NCube/papyrus huggingface dataset:
Évaluation de la variabilité du transfert d’immunité passive dans les troupeaux laitiers du Québec

Calves are born almost agammaglobulinemic, so they must ingest immunoglobulins from their mother's colostrum; it’s the transfer of passive immunity (TPI). An adequate TPI reduces the risk of mortality and morbidity during the first weeks of life. A high percentage of success of TPI in herds maximizes the chances of having a herd with healthy calves. The objectives of this herd-level study were to quantify the prevalence of adequate TPI, and to investigate its association with colostrum management. A total of 59 Quebec commercial dairy herds were selected by convenience to participate to this observational study. In every participating herd, a minimum of 14 blood samples from Holstein calves were sampled to estimate their prevalence of adequate TPI using a digital Brix refractometer. Samples of colostrum served to each of these calves were collected to evaluate immunological quality using a digital Brix refractometer and bacteriological quality using Petrifilm systems. A questionnaire on colostrum management practices was completed by dairy producers to assess on-farm practices. The herd-level prevalence of adequate TPI (defined as the percentage of calf with serum Brix degree ≥ 8.4%) success ranged from 24% to 100%, and the median was 67%. In the multivariable linear regression models, the prevalence of adequate TPI was associated with the prevalence of adequate volume (defined as the percentage of calves receiving ≥ 2 liters of colostrum at first meal), prevalence of adequate colostrum quality (defined as the percentage of calves receiving a colostrum with ≥ 20,9 Brix degrees), and prevalence of adequate time to the first meal (defined as the percentage of calves receiving colostrum within ≤3h after birth), but was not associated with the gender or bacterial contamination prevalence. In summary, the prevalence of success of TPI varied greatly and was influenced by management practices of dairy farmers.

Keyphrases: Colostrum, Bacteriological quality, Immunological quality, Passive immunity transfer, Dairy herd, Brix refractometer
Développement d’une méthode informatique appliquée à la quantification immunohistochimique du mastocyte et du macrophage M1 et M2 lors de la guérison cutanée chez le cheval

The goal of this randomized and controlled study was to develop a reliable and accessible quantification method for immunohistochemically-stained tissues and to quantify the temporal and anatomical pattern of mast cells and M1/M2 macrophages during equine wound healing. Two full-thickness skin wounds were created on each distal forelimb and hemithorax, respectively, of four mixed breed mares (n= 4). Samples were taken at days 2, 7, 14 and 21 post wounding and stored (n = 28). Immunohistochemistry was performed to study mast cell (CD117) distribution and double immunohistochemistry was performed with M1 (CD86), M2 (CD204) and pan macrophage (CD14) markers. An ImageJ quantification method was developed and compared with a traditional manual counting on 6 specimens. Stained cells on the other 22 samples were then quantified with the computer-based method. For the validation of the method, an intra- and interoperator Intraclass correlation coefficient (ICC) of 0.90 (p < 0.01) and 0.69 (p < 0.01) were found. An ICC value of 0.67 (p < 0.05) was found between the ImageJ method and manual counting. No significant difference of mast cell numbers was observed in relation to anatomical location (thorax vs limb) or time of healing. M2 macrophages showed a spindle or rounded shape while general macrophages showed a round, fried-egg or dendritic morphology. The quantification method developed is reliable, reproducible, available and free. Future studies should, with equine-specific antibodies, further characterize mast cell and macrophage implication in wound healing and chronically-inflamed limb wounds of horses.

Keyphrases: Quantification, Equine, Immunohistochemistry, M1 and M2 macrophages, Mast cells, Skin
Identification des récepteurs cholinergiques impliqués dans le fonctionnement du cortex visuel du rongeur

The cholinergic system is involved in attention, learning and memory and cholinergic receptors regulate multiple functions of the central nervous system. Nevertheless, their role in modulating the properties of the visual cortex remains to be established. One of the objectives of this thesis was to study the role of muscarinic receptors involved in the normal function of the visual cortex. We have been able to determine that the muscarinic receptors are involved in the establishment of many visual properties such as the size of the receptor fields, contrast sensitivity, spatial frequency selectivity and accuracy of the cortical connectivity. The other objective was to identify the cholinergic receptors involved in the potentiation of visual abilities. We improved the cognitive processing of visual information by electrical stimulation of the basal forebrain (the nucleus where the cholinergic cell bodies are located) and by cholinergic stimulation using donepezil, an acetylcholinesterase inhibitor. The repeated combination of visual and cholinergic stimulations (whether electrical or pharmacological) similarly enhances visual cortical activity. However, the receptors involved are not the same. Following the pharmacological stimulation, it is mainly the muscarinic receptors that influence visual acuity with a delay in the receptors expression and this modulation is earlier for the electrical stimulation. These results demonstrate that repetitive coupling of cholinergic stimulation and visual stimulation can enhance visual cortical activity. Knowing the cholinergic receptors involved will allow in a near future to target them directly to improve cortical function.

Keyphrases: Vision, Muscarinic receptors, Nicotinic receptors, Cholinergic stimulation, Cortical activity, Acetylcholinesterase inhibitors, Basal forebrain
Étude des adaptations spécifiques à la pratique des activités d’armer : facteurs de risque et prévention des pathologies de l’épaule

The shoulder joint complex is largely involved in the tennis strokes. Particularly, the tennis serve applies high mechanical constraints and requires extreme joint positions making the shoulder vulnerable to injuries. Intensive tennis practice leads to musculoskeletal and functional adaptations that are thought to be beneficial to performance. However, it remains unclear when they become unbalanced or excessive that increases the risk of injury. The prospects are scouted from 5 years old, but little is known on their specific shoulder characteristics, risk factors for injury and pathomechanics. Such knowledge would be useful to optimize their monitoring by coaches. This thesis aimed to characterize the young tennis player's shoulder, identify risk factors for injury and describe the shoulder pathomechanisms related to the tennis serve. To characterize the young tennis player’s shoulder, 67 asymptomatic tennis players aged 7 to 13 years old were divided into three groups according to their biological age. The comparison between our three groups highlighted that the glenohumeral ranges of motion and the shoulder muscle strength adaptions occurred from an early age. Then to bring risk factor for shoulder injuries to light, these parameters were also compared between 31 players with a history of shoulder pain and 60 asymptomatic players. Players with a history of shoulder pain presented a larger glenohumeral joint total rotation range of motion as well as a weakness of the glenohumeral external rotator muscles and the scapular stabilizer muscles. A longitudinal study, using a latent profile transition analysis, was conducted to determine whether the factors previously identified were the cause or consequence of the shoulder injury. Furthermore, in the aim to describe the shoulder pathomechanisms related to the tennis serve motion, the glenohumeral and scapulothoracic kinematics of the tennis serve were compared between 13 players without and 15 with a history of shoulder pain. Players with a history of shoulder pain adapted their glenohumeral and scapulothoracic kinematics at the end of the cocking phase to probably preserve the sub-acromial space and the rotator cuff tendons during the tennis serve. Finally, the previous study was completed by a study analyzing the shoulder biomechanics of a tennis serve before and after the fatigue of the lower trapezius. The weakness of the scapular stabilizer muscles impaired the scapular kinematics and decreased the activation of the anterior shoulder muscles that may jeopardize the shoulder joint anatomical structures. These findings bring new knowledge to improve the young players monitoring and the injury prevention. Particularly, it highlights the importance to strengthen the stabilizer muscles (glenohumeral external rotator muscles and scapular stabilizer muscles).

Keyphrases: tennis, kinematics, young, muscle strength, range of motion, muscle activation, overhead sport, electromyography
Nucleotide Complementarity Features in the Design of Effective Artificial miRNAs

The importance of miRNA in gene regulation has been well established; however, the precise mechanism of its target recognition process is still not completely understood. Among the known factors, nucleotide complementarity, accessibility of the target sites, and the concentration of the RNA species, and site cooperativity were deemed important. Using these known rules, we previously designed artificial miRNAs that inhibit cancer cell growth by repressing the expression of multiple genes. Such guide sequences were delivered into the cells in the form of shRNAs.  HIV is an RNA virus. We designed and tested guide RNAs that inhibit its replication by directly targeting the viral genome and cellular factors that the virus requires in my first project. Using an updated version of the design program, mirBooking, we become capable to predict the concentration effect of RNA species more accurately. Designed guide sequences provided cells with effective resistance against viral infection. The protection was equal or better than those that target the viral genome directly via near-perfect complementarity. However, the repression levels of the viral and cellular factors could not be precisely predicted. In order to gain further insights on the rules of miRNA target recognition, the rules of base pairing beyond the seed was further investigated in my second project. By designing guide sequences that partially match the target and analysing the repression pattern, we established a unifying model of miRNA target recognition via Ago2 protein. It shows that once the seed is base-paired with the target RNA, the formation of an RNA duplex is interrupted at the central portion of the guide strand but resumes further downstream of the central portion following a distinct order. The implementation of the discovered rules in a computer program, MicroAlign, enhanced the design of efficient artificial miRNAs.  In this study, we not only confirmed the contribution of non-seed nucleotides to the efficiency of miRNAs, but also quantitatively defined the way through which they work. The currently popular view that miRNAs can effectively target all genes equally with only seed matches may require careful re-examination.

Keyphrases: miRNA, Semance, Ago2, Seed, HIV, Artificial miRNA, Multi-targeting, Target recognition, Nucleotide complementarity
Modélisations de maladies des motoneurones en utilisant le poisson zébré

Hereditary spastic paraplegias (HSP) are a group of heterogeneous neurodegenerative diseases affecting upper motor neurons, causing progressive gait dysfunction and more than 60 genes have been linked to this disease. On the other hand, amyotrophic lateral sclerosis (ALS) is a late-onset progressive neurodegenerative disorder that affects both upper and lower motor neurons, leading to muscle atrophy with spasticity and death in two to five years due to respiratory failure. These two motor neuron disorders, while separate, share common genes and pathological mechanisms and as such, increasing our knowledge about their similarities and differences can help us have a better understanding of each of them individually. In order to study these two diseases, we used previously characterized zebrafish models and developed new ones to deepen our understanding of the pathophysiological mechanisms of HSP and ALS. In the first part of this thesis, we identified ER stress as a new pathological mechanism at play in HSP due to spastin loss-of-function and showed that ER stress modulators are able to rescue the locomotor phenotype. We also identified a new gene causative of HSP, CAPN1 (SPG76), provided in vivo validation of its loss-of-function pathogenicity and identified microtubule networks disorganization as one of the main defects. In the second part of this thesis, we generated several new zebrafish models to study ALS. Two transgenic lines expressing either a wild-type or a mutant TDP-43 protein under the control of an inducible promoter allowed us to recapitulate previous findings obtained with mRNA injections and identify transcriptomic changes due to the mutant protein that are in line with recent transcriptomic data obtained in mouse models. We also generated two new lines with knock-in of ALS-causative point mutations in the tardbp and fus zebrafish endogenous genes using the CRISPR/Cas9 technology. These results underscore the value of the zebrafish model to study motor neuron disorders and their pathophysiological mechanisms as well as open new therapeutic avenues.

Keyphrases: stress RE, TDP-43, FUS, spastin, CRISPR/Cas9, calpain 1, Amyotrophic lateral sclerosis, hereditary spastic paraplegia, zebrafish, ER stress
Étude des kinases RSK : de l’interactome aux fonctions biologiques

The Ras/MAPK signaling pathway regulates many biological functions and plays a key role in transducing extracellular signals to intracellular target proteins. Inappropriate regulation of this pathway leads to a variety of diseases and genetic syndromes, including cancer or diabetes. This signaling pathway regulates the activity of ERK1/2 protein kinases, which have many cellular substrates, and therefore regulates significant biological processes. Among these substrates, there is the RSK (p90 ribosomal S6 kinase) family of protein kinases, which is composed of four isoforms (RSK1-4). Although several cellular substrates have been identified for the RSK1 and RSK2 isoforms, the biological functions of RSK kinases and the molecular mechanisms regulating them are still poorly understood. Thus, to improve our knowledge of the RSK family, we used several approaches. First, we determined the cellular partners of the RSK kinases using a proximity-based labeling technique. This first step allowed us to identify the p120ctn protein as a new substrate of RSK kinases, but also to demonstrate the role of these proteins in the regulation of intercellular junction’s integrity. Additionally, by focusing on a particular domain of RSK kinases still unstudied, our second study also provided new insights into the different interactions of RSK proteins. Finally, we demonstrated that the binding of the RSK2 isoform with the Scribble protein inhibits its activation by the Ras/MAPK signaling pathway. Consequently, by establishing large-scale studies to determine the specific interactions of each RSK isoform, we have identified several new cellular partners of these proteins and their associated functions. This step is crucial to understand and characterize the role of the RSK proteins, particularly with respect to their described functions in cancer.

Keyphrases: phosphorylation, cancer, RSK, MAPK, p120ctn, Scribble, cell signaling, intercellular junctions
Expanding the immune self : impact of non-canonical translation on the repertoire of MHC I-associated peptides

On their surface, nucleated cells present major histocompatibility complex class I (MHC I) molecules in complex with short peptides, that we will refer to as MHC I-associated peptides (MAPs). These MAPs derive from the degradation of cytosolic proteins by the proteasome and provide an integrative view of the inner state of cells to CD8+ T cells, which can, in turn, eliminate abnormal cells, e.g., those presenting viral MAPs or tumor-specific antigens (TSAs).  With the growing body of evidence suggesting that translation does occur outside of protein-coding transcripts, we tried to evaluate the impact of non-canonical translation on the repertoire of MAPs. Combining RNA-sequencing and mass spectrometry to analyze the MAP repertoire of B-lymphoblastoid cell lines, we uncovered that ~ 10 % of the MAP repertoire derives from such non-canonical translation events, including (i) the out-of-frame translation of protein-coding transcripts or (ii) the translation of non-coding regions (UTRs, introns, etc.) or transcripts (antisense, pseudogene, etc.). Interestingly, our data suggest that the biogenesis of cryptic and conventional MAPs differs, as cryptic MAPs derive from unstable transcripts generating short proteins that might be degraded in a proteasome-independent fashion.  Because the global DNA hypomethylation observed in cancer cells tend to de-repress non-coding transcripts, we developed another proteogenomic approach to probe the cryptic MAP repertoire of two murine cancer cell lines (EL4 and CT26) and seven humor primary tumor samples (four B-lineage acute lymphoblastic leukemias and three lung tumor biopsies). This second analysis revealed that ~ 90% of TSAs are cryptic TSAs. Interestingly, most of those TSAs derived from cancer-restricted yet non-mutated sequences, such as endogenous retroelements, thereby suggesting that such TSAs could be shared between patients. Lastly, our validation study in mice demonstrated that at least two parameters can influence the in vivo protective effect of TSAs, namely TSA expression in cancer cells and the frequency of TSA-specific T cells. Altogether, our proteogenomic studies on the MAP repertoire of normal and cancer cells demonstrate that cryptic MAPs significantly expand the immune self and, consequently, the scope of CD8+ T cell immunosurveillance.

Keyphrases: Major histocompatibility complex class I, Non-canonical translation, Tumor-specific antigens, T lymphocytes, Cancer immunotherapy, Proteogenomics, Mass spectrometry, Next-generation sequencing
Overrepresentation and disparity of Black children reported under the child protection system : the need for effective cross-system collaborations

This three-paper dissertation examines the overrepresentation of Black children reported to  child protection services in Canada. The first and second papers examine rates of service disparities using clinical-administrative data provided by a child protection agency for a sample of Black, White, and other visible minority children residing in Montreal, Quebec. Findings from the first paper reveal that compared to White children, Black children’s protection reports were five times more likely to be screened in, substantiated, and brought to court. Black children were also five times more likely than White children to enter out-of-home placement. Findings from the second paper demonstrate disparity in exits from the child protection system through comparison of Black, White and other visible minority children on time spent in out of home placement and likelihood of family reunification. Of these three groups, Black children spent the longest time in out-of-home placement and had a lower proportion of children experiencing family reunification. This decreased likelihood of reunification was statistically associated with three variables: placement instability, age of the child and type of maltreatment.  The accessibility of support services within a child’s community to help moderate exposure to risk conditions has been offered as a possible solution in addressing the overrepresentation of Black children.  The third paper in this dissertation uses qualitative inquiry employing a thematic approach to highlight some of the challenges faced by a collaboration between a child protection agency and community organization. The creation of the partnership sought to reduce overrepresentation of Black children receiving services from the child protection system.  It aimed to improve socioeconomic conditions faced by Black families by providing access to support services to address their needs in a culturally adapted manner.  In depth-interviews from members of the stakeholder committee composed of management staff from both the child protection agency and community organization cited challenges pertaining to the child protection agency’s organizational context, level of socio-political support and organizational culture as obstacles to an effective partnership.   Together, these three papers document the nature and potential causes of overrepresentation and disparity faced by Black Canadian children.  It suggests that the disproportionate need faced by Black families is an important factor explaining their differential treatment within child protection systems. This study also highlights some of the potential barriers in implementing solutions.

Keyphrases: Child protection, Black children, Overrepresentation, Disparity, Collaboration, Partnership, Partnenariat, Community intervention