NCube/papyrus huggingface dataset:
Le temps sédentaire au travail et les bureaux actifs : compréhension des différences entre les bureaux actifs

In our industrialized countries, sedentary behaviours lead to health issues for many workers, as the physical demands of their work are now insufficient. To answer this problem, the research focuses on active workstations (standing, with pedals or treadmill workstations) which compared to the conventional workstation allow workers to increase physical load at work and thus, reduce daily sedentary time. When compared to the conventional (sit) workstation, active workstations have effects on physiological and biomechanical biomarkers related to better health. Also, they offer some advantages over workers’ productivity and wellbeing at work. Despite the accumulation of knowledge about active workstations, the differences between active workstations are still unknown. This thesis is aimed at understanding and comparison between active workstation types, specifically their impacts on sedentary time at work, their effects on physiological and biomechanical biomarkers and their effects on productivity and well-being at work. The results and the discussion are developed around a systematic review article (Dupont et al., 2019) and an article from an experimental research submitted in October 2019. First of all, the benefits associated with each type of active workstation (i.e. standing, cycling, treadmill) may not be equivalent. Cycling and treadmill workstations appear to provide greater short-term physiologic changes than standing workstations that could potentially lead to better health. Cycling, treadmill and standing workstations appear to show short-term productivity benefits, while treadmill workstations reduce the performance of computer-related work. Secondly, in the short term (2 weeks), the introduction of a standing workstation and a pedal workstation in their office allows workers to accumulate an average of 132 minutes of active time (i.e. work done with standing and/or cycling workstations) per day, which represents 46% of the total time spent in their personal workspace. As a result, workers reduce their total desk-sitting time by half and sat on average 30 minutes per sedentary bout. Based on our findings, adding two active workstations to an office worker’s helps reduce sedentary time at work.

Keyphrases: Active workstation, Sedentary, Occupational health
Investigating the localization mechanism of Bsg25D mRNA in Drosophila melanogaster

The subcellular transport and localized translation of mRNA molecules is emerging as a highly prevalent and important process for controlling asymmetric protein distribution in cells. A candidate mRNA, Bsg25D, known to localize to centrosomes and astral microtubules in Drosophila embryos during early events of embryogenesis, was selected to determine the role and importance of mRNA targeting to the mitotic apparatus during cell division. The localization of Bsg25D to centrosomes in Drosophila embryos is conserved between species such as D. melanogaster, D. simulans and D. yakuba. Bsg25D encodes a protein closely related to centrosome-associated proteins Ninein (Nin) and Ninein-like protein (Nlp) in mammalian cells. Structure function analysis revealed that the coding and 3’UTR of Bsg25D are necessary for its targeting pattern, suggesting that a cis-regulatory motif that drives its localization, is in the coding + 3’ UTR region.

Keyphrases: Centrosomes, Hybridation in situ de fluorescence, mRNA localization, Fluorescent in situ hybridization, Embryogenesis
La protéine MAP kinase-activated protein kinase-2 n’est pas essentielle lors de la phase inflammatoire du processus de guérison après un infarctus du myocarde chez la souris

The first phase of reparative fibrosis following a myocardial infarct (MI) is an inflammatory response. Without inflammation, scar formation is impaired, which leads to heart rupture. A strong response can also lead to heart rupture due to excessive ECM degradation. Efficient ways of controlling inflammation are constantly being explored to improve the prognosis in patients. In response to cellular stress, MAP kinase-activated protein kinase-2 (MK2) is activated by p38α and β. This protein serine/threonine kinase mediates the inflammatory process by stabilising pro-inflammatory cytokine mRNA. MK2-deficent mice (MK2-/-) show an impaired expression of cytokines, such as IL-1β and IL-6, in response to lipopolysaccharide injection. The objective of this study was to determine if the absence of MK2 impaired the inflammatory phase following an MI induced by permanent ligation of the left anterior descending artery (LADL) in 12-week-old male MK2+/+ and MK2-/- litter mate mice. This study shows that mortality was significantly reduced in MK2-/- mice. Echocardiographic imaging showed that heart function was affected in similar ways in MK2+/+ and MK2-/- mice whereas heart structure was less affected MK2-/- mice. Masson's trichrome staining revealed no difference in scar size and collagen content. No differences were observed in neutrophil and macrophage recruitment. The use of a RT2 Profiler PCR Array specific to cytokines showed that mRNA fold expression appeared to be reduced in MK2-/- healthy tissues but that the inflammatory response was not impaired. In conclusion, MK2 was not essential for the inflammatory phase of post-MI wound repair in the male mouse heart.

Keyphrases: MK2, Inflammation, Fibroblastes, Cardiofibroblastes, Myocardial infarct, Fibroblasts, Cardiofibroblasts, Reparative fibrosis
DNMT3A P904L : un nouveau variant dans la tumeur de Wilms

Wilms tumours are the most common kidney tumour in children. As of now, almost 80 % to 90 % of the patients survive but there is still some who do not respond. This project objective is to study the novel mutation P904L in the DNMT3A gene discovered in a relapse Wilms tumour’s patient. The impact of this variant is unknown, but mutations in DNMT3A are frequently found in cancer. The context of the mutation in the patient and the recurrence of this mutation in other cancers and syndrome make us believe that it is affecting the function of the DNMT3A protein. Loss of function and some mutations of DNMT3A are known to affect crucial characteristics of cancers such as differentiation and immortalization. It is also known that Wilms tumours are made of undifferentiated or embryonic looking cells. We supposed that the impact of the mutation on DNMT3A protein contribute to the development of the tumour. To prove that this new mutation is affecting the protein and the development of the tumour, we used both functional assays and next generation sequencing technologies. Because DNMT3A is a gene affecting the methylation of the DNA and thus regulating gene expression, we used expression profile to assess the impact of the mutation on the enzyme DNMT3A. We demonstrate that the new mutation P904L causes a loss of function of the DNMT3A protein. This mutation affects the self-renew and the migration of the cells. Moreover, it modulates the response to drugs. We also found that the mutation modulates the gene expression in the cell line and this modulation is coherent with the expression pattern of the patient. In conclusion, we suggest three mechanisms by which this new mutant contributes to the development and progression of Wilms tumours. We also show that there is a need to further our knowledge of this tumour in order to propose new therapeutics options to non-responsive patient.

Keyphrases: DNMT3A, Cancer, Mutation, Wilms Tumour, Epigenetics
Structure et localisation du complexe ESX-3 dans les mycobactéries

A novel, type VII secretion system (T7SS) was recently discovered in Mycobacteria. Five subsystems, called ESX-1 to ESX-5, have been identified, with the ESX-3 being the most conserved. The ESX-3 system is essential for growth and pathogenesis, and has been implicated in iron transport and secretion of effector proteins into the host. The secreted proteins are shown to prevent phagosome maturation by interacting with the ESCRT machinery of the macrophage. To characterize the structure and mechanism of secretion employed by the T7SS, we use the ESX-3 system from Mycobacterium tuberculosis (Mtb) and recombinantly express it in M. smegmatis and M. marinum cells. By combining Fast Protein Liquid Chromatography (FPLC) and Single Particle electron microscopy analysis, we have reconstructed several in vitro models that contain at least three of the ESX-3 cluster proteins and may represent the dynamic nature of the core complex. Using fluorescent light microscopy (fLM) and super-resolution structure illumination microscopy (SR-SIM), we localized the ESX-3 complex to the lateral pole in M. marinum cells. We also used super-resolution photoactivated localization microscopy (PALM) in correlation with cryo-electron tomography (cryo-ET) of whole M. marinum cells to localize and reconstruct an in vivo 3D model of the ESX-3 secretion system. By combining the single particle reconstructions and the cryotomography data, we discuss a possible mechanism of ESX-3 secretion. Such analysis may support future inhibitor screens to prevent mycobacterial infections.

Keyphrases: T7SS, ESX-3, structure, Microscopie corrélative PALM-cryo-ET, Localization, Model, Correlative PALM-cryo-ET
Adaptation de la levure à la suite des perturbations du mécanisme de contrôle de qualité de l'ARN

The life-cycle of RNA is determined by several processing steps, which allow the cell to export and translate a coding transcript. The cell has developed an astonishingly complex mechanism to ensure the integrity of RNA processing steps. The quality control mechanism of RNA balances the biosynthesis and degradation of various transcripts, adding another layer of gene regulation to the complex system of gene expression. The exosome is a central piece of the RNA quality control mechanism as it degrades many of the aberrant or non-functional RNAs in the nucleus and the cytoplasm. This project characterizes and highlight a response to mutation of components from the RNA quality control mechanism in Saccharomyces cerevisiae. These perturbations include functional components of the exosome (Csl4 and Dis3), a cofactor of the nuclear exosome (Rrp6), an essential protein for pre-rRNA processing (Enp1) and a component of RNA export machinery (Srm1). Here, I present bioinformatics approaches to characterize the cellular response at a level of transcript expression and polyadenylation size. The stress response embedded in the gene expression profile is highly similar between the mutants. This work suggests a generic response to a failure in different components of the RNA quality control machinery.

Keyphrases: bioinformatic, transcriptomic, RNA quality control, exosome, polyadenylation
Investigation génétique de NAFLD dans le diabète de type 2 via construction d’un modèle de prédiction de la maladie et par criblage du locus PNPLA3-SAMM50

Non-alcoholic fatty liver disease (NAFLD) is a liver disorder more frequent in type 2 diabetes (T2D) and is associated with complications such as mortality. For this reason, establishing non-invasive tools for predicting NAFLD is crucial. My master’s project aimed to establish genetic markers for NAFLD in T2D using two strategies: 1) a non-targeted selection of genetic markers (SNPs) by the LASSO method and 2) a targeted selection of SNPs reported as associated with the disease or its related abnormalities. A population involving 4098 patients with T2D and Caucasian ancestry was used. Summary statistics data of pangenomic studies were exploited for the selection of SNPs to be involved in the polygenic risk score (PRS). I also designed a model of 3210 SNPs adjusted by covariates and able to predict the high rates of ALT (AUC=0.69) and non-cardiovascular death (AUC=0.66). Mapping of the candidate locus PNPLA3-SAMM50 allowed the observation of diversity in terms of genetic association with the metabolic abnormalities such as ALT (surrogate of NAFLD) (rs2294915, P = 1.83x10-7), non-cardiovascular death (rs2294917, P = 3.9x10-4) and the efficiency of the intensive antidiabetic therapy within a subgroup in the population (individuals with GG of rs16991236, P = 0.007). My studies allowed for a better understanding of the genetic background of NAFLD in T2D and open perspectives for establishing more adequate tools for diagnosis and follow-up of the disease.

Keyphrases: NAFLD, SNP, PNPLA3-SAMM50, Type 2 diabetes, Non-cardiovascular death, Polygenic risk score
La maladie de Parkinson est-elle une maladie auto-immune ? À la recherche des acteurs moléculaires de la MitAP

Mitochondrial dysfunction is associated with many neurodegenerative diseases. Indeed, several proteins involved in these diseases, such as PINK1 and Parkin proteins in Parkinson's disease, are involved in the protein recruitment required for mitochondrial homoeostasis. In the absence of these proteins, a new mechanism is set up: the formation of vesicles derived from mitochondria (MDVs). Our team has demonstrated that this mechanism is responsible for the mitochondrial antigen presentation (MitAP) and that the PINK1 and Parkin proteins play a repressor role on this pathway and that this new presentation pathway is capable of activating CD8 + T cells in vivo. These discoveries bring the immune system as a new player in neurodegenerative diseases. However, the proteins involved in MitAP remain to be identified. Two projects have been initiated to better characterize MitAP. The first was to develop a mitochondrial isolation protocol to identify new molecular partners for MDV formation at the mitochondrial level. The second project initiates the study of the immunopeptidoma of antigen presenting cells to identify the mitochondrial peptides presented on the cell surface. The identification of these proteins is essential to understand the mechanism of MDVs and the functioning of MitAP involved in Parkinson's disease. The protein partners of this molecular pathway may have a role in neurodegenerative diseases and may be therapeutic targets or biomarkers.

Keyphrases: Parkinson's Disease, Immune System, Mitochondria, Mitochondrial Antigen Presentation
Impact du sexe sur l’immunogénicité, l’efficacité et l’innocuité du vaccin contre la grippe saisonnière : revue systématique

Every year, seasonal influenza is an important cause of morbidity and mortality, despite being vaccine-preventable. Several studies have demonstrated that sex factors (genes and hormones) impact individuals’ susceptibility and response to infectious diseases and vaccines. However, most studies do not explicitly assess sex differences in vaccine response despite collecting this data, but rather adjust for sex.  The purpose of my dissertation is to synthesize the current evidence on sex differences in response to seasonal influenza vaccine in an attempt to guide sex-specific recommendations in influenza vaccines administration. Therefore, we conducted a systematic review to analyze available evidence on sex differences in immunogenicity, efficacy, effectiveness and/or safety of the seasonal influenza vaccine. Available data show no sex differences in the immunogenicity and effectiveness of seasonal influenza vaccine, while higher rates of adverse events following immunization (AEFIs) seem to occur in females. However, evidence of higher quality is needed to better understand sex differences in response to influenza vaccine.

Keyphrases: Influenza, Genre, Flu, Vaccines, Sex differences, Gender differences, Immunogenicity, Effectiveness, Efficacy, Safety
Impact des antibiotiques céfprozil et céfoxitine sur le microbiote Eggerthella lenta, lié au métabolisme du cardiotonique digoxine

Digoxin is a widely used cardiotonic drug in the management of heart failure and atrial fibrillation. It has been known since the early 1980's that the main metabolite of digoxin, dihydrodigoxin, is synthesized by the gut microbiome during first pass metabolism and is exclusively produced by the bacteria Eggerthella lenta. In a clinical study done in the U.S.A., there were 14% of high metabolizers, for whom over 40% of the oral digoxin dose is transformed to the inactive metabolite and rapidly eliminated. Digoxin toxicity is the leading cause of hospitalization from medication's secondary effects. The toxicity events are often associated with the addition of an antibiotic (mostly from the macrolides class) to the patient's drugs regiments. The theory explored in this project could help explain the toxicity events in metabolizers. These patients have a higher daily digoxin maintenance dose to counteract the effects of the microbiome and are then prescribed antibiotics for an infection unrelated to their heart condition. The antibiotic alters E. lenta negatively, which cannot metabolize digoxin anymore and therefore augments the bioavailability of the cardiotonic. If the plasmatic concentration reaches dangerous levels (over 2ng/ml of plasma), the patients face adverse effects that include death. In the present project, we evaluated the susceptibility of E. lenta to two second generation cephalosporins, in vivo and in vitro.  With the 18 healthy volunteers that were exposed to 2x500mg of cefprozil daily for 7 days, we observed a diminution of the abundance of the bacteria of interest by 58,3% from the initial levels. This change did not however produce statistically significant tests results. For the complete fecal microbiome that were cultivated in vitro, with or without cefprozil, the difference between the two conditions resulted in a statistically significant p-value of 0.0457, confirming the sensitivity of E. lenta to this cephalosporin. These results validate an important premise for the demonstration of the importance of the gut microbiome in the pharmacokinetics of digoxin and the clinical management of the drug to avoid toxicity events in clinical practice.

Keyphrases: Microbiome, Eggerthella lenta, Eubacterium lentum, Next-Generation Sequencing (NGS), Whole Genome Shotgun (WGS), Bioinformatics, Pharmacology, Pharmacokinetics, Cardiology, Heart Failure
Optimisation d’un système microfluidique pour le test d’agents thérapeutiques avec la radiothérapie

At least 60% of cancer patients will receive radiotherapy (RT) as part of their treatment. The efficacy of radiotherapy in the treatment of cancer is limited by the phenomenon of radioresistance of cancer cells and by the toxicity of radiation on healthy tissues. The discovery of new radiosensitizers and radioprotectors is essential to overcome these challenges. 3D cellular models such as spheroids emerge motivated by the need for better preclinical models. The objective of the project was to optimize a microfluidic system for easy, fast and low-cost testing of therapeutic agents with RT on spheroids. The developed microfluidic system allows the formation of 336 homogeneous spheroids in two days with minimal user intervention. The spheroids are distributed in 16 culture chambers separated by a magnetic valve system to avoid bystander effects between irradiated and unirradiated spheroids. A new irradiation technique has been developed to expose a system with 4 different radiation doses. In total, 4 radiation doses and 4 concentrations of therapeutic agents can be tested per system. Using this approach, the efficacy of three agents with RT was evaluated with clonogenic assays.  Radiosensitizing properties of Talazoparib, a PARP inhibitor, on soft tissue sarcoma (STS) cells cultured as spheroids at 2 Gy were demonstrated. The developed system enables the evaluation of therapeutic agents with RT and contributes to the wide adoption of spheroids as a preclinical model.

Keyphrases: Radiotherapy, Radiosensitizer, Radioprotector, Spheroid, Microfluidic, Repurposing, Sarcoma, Orthovoltage
Understanding the role of the matricellular protein SMOC-2 in renal cell carcinoma

Matricellular proteins (MPs) are non-structural ECM macromolecules induced transiently during development, tissue repair and remodeling, and inflammation. Expression of MPs can be triggered by acute tissue injury and their sustained expression can contribute to chronic disease. MPs primarily act to mediate tissue remodeling events by facilitating interactions and signals from the ECM to the surrounding cellular niche. Using published RNA-seq data from two distinct models of kidney injury, Folic Acid (FA) and Unilateral Ureteral Obstruction (UUO), we analyzed the expression profile of various members of well-known MP families during the acute and fibrotic injury phases. We reveal novel MPs implicated in renal injury and present informative networks between members of each MP family using bioinformatic tools. mRNA expression of select candidate MPs were confirmed by Western blot.  To extend our understanding of translatable mechanisms in repair and matrix remodeling, we chose SMOC-2 as our MP model to study in Renal Cell Carcinoma (RCC) which has strong metastatic tendencies. SMOC-2 overexpression and recombinant protein treatment of RCC cell lines (786-O, ACHN) were shown to induce a metastatic EMT profile by Western blot analysis, supported by functional assays (proliferation, migration). Silencing SMOC-2 by siRNA showed the contrary results.  Taken together, our work utilizes the understanding of temporal expression patterns of MPs to gain insight into mechanisms and conditions that support persistent activation in chronic injury states. Overall, our work with SMOC-2 provides a valuable perspective and template to approach studying and characterizing novel MPs in diseases involving pathological matrix remodeling and repair.

Keyphrases: matricellular protein, epithelial-to-mesenchymal transition, folic acid, unilateral ureteral obstruction, extracellular matrix, renal cell carcinoma, cancer metastasis
Détection et suivi des singularités de phase par le suivi des fronts de dépolarisation dans un modèle informatique de ﬁbrillation auriculaire

Atrial fibrillation affects a growing number of individuals each year. These patients are subject to severe complication such as AVCs if a treatment is not applied to their condition. One possible therapeutic approach is catheter ablation of the problematic tissue with heat or cold. This method targets fibrillation sources known as rotors. To allow for a more efficient and personalizable treatment, detection of such rotors is done through electrical or optical signal cartography. The resulting map of membrane potentials can then be used to find the center of the target rotors: phase singularities (PS). PS analysis allows a deeper understanding of AF dynamics. Moreover, tracking these reentries is essential for the evaluation of PS lifespan. The sources with longer the lifespans can be identified as stable and kept as possible candidates for ablative therapy. The projects objective is to improve PS detection and tracking algorithms We have developed 2D atrium models with dynamic (beat-to-beat variation), ionic (potassium channel conductance) and structural (fibrosis) heterogeneities. Episodes of atrial fibrillation were simulated for each model. The developed method allows for precise PS tracking for the simulated cases of AF. The error rate of the method is dependent of the temporal resolution and the complexity of the fibrillation dynamics. By applying a post-processing correction method and a threshold to the lower lifespan values ( ps = 15ms) it is possible to highlight longer lasting rotors that could be considered permanent when the temporal resolution is sufficiently low (dt = 0.1ms). The result of the following project allows for easier AF dynamics analysis for simulated 2D sheet cases. The method is theoretically applicable to 3D cases if the algorithm is adapted to such models.

Keyphrases: Arrythmies, Phase, Source, Atrial ﬁbrillation, Phase singularity, Arrhythmia, Tracking, Source, Rotors, Reentry