NCube/papyrus huggingface dataset:
Impact de l’IL-15 dans un modèle murin de la sclérose en plaques

Multiple sclerosis (MS) is a chronic, inflammatory disease of the central nervous system (CNS). This disease is characterized by demyelination and immune cell infiltration in the CNS. Studies have shown that the immune system plays a key role in MS pathogenesis. Our laboratory identified the cytokine, interleukin 15 (IL-15), as a potential effector in MS development. IL-15 has been shown to be elevated in the blood and lesions of MS patients; however, its implications or its mechanisms of action in MS are not well defined. The goal of this project was to assess the role of IL-15 in the experimental autoimmune encephalomyelitis (EAE) animal model of MS. In this project, we injected peripheral IL-15 for 8 days to EAE mice and followed their clinical score. We also harvested the CNS and the spleen for cytometry analysis. Our results showed that peripheral injection of IL-15 caused a more severe EAE, and changed the frequency of CD8 T lymphocytes and NK cells in the periphery and CNS. We also showed that CD8 T cells in the periphery and CNS have increased IL-15 receptor expression after the IL-15 injection. Overall, our data show that peripheral IL-15 plays a role in the progression of EAE and affects the phenotype and number of immune cells.

Keyphrases: EAE, Neuroinflammation, Lymphocyte T CD8, Multiple sclerosis, CD8 T cells, NK cells, Immune cell infiltration
Effets d’âge et de sexe sur la synchronisation de l’EEG en sommeil : analyses multivariées par apprentissage machine

Aging is associated with significant changes in sleep. However, few studies evaluated how sex modulates the effects of aging on sleep, and the results show a large discrepancy in the literature. The objective of this study is to identify sleep features (polysomnographic sleep and quantitative sleep EEG variables), allowing to classify 299 participants aged between 20 and 70 years, according to the age group (young : 20-40 and older : 41-70 years) and by sex (women, men), using machine learning. The results obtained for the age classification show a decoding accuracy of 96% with a low error percentage and requires a combination of 19 features. We noticed that the amplitude and the Z-negative slope of the slow waves as well as the alpha/sigma ratio are present in 90 to 100% of the best combinations for the age classification. The decoding accuracy obtained for sex classification decreases to 72% and requires a combination of 15 features. We observed that sleep latency, alpha absolute spectral power, theta/alpha ratio and spindle frequency are occurred between 7 and 9 times in the best combinations for sex classification. Women showed a higher decoding accuracy than men (87% vs 57% respectively). The decoding accuracy obtained for classifying subjects according to 4 classes (young women, young men, older women, older men) is 71%, which is only 1 % less than that obtained for the classification by sex. Considering that the appropriate classification attributable to chance for two classes is 50% and that for four classes is 25%, the algorithm shows a significantly higher performance to classify by age and sex than by sex alone. We noticed that absolute sigma spectral power, amplitude of sleep spindles as well as amplitude, frequency and Z-negative slope of slow waves occurred in all the best combinations for age and sex classification. Older women showed again a higher classification percentage (87%) than the young women, young men and older men. The results confirm that it is possible to classify participants according to age and sex based on their sleep characteristics, but that it is easier to classify subjects according to age than by sex. Although the best classification combinations include polysomnographic features, EEG quantified variables (spectral and characteristics of slow-wave oscillations) are found more frequently in the best combinations suggesting that cerebral synchrony is a key factor in age and sex difference on sleep.

Keyphrases: EEG, Sleep, Aging, Sex differences, Machine learning
La synthèse de NETs par les angiopoïétines -1 et -2 contribue à des activités pro-inflammatoires et pro-angiogéniques

Angiopoietins (Ang1 and Ang2) are proteins known for their implication in angiogenesis. The discovery of their receptor (Tie2) on neutrophil surface led to numerous studies about their role in pro-inflammatory activities of neutrophils, like neutrophil adhesion onto endothelial cells (EC), pro-survival activity and synthesis and release of various cytokines. Recently, it has been reported that neutrophils have the capacity to release Neutrophil Extracellular Traps (NETs), nuclear DNA extruded in a web-like structure in response to infection or inflammation. Since angiopoietins can activate neutrophils, we address if they can induce NETs release, and if these NETs have an in vitro effect in pro-inflammatory and pro-angiogenic activities. Neutrophils were isolated from blood of healthy volunteers in accordance with the guidelines of the Montreal Heart Institute’s ethical committee. We observed that Ang1 and Ang2, alone or combined (10 nM; 3 hours) increase NETs release (≈2.5-fold) as compared to PBS-treated neutrophils. This NETosis is Tie2-dependent, and requires intracellular participation of PI3K, p38 and p42/44 MAPK pathways, ROS production, intracellular calcium release, and protein arginine deiminase 4 (PAD4) activation. These isolated NETs induced neutrophils and endothelial cells activation, leading to neutrophil adhesion onto human extracellular matrix (hECM) and human umbilical vein endothelial cells (HUVEC) and in vitro HUVEC capillary-like tube formation. This study is the first one to report the capacity of both angiopoietins to promote the release of NETs and to demonstrate that angiopoietins-mediated NETs contribute to pro-inflammatory and pro-angiogenic activities.

Keyphrases: Neutrophils, Neutrophil Extracellular Traps (NETs), Angiopoietins, Endothelial Cells, Cytokines, Adhesion Molecules, Cell Activation, Chemotaxis, Inflammation, Angiogenesis, Human
Fabrication de microstructures pour le recrutement de protéines synaptiques par polymérisation à deux photons

This thesis presents a technique allowing the implementation of electrodes’ surfaces for the optimisation of neuronal connexions. It was established that micrometric beads with a positive charge stimulate the formation of synaptic junctions on their surfaces. It was suggested by Dr. Santiago Costantino that it was possible to link those beads on the electrodes’ surface using the connection between biotin and streptavidin-coated beads. But, those connections demonstrated to be too weak to link the beads efficiently. Alternatively, we recreated those synaptic junctions using others conductive structures comparable to beads. Those structures were fabricated using a Ti:Sa laser at 800nm that allows the two-photon reduction of micro structures made of silver nitrate integrated in a polymer of polyvinylpyrrolidone (PVP). Those structures have an average height of 4.5±0.6µm and a diameter a mid-height of 8.8±1.6µm. Their resistivity is 4x10-3 Ω·m. The analysis of the synaptophysin and the PS95, two proteins widely found in the pre-synaptic and post-synaptic regions, demonstrates a significant accumulation around the structures. This confirms that microfabrication of structures of PVP and silver stimulates the formations of synaptic junction and allows the optimisation of neuronal connections on electrodes.

Keyphrases: synapse, Electrode, neuron, synapse, polymer, photo reduction, two-photon polymerisation
Techniques de spectroscopie proche infrarouge et analyses dans le plan temps-fréquence appliquées à l’évaluation hémodynamique du très grand prématuré

This master’s thesis is divided into two main sections discussing 1) near infrared spectroscopy (NIRS) techniques and signal analysis, and 2) the design and development of a multimodal NIRS probe to measure cerebral oxygen metabolism in newborns. NIRS is based on the measure of the optical properties of biological tissue, namely the absorption (μa) and scattering (μs') coefficients. These coefficients allow the estimation of oxy- and deoxyhemoglobin concentrations in the tissue. These optical techniques have great potential to monitor brain health in neonate at the bedside. The first part of the master’s thesis describes specific NIRS techniques used for neonatal applications. These modalities measure the hemoglobin oxygen saturation and peripheral systemic perfusion. Both parameters have been monitored in extremely preterm infants and showed significant differences in infants with hemorrhages compared to healthy controls. These differences were observed in the time-frequency domain with the use of wavelets analysis. Chapter 1 details the theory behind NIRS and the wavelets time-frequency analysis. The results of the study are presented in Chapter 2, in the form of a manuscript submitted to the Scientific Reports (Nature Publishing Group). Chapter 3 proposed a general and extended discussion on the results of the study as well as a return on Chapter 1 and Chapter 2. The second part of the master’s thesis (Chapter 4) details the design and development of a multimodal probe combing frequency-domain NIRS and diffuse correlation spectroscopy. The probe allows the measure of cerebral hemoglobin oxygen saturation and an index of cerebral blood flow. Both of these parameters serve to estimate an index of cerebral oxygen metabolism. The probe was designed for bedside monitoring of brain health in neonate.

Keyphrases: Neonatology, Brain imaging, Near infrared spectroscopy (NIRS), Continuous wavelet transform, Prematurity, Signal processing, Hemorrhage
Caractérisation du profil lymphocytaire B et de la réponse vaccinale des enfants exposés non infectés par le virus de l'immunodéficience humaine

In early life, HIV-exposed uninfected (HEU) children experience higher rates of morbidity and mortality. Studies revealed evidences of alterations in their immunological profile that are associated, in part, with maternal parameters related to HIV infection including in utero exposure to HIV, antiretroviral therapy (ART) and the pro-inflammatory placental environment. Here, we performed a longitudinal profiling of the B cell subsets and response to tetanus vaccine in HEU children during their 1st year of life.  HEU children (n = 68) from the CMIS Cohort were stratified based on the zenith of the maternal viral load  (VL; ≤40 vs. >40 copies/ml plasma) and the nadir of the maternal CD4 count (<500 vs. ≥500 cells/mm3) during pregnancy. Newborns received prophylactic ART (AZT/3TC) from 12h after birth until week 4 or 6. Blood mononuclear cells were isolated at birth, 6, and 12 months of age. CD19+ B cell subsets (naïve; transitional T1/T2; classical, activated and atypical memory; plasmablasts) were analysed by flow cytometry using CD10, CD20, CD21, CD27 and surface IgM markers. Tetanus-specific B cells and the IgG secreting activity of the memory fraction were studied using fluorescent tetanus toxoid C fragment (TTCF) oligomers and an ELISpot assay.  HEU infants born to mothers with a detectable VL during pregnancy had increased proportions of plasmablasts (p=0,0449) and a lower frequency of CD19+ B cells (p=0,0174) at birth in addition to having an expanded percentage of IgM+ classical memory B cells at 12 months (p=0,0367). Infants whose mothers had an impaired CD4 immunity throughout pregnancy (<500 cells/mm3) presented with greater frequencies of plasmablasts (p=0,0458) and IgM+ activated memory B cells (p=0,0071) at birth and 6 months respectively. These results suggest an early maturation of the B cell compartment and an alteration of the class switching mechanism in infants born to mothers with either a detectable VL or a low CD4 count. No relevant difference was noted in the TTCF-specific B cell subsets and the ability of memory B cells to generated specific antibodies. Overall, the severity of the maternal parameters in terms of VL and CD4 count had little impact on the ontogeny of the B cells subsets and their capacity to respond to vaccination.

Keyphrases: Lymphocytes B, HIV, B Cells, HIV-Exposed Uninfected Children, Tetanus, Vaccine Response
Sélection et étude de peptides inhibiteurs multi-cibles visant les Mur ligases chez Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen responsible of many nosocomial infections around the world.  Among cystic fibrosis patients, lung infections caused by this bacterium are the major cause of morbidity and mortality and thus developing new antipyocyanic agents, capable to fight this pathogen in an efficient and sustainable manner, is now a necessity to improve the quality and the life expectancy of these patients. To realize this, the peptidoglycan is one of the best targets for the development of antibacterial agents given the essential role of this polymer in bacterial survival. The Mur ligases (MurC, MurD, MurE and MurF), a family of very similar enzymes that have an essential role in the peptidoglycan biosynthesis pathway, are today not targeted by any antibiotic and are promising targets for the development of effective and sustainable antibacterial agents that target several of them. In this study, the Mur ligases of Pseudomonas aeruginosa were purified and used as targets in an innovative strategy to select peptides with affinity for the four Mur ligases. For this purpose, two peptide libraries were screened using an optimized version of the phage display technique and six selected peptides were evaluated for their specific affinity for the Mur ligases.

Keyphrases: Pseudomonas aeruginosa, Mur ligase, Cystic fibrosis, Peptidoglycan, Phage display, Antibacterial peptide, Multi-target
Implication des topoisomérases de type 1A dans la réplication stable et constitutive de l'ADN

Normal DNA replication in Escherichia coli begins at oriC. However, during transcription, certain factors (rnhA-, negative supercoiling) may trigger the formation of an R-loop, a DNA-RNA hybrid which can serve as a primer for constitutive stable DNA replication (cSDR). Recent genetic evidence has suggested that growth, segregation and filamentation defects in the topA topB double mutant are partially linked to cSDR. To confirm these observations and to better understand the function of topoisomerase 1A in the regulation of R-loop-dependant replication, we developed a new technique which can detect and measure cSDR in vivo at the cellular level. Growing cells are first exposed to spectinomycin, which prevents them from initiating replication at oriC, without affecting cSDR. DNA synthesis is next measured by the incorporation of a thymidine analogue, EdU (5-ethynyl-2´-deoxyuridine). The detection of these incorporated molecules is accomplished through their interaction with the Alexa Fluor 488 dye, using a click-it reaction. The level of fluorescence is then measured by flow cytometry. Using this protocol, we were able to confirm the presence of cSDR in the topA topB E. coli mutant. Furthermore, we detected a higher level of cSDR in this double mutant than in the topA single mutant. These results suggest that topB suppression amplifies cSDR-related phenotypes in the topA mutant. However, no cSDR was detected in the topB mutant, and topB suppression in the rnhA mutant did not magnify its cSDR-related phenotypes. We thus propose that the topoisomerase III enzyme shares an important function with topoisomerase I in chromosome segregation, and also that this function is essential when the cell undergoes cSDR. Our results also demonstrated that Topo I is the major Topo 1A involved in R-loop and cSDR regulation.

Keyphrases: R-loop, topA, topB, rnhA, RNase H, Topoisomerase
Expansion of the CD8 memory T cells : implications for the self-renewal gene Hoxb4

CD8 memory T (Tm) cells provide life long protection against recurrent infections and are maintained through self-renewal mechanisms. Hematopoietic stem cells (HSC) also possess the capacity to slowly self-renew assuring their long-term maintenance. Both cell types use the bone marrow as their preferred proliferation niche. CD8 Tm and HSC partially share a transcriptional profile including some genes known to control self-renewal. Hox genes are expressed in HSCs, among them Hoxb4 is a potent enhancer of HSC expansion in vitro and in vivo. Based on the similarities between HSC and Tm cells, we hypothesize that genes involved in HSC self-renewal, like Hoxb4, will promote CD8 Tm cell expansion. To test this hypothesis, we have determined the effect of Hoxb4 overexpression in T cells from young and old transgenic mice, and on the engraftment and maintenance of CD8 Tm cells after transplantation into immunocompetent or immunodeficient mice. At the steady-state, the composition and phenotype of the naïve and memory T cells were not affected by Hoxb4 overexpression. To study CD8 Tm cell maintenance, the Hoxb4 and the OT-1 transgenic mice were crossed; the latter express a T cell receptor that recognizes the ovalbumin (OVA) peptide, presented by major histocompatibility complex class I. Using this model, we generated in vitro large numbers of monoclonal and OVA specific CD8 Tm cells for adoptive transfer experiments. The number and the phenotype of Tm cells generated in culture were not affected by Hoxb4 overexpression. These cells were transplanted into wild type mice to evaluate their engraftment and long-term maintenance. After transplantation in either immunocompetent or immunodeficient mice, Hoxb4 overexpressing Tm cell engraftment or maintenance was not enhanced when compare to wild-type Tm cells. These results demonstrate that Hoxb4 does not promote CD8 Tm cell self-renewal. Further studies will try to identify the factors controlling CD8 Tm cell self-renewal.

Keyphrases: Hoxb4, CD8 memory T cells, hematopoietic stem cells, self-renewal, homeostatic proliferation, transgenic mice model
L'homodimérisation du CD40 et son implication indirecte dans l'asthme allergique

The CD40 is a member of the TNF receptor family. It is a type I transmembrane glycoprotein, expressed on the surface of hematopoietic and non-hematopoietic cells. Its main ligand, the CD154, belongs to the Tumor necrosis factors (TNFs) superfamily. The trimeric soluble or membrane CD154 binds to the monomeric CD40 and induces its oligomerization as well as its homodimerization. It is well known that CD154 binds to three other receptors belonging to the family of integrins: αIIbβ3, α5β1, and αMβ2 (Mac-1). The interaction of CD40/CD154 plays a key role in the regulation of the immune response. On the other hand, studies have shown that this couple is overexpressed and this interaction is amplified in inflammatory and autoimmune diseases, such as allergic asthma. In addition, several studies have demonstrated the beneficial effect of blocking the binding of CD40 to its major ligand CD154, in various diseases. Currently, blocking this axis is a targeted strategy to develop new immunotherapies, however, it has several side effects. That’s why we have focused on the homodimerization of CD40, in order to study the effects of its inhibition. Our group has already demonstrated that cysteine 238 (Cys238) from the intracellular domain of the CD40 mediates the formation of disulfide bond CD40 homodimer (db-CD40). Furthermore, the use of the antioxidant NAC inhibits this homodimerization. Thus, the ROS could be involved in the formation of CD40 homodimers. Moreover, it’s important to note that NADPH Oxidase (NOX) is the major intracellular source of ROS. So, we hypothesize that the homodimerization of CD40 requires specific signals involved in the production of ROS, and this homodimerization could lead to the development of diseases such as allergic asthma. In order to confirm it, our objectives are to: 1) Determine the signaling pathways required for the formation of the CD40 homodimer. 2) Determine if CD40 is the only receptor involved in the development of allergic asthma. Indeed, we have generated an allergic mice model, sensitized to ovalbumine. In this project, our results have demonstrated the involvement of ROS and NOX in the formation of db-CD40 homodimer. Indeed, NOX produces ROS that oxidize Cys238. Moreover, we have shown that blocking the interaction CD40/CD154 attenuates asthma in ovalbumin-sensitized mice. In fact, intratracheal administration of MR-1 (anti-CD154) or FGK (anti-CD40) antibodies significantly decrease cellular influx to the airways, and attenuated the development of Methacholine induced AHR. In addition, treatment with either MR-1 or FGK locally abrogated IgE class switching.

Keyphrases: CD154, CD40, ROS, NOX, db-CD40 homodimer, asthma
Effet des pesticides sur la diversité bactérienne des champs agricoles et la capacité des bactéries à les dégrader

This study presents the characterization of bacteria involved responsible in-vivo bioremediation of herbicides Diuron and Linuron. Microbial biodiversity was analyzed using 16S RNA amplicon sequencing methods for six soil samples of two different biofilters, sampled three times a year over three year period. Illumina MiSeq amplicon sequencing coupled with bioinformatics and statistical analysis showed that the Actinobacteria group are most abundant in soil noncontaminated by pesticides accounting for up to 45% of bacteria, whereas subsequent exposure of soil to pesticides altered the biodiversity and the abundance of each group of bacteria present in a given soil sample. Proteobacteria were found to be the most abundant after three successive exposures to pesticides during the growing session. Once pesticide exposure stopped during the winter period, the biodiversity of our soil had a tendency to recover. Rhodanobacter spathiphyllum and Geobacillus stearothermophilus were isolated from a soil sample exposed to pesticides and showed optimal growth in the presence of Diuron in liquid minimal medium compared to conditions without the pesticide. The results of degradation of Diuron and Linuron by R. spathiphyllum in minimal medium, were confirmed by High Performance Liquid Chromatography-Mass Spectrometry (HPLC-MS), and showed a better degradation of Linuron (from 20 μg/ ml to 0.9 μg/ml and Diuron (from 40 μg/ml to 31 μg/ml) by R. spathiphyllum and (from 40 μg/ml to 37 μg/ml) by G. stearothermophilus. The degradation of Diuron by R. spathiphyllum seems to produce by-products that inhibit its growth.

Keyphrases: Diuron, Linuron, Microbiology of pesticides, Bioremediation, Biofilters, Biodiversity of soil
Cost-effectiveness of NASH screening

Nonalcoholic fatty liver disease (NAFLD) is the most common liver disease in Western countries. No studies have examined the cost-effectiveness of screening for nonalcoholic steatohepatitis (NASH), its advanced form.  We performed a cost-utility analysis of annual non-invasive screening strategies using third-party payer perspective in a general population and compared it to screening in a highrisk obese or diabetic population. Screening algorithms involved well-studied techniques including NAFLD fibrosis score, transient elastography (TE), and acoustic radiation force impulse (ARFI) imaging for detecting advanced fibrosis (≥ F3); and plasma cytokeratin-18 for NASH detection. Liver biopsy and magnetic resonance elastography (MRE) were compared as confirmation methods. Canadian dollar costs were adjusted for inflation and discounted at a 5% rate. Incremental cost-effectiveness ratio (ICER) of ≤$C50,000 / quality adjusted life year (QALY) was considered cost-effective.  Compared with no screening, screening with NAFLD fibrosis score/TE/CK-18 algorithm with MRE as confirmation for advanced fibrosis had an ICER of $C26,143 per quality-adjusted life year (QALY) gained. Screening in high-risk obese or diabetic populations was more cost-effective, with an ICER of $C9,051 and $C7,991 per QALY gained respectively. Liver biopsy confirmation was not found to be cost-effective.  Our model suggests that annual NASH screening can be cost-effective, particularly in high-risk obese or diabetic populations.

Keyphrases: Nonalcoholic fatty liver disease (NAFLD), Nonalcoholic steatohepatitis (NASH), Cost-utility, Elastography, Screening, Cost-effectiveness