VictorJuiz/thesis huggingface dataset:
Assessing the immunomodulatory effects of Ganoderma lucidum and Coriolus versicolor on the cancer killing capacity of natural killer cells

Ganoderma lucidum and Coriolus versicolor are medicinal mushrooms with diverse immunomodulatory properties. This work demonstrates the effects of mushroom extracts on the survival of different cancer and natural killer (NK) cell lines (NK-92, CD16+IL-2+NK-92, KHYG-1) and NK cytotoxicity against different cancers. G. lucidum ethyl acetate and C. Versicolor aqueous extracts completely inhibited the growth of all tested cancer targets at 100 ug/mL, whereas G. lucidum aqueous extract enhanced NK-92 cell survival. At a 5:1 effector to target ratio, aqueous G. lucidum and C. Versicolor extract significantly enhanced the cytotoxicity of NK-92 and KHYG-1 against leukemia, multiple myeloma (2.2x fold increase), and breast cancer. G. lucidum aqueous extract pretreated CD16+IL-2+NK-92 cells in combination with Herceptin demonstrated 2x higher killing against ovarian cancer compared to untreated CD16+IL-2+NK-92. Five distinct fractions from the crude aqueous extract were isolated and shown to have promising NK immunostimulatory activity that merits further investigation into their bioactive components.

Keywords: antibody dependent cytotoxicity
cell therapy
Coriolus versicolor
Ganoderma lucidum
immunotherapy
natural killer cells
Advisor: Keating, Armand
Coronavirus Evolution and Immune Evasion

Coronaviruses are emerging pathogens that threaten human health and prosperity. Each year, hundreds of millions of people are infected with continually circulating coronaviruses that cause the common cold in healthy individuals and kill the most vulnerable of us. Coronaviruses adapt to environmental change at a remarkable rate. The HCoV-229E coronavirus has adapted and evolved over the last 50 years by mutating residues in the receptor-binding loops of the receptor binding domain (RBD) of its spike (S) protein. These sequences phylogenetically segregate into Classes whose viruses have successively replaced one another in the human population. These Classes possess different receptor (hAPN) and antibody binding characteristics and the crystal structures of RBD-hAPN complexes have been solved. Structural insights into the ever-changing RBD and its interaction with hAPN show the use of secondary structure-less loops facilitate tremendous structural variability, a trait that likely enables changes in viral fitness and immune evasion.

Keywords: Adaptation
Coronavirus
Crystallography
Evolution
Immune
Phylogeny
Advisor: Rini, James M
Alcohol Use and Emerging Adult Development: A Latent Profile Analysis of Community Drinkers

Latent profile analysis was used to establish profiles of emerging adult development and then test associations with drinking behaviors both concurrently and prospectively. To differentiate between different patterns of emerging adult drinking, 153 regular drinkers from the community (ages 18-24 years; M = 20.9, SD = 1.9) completed the Inventory of Dimensions of Emerging Adulthood (IDEA) and measures of alcohol use, motives and consequences. The EA-Consistent (90%) profile had elevated scores on the five typical IDEA subscales; the Non-Exploring EA profile (10%) had low scores on four dimensions. The Non-Exploring EA profile consumed significantly less alcohol, experienced fewer alcohol consequences, and had lower social and enhancement motives at baseline and lower scores on drinking volume, alcohol consequences, and social motives at the one-year follow-up. The findings provide support that emerging adult development profiles reflect different patterns of alcohol use and differentiate between those with lower- vs. higher-risk alcohol use.

Keywords: alcohol problems
alcohol use
binge drinking
drinking motives
emerging adult development
latent profile analysis
Advisor: Goldstein, Abby L
Novel Mechanism of Thrombosis: Role of β3 Integrin PSI Domain in Blood Coagulation

Integrin αIIbβ3 is a key receptor in platelet adhesion/aggregation. We recently showed the plexin-semaphorin-integrin (PSI) domain of β3 has thiol isomerase activity. We developed four monocloncal antibodies (mAbs) that bind PSI and inhibit thiol isomerase activity, platelet adhesion/aggregation and thrombosis. The inhibitory effect of the mAbs was much stronger in vivo than in vitro (anticoagulated), suggesting that anti-PSI mAbs decrease blood coagulation. The anti-PSI mAbs were shown to inhibit blood clot retraction. Anti-PSI mAb-treated platelet-rich plasma decreased fibrin network formation in laser scanning and spinning disk confocal microscopy. In thromboelastography, anti- PSI mAbs inhibited blood coagulation. Furthermore, anti-PSI B1 significantly inhibited blood coagulation more than other anti-β3 mAbs (JAN D1, M1 and Abciximab precursor 7E3). This supports a novel role of PSI in enhancing blood coagulation, particularly through intrinsic pathway factors. For the first time, αIIbβ3 has been targeted at an allosteric region (PSI). This novel anti-thrombotic inhibits platelet aggregation and blood coagulation without increasing bleeding or requiring combinatorial therapy.

Keywords: cell-based blood coagulation
integrin αIIbβ3
PSI domain
thiol isomerase
thromboelastography
thrombosis
Advisor: Ni, Heyu
Socio-Structural inference in Stereotype and Impression Formation

Recent advances in stereotyping and prejudice literature, such as the Stereotype Content Model, explain the content of stereotypes in terms of common aspects of social structure. Yet despite this, the question of how these common aspects of social structure may direct stereotype formation remains unaddressed. In this article, we outline a theory for how common social contexts predict common behavioral tendencies and traits in the individuals and groups within these common social contexts. These common traits could then be represented in a prototype, and used to draw inferences about the traits of novel groups and individuals, directing stereotype and impression formation. Across 3 studies, we show support for 2 key assumptions of this model: that these prototypes should significantly explain stereotypic trait content, and that using these prototypes to infer stereotypes is more explanatory of the correlation between these prototypes and stereotypes than the reverse.

Keywords: Archetype
Impression-Formation
Social Psychology
Stereotype
Stereotype Formation
Traits
Advisor: Cunningham, William A
Regeneration of Neurons in the Inner Ear by Reprogramming Spiral Ganglion Glial Cells

Disabling hearing loss affects over 5% of the world’s population and impacts the lives of individuals from all age groups. A leading cause of hearing loss is the degeneration of primary auditory neurons through exposure to noise, infection, ototoxic drugs and/or aging. Primary auditory neurons are the sensory neurons of the auditory system that receive input from mechanosensory hair cells in the cochlea. Hence, it may be possible to restore hearing by regenerating these primary auditory neurons. A direct reprogramming approach can be used to convert the resident spiral ganglion glial cells into induced neurons to restore hearing. This thesis lays the groundwork for future steps in regenerating the peripheral auditory system by demonstrating the reprogramming of both neonatal and adult glia. In the coming years, reprogramming of spiral ganglion cells has the potential to become one of the leading biological strategies to treat hearing impairment.

Keywords: adult
glia
hearing
in vitro
regeneration
spiral ganglion
Advisor: Dabdoub, Alain
Rescuing TTC7A mutant phenotypes associated with Very Early Onset Inflammatory Bowel Disease via high throughput drug screening

Mutations in tetratricopeptide repeat domain 7A (TTC7A) cause a severe form of Very Early Onset Inflammatory Bowel Disease (VEOIBD). Since 2013, >52 patients were reported with TTC7A-deficiency, having poor survival outcomes with combined primary immunodeficiency and severe intestinal phenotypes, including apoptotic enterocolitis and multiple intestinal atresia. Human TTC7A-knockout cells demonstrated abnormal phenotypes related to morphology and apoptosis. ttc7a-mutant zebrafish displayed abberant intestinal features, recapitulating patient disease features and establishing a novel model system for TTC7A and VEOIBD. A high-throughput drug screen identified FDA-approved drugs that rescued the apoptotic phenotype in the knockout cells. Hits of interest were further validated with orthogonal cell and zebrafish phenotypes. Our lead compound, a drug used to treat inflammatory diseases, was identified as a novel therapy to rescue TTC7A-deficiency phenotypes. Since there is no treatment option for TTC7A-deficiency and the pathobiology remains unclear, target-agnostic phenotypic drug discovery was an efficient strategy to identify novel therapeutics.

Keywords: Drug screen
IBD
phenotypic drug screen
TTC7A
VEOIBD
zebrafish
Advisor: Muise, Aleixo M
The Role of Diacylglycerol Kinase Epsilon (DGKE) in Regulating Cellular Phosphoinositide Levels in Endothelial Cells

Atypical hemolytic uremic syndrome (aHUS) is a rare kidney disease that leads to thrombosis of the kidney microvasculature. A majority of aHUS patients with some genetic diagnosis display complement abnormalities. However, mutations in complement-independent genes, such as diacylglycerol kinase epsilon (DGKE) have also been shown to lead to aHUS. DGKE is a lipid kinase that is involved in the phosphatidylinositol-cycle (PI-cycle) that regenerates and breaks down various phospholipids. Unfortunately, DGKE-aHUS patients do not benefit from current therapy options and the pathophysiology of DGKE deficiency is not well understood. We aimed to study the role of DGKE in regulating PI-cycle phospholipids in endothelial cells. Using orthogonal approaches, we found that DGKE deficiency in endothelial cells leads to reductions in various PI-cycle phosphoinositides. In addition, DGKE-null mice did not develop TMA or renal impairments as a function of age, and likely require an immunological challenge to recapitulate aHUS pathology.

Keywords: Atypical Hemolytic Uremic Syndrome (aHUS)
Diacylglycerol Kinase Epsilon (DGKE)
Endothelial Cells
Phosphoinositides
Phospholipids
Thrombotic Microangiopathy
Advisor: Lemaire, Mathieu
Role of Acid Sphingomyelinase in Murine Placentation

Growing evidence has implicated bioactive sphingolipids and their associated enzymes in proper placentation. Previous experiments done in our lab have showed compromised placental development and function in mice deficient for aSMase (aSMase-KO). We hypothesized that aSMase is involved in trophoblast lineage differentiation either through its product CER or derivatives of it. Here we show an altered sphingolipid profile in aSMase-KO placentas with increased levels of SM16:0 and decreased levels of S1P, results in line with human studies on abnormal placentation. During normal placentation, we found Smpd1 mRNA expression to be significantly increased around d13.5 while protein expression was localized to the SpT and labyrinth layers of the murine placenta with staining present in several S-TGCs. Analysis of potential trophoblastic differentiation defects in aSMase-KO placentas revealed decreased mRNA expression of Prl7c1, a marker of glycogen and SpA-TGCs.

Keywords: Acid Sphingomyelinase
Murine Placenta
Placentation
Sphingolipids
Advisor: Jurisicova, Andrea
Risk factors for low physical activity levels in preschool-aged children in urban Bangladesh

Physical activity (PA) is a known determinant of health and is important in the development of young children. Risk factors for PA may be different in low- and middle-income countries, such as urban Bangladesh, where the environment is densely populated and nutritional deficits are common. We aimed to describe the PA levels of preschoolers in Dhaka, Bangladesh, as well as estimate the associations between preschooler PA levels and household and nutritional factors. We conducted a cross-sectional, observational study, collecting accelerometry, hemoglobin concentration, socioeconomic status, anthropometry, and data on the home built environment. Linear mixed-effects models were used to assess the associations between PA and the exposures of interest. The entire sample were found to meet Canadian preschooler PA guidelines for daily activity. There were no associations between PA and characteristics of the built environment of the home, nor hemoglobin concentration, suggesting a need for further exploration of potential influential factors.

Keywords: Accelerometry
Anemia
Bangladesh
Built environment
Physical activity
Advisor: Roth, Daniel E.
EFFECTS OF FLAXSEED AND ITS COMPONENTS ON THE INTESTINAL MICROBIOTA AND MAMMARY GLAND MICRORNA SIGNATURE IN FEMALE C57BL/6 MICE

Flaxseed (FS) is an oilseed rich in α-linolenic acid, lignans, and dietary fiber. Due to this unique composition, FS has potential to affect the health of the gut and breast. This study determined the effect of FS and its components, FS oil (FSO) and secoisolariciresinol diglucoside (SDG), on the gut microbiota, serum concentration of microbial-derived SDG metabolites, and mammary gland microRNA signature. It was found that animals maintained on 10% FS experienced the most prominent changes in gut microbiota composition and diversity compared to other groups. Higher concentrations of SDG metabolites were detected in the 10% FS and SDG diet groups, while not detectable in FSO or control. Lastly, four microRNAs in the mammary gland were downregulated in the experimental diet groups indicating that the mammary gland microRNA signature responded to FS and its components.

Keywords: flaxseed
gut microbiota
mammary gland
microRNA
Advisor: Comelli, Elena M.
Thompson, Lilian U.
Tumour Suppressor Tuberous Sclerosis Complex 1 Protein is Decreased in the Presence of VEPH1 in Some Cancer Cell Lines

The VEPH1 homolog in Drosophila melanogaster has been shown to inhibit the tumour suppressors Tsc1/2 complex function, resulting in increased TOR activity. This study aimed to investigate the role of VEPH1 in human mTORC1 signalling pathway. TSC1 did not coimmunoprecipitate or colocalize with VEPH1 under the conditions of these experiments. In cell lines (SKOV3 ovarian cancer cells, HepG2 hepatocellular carcinoma cells, ES-2 ovarian cancer cells) cultured in presence or absence of VEPH1 expression, TSC1 protein level decrease was associated with VEPH1 expression. Interestingly, in SKOV3 cells with Doxycycline inducible VEPH1 expression, TSC1 protein levels were not altered upon induction of VEPH1 expression. The decrease in TSC1 in SKOV3 cells appears independent of PI3K, MAPK, or serum stimulation and did not appear to impact mTORC1 activity. This study suggests that unlike its Drosophila homolog, VEPH1 does not regulate mTORC1 signalling in SKOV3 cells.

Keywords: cancer
melted
mTOR
TSC1
VEPH1
Advisor: Brown, Theodore J
Sensitivity and Specificty of a Multimodal Approach for Concussion Assessment in Youth Athletes

Background: Concussions are a heterogeneous and complex injury that may negatively impact the lives of youth. Multimodal assessment is recommended, however, validation of concussion measures in youth athlete populations remains limited. Purpose: To explore the sensitivity and specificity of a multimodal approach compared to individual clinical measures for the assessment of concussion in youth athletes at symptomatic and asymptomatic time points following concussion. Methods: A prospective, longitudinal cohort study with matched non-injured controls was used. Youth athletes (10-18 years) were assessed using a multimodal approach consisting of cognitive, balance, strength and symptom measures. Results: Cognitive, balance, and strength measures were sensitive and specific to declines in performance following a concussion. Multimodal assessment can more accurately distinguish between concussed and non-injured controls compared to stand-alone measures when post-concussion symptoms resolve. Conclusions: Findings may help guide clinical decision making and contribute to future research exploring approaches to concussion assessment in youth athletes.

Keywords: Assessment
Concussion
Multimodal
Sensitivity
Specificity
Youth Athlete
Advisor: Reed, Nick
The role of the coding sequence in regulating human mRNA stability

Proper control of mRNA stability is key in the regulation of gene expression, with half-lives varying considerably transcriptome-wide. While sequence elements regulating mRNA decay are classically attributed to the untranslated regions (UTRs) of the transcript, recent work across a range of non-human model systems has uncovered a conserved decay mechanism triggered by codon usage within the coding sequence (CDS). Here, I use the human ORFeome (hORFeome) collection, a library of human CDSs flanked by universal synthetic UTRs, to demonstrate that hORF constructs with different CDSs possess a wide range of stability comparable to that of endogenous transcripts. This CDS-mediated diversity in mRNA decay requires translation. I further identify codon and amino acid usage to be key elements driving this variation in stability and outline their relative impacts in yeast and humans. Overall, the hORFeome collection represents a powerful framework for deconvoluting the effects of CDSs and UTRs on stability transcriptome-wide.

Keywords: mRNA stability
post-transcriptional regulation
RNA
RNA sequencing
Advisor: Rissland, Olivia S
Ellis, James
Evaluation of GCaMP3 Protoplasts for the Analysis of Ca2+ Signaling in Plant Immunity

Ca2+ serves as a common second messenger in diverse eukaryotic cells. However, measuring in planta Ca2+ levels has been difficult. Recently, the fluorescence-based Ca2+ visualization indicator, GCaMP3 has emerged as a tool to visualize Ca2+ signals in plant cells; in particular, stress-related Ca2+ signals were successfully captured in GCaMP3 expressing leaf discs. In this study, the usage of GCaMP3 in protoplasts was evaluated. Upon stress-related stimuli, stress-induced Ca2+ signals were captured in Arabidopsis thaliana protoplasts using a fluorescence microscope and a plate reader. The signal pattern was faster and quicker but fundamentally similar to that of leaf discs, indicating that protoplasts can be used for Ca2+ visualization study. Furthermore, transfection of GCaMP3 in protoplasts was evaluated. Upon the bacterial elicitor flg22 treatment, Ca2+ signal was seen once by transfecting GCaMP3. Taken together, protoplasts can be used for investigating stress-induced Ca2+ signals using GCaMP3; however, transfection protocol has to be optimized.

Keywords: Calcium
Calcium signaling
Fluorescence
Plant immunity
Protoplasts
Advisor: Yoshioka, Keiko
Assessment of Bioaerosol Samplers for the Detection and Quantification of Influenza Virus and Compounds that Potentially Influence Influenza Virus Replication

Bioaerosol samplers are used to detect and characterize influenza virus bioaerosols but current guidelines for sampler selection are lacking. We examined four bioaerosol samplers using artificial bioaerosols and the ferret model of IAV infection. Samplers included a PTFE filter, NIOSH cyclone sampler, Andersen impactor, and SpinCon®. The PTFE filter and NIOSH cyclone sampler retained vRNA and infectious artificial bioaerosols. All bioaerosol samplers collected vRNA and the PTFE filter and NIOSH cyclone sampler retained infectious virus from infected ferrets. Ease of use, and infectious virus retention make the PTFE filter and NIOSH cyclone sampler suitable for the collection of IAV. We also examined the ability of digoxin to inhibit H1N1 replication. H1N1 viral loads decreased after incubation with digoxin while minimal cellular metabolic inhibition was observed. Digoxin in combination with oseltamivir, examined to determine the additive effects, also decreased viral loads in vitro. Digoxin appears to inhibit H1N1 replication in vitro.

Keywords: Antivirals
Bioaerosols
Bioaerosol samplers
Cardiac glycosides
Emission
Influenza
Advisor: Mubareka, Samira
Identification of Novel Folding Factors Involved in Oxygen-Dependent and Oxygen-Independent Disulfide Bond Formation of VEGFA165

Regulation of vascular endothelial growth factor (VEGF) has been studied at the transcription and translational levels in many physiological and pathological conditions, but the folding mechanisms leading to the functional 3-D conformation and secretion of VEGF under normoxia and anoxia remain to be poorly understood. To identify novel interactors involved in the folding of vascular endothelial growth factor (VEGF), proximity dependent labelling was performed in Hek293 cells expressing Flag-APEX2-VEGF fusion protein. Fusion protein expression, secretion, ER localization and APEX2 activity was validated in Flag-APEX2-VEGF and Flag-APEX2 expressing cells. The proteomes of Flag-APEX2-VEGF and APEX2 without a cargo protein were compared to identify potential unique Flag-APEX2-VEGF interactors under normoxia and anoxia. Our data suggests APEX2 is highly active in the ER and can be used to identify unique interactors of ER-tagged Flag-APEX2-VEGF under normoxia and anoxia.

Keywords: APEX2
endoplasmic reticulum
hypoxia
protein folding
proximity dependent labeling
VEGFA
Advisor: Koritzinsky, Marianne
An Arf-GEF Pathway for Regulating Actomyosin at Adherens Junctions: the Role of an Adaptor Protein

Cytoskeletal regulation is essential for morphogenesis during development. One down-regulator of actomyosin in the Drosophila embryo is the Arf-GEF Steppke. I investigated how Steppke is recruited to myosin-enriched adherens junctions. Its coiled-coil (CC) domain was shown to be necessary and sufficient for Steppke localization, while its PH domain was found to be dispensable. Homodimerization of Steppke’s CC domain also had minimal effect. Thus, I pursued Steppke’s adaptor, Stepping stone (Sstn). The proteins co-localized in vivo, Sstn was required for Step localization, and the proteins interacted directly through hydrophobic residues of their respective CC domains in vitro. A separate conserved region (CR) in Sstn was necessary and sufficient for Sstn localization, while its CC domain was dispensable. Remarkably, replacing the CC domain of Steppke with the CR of Sstn conveyed proper localization to Steppke. Thus, Steppke is recruited to actomyosin-rich adherens junctions through direct interaction with the adaptor protein Sstn.

Keywords: Actomyosin
Development
Dorsal Closure
Drosophila
Stepping stone
Steppke
Advisor: Harris, Tony
The Cognitive Sequelae of Paediatric Concussion: Understanding Outcomes and Exploring Opportunities for Intervention

Background: Children and youth are at risk of experiencing persistent cognitive challenges after concussion. However, there is a lack of characterization of these outcomes and a paucity of treatment interventions. Objective: (1) To characterize working memory post-paediatric concussion; and, (2) to explore the therapeutic potential of transcranial direct current stimulation (tDCS) for youth experiencing persistent cognitive symptoms. Methods: (1) Systematic review methodology was applied to synthesize the literature on working memory outcomes. (2) A pilot quasi-randomized control trial was conducted to explore the feasibility, tolerability, and clinical efficacy of tDCS. Results: (1) Working memory is vulnerable to insult in paediatric concussion, yet outcomes are variable. (2) tDCS shows the potential to enhance cognitive skill acquisition. Barriers to feasibility must be addressed. Conclusions: This dissertation contributes to a better understanding of the cognitive outcomes of paediatric concussion and will inform future research exploring therapeutic interventions for persisting cognitive symptoms in youth.

Keywords: Concussion
Neuromodulation
Neuroplasticity
Paediatrics
Transcranial direct current stimulation
Working memory
Advisor: Beal, Deryk S