NCube/papyrus huggingface dataset:
Decoding protein networks during porcine reproductive and respiratory syndrome virus infection through proteomics

Porcine reproductive and respiratory virus (PRRSV) is a pathogen of high importance in the porcine industry because it can lead to significant economic losses. One of the cell lines routinely used for research and vaccine production is MARC-145 (African green monkey kidney cells). Molecular interactions between the host cells and the virus are essential to understand how the virus uses the cell machinery to replicate and infect neighbouring cells. Our goal was to analyze the proteomic changes involved during the PRRSV infection in MARC-145 cells, including the composition of the infected cells' virions and exosomes. The infected and non-infected cells' supernatants were purified to obtain the host cells' virions and exosomes. Extracted proteins were further analyzed by High-Resolution-Quadrupole-Hybrid-Orbitrap mass spectrometry and classified according to molecular function and subcellular localization. The need for obtaining reliable proteomics data led to the next goal of optimizing the infection of MARC-145 cells with PRRSV. To assess the efficiency of the infection, we synchronized the infection, used a virus tagged with an enhanced green fluorescent protein (EGFP) and added polycations at different concentrations to stimulate the binding of the viral particles to the cell. To verify the percentage of infected cells, we used fluorescence microscopy and flow cytometry. Our findings suggest the cellular proteins affected during the PRRSV infection could play important roles in host immune response and/or the viral life cycle. The efficiency of the use of polycations was demonstrated to be effective in increasing PRRSV infection.

Keyphrases: Porcine reproductive and respiratory syndrome virus (PRRSV), Host-virus interactions, Exosomes, Polycations, Proteins, Mass spectrometry, Exosomes, Spinoculation
Regulation of granulosa cells during follicular development and ovulation

The efficiency of bovine reproduction has considerably decreased in recent decades and this decrease constitutes a major economic problem. To better counter this problem, the physiology of ovarian steroidogenic cells including granulosa (CG) cells needs to be better understood during the later stages of follicular growth, ovulation and luteinization. In this sense, we have previously identified various genes induced in the CGs of bovine ovulatory follicles by LH / hCG including Ankyrin-repeat and SOCS-box protein 9 (ASB9). However, ASB9 mechanisms of action in GC were still undefined. The objectives of this study were to elucidate the role of ASB9 in CG as well as its effects on target partners PAR1, TSG6 and TAOK1, and on MAPK signaling. An in vivo model of GC from follicles at different developmental stages: small follicles (SF), dominant follicles (DF), and ovulatory follicles (OF) and an in vitro model of cultured GC along with the CRISPR/Cas9 approach to inhibit ASB9 were used. Inhibition of ASB9 in GC resulted in significant increase in PAR1, PCNA, CCND2, and CCNE2 and significant decrease in TAOK1, TNFAIP6, and CASP3 expression. From in vivo samples, PAR1 was differentially expressed in DF as compared to OF while TSG6 and TAOK1 were induced in OF. Further analyses showed an increase in GC number and a decrease in apoptosis and caspase3/7 activity following ASB9 inhibition. Western blot analyses demonstrated that ASB9 induction in OF by hCG was concomitant with a significant decrease in MAPK3/1 phosphorylation levels while pMAPK3/1 increased following ASB9 inhibition. These results provide strong evidence that ASB9 is a regulator of GC activity and function by modulating MAPK signaling pathway likely through specific binding partners such as PAR1, therefore controlling GC proliferation. These results contribute to a better understanding of ovarian activity and bovine reproduction.

Keyphrases: ASB9, MAPK, Ovulation, Bovin, Reproduction, Granulosa cells, Proliferation, Ovary, Bovine, Fertility
Exploration de l’impact d’un programme de danse-thérapie sur la mobilité de personnes atteintes de condition neurologique : un devis expérimental à cas unique

Background: Several therapeutic approaches are used to improve mobility in rehabilitation settings. Dance therapy is one of the innovative approaches for populations with neurological disorders. A quasi-experimental study with a control group did not provide evidence to support the effectiveness of a 12-week weekly outpatient dance therapy program for persons with physical disability (DTPD) aimed at improving their mobility. Given the perceived benefits of the intervention, further investigation was important. Method: We conducted a single case experimental design (SCED) with the Tau-U statistic over 28 weeks with repeated measures (4 tools to assess mobility) in the pre-dance phase (A1), dance program phase (B) and post-dance phase (A2). The Flow State Scale and the Activity-specific balance confidence scale (ABC) provided scores pre-and post intervention. Results: Five participants significantly (p <0.05) improved scores for the Mini BESTest (MBT), 2/5 for the 4 Square Step Test (4Sq) and 4/5 for the Multi-Directional Reach Test – Behind (MDRT- behind) with very large effect sizes (ES). Aggregated ES for A1 and A2 went from moderate to very large. Changes on the FSS and ABC scales were not significant. Personal objectives were perceived and measured as attained. Conclusions: These results support the effectiveness of the DTPD program for adults with neurological conditions, and for the use of SCED with the Tau-U statistic to explore effectiveness of dance interventions for heterogeneous cohorts. The tools used to measure mobility appear promising to detect changes due to dance.

Keyphrases: condition neurologique, Rehabilitation, dance therapy, physical disability, Single Case Experimental Design, neurological condition, mobility, Tau-U statistics
Caractérisation des réponses contre des antigènes spécifiques aux tumeurs cryptiques pour le développement de thérapies contre les leucémies aiguës

The treatment of acute myeloid and lymphoblastic leukemia has seen significant advances in the past decade. Despite this progress, the relapse rate remains high and the medical need is real. These leukemias are characterized by an aberrant expression of antigens, some from mutated proteins but also from sequences of DNA that were reported as non-coding. Responses against these “cryptic” neoantigens remains uncharacterized. In order to verify whether a diverse repertoire of T cell receptors (TCR) does recognize these neoantigens, mononuclear cells from peripheral blood of healthy patients are isolated and enriched with naive CD8+ T cells. The expansion and activation of these cells are then carried out with autologous dendritic cells loaded with the antigen of interest and then sorted using HLA-peptide specific multimers. RNA from cells with TCR specific for leukemic tumor-specific antigens (TSA) is isolated in order to perform TCR-beta sequencing. Cell expansion was sufficient to perform the sequencing of cells identified as positive by staining with dextramers. A T-cell response is obtained for 50% of the neoantigens tested with reactivity shown by ELISpot and resulting in a secretion of inflammatory cytokines. T lymphocytes specific to the TSA of interest are therefore present in the peripheral blood of healthy donors. Sequencing of these cells made it possible to identify clonotypes for which a strong anti-leukemic response can be expected. It would be interesting to use these cryptic tumor-specific clonotypes in the development of new adoptive immunotherapy treatments.

Keyphrases: Cryptic tumors, Leukemias, Neoantigens, Tumor-specific antigens (TSA), Immunotherapy, Major histocompatibility complex
Étude de la longueur des télomères cardiovasculaires et de leur modulation pharmacologique chez le rat hypertendu

Objective: Hypertension is associated with cardiovascular hyperplasia, an increased cell turnover and a decrease in telomere length. We postulated that the reversal of hyperplasia by selective apoptosis observed with renin-angiotensin inhibitors (RASi) in the spontaneously hypertensive rat (SHR) is associated with a modulation of cardiovascular telomere length. Methods: Relative weight of the left ventricle (LV) and its DNA content were measured. In the aorta, hypertrophy was measured histologically and hyperplasia was measured through smooth muscle cell (SMC) count. Telomere restriction fragment (TRF) length was measured using Southern blot. Those measures were taken on SHR treated with either a placebo, a RAS inhibitor (enalapril or losartan) or hydralazine for 21 days, as well as on Wistar-Kyoto (WKY) normotensive rats. Results: RAS inhibitors partially normalized DNA content in the LV and completely normalized the SMC count in the aorta. Comparatively to the WKY rats, SHR-placebo displayed a higher percentage of short TRF in the LV (50,2% vs 64,6%; p<0,05) as well as a shorter mean TRF length (62,6 Kb vs 57,1Kb; p<0,05). Those differences were eliminated by enalapril and losartan, but not with hydralazine. In the aorta, preliminary results did not yield to significant differences. They suggest that SHR-placebo have longer telomeres than WKY rats and that RAS inhibitors tend to normalize this difference. Conclusion: RAS inhibitors normalized telomere length in the LV. We speculate that RAS inhibitors act as senolytic agents and preferentially eliminate cardiac fibroblasts with short telomeres. In the aorta, more studies are required to confirm the possible differential regulation specific to this tissue.

Keyphrases: Hypertension, Telomeres, RAS inhibitors, Senolysis, Hyperplasia, Left ventricle, Cardiovascular remodeling
Effets d’une dysbiose sur la perméabilité intestinale et sur la taille de l’infarctus du myocarde reperfusé chez le rat

A lot of evidences suggest that the composition of the gut microbiota may play a role in certain conditions such as hypertension, obesity, diabetes and many others. The aim of our experiment is to demonstrate that the intestinal microbiota modulated by diets enriched in omega-3 fatty acid (w-3) or in omega-6 fatty acid (w-6) with or without a supplement in probiotics, could influence differently the size of a myocardial infarction. To do this, microbiota transplants from rats fed a w-3 or w-6 diet combined or not with intake of probiotics were performed for 10 days on rats whose microbiota had previously been suppressed by antibiotic therapy. Then, the anterior coronary artery was occluded for 30 minutes in the transplanted rats and the size of their infarction was measured after 24 hours of reperfusion. Intestinal resistance, plasma LPS (lipopolysaccharides) concentration, myocardial accumulation of neutrophils, activation of the NF-kB (nuclear factor-kappa B) pathway, activation of the RISK (Reperfusion Injury Salvage Kinase) cardioprotection pathway and microbiota composition are the other parameters that were measured. Our results demonstrate a larger infarct size in animals transplanted with the w-6 microbiota without probiotics compared to other groups (including the w-6 microbiota with probiotics group. These results indicate that a microbiota from a diet enriched in w-6 produces deleterious effects that increase the size of the myocardial infarction compared to a microbiota from a diet enriched in w-3 and taking probiotics can reduce the size of the myocardial infarction.

Keyphrases: Inflammation, Gut microbiota, Myocardial infarction, Gut permeability
Sélection visuelle basée sur un phénotype migratoire, isolation et caractérisation de cellules uniques métastatiques

The characterization of biological samples depends heavily on the optical microscope. However, it is technically challenging to isolate rare cells among a heterogeneous culture solely based on visual inspection at the microscope. Indeed, characteristics like location, morphology or displacement do not necessairly have specific related molecular markers. In order to solve this issue, the laboratory where I accomplished my master internship developped the Single Cell Magneto Optical Capture (scMOCa) wich uses commun reagents and a low powered laser to attach ferromagnetic beads on the cell plasma membrane and isolate the cells of interest with magnetic tools. The present work reports the application of scMOCa to the metastatic cell migration and the implemented adaptations to the technique in order to carry out the project, especially by increasing the number of single cells being isolated by a factor of 250. This adaptation requiered the study of photobleaching, phenomenon at the foundation of scMOCa. Briefly, the experiment consists to capture the cells presenting the most important migratory phenotypes, defined by their track analysis, among a heterogeneous metastatic cell culture. The experimental results show that the migratory phenotypes are preserved after several cell divisions. Also, the relative gene expression highlights some genes and gene groups owned to cellular migration.

Keyphrases: cancer, photoblanchiment, Single-cell, cellular isolation, metastasis, cellular migration, sequencing, photobleaching
Le rôle des importines dans le ciblage à la membrane nucléaire interne de la glycoprotéine M de l'herpès simplex de type 1

Glycoprotein M (gM) is a viral transmembrane protein that is conserved in the Herpesviridae family. Despite its non-essential role in vitro in most viruses of the Alphaherpesvirinae subfamily, including herpes simplex virus type 1 (HSV-1), gM is involved at several stages of their viral cycle and its depletion leads to a decrease in viral production. To perform its various functions, gM is dynamically targeted to several cellular compartments during infection, including the nucleus, the trans-Golgi Network and the plasma membrane. In HSV-1, gM is the first glycoprotein detected at nuclear membranes as early as 4 hours after the onset of infection. Previous experiments conducted in our laboratory have shown that the localization of gM to the nucleus at 4hpi is an active, viral-dependent and specific process that follows its translation at the endoplasmic reticulum. However, its function at the nucleus is still not elucidated, nor is the mechanism by which it reaches this compartment early during infection. Moreover, none of gM's known interacting partners have been identified as participants in this targeting, raising questions about the mechanism used by the viral glycoprotein. Our hypothesis is that gM takes advantage of the nucleocytoplasmic transport of the cell to be actively targeted to the inner nuclear membrane via importins.  In order to study the role of the importins in the localization of gM early in the infection, each importin was depleted by interfering RNA in 143B cells. After a 4-hour infection, gM localization was determined by confocal microscopy followed by 2D and 3D qualitative analysis. The results obtained from these experiments suggest that importins do not significantly participate in the targeting of gM to nuclear membranes at 4hpi. These observations open the door to other transport mechanisms that will need to be studied in order to better understand the targeting of gM to this compartment and to eventually determine its role(s) in the herpes viral cycle.

Keyphrases: HSV-1, Glycoprotein M, Importins, Nuclear membranes, Nucleocytoplasmic transport, Interfering RNA, Transmembrane proteins, Confocal microscopy
The role of poly(C)-binding protein 1 in HSV-1 Infection

During herpes simplex virus type 1 (HSV-1) infection, four types of nuclear capsids are made: procapsids and A-, B- and C-capsids. Of the four capsids, only C-capsids contain the viral DNA and will become infectious progeny. A level of regulation occurs during nuclear egress that ensures only C-capsids exit the nucleus. The mechanism that underlies this phenomenon is presently unknown. Current research suggests the viral protein pUL25 alters the conformation of the viral nuclear egress complex (NEC) that forms a flat hexameric coat on nuclear membranes by the introduction of pentamers and therefore the induction of membrane rounding and viral budding. However, questions remain for how A-, B-, and C-capsids are differentiated within the nucleus to ensure C-capsid specific egress since pUL25 is found on all capsid types. Here we investigate how host proteins may play a role in nuclear egress of C-capsids. Based on the lab’s previous study where host protein poly(C)-binding protein 1 (PCBP1) was found specifically on C-capsids via mass spectrometry, we explore the role of PCBP1 in HSV-1 infection. Using plaque assays we show that PCBP-1 is important for viral infection, as in its absence titers decrease and when PCBP1 is over expressed titers increase. This result does not seem to be due to PCBP1 affecting gene expression of immediate early, early, or late viral gene subsets, nor does it seem to affect genome replication or encapsidation. PCBP1 knockdown does not cause an accumulation of capsids or mature particles as assessed by electron microscopy, but it does increase the number of enveloped B-capsids observed in the perinuclear space (PNS). Depletion of PCBP1 also decreases the level of pUL24, a viral protein implicated in viral nuclear egress. Our results suggest that PCBP1 could be regulating pUL24 for proper activity in nuclear egress, such that when PCBP1 is depleted, more B-capsids are able to bud through the PNS. This research constitutes a starting point for further analysis into the exact mechanism of PCBP1 in HSV-1 infections. In addition, it may provide important clues to elucidate how pUL24 supports nuclear egress.

Keyphrases: Herpes simplex virus type 1, PCBP1, Nuclear egress, hnRNP E1
Rôle du complexe LINC dans la propagation du virus de l’herpès simplex de type 1

HSV-1 is widely used to study viral cycles and host-pathogen interactions of Herpesvirdidae, because it replicates quickly and efficiently in many cells types. The transcription, replication and capsid assembly of HSV-1 take place in the nucleus of the infected cell. The assembled HSV-1 capsid must exit the nucleus to continue the viral cycle. The nuclear membranes constitute a barrier for the nuclear egress of nucleocapsids (125 nm) given the exclusion size of the nuclear pores is approximately 40 nm. The nucleocapsids therefore pass through the nuclear membranes by an envelopement-deenvelopement process. The capsids acquire an envelope from the inner nuclear membrane when they are released into the perinuclear space. This primary viral envelope then fuses with the outer nuclear membrane, enabling the capsid to reach the cytoplasm. Situated between the two nuclear membranes is the linker of the nucleoskeleton and cytoskeleton (LINC) complex. It is involved in the maintenance of the perinuclear space, nuclear positioning and force transmission between the nucleus and the cytoplasm. The LINC complex is composed of two families of proteins, SUN and KASH proteins. SUN proteins are found in the inner nuclear membrane, their N-terminal interacts with the nucleoskeleton and the C-terminal includes a conserved domain, the SUN domain, which interacts in the perinuclear space with the conserved domain of KASH proteins. The implication of the LINC complex in the propagation of the pseudorabies virus (PrV), a member of the alphaherpesviruses, has already been demonstrated. Since PrV is part of the same family as HSV-1, we hypothesized it may also play a role in HSV-1 propagation. My work shows that overexpression of a dominant negative form of SUN2 or its depletion shows a proviral effect on HSV-1 propagation. This result differs to what has been previously found for PrV, where SUN2 displays an antiviral phenotype. This work confirms our hypothesis but reveals a more complex scenario than anticipated.

Keyphrases: SUN, KASH, Propagation virale, HSV-1, Nuclear envelope, Protein overexpression and depletion, Viral propagation
Association entre la stéatose hépatique non alcoolique et les hyperchylomicronémies familiale et multifactorielle

Nonalcoholic fatty liver disease (NAFLD) is a disorder caused by hepatic triglyceride accumulation. It ranges from hepatic steatosis to steatohepatitis with fibrosis. Obesity and other elements of the metabolic syndrome, such as hypertriglyceridemia and type 2 diabetes, are risk factors for NAFLD, which affects between 20% and 29% of Canadians. These statistics are alarming, especially knowing that there is still no treatment for this condition and considering the increasing prevalence of obesity. Lipoprotein lipase (LPL) hydrolyzes triglycerides contained in very low-density lipoproteins (VLDL) and chylomicrons. LPL is often down-regulated in the metabolic syndrome and some patients may present triglycerides level higher than 10 mmol/L, as multifactorial chylomicronemia syndrome (MCS). Chylomicronemia also characterizes total LPL deficiency, known as familial chylomicronemia syndrome (FCS). FCS and MCS are two dyslipidemias associated with severe hypertriglyceridemia, which is associated with increased risk of recurrent acute pancreatitis. Whereas FCS is monogenic, MCS is polygenic and directly related to the metabolic syndrome with a significant influence of the environment. Results of the present study compare the expression of NAFLD in FCS and MCS patients. NAFLD was assessed using transient elastography performed in 18 FCS and 18 MCS patients matched for age and sex. Controled attenuation parameter (CAP) score ≥ 280 dB/m, suggesting NAFLD expression, were observed in 50% of FCS and 83.3% of MCS. The difference between degrees of hepatic steatosis in both groups is significant with a p-value of 0.036. In addition, only 22.2% of FCS with NAFLD are obese compared to 71.4% for MCS (p = 0.001). It is also interesting to note that FCS patients have NAFLD even in the presence of a very low body mass index (BMI<18 kg / m2). Besides, CAP score in FCS was negatively correlated with the number of acute pancreatitis (p=0.004). Our study shows that NAFLD was frequently observed in FCS and MCS but occurred independently of BMI and could be associated with a lower occurrence of acute pancreatitis.

Keyphrases: Hyperchylomicronemia, Dyslipidemia, Triglycerides, Familial chylomicronemia syndrome, Hepatic steatosis, Hepatic fibrosis, Transient electrography
Les corrélats du sexe et du genre dans les différences sexuelles du fonctionnement cognitif : une étude exploratoire

The correlates of sexually dimorphic cognition are not yet fully understood since many biological and psychosocial variables modulate these cognitive abilities in synergy. Sex and gender correlates of sexually dimorphic cognition were assessed in a sample of individuals ages 18-45 years (N=87) from diverse sexual orientations. Sex hormones (estradiol, testosterone and progesterone) were assessed via saliva samples at four timepoints throughout testing. Gender-roles, sexual orientation and socio-demographics were measured via self-report questionnaires. Contraception being an important variability factor was assessed via self-report questionnaires. Participants completed mental rotation and verbal fluency tasks as well as the Trier Social Stress Test afterwards. The stress reactivity aspect was evaluated but was not one of the main objectives of the current study as previous publications have investigated this already. Men performed better than women at mental rotation, while no significant difference was found for verbal fluency. Significant positive associations were observed between estradiol and word fluency for the naturally cycling women compared to the women using oral contraception but not for progesterone and testosterone. While controlling for sex hormones, a significant interaction effect of sex and gender-roles was identified showing that masculine women performed better than other women groups at the mental rotation task. These exploratory results suggest an effect principally driven by sex and sex hormones on cognitive performance that may also be influenced by psychosocial factors.

Keyphrases: sexually dimorphic cognition, sex differences, sex hormones, sexual orientation, gender-roles