The Coronavirus disease 2019 (COVID-19) pandemic has highlighted the critical need for accurate and sensitive diagnostic tools for detecting the SARS-CoV-2 virus. The nucleocapsid (N) protein is essential for virus replication and plays vital roles in virus assembly, packaging, and RNA transcription. This protein is a crucial component of the viral particle and is less prone to mutations than the other essential proteins in SARS-COV-2. All of these make the N protein a reliable target for virus detection. Aptamers, single-stranded oligonucleotides that can specifically bind to target molecules, have been proposed as a promising alternative to antibodies for detecting and treating viral infections. This study aimed to select DNA aptamers against the N protein of SARS-CoV-2 using capillary electrophoresis (CE) and validate the binding specificity of the aptamers. After selecting seven clones, a preliminary binding validation was performed, and the two best binding clones were identified as ECK4 and ECK6. The structures of the aptamers were then modified by removing the primer regions from the original sequence, and the binding capacity of the truncated aptamers was confirmed. Dissociation constant (KD) values were calculated to provide further supportive information for the quality of the two clones. Additionally, Biolayer interferometry (BLI) was used to calculate Apparent KD as an alternative technique and provided consistent results with CE. Our results demonstrate the successful selection of aptamers for the N protein of SARS-CoV-2 using CE-SELEX. Confirming the aptamers' binding capacity to N protein paves the way for developing aptamer-based diagnostics for COVID-19.

The recent pandemic has reminded the public that basic research in virology is pivotal for human health. Understanding the mechanisms of successful viral replication and the role of host factors can help to combat viral infections and prevent future pandemics. Our lab has published the first SARS-CoV-2 RNA-protein interaction atlas, laying the foundation to investigate the interplay between viral RNA and host RNA binding proteins (RBP). Based on this, my project created the largest collection of binding profiles of host and viral RBPs on SARS-CoV-2 RNA to date. This revealed the host protein SND1 as the first human RBP that specifically binds negative sense viral RNA at the 5´ end, a region associated with viral transcription initiation. The binding profile shares similarities with the viral RBP nsp9, which binds the 5´ ends of positive and negative sense SARS-CoV-2 RNA. Depletion of SND1 shows reduced levels of viral RNA revealing it as a proviral host factor. To decode the underlying molecular mechanism, I characterized the protein-protein interactions of SND1 in SARS-CoV-2 infected and uninfected cells. Infection remodels the protein interactors of SND1 from general RNA biology to membrane association and viral RNA synthesis. Upon infection, SND1 specifically interacts with nsp9, the RBP that shares the same binding region on the negative strand of SARS-CoV-2 RNA. Recent work demonstrates that nsp9 is NMPylated in vitro suggesting a functional role of nsp9 in priming of viral RNA synthesis. I was able to show that nsp9 is covalently linked to the 5´ ends of SARS-CoV-2 RNA during infection of human cells. Analysing the covalent bond of nsp9 with the viral RNA on nucleotide level shows close proximity to the initiation sites of viral RNA synthesis, suggesting that nsp9 acts as a protein-primer of SARS-CoV-2 RNA synthesis. SND1 modulates the distribution of nsp9 on the viral RNA, since depletion of SND1 results in imbalanced occupancy of nsp9 at the 5´ends of viral RNA. This study is the first to provide evidence for the priming mechanism of SARS-CoV-2 in authentic viral replication and further reveals how this mechanism is modulated by the host RBP SND1. Detailed knowledge about priming of viral RNA synthesis can help to find targeted antivirals that could be used to fight coronaviral infections. / Die letzte Pandemie zeigte erneut, das Grundlagenforschung im Bereich der Virologie essentiell für die Gesundheit des Menschen ist. Das Wissen über Schlüsselelemente erfolgreicher viraler Replikation und der Relevanz humaner Proteine darin kann helfen Infektionen zu bekämpfen und künftige Pandemien zu verhindern. Unser Labor publizierte das erste SARS-CoV-2 RNA Protein-Interaktom und legte dabei den Grundstein für die Forschung am Zwischenspiel viraler RNA und humanen RNA Bindeproteinen (RBPs). Basierend darauf, generierte mein Projekt die bislang größte Sammlung an Bindeprofilen humaner sowie viraler RBPs auf der SARS-CoV-2 RNA. Dabei zeigte sich der Wirtsfaktor SND1 als das erste human RBP das in der Lage ist den Negativstrang der viral RNA zu binden, spezifisch an dessen 5´ Ende welches mit der Transkriptionsinitiierung assoziiert ist. Diese Bindestelle ist ähnlich zu dem viralen RBP nsp9, welches die 5´ Enden der positiv und negativ RNA bindet. Das Fehlen von SND1 in der Wirtszelle führt zu reduzierten Mengen viraler RNA und impliziert daher einen proviralen Einfluss von SND1. Um den zugrundeliegenden molekularen Mechanismus zu verstehen, betrachtete ich die Protein-Protein Interaktionen von SND1 in SARS-CoV-2 infizierten und uninfizierten Zellen. Dabei zeigte sich, dass durch die Infektion die Interaktionspartner von SND1 von genereller RNA Biologie zu Membranassoziierung sowie viraler RNA Synthese verschiebt. Mit Infektion der Zelle interagiert SND1 spezifisch mit nsp9, das RBP welches dieselbe Binderegion am Negativstrang mit SND1 auf der SARS-CoV-2 RNA teilt. Neuste in vitro Studien zeigen, dass nsp9 NMPyliert wird und deuten damit eine Relevanz von nsp9 in Priming an. Ich konnte im Kontext authentischer viraler Replikation zeigen, dass nsp9 kovalent an die 5´ Enden der SARS-CoV-2 RNA gebunden ist. Bei genauerer Untersuchung der kovalenten Bindung von nsp9 an der viralen RNA auf Nukleotidebene zeigt, dass diese Nahe der Initiationsstelle der Transkription liegen, was eine Relevanz von nsp9 als Protein-Primer in der SARS-CoV-2 RNA Synthese impliziert. Die Richtige Verteilung von nsp9 auf der viralen RNA wird von SND1 moduliert, da Abwesenheit von SND1 zu einem Ungleichgewicht von nsp9 an den 5´ Enden führt. XII Diese Studie ist die Erste, die Evidenzen für den Primingmechanismus von SARS-CoV-2 in authentischer viraler Replikation zeigt und wie diese durch SND1 moduliert wird. Detailliertes Wissen über das Priming viraler RNA Synthese kann dabei helfen gezielte nach antiviralen Substanzen zu suchen, die dabei helfen könnten Infektionen durch Coronaviren zu bekämpfen.

Three types of 2-alkenylthiazolines were designed and synthesized by a two-step method starting with 2-methylthiazoline and aromatic aldehydes, alkyl aldehydes and alkenyl aldehydes, respectively. Diels-Alder reactions of several 2-styryl-1,3-thiazolines with maleic anhydride in toluene were attempted. Expected Diels-Alder products were not observed or separated. Only starting materials were recovered. Several 2-alkenyl-1,3-thiazolines were successfully reacted with benzoyl chloride to form the N-benzoyl mono-substituted products. This is in sharp contrast with the di-benzoylation of 2-methylthiazoline reported previously by the Pittman group. 2-Methylbenzothiazole was reacted with different folds of aroyl chlorides. However, only di-aroylation products were observed even when a 1:1 2-methylbenzothiazole:aroyl chloride ratio was employed. Finally, N-methyl cyclic ketene N,O- and N,S-acetals were reacted with different alkylsulfonyl chlorides, respectively. Only di-substituted products were found in the N,O-acetal reacitons and only mono-substituted products were found in the N,S-acetal reactions even when different folds of sulfonyl chloride was employed.

No description available.

No description available.

Caloxin2A 1 is a novel peptide that inhibits the activity of Plasma Membrane Calcium ATPase (PMCA). PMCA is known to play a role in homeostasis of cytosolic calcium and cell signaling. There are 4 genes (PMCA1-4) that code for the various isoforms of the calcium pump. Based on hydropathy plots, PMCA proteins have 5 putative extracellular domains. We screened combinatorial peptide phage display library for binding to specific extracellular targets. Caloxin 2A1 was obtained as a peptide sequence that would bind to the 2nd putative extracellular domain of PMCA 1 isoform. Caloxin2A1 selectively inhibited the Ca2+-Mg2+ ATPase activity in human erythrocyte leaky ghosts that express mainly PMCA 4 isoform. It produced 50% inhibition of the pump activity at 0.4 mM. Caloxin2A1 inhibited the formation of the acid stable 140 kDa acyl phosphate in the reaction cycle of the calcium pump in the human erythrocyte leaky ghosts. It also produced endothelium dependent relaxation in the pig coronary artery. The random peptide phage display library was screened again with higher stringency to obtain caloxin with higher affinity in order to be cost effective and with greater therapeutic potential. This time, the targets were the 2nd putative extracellular domain of PMCA 1 and 2nd and 3rd putative domains of PMCA 4. The peptides selected for binding to the 2nd putative extracellular domain of PMCA 4 selectively inhibited the Ca2^+-Mg^2+ ATPase activity in human erythrocyte leaky ghosts but with a similar affinity as Caloxin2A1. The peptide selected for binding to the 3rd putative extracellular domain of PMCA 4 was hydrophobic and water insoluble. Substitution of its C-terminus amino acid with lysine residue made the peptide water-soluble and it did inhibit the Ca^2 +-Mg^2 + ATPase with slightly higher affinity. However, the inhibition was due to hydrophobicity of the peptide as the randomized version of the peptide also produced inhibition. We have obtained the first selective inhibitor of PMCA and shown that perturbing extracellular targets can affect protein activity even though most of the functional groups of this protein are in the cytosol. / Thesis / Master of Science (MS)

Problem: Herpes simplex virus type-2 (HSV-2) is one of the most prevalent sexually transmitted infections in the world, and rates of infection are higher in women compared to men. Furthermore, vaccines developed against HSV-2 have failed at various stages of clinical trials, due to their inability to induce protective mucosal immunity. In animal models, intranasal (IN) immunization with attenuated HSV-2 (TK−) virus has been shown to confer protection against wildtype HSV-2 challenge. Since IN immunization serves as a more practical and less intrusive vaccination strategy, further studies are warranted to characterize optimal immune responses following IN immunization. We have previously demonstrated that estradiol (E2) treatment promotes enhanced protection against HSV-2 through enhanced anti-viral T cells responses. However, the effect of E2 on B cell responses, which were recently shown to be critical in protecting the host following IN immunization, remain poorly understood. Therefore, in this study we aimed to examine if following IN immunization, E2 enhances the memory B cell (MBC) and antibody-secreting plasma cell populations within the secondary lymphoid tissues and nasal effector sites, and whether this enhancement leads to an overall better protection against intravaginal IVAG WT-HSV-2 challenge. Methodology: Ovariectomized (OVX) mouse model of HSV-2 were pre-treated with E2 or placebo pellets. Subsequently, both groups were immunized intranasally with TK- HSV-2. Four weeks later nasal associated lymphoid tissues, nasal mucosa, cervical and iliac lymph nodes, spleen and vaginal tract were collected and processed and MBC and antibody-secreting plasma cells were characterized by flow cytometric analysis. HSV-2 specific IgM and IgG antibody responses in serum and vaginal secretions were measured by ELISA. In parallel experiments, animals were IVAG challenged with WT-HSV-2 and the B cell subsets were characterized as above. Results: The formation of MBC subsets, as seen by the presence of CD19+ IgD- cells and the heterogenous expression of CD73, CD80, and PD-L2, were observed four-weeks post immunization within the cervical and iliac lymph nodes and spleen, which were further enhanced in the presence of E2. Additionally, E2-treated mice had increased number of B220- CD138+ IgG2c+ plasma cells within the nasal mucosa following immunization. These enhancements translated into increased levels of HSV-2 specific IgG2b and IgG2c antibodies within the serum and vaginal secretions of E2-treated mice at four-weeks post IN immunization. Upon IVAG challenge, E2-treated mice, but not control mice, were protected. Since the antibody isotypes that were enhanced in E2 treated mice are correlated with Th17 responses, E2 mediated antibody enhancement was tested in IL-17 knockout mice. E2 treatment in IL-17-knockout mice failed to induce similar responses observed in WT mice, indicating that the enhancement of B cells and antibodies seen following E2 treatment was mediated in an IL-17 dependent manner. Conclusion: This study highlights the importance of sex-dependent differences in vaccine-induced immunity. Specifically, the findings from this study will provide valuable information for the design of a potentially efficacious mucosal vaccine strategy, whereby immunization in the context of E2 could significantly enhance antigen-specific antibody responses in the genital tract. / Thesis / Master of Science (MSc)

At the site of vascular injury platelet aggregation serves to stem blood flow, initiate the inflammatory response, and stimulate wound healing. Platelets become stimulated, release their granule contents, and become adherent to one another. Platelet granules contain important clotting factors and regulators of aggregation. Disabled-2 (Dab2) is a negative regulator of platelet aggregation released from platelet α-granules. Dab2 binds to the αIIbβ3 integrin, through the PTB domain, and blocks fibrin binding to the integrin which serves as the major cause of platelet-platelet interactions. Dab2 is also capable of binding to sulfatides, through the N-PTB region, expressed on the outer leaflet of adjacent cells. Dab2-sulfatide binding decreases Dab2's ability to interact with the αIIbβ3 integrin, however sulfatides activate and stimulate platelet-platelet and platelet-leukocyte aggregation. Sulfatide addition to platelets stimulates increased αIIbβ3 integrin and P-selectin expression through stimulation of continued platelet degranulation, and these surface receptors mediate platelet heterotypic and homotypic aggregation. Here, we show that Dab2 N-PTB binding of sulfatides serves to increase the inhibitory affect of Dab2. Sulfatide stimulation of platelet degranulation can be blocked by the addition of N-PTB. Inhibition of sulfatide induced αIIbβ3 integrin and P-selectin expression result in decreased platelet-platelet aggregation under flow. N-PTB also blocks sulfatide induced platelet-leukocyte interactions and aggregation. Experimental data supports the hypothesis that Dab2-sulfatide binding serves to increase the inhibition of platelet aggregation. / Master of Science

Thrombosis, the major cause of heart attack and strokes,1 is triggered by localized clotting of the blood as the result of deregulated platelet aggregation. During the repair of vascular injury, clotting usually occurs when platelets adhere to each other at the site of vascular injury in order to stop bleeding.2 Distinct protein receptors and adhesive ligands together with the blood flow conditions govern this process. One of the negative regulators in platelet aggregation is Disabled-2 (Dab2), a modular protein that is released upon platelet activation to the extracellular platelet surface.3 Dab2 inhibits platelet aggregation through its phosphotyrosine-binding (PTB) domain by competing with fibrinogen for ï ¡IIï ¢3 integrin binding on the activated platelet surface.3 Sulfatides are also found on the platelet surface,4 interacting with adhesive and coagulation proteins5-7 and, thus, they are thought to play a major role in haemostasis and thrombogenesis. Here, we show that the Dab2 PTB domain specifically interacts with sulfatides through two conserved basic motifs. The sulfatide-binding site overlaps with that of phosphatidylinositol 4,5-biphosphate (PtdIns(4,5)P2) in the PTB domain. Whereas sulfatides recruit the Dab2 PTB domain to the platelet surface, thus sequestering the protein from thrombin-mediated platelet aggregation, the phosphoinositide mediates its internalization. Experimental data support the hypothesis that two pools of Dab2 co-exist at the platelet surface and that the balance between them controls the extent of the clotting response. / Master of Science

Mémoire numérisé par la Direction des bibliothèques de l'Université de Montréal.