogeneity of the mutation rates across skin cancer genomes and that transcription-coupled NER extends beyond the gene boundaries reducing the intergenic mutation rate. Mutational profile in XP-V tumors and experiments with POLH-KO cell line revealed the role of polymerase {eta} in the error-free bypass of (i) rare TpG and TpA DNA lesions, (ii) 3 nucleotides in pyrimidine dimers, and (iii) TpT photodimers. Our study unravels the genetic basis of skin cancer risk in XP and provides insights into the mechanisms reducing UV-induced mutagenesis in the general population.

cancer biology↗

bioRxiv2022

Uncoupling from transcription protects polyadenylation site cleavage from inhibition by DNA damage

Pre-mRNA 3-end processing by cleavage and polyadenylation (CPA) is a nuclear process in which RNA polymerase II (Pol II) transcripts are cleaved at the polyadenylation site (PAS cleavage) before addition of a poly(A) tail. While PAS cleavage is usually coupled to transcription termination, for some pre-mRNAs it occurs post-transcriptionally, i.e. after pre-mRNA release from chromatin to nucleoplasm through a downstream co-transcriptional cleavage (CoTC) event. DNA-damaging agents such as ultraviolet-C (UV) irradiation trigger rapid shutdown of pre-mRNA 3-end processing. However, specific compensatory mechanisms exist to ensure efficient 3-end processing for some pre-mRNAs encoding proteins involved in the DNA damage response (DDR), such as the p53 tumor suppressor protein. Here, we show that PAS cleavage of the p53 pre-mRNA occurs in part post-transcriptionally, in a PCF11-independent manner, in the nucleoplasm, following a CoTC-type event. Upon UV-irradiation, cells with an engineered deletion of the p53 CoTC site exhibit impaired 3-end processing of the p53 pre-mRNA, decreased mRNA and protein levels of p53 and its transcriptional target, p21, and altered cell cycle progression. Finally, using a transcriptome-wide analysis of PAS cleavage, we identified additional-including DDR related-pre-mRNAs whose PAS cleavage is maintained in response to UV and occurs post-transcriptionally. These findings indicate that CoTC-type cleavage of pre-mRNAs, followed by PAS cleavage in the nucleoplasm, allows specific pre-mRNAs to escape 3-end processing inhibition in response to UV-induced DNA damage.

molecular biology↗

bioRxiv2022

Development of methylation-based biomarkers for breast cancer detection by model training and validation in synthetic cell-free DNA

Circulating tumour-derived DNA (ctDNA) carries the genetic and epigenetic characteristics of the tumour from which it is derived and can give information about the biology and tissue origins of the underlying tumour. DNA methylation is an epigenetic mark that is specific to individual tissues and, as methylation profiles are disrupted in tumours, they can indicate the tissue of origin and cancer type of ctDNA. We have developed a set of methylation biomarkers for detecting breast cancer in plasma cell-free DNA (cfDNA). First, we mined publicly available methylation datasets to create synthetic methylation profiles that were modelled to reflect cfDNA from healthy subjects and cancer patients. These profiles were restricted to the most differentially methylated CpGs between breast tumour samples and haematopoietic cells. Regularised logistic regression models were trained using 10-fold cross-validation on synthetic cfDNA datasets with distinct fractions of breast tumour DNA spiked in silico into healthy cfDNA with the addition of 10% of a mix of different tissues. Initial validation with synthetic cfDNA permitted detection of breast cancer-derived DNA with as little as 0.25% tumour DNA spiked in silico into healthy subject cfDNA with an area under ROC curve (AUC) of 0.63. Performances of classifiers increased with increased fractions of spike-in tumour DNA (AUCs 0.77 and 0.93 at tumour DNA fractions 0.5% and 1% respectively). We then combined the most discriminative CpG markers from our models with methylation markers of breast cancer that had already been published to obtain a single marker set. In vitro testing of MCF-7 breast cancer cell line DNA spiked into leukocyte DNA showed highly significant correlation for individual markers between laboratory-measured and published methylation data for MCF-7 and leukocytes (R > 0.89, P < 2.2 x 10-16). These preliminary data indicate promising results for detection of breast cancer cell line DNA using this methylation marker set, which now require testing in cfDNA from breast cancer patients and healthy controls.

cancer biology↗

bioRxiv2022

The first horse gut microbiome gene catalog reveals that rare microbiome ensures better cardiovascular fitness in endurance horses

Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance, but the extent of their functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built the first equine gut microbial gene catalog comprising more than 25 million non-redundant genes representing 4,696 genera spanning 95 phyla. The unprecedented resolution unrevealed functional pathways relevant for both the structure of the microbiome and the host health and recovered 369 novel metagenome-assembled bacterial genomes, providing useful reference for future studies. Integration of microbial and host omic datasets suggested that microbiomes harboring rare species were functionally dissimilar from those enriched in Lachnospiraceae taxa. Moreover, they offered expanded metabolic pathways to fine-tune the cardiovascular capacity through mitochondria-mediated mechanisms. The results identify an associative link between horse endurance capability and its microbiome gene function, laying the basis for nutritional interventions that could benefit endurance athletes.

microbiology↗

bioRxiv2021

The natural adaptation and human selection history of African sheep genomes

African sheep manifest diverse but distinct physio-anatomical traits which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous African sheep genomes sequenced at an average depth of [~]54x for 130 samples (Ethiopia, Libya) and [~]10x for 20 samples (Sudan), representing sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups that correspond to altitudinal geographic origins and tail morphotypes. Comparative genomic analysis identified targets of selection spanning conserved haplotype structures overlapping genes and gene families relating to hypoxia responses, caudal vertebrae and tail skeleton length, ear morphology, and tail fat-depot structure. Our findings provide novel insights underpinning variation and response to human selection and environmental adaptation, and possible pleiotropic gene interactions in indigenous African sheep genomes, which guaranteed the successful establishment of the species on the continent.

genomics↗

bioRxiv2021

Copy number variations with adaptive potential in caribou (Rangifer tarandus): genome architecture and new annotated genome assembly

BackgroundRangifer tarandus (caribou and reindeer) has experienced recent drastic population size reductions throughout its circumpolar distribution. In efforts aimed at preserving caribou in North America and reindeer in Eurasia, genetic diversity conservation is of utmost importance, particularly the adaptive genetic diversity. To facilitate genomic studies of the caribou population, we improved genome assembly and annotation by combining long-read, linked-read and RNA sequencing technologies. As copy number variations (CNVs) are known to impact phenotype and are therefore likely to play a key role in adaptation, we investigated CNVs among the genomes of individuals representing three ecotypes of caribou (migratory, boreal and mountain). ResultsUsing de novo transcriptome assembly and similarity with annotated human gene sequences, we identified 17,394 robust gene models embedded in a new highly contiguous genome assembly made of 13,994 scaffolds and presenting the highest N50 reported to date. A BUSCO analysis supported the high accuracy of this assembly, 90% of which being represented by only 131 scaffolds. Genome level comparisons with domestic ruminant species showed high synteny within this clade. A total of 1,698 large CNVs (length > 1kb) were identified, including 332 overlapping coding sequences annotated for functions related to immunity, musculoskeletal development or metabolism regulation and others. While the CNV distribution over the genome revealed 31 CNV hotspots, 43 large CNVs were particularly distinctive of the migratory and sedentary ecotypes and included genes annotated for functions related to cardiac development, fatty acid regulation, cold responses, locomotory behavior or environmental perception (hearing and sight), that can be related to the expected adaptations. ConclusionsThis work includes the first publicly available annotation of the Rangifer tarandus genome and the first genome assembly allowing genome architecture analyses. This robust annotation based on truly expressed sequences showed a distribution overlapping many CNVs that are promising candidates given the annotations supporting their involvement in adaptation. This new highly contiguous assembly will allow relative localization of genetic variations and features and will be a valuable resource for molecular tool development and genomic studies aimed at describing and preserving this species.

genomics↗

bioRxiv2021

Microstructural variation in the human striatum using non-negative matrix factorization

The striatum is a major subcortical connection hub that has been heavily implicated in a wide array of motor and cognitive functions. Here, we developed a normative multimodal, data-driven microstructural parcellation of the striatum using multiple magnetic resonance imaging-based metrics (mean diffusivity, fractional anisotropy, and the ratio between T1- and T2-weighted structural) from the Human Connectome Project Young Adult dataset (n=329 unrelated participants, age range: 22-35, F/M: 185/144). We further explored the biological and functional relationships of this parcellation by relating our findings to motor and cognitive performance in tasks known to involve the striatum as well as demographics. We identified 5 spatially distinct striatal components, for each hemisphere. We also show the gain in component stability when using multimodal versus unimodal metrics. Our findings suggest distinct microstructural patterns in the human striatum that are largely symmetric and that relate mostly to age and sex. Our work also highlights the putative functional relevance of these striatal components to different designations based on a Neurosynth meta-analysis.

neuroscience↗

bioRxiv2021

Understanding the holobiont: crosstalk between gut microbiota and mitochondria during endurance

Endurance exercise has a dramatic impact on the functionality of mitochondria and on the composition of the intestinal microbiome, but the mechanisms regulating the crosstalk between these two components are still largely unknown. Here, we sampled 20 elite horses before and after an endurance race and used blood transcriptome, blood metabolome and fecal microbiome to describe the gut-mitochondria crosstalk. A subset of mitochondria-related differentially expressed genes involved in pathways such as energy metabolism, oxidative stress and inflammation was discovered and then shown to be associated with butyrate-producing bacteria of the Lachnospiraceae family, especially Eubacterium. The mechanisms involved were not fully understood, but through the action of their metabolites likely acted on PPAR{gamma}, the FRX-CREB axis and their downstream targets to delay the onset of hypoglycemia, inflammation and extend running time. Our results also suggested that circulating free fatty acids may act not merely as fuel but drive mitochondrial inflammatory responses triggered by the translocation of gut bacterial polysaccharides following endurance. Targeting the gut-mitochondria axis therefore appears to be a potential strategy to enhance athletic performance.

systems biology↗

bioRxiv2020

Low doses of radiation therapy increase the immunosuppressive profile of lung macrophages via IL-10 production and IFNγ/IL-6 suppression: a therapeutic strategy to counteract lung inflammation?

Severe pneumonia and acute respiratory distress syndrome (ARDS) have been described in patients with severe COVID-19. Recently, early clinical data reported the efficacy of low doses of radiation therapy (RT) in the treatment of ARDS in patients with severe COVID-19. However, the involved mechanisms remained unknown. Here, we used airways-instilled lipopolysaccharide (LPS) and influenza virus (H1N1) as murine models of pneumonia, and Tolllike receptor (TLR)-3 stimulation in human lung macrophages. Low doses RT (0.5-1 Gy) decreased LPS induced pneumonia, and increased the percentage of Nerve- and Airway-associated Macrophages (NAMs) producing IL-10. During H1N1 viral infection, we observed decreased lung tissue damage and immune cell infiltration in irradiated animals. Low doses RT increased IL-10 production by infiltrating immune cells into the lung. Irradiation of TLR-3 ligand-stimulated human lung macrophages ex vivo increased IL-10 secretion and decreased IFN{gamma} production in the culture supernatant. The percentage of human lung macrophages producing IL-6 was also decreased. Our data highlight one of the mechanisms by which low doses RT regulate lung inflammation and skew lung macrophages towards an anti-inflammatory profile. These data provide the preclinical rationale for the use and for the optimization of low doses RT in situations such as COVID-19-induced ARDS.

immunology↗

bioRxiv2018

Cell-lineage specificity of primary cilia during epididymis post-natal development

Primary cilia are sensory organelles that orchestrate major signaling pathways during organ development and homeostasis. By using a double Arl13b/mCherry-Cetn2/GFP transgenic mouse model, we characterized the spatio-temporal localization of primary cilia in the epididymis, from birth to adulthood. We report here a constitutive localisation of primary cilia in peritubular myoid cells and a dynamic profiling in differentiated epithelial cells throughout post-natal development. While primary cilia are present at the apical pole of the undifferentiated epithelial cells from birth to puberty, they are absent from the apical pole of the epithelium in adults, where they appear exclusively associated with cytokeratin 5-positive basal cells. Exogenous labeling of primary cilia marker Arl13b and IFT88 confirmed the cell lineage specific localization of primary cilia in basal cells and myoid cells in human epididymides. From whole epididymis tissues and serum-free cultures of DC2 murine epididymal principal cell lines we determined that primary cilia from the epididymis are associated with the polycystic kidney disease-related proteins polycystin 1 (PC1) and polycystin 2 (PC2), and Gli3 Hedgehog signaling transcription factor. Thus, our findings unveil the existence of primary cilia sensory organelles, which have the potential to mediate mechano/ chemo-signaling events in the epididymis.

developmental biology↗