NCube/papyrus huggingface dataset:
Decoding protein networks during porcine epidemic diarrhea virus (PEDV) infection through proteomics

Porcine epidemic diarrhea virus (PEDV) is responsible for severe economic losses. The PEDV epidemics have destroyed more than 10% of the US swine population in the past 3 years. Unfortunately, the insufficient understanding of virus-host interactions impedes the development of an effective vaccine against PEDV. Virus-host interactions are highly dynamic and may involve multiprotein complexes. Growing evidence indicates that extracellular microvesicles (EMV) and composition of the viral particles play an important role in viral pathogenesis and modulation of host immune responses to infection. Additionally, it could be expected that the composition of porcine epidemic diarrhea (PED) virions is cell type dependent, due to the differential incorporation or association of host cell proteins into or with virions. Consequently, the characterization of the proteomic profiles of the EMV, produced by the PEDV-infected cells, and identification of the host proteins that are specifically encapsidated into the virions are important for our further understanding of virus-host interactions. To accomplish this objective, we produced and purified PEDV virions and EMV and analyzed their protein composition using a proteomic approach. In order to investigate the spatial-temporal regulation of viral infection and due to the low overall infectivity of the virus, a certain optimization of the PEDV infection was needed. To this end, we synchronized and increased virus entry into the cells. This allowed us to study the proteomic patterns of the PEDV-infected cells in a time-resolved mode. We found that PEDV infection affected the abundance of various host proteins associated with microvesicles produced by the infected cells. More precisely, our proteomic data revealed that proteins involved in nucleic acids binding, metabolic processes and immune response pathways were among the most affected by the PEDV infection. Interestingly, host proteins involved in cell cycle regulation and cytoskeletal system also were affected in abundance, which is not surprising since several investigators have reported that cytoskeletal proteins are actively participating in moving the viral components to the assembly site, and that many viruses manipulate DNA repair and cell cycle. The present study has demonstrated the incorporation of numerous cellular proteins into the PED virions. Additionally, we demonstrated that treatment of PEDV virions with polycations (positively charged molecules) induced a nine-fold increase in the efficiency of viral entry and infection. Thus, polycations can be used for the optimization of PEDV infection and improved vaccine production. To the best of our knowledge, this is the first study of the composition of PED virions and microvesicles produced by PEDV infection.

Keyphrases: Porcine epidemic diarrhea virus, Proteomics, Polycation, Polybrene, DEAE-dextran, Virion composition, Microvesicles
Étude de l’expression et de la fonction du gène Ankyrin-repeat and SOCS-Box protein 9 (ASB9) dans le follicule ovulatoire bovin

Dairy cows fertility has been declining steadily worldwide for the last fifty years. This decline in fertility is a major concern for the dairy industry in Canada since it results in significant economic losses each year. Yet, the molecular mechanisms associated with fertility decline are still not fully investigated. In this regard, the regulation of Ankyrin-repeat and SOCS Box protein 9 (ASB9) in the ovarian follicle has been recently reported, for the first time, by our laboratory. We have identified ASB9 as a differentially expressed gene in granulosa cells (GC) of bovine ovulatory follicles. However, the biological role of ASB9 in GC was still unknown. We hypothesized that ASB9 expression would be induced by the luteinizing hormone (LH) in GC and that ASB9 would contribute to the control of GC function. GC were obtained from small follicles (SF: 2-4 mm), dominant follicles at day 5 of the estrous cycle (DF) and ovulatory follicles 24 h post-hCG injection (OF). RT-qPCR and western blot analyzes demonstrated an induction of ASB9 expression in the OF by hCG both at the mRNA and protein levels. Moreover, the expression of ASB9 in follicular walls was significantly induced from 12 h post-hCG and reached a maximum induction 24 h post-hCG or 24 h following the endogenous LH surge as compared to 0 h. Yeast two-hybrid screening of a cDNA library from ovulatory follicles resulted in the identification of 10 ASB9 binding partners, which included tumor necrosis factor alpha-induced protein 6 (TNFAIP6), hypoxia inducible factor 1, alpha subunit (HIF1A) and cytochrome B (CYTB). Inhibition of ASB9 through the CRISPR-Cas9 approach resulted in increased GC proliferation and modulation of target genes expression such as steroidogenic enzyme CYP11A1. These results confirm a physiologically relevant role of ASB9 in the ovulatory follicle by regulating GC proliferation and function, targeting specific proteins that may be degraded and, possibly by contributing to the final differentiation of GC into luteal cells. The results of this study could lead to a better understanding and control of the ovarian function by identifying target genes associated with fertility in dairy cows.

Keyphrases: ASB9, Ovulation, LH, hCG, CRISPR-Cas9, Ovary, Granulosa cells, Ovulatory follicle, Dairy cow, Fertility, Yeast two-hybrid
Évaluation de l’utilité clinique d’une méthode de dépistage de l’hématurie féline

Hematuria is defined as an increased number of erythrocytes in urine. It indicates a urinary disorder. The important occurrence of hematuria in lower urinary tract disease makes hematuria a good potential biomarker of those disorders. A non-invasive screening test for feline hematuria has just been developed. It consists of white granules, dispersed on the cat litter, which turn blue when in contact with hemoglobin. The goal of this memoire is to report the results of the study of this screening test and to contextualize the assessment with a review on feline hematuria monitoring in the context of lower urinary tract disorders. Previous studies on the test (Gara-Boivin, del Castillo et al. 2018, Khenifar, del Castillo et al. 2018, Khenifar, del Castillo et al. 2018) demonstrated a good detection threshold, around 12[8-16] red blood cells per high power field upon microscopic examination. This study evaluated the test product with 80 cats, both in veterinary clinics and in the household. The test performances are considered as very good, with a 91.5% sensitivity, a 90.9% specificity, a 93.5% positive predictive value and a 88.2% negative predictive value.   The hematuria chromogenic screening test demonstrate the required characteristics for a reliable use in the follow-up of feline hematuria. Studies on a larger cat population and further studies on the management of lower urinary tract disorders are currently underway.

Keyphrases: urolithiases, hematuria, cat, lower urinary tract disease, screening test, feline idiopathic cystitis, urolithiasis, urinary tract infection, sensitivity, specificity, predictive values
Caractérisation des déchirures méniscales équines et de leur relation avec l’ostéoarthrose fémorotibiale

There is limited information available concerning normal equine meniscal morphology, its degeneration and role in osteoarthritis (OA). The objectives of the present study were to characterize normal equine meniscal morphology and lesions and explore the relationship between equine meniscal degeneration and femorotibial OA. In this ex vivo cadaveric study, menisci were harvested from 7 normal joints (n = 14 menisci) and 15 with OA (n = 30 menisci). A macroscopic femorotibial OA score (cartilage degeneration and osteophytosis) was employed to measure disease severity (modified from Olive at al 2010). The meniscal surfaces (regions: cranial, body and caudal) were scored for macroscopic fibrillation and tears (1-4). Histological sections were also scored for fibrillation and tears (0-3) and inner border degeneration (0-3). Partial meniscal tears were present on both meniscal surfaces in all 3 regions and most frequently identified on the femoral surface of the cranial medial meniscal horn. There was a positive correlation between the global medial meniscal macroscopic scores and osteophyte (r=0.7, p=0.002) and cartilage degeneration (r=0.5, p=0.03) scores within the medial femorotibial joint. The global medial meniscal macroscopic score was greater (p=0.004) in the advanced OA joints compared with controls. The main limitation was that menisci were principally from slaughterhouse specimens without a clinical history. This study is the first to describe normal equine meniscal morphology and lesions. Meniscal lesions were identified in all segments and on both articular surfaces. While meniscal degeneration significantly correlated with OA severity in the equine medial femorotibial joint, the relationship between OA and meniscal pathology remains to be elucidated.

Keyphrases: Equine, Meniscus, Tear, Femorotibial, Osteoarthritis
Étude de la contamination des carcasses de poulets de chair par Salmonella aux différentes étapes du procédé d’abattage et dans l’environnement de deux abattoirs au Québec

Salmonella is one of the most common foodborne pathogens associated with human foodborne illnesses worldwide. Animal products, especially poultry meat, are considered the main source of contamination. Each stage of the production chain can have an impact on the prevalence of Salmonella in poultry products, from the farm to the table. Several control strategies have been developed to control the contamination of poultry carcasses by Salmonella along the food production chain in order to improve the microbial quality of the final product, but so far, none of them allowed for the complete eradication of the bacteria in poultry meat at slaughter plants. In addition, there is limited knowledge on the distribution, prevalence and sources of contamination of the poultry meat product by this pathogen in Canadian broiler slaughtering establishments. The objective of this study was to generate new knowledge on the prevalence and distribution of Salmonella on broiler chicken carcasses and in the environment of two poultry slaughterhouses in Quebec. Also, we aimed to find, using molecular characterization techniques on the Salmonella isolates recovered from the two plants, the main sources of contamination of poultry carcasses. Eight visits were conducted in each slaughterhouse during the 6 months sampling period. A total of 379 carcass rinsates were collected in two poultry slaughterhouses at 5 critical steps. Samples were also recovered from seven critical sites of the process of the slaughterhouse environment. overall, 42.3% of carcasses sampled were contaminated with Salmonella. The bleeding step was significantly the most contaminated step, with a gradual decrease of the contamination along the slaughtering process. Furthermore, the defeathering device and the evisceration machine were the most contaminated critical sampling sites of the environmental samples analyzed. v The most frequently isolated serotypes, both from carcasses and environmental surfaces, for both slaughterhouses, were S. Heidelberg, S. Kentucky and S. Schwarzengrund. Our study suggests that birds arriving to the establishment, with their positive status as well as the environment of the slaughter plant represent the main sources of carcass contamination. Also, the results obtained by the high resolution melting (HRM) analysis showed that when a flock at the arrival to the slaughter plant is contaminated by the HRM S. Heidelberg 1-1-1 profile, the probability that carcasses sampled after chilling will be contaminated by the same profile is significantly higher. Finally, the carcass status of a contaminated flock is also significantly associated with the positive status of the previous flock contaminated by this same HRM profile.

Keyphrases: Salmonella, HRM, Poultry, Slaughterhouse, Sources of contamination, Carcass rinsate
Etude épidémiologique de la résistance de Salmonella Dublin, Campylobacter spp et Escherichia coli et l’usage des antimicrobiens chez les veaux de lait du Québec

Antimicrobial resistance is now a global concern as well as in Canada and Quebec. Animal production in general, including cattle, contributes to this complex problem through antimicrobial drug use. The hypothesis of this study was that milk-fed veal calves are a source of Salmonella Dublin, Campylobacter spp and Escherichia coli resistant to antimicrobials in Quebec. The study was conducted from August 2016 to October 2017 using samples of caecal contents collected from animals slaughtered in two federal inspection abattoirs in Quebec. Firstly, the antimicrobial resistance prevalence and patterns of the three bacteria were evaluated. The results showed multidrug resistance in the three bacteria. Some of the antimicrobial drugs concerned, such as amoxicillin-clavulanic acid, ceftriaxone and ciprofloxacin, are of high importance for human health. Next, the association between antimicrobial use in calf batches and resistance in E. coli was studied. The use of polypeptides (bacitracin) was significantly associated with a decrease in resistance to ampicillin and tetracycline. Finally, other risk factors associated with the presence of multidrug-resistant E. coli in calf batches were studied. The results showed that the batch size (small batches) was a risk factor for multidrug resistance in E. coli. The results obtained from this study should help to guide government and milk-fed veal industry decision-makers in setting up measures for the prevention and control of antimicrobial resistance in milk-fed veal calves.

Keyphrases: Salmonella Dublin, Campylobacter spp, Escherichia coli, Antimicrobial resistance, Salmonella Dublin, Campylobacter spp, Escherichia coli, Milk-fed veal calves, Risk factors, Multidrug resistance
Concentration sérique de la lipase DGGR chez le chat lors d’insuffisance rénale

1,2-o-dilauryl-rac-glycero-3-glutaric acid-(6’-methylresorufin) ester (DGGR) lipase appears to be a useful test for the antemortem diagnosis of pancreatitis and a cost-effective method compared to the feline pancreas-specific lipase (Spec fPL) test but little is known about the influence of comorbidities, in particular renal insufficiency on DGGR lipase in the cat. The aim of this clinical prospective and controlled study was to evaluate the influence of renal function on serum DGGR lipase in the cat. Thirty-one sick cats with a normal semi-quantitative test for the estimation of feline pancreatic immunoreactivity (SNAP fPL) were enrolled. This group was then subdivided into cats with renal insufficiency (RI+ group) and those without renal insufficiency (RI- group). A further 18 healthy cats without renal insufficiency were recruited as the control group. Serum samples were collected from cats and were analyzed for DGGR lipase activity and creatinine. Analysis of data revealed that the RI+ group had significantly higher DGGR lipase concentrations as compared to the control group (P < 0.05). DGGR lipase was also positively associated with serum creatinine levels (P < 0.05), and this parameter accounted for 19.6%. In conclusion, our study confirmed that the presence of renal insufficiency had a significant effect on serum DGGR lipase levels in the cat. Cats within the RI+ group had significantly higher serum levels of DGGR lipase than did the healthy controls. Furthermore, 37% of the cats in the RI+ group had values higher than the reference range for DGGR lipase. Mild increases in serum DGGR lipase should be interpreted with caution in cats with renal insufficiency.

Keyphrases: SNAP fPL, DGGR lipase, Renal insufficiency, Pancreatitis
Épidémiologie et pathologie des dermatopathies chez les bélugas (Delphinapterus leucas) de l’estuaire du Saint-Laurent

The objectives of this study were 1) to establish a classification system of skin lesions in belugas from the St. Lawrence Estuary based on macroscopic appearance, and 2) to estimate the frequency and causes of skin lesions categories (SLC) in this population. The presence of 18 SLC was assessed using 26,020 photographs, representing 5,388 randomly selected individual sightings of beluga, collected from 2003 to 2014. At least one SLC was seen in half of neonate sightings. At least one SLC was present in >90%, and two to three SLC were seen in >50% of gray and white beluga individual sightings. In individual sightings of gray and white belugas, “rake marks” were the most common SLC, while “single linear fissures” were most common in individual sightings of neonates. Seasonal and postnatal molting were suspected in St. Lawrence Estuary belugas. In addition, cutaneous lesions from 111 stranded belugas were characterized microscopically. Apart from needle-like foreign bodies found within some “pinhole erosions” and a gamma-herpesvirus found by PCR in a wound, the potential cause and significance of most SLC described here remain undetermined. This is the first study which investigates skin conditions in the St. Lawrence Estuary beluga population. It provides relevant baseline data for future use of skin lesions for evaluating the health of belugas.

Keyphrases: Delphinapterus leucas, pathologie, photo-identification, beluga, Delphinapterus leucas, dermatology, diseases, lesions, pathology, photo-identification, skin, St. Lawrence Estuary
The social and interpersonal dimensions of measuring loss of autonomy : expectations among family caregivers and home care social workers in Québec

Problematic: The ever-increasing numbers of older people experiencing physical and cognitive health changes leading to loss of autonomy requires an inclusive and efficient assessment process from healthcare professionals to ensure they are receiving proper support and services. The presence of the family caregiver during the assessment is an important element that could influence its results. In public healthcare services, little is known about how expectations can influence the assessment process and outcome.  The objective of this study is to explore the concept of expectations in the context of loss of autonomy assessment (OEMC) through Québec homecare services from the triadic perspective of the family caregivers, homecare social workers and the institution. Methodology: To study this phenomenon, a variety of data-gathering techniques were employed using a reflexive, focused ethnographic methodology that explored this notion from a macro and a micro perspective. An extensive literature review examined the notion of autonomy to gain an in-depth understanding of its interdisciplinary meaning, individual interviews were conducted with social workers working at a Montreal CIUSSS and family caregivers as well as a discussion group with a group of caregivers. Also, to provide the context of the current healthcare system, articles and publications on the systemic reorganizations according to New Public Management and LEAN protocols and the corresponding effect on the working environment of professional social workers are included as the third part of the triad of expectations. Results: The results demonstrated that family caregiver’s expectations for services and support for their care recipients are influenced by the assessment process itself and there are blurred boundaries between their expectations for service and the needs of their elderly family members. As well, social workers sometimes find themselves caught between the pressures and expectations of performance and productivity of the organization and their own expectations of family members to provide care, until, the caregivers themselves become clients in their own right.  Conclusion: The results of this study demonstrates that the interaction of expectations from the three above-mentioned perspectives creates an environment of frustration and unmet expectations on the part of social workers and family caregivers. This is also influenced by the current working environment in the public health care system that is reflected in budget constraints and the inconsistency in the provision of services and supports to consumers. This phenomenon can contribute to the ‘clientization’ of family caregivers wherein administrative imperatives increasingly influence the service relationship.

Keyphrases: Healthcare, Social workers, Elderly, Aging, Autonomy, Loss of autonomy, Caregivers, Evaluation instruments, Expectations, New public management, Austerity
Rôle du NKG2D et ses ligands dans un modèle murin de la sclérose en plaques

Multiple sclerosis (MS) is considered the prototypic inflammatory disease of the central nervous system (CNS). Lesions in the CNS of MS patients are characterized by myelin sheath destruction, oligodendrocyte death, axonal and neuronal damage, and activation of glial cells. It is well established that the immune system (IS) participates in the pathogenesis of MS. Nevertheless, the contribution of specific immune mediators to injury remains to be defined.  NKG2D is an activating receptor expressed by numerous immune effector cells including subsets of CD8 and CD4 T lymphocytes. NKG2D binds to various ligands (NKG2DL), which include Rae-1(alpha to epsilon), MULT1, and H60 (a to c) in mice. NKG2DL are induced by environmental triggers (e.g. inflammation) suggesting that these proteins alert the IS to abnormal cells. Our laboratory has previously shown that human oligodendrocytes express at least one NKG2DL in MS lesions but not in control brains. Moreover, CD8 T cells in MS lesions are detected in close proximity to NKG2DL expressing cells. We have also established that disruption of the NKG2D-NKG2DL interaction inhibits killing of human oligodendrocytes by activated immune effector cells in vitro. One group showed that blockade of NKG2D diminished disease severity in the MS mouse model: experimental autoimmune encephalomyelitis (EAE). Overall, these results imply that the NKG2D-NKG2DL interaction can contribute to the pathogenesis of MS and its animal model EAE. However, whether specific NKG2DL are upregulated in vivo during the development of EAE and could potentially be targeted is still unresolved.  We used EAE models, to assess the expression of NKG2DL during different disease stages and to study NKG2D contribution. We used flow cytometry, qRT-PCR, western blot and ELISA approaches.  We observed that MULT1, one specific ligand of NKG2D, is upregulated in the CNS of EAE mice and such elevated expression correlated with disease severity. Moreover, MULT1 was released in the cerebrospinal fluid during EAE and soluble MULT1 increased the effector properties of immune cells. In contrast, expression of other ligands did not vary throughout disease. Finally, adoptive transferred of activated autoimmune T cells into NKG2D deficient recipient mice induced a significantly less severe disease than the transfer into wild type counterparts. The proportion of infiltrated cells in the CNS correlated with disease severity. Our results suggest that NKG2D and specific ligands could play a role in the pathogenesis of EAE and potentially MS.

Keyphrases: EAE, NKG2D, MULT1, Multiple sclerosis, flow cytometry