VictorJuiz/thesis huggingface dataset:
Tumour Suppressor Tuberous Sclerosis Complex 1 Protein is Decreased in the Presence of VEPH1 in Some Cancer Cell Lines
Keywords: cancer
melted
mTOR
TSC1
VEPH1

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.
Sensitivity and Specificty of a Multimodal Approach for Concussion Assessment in Youth Athletes
Keywords: Assessment
Concussion
Multimodal
Sensitivity
Specificity
Youth Athlete

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.
The role of the coding sequence in regulating human mRNA stability
Keywords: mRNA stability
post-transcriptional regulation
RNA
RNA sequencing

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.
Evaluation of GCaMP3 Protoplasts for the Analysis of Ca2+ Signaling in Plant Immunity
Keywords: Calcium
Calcium signaling
Fluorescence
Plant immunity
Protoplasts

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.
Assessment of Bioaerosol Samplers for the Detection and Quantification of Influenza Virus and Compounds that Potentially Influence Influenza Virus Replication
Keywords: Antivirals
Bioaerosols
Bioaerosol samplers
Cardiac glycosides
Emission
Influenza

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.
Identification of Novel Folding Factors Involved in Oxygen-Dependent and Oxygen-Independent Disulfide Bond Formation of VEGFA165
Keywords: APEX2
endoplasmic reticulum
hypoxia
protein folding
proximity dependent labeling
VEGFA

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.
An Arf-GEF Pathway for Regulating Actomyosin at Adherens Junctions: the Role of an Adaptor Protein
Keywords: Actomyosin
Development
Dorsal Closure
Drosophila
Stepping stone
Steppke

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.
The Cognitive Sequelae of Paediatric Concussion: Understanding Outcomes and Exploring Opportunities for Intervention
Keywords: Concussion
Neuromodulation
Neuroplasticity
Paediatrics
Transcranial direct current stimulation
Working memory

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.
An Investigation of Lipid Transport between the Endoplasmic Reticulum, Peroxisomes and Lipid Droplets
Keywords: Intracellular lipid transfer
Lipid droplet
Membrane contact sites
Oxysterol binding proteins
Peroxisome

The interplay between peroxisomes and the endoplasmic reticulum (ER) and lipid droplets (LDs), is suggested to be important for peroxisome maintenance and metabolic functions. It is hypothesized that peroxisomes receive lipids from these two organelles as a source of lipids for growth and proliferation and substrates for metabolic activities. However, how lipids are exchanged between these organelles is poorly understood. Using RNA interference analysis, I have demonstrated that depletion of a peroxisome membrane protein ACBD5 decreased LDs size upon oleic acid loading. Consistently, induction of LD growth and proliferation by oleic acid in patient fibroblasts lacking peroxisomes were impaired, suggesting a role of peroxisomes in LD maintenance. Oxysterol binding protein (OSBP)-related proteins (ORPs), were implicated in the transport of lipids at ER-peroxisome contact sites. Using the peroxisome membrane expansion assay and overexpression subcellular localization studies, I had shown that ORP6 is a potential cholesterol transporter at ER-peroxisome contact sites.
Pathogenesis of Integrin αIIb-mediated Fetal and Neonatal Alloimmune Thrombocytopenia: The Effect of Maternal Antibodies on Hematopoietic Stem Cells
Keywords: alloimmune
hematopoietic stem cells
human platelet antigen
thrombocytopenia
αIIbβ3 integrin

Fetal and neonatal alloimmune thrombocytopenia (FNAIT) is a life-threatening disorder caused by maternal immune responses to fetal platelet antigens, particularly αIIbβ3 integrin. Interestingly, although αIIb and β3 have similar genetic polymorphic frequencies, the reported incidence of αIIb-mediated FNAIT is at least 20 times less than β3-mediated FNAIT, the mechanism of which is unknown. Since hematopoietic stem cells (HSCs) express αIIb, I tested whether HSCs are affected in αIIb-mediated FNAIT. A mouse model was established in which fetal death was more frequently observed compared to the β3-mediated FNAIT model. Maternal anti-αIIb antibodies bound fetal HSCs in vivo, and impaired HSC migration was observed in embryonic day (E) 14.5 fetuses and post natal day one (PND1) neonates. I found that the liver may be a site of macrophage-mediated clearance at E14.5, prior to complete splenic development. PND1 HSC distribution was also irregular: significantly decreased in bone marrow and blood and significantly increased in lung and spleen.
Connectivity Coarse Filter Approach for Marine Protected Area Network Design
Keywords: Biophysical Model
Climate Change
Marine Protected Area
Marxan
Pelagic Larval Duration
Spatial Ecology

Human use of the ocean is impacting biodiversity sustainability. To mitigate human pressure, governments have committed to protecting 10% of their oceans/coasts as Marine Protected Areas (MPAs). Determining the most effective placement of MPAs for conserving biodiversity should be done at a network scale such that MPA networks are placed to provide the greatest protection for multiple species. I propose a methodology to determine priority conservation areas for distinct species assemblages, located at different depths, to determine MPA network placement, using the Pacific Ocean in Canada as a case study. I found dispersal ability had a larger impact on MPA network configuration for species spending a long time as larvae compared to species spending a short time as larvae, and that climate change is likely to shift priority-area locations. The methodology proposed for MPA design relies on limited data and can be applied to other regions and ecosystems.
Characterization and Measurement Circuit Design for a Novel Low Noise and High Sensitivity MEMS Capacitive Accelerometer
Keywords: Accelerometer
Capacitive
Circuit
MEMS
Noise

A novel MEMS capacitive accelerometer was characterized and tested using a specifically designed low noise measurement circuit. The accelerometer architecture results in a low noise, highly sensitive single-axis device. Numerical simulations were conducted on the mechanical and electrical properties of the accelerometer and then verified experimentally. The accelerometer has a -3 dB bandwidth of 150 Hz, single-sided measurement range of 12 g and an estimated noise floor of 0.83 μg/√Hz which gives it a dynamic range of 121.5 dB. The core of the measurement circuit uses a transimpedance amplifier gain stage and a precision diode rectifier to demodulate the signal from the carrier wave. It has a noise floor of approximately 0.7 μV/√Hz and a range of ±10 V and was used to experimentally measure an accelerometer noise floor of 0.94 μg/√Hz.
Evaluation of a Motor Imagery Electroencephalography Brain-computer Interface as an Access Technology for Children
Keywords: Access technology
Brain-computer interface
Electroencephalography
Motor imagery
Pediatric

Brain-computer interfaces (BCIs) have been proposed as an access technology for children with severe motor impairments. This study created an electroencephalography (EEG) pediatric BCI driven by motor imagery (MI) and evaluated its performance when controlled by 11 typically developing children aged 9-14 years. The online BCI demonstrated a limited ability to classify left versus right hand MI using spatial features (average 52±9%). Average classification in a retrospective analysis of a MI task versus rest, reached 70±3% indicating the potential for successful BCI control. Small or absent event-related desynchronization in participant-specific topographic representations of MI activity suggest that pediatric brains may not produce MI-related EEG patterns comparable to those of adults. EEG signal features known to be robustly discriminatory and effective in adults may not be appropriate for the pediatric population. Future pediatric MI-BCI studies should recruit larger cohorts of children and youth to test the generalizability of the present findings.
Variations in Silviculture Practices Alters the Composition and Degradation of Soil Organic Matter in the Snowden Demonstration Forest, British Columbia
Keywords: Forest harvesting
Gas chromatography-mass spectrometry
Nuclear magnetic resonance
Pacific Northwest
Sequential biomarker analysis
Soil organic matter

Forest management practices such as clear-cutting may result in the loss of soil carbon (C) potentially accelerating global warming from enhanced soil priming. Green tree retention (GTR) is an emerging silviculture treatment that retains forest cover and is suggested to be a better alternative. However, molecular-level analysis of soil organic matter (SOM) of GTR is lacking. Two different GTR practices and clear-cutting were evaluated at the Snowden Demonstration Forest. SOM biomarkers were analysed with gas chromatography-mass spectrometry (GC-MS) complimented with solid-state 13C nuclear magnetic resonance (NMR). Results suggests that harvesting of forest biomass resulted in significant differences in the composition of SOM (specifically lignin-derived inputs) compared to the uncut treatment 13 years post-harvest. Additionally, degradation of bulk soil (alkyl/O-alkyl ratio) was a result of lignin oxidation by fungi. Analysis of SOM with forest management practices employed in the logging industry will assist with the development of sustainable forest management practices.
The role of trophic interactions in shaping species persistence and coexistence outcomes
Keywords: coexistence
community ecology
herbivory
persistence
pollination
population ecology

What maintains species diversity? While trophic interactions are hypothesized to promote species diversity, there are few empirical tests of how trophic interactions influence rare species persistence and coexistence. Here, I ask how fitness in rare plant species is indirectly influenced by the surrounding community via pollinator interactions. I found that the surrounding community can increase rare species fitness, but only when neighbouring species have a similar pollinator niche. This suggests that the effect of the surrounding community on rare species fitness depends on the overlap in trophic partners (mutualists, antagonists), and by promoting rare species fitness and persistence, trophic interactions can facilitate rare species establishment, invasion, and potentially coexistence in communities. I test these questions in an on-going experiment asking how herbivory influences plant species coexistence. Together, these results suggest that trophic interactions play a critical role in maintaining species diversity via rare species persistence, invasion and coexistence in communities.
Modulation of Wnt and Notch Signalling Pathways for Sensory Hair Cell Regeneration in the Mammalian Auditory Organ
Keywords: Development
Hearing
Mouse cochlea
Notch
Regeneration
Wnt

I investigated the temporal pattern and underlying mechanisms of the transient regenerative response to canonical Wnt activation in the neonatal mouse cochlea. Ectopic Wnt activation in vitro in typically quiescent embryonic day (E) 13.5 and postnatal day (P) 0 cochleae promoted prosensory and supporting cell proliferation, respectively; however, this effect was no longer observed at P5. This age-dependent decline in proliferative capacity occurred despite similar levels of β-catenin accumulation in cochleae following transient exposure to the Wnt activator at all three developmental stages, suggesting that barriers to Wnt-mediated regeneration lie downstream of β-catenin stabilization and might be related to a lack of key transcription factors or limited access to downstream target genes. Furthermore, maintaining Wnt activation in early neonatal stages promoted changes in the expression of specific Wnt and Notch pathway genes and extended the window for hair cell induction in response to Notch signalling inhibition.
An Examination of Interaction Dynamics During Sibling Conflict using Dynamic Structural Equation Modelling
Keywords: Conflict Resolution
Interaction Processes
Sibling Dynamics
Sibling Interaction

Micro-processes of sibling interactions are associated with important aspects of child development (Dirks et al., 2015; Gass, Jenkins Dunn., 2007; Pike, Coldwell Dunn., 2005; Stocker, Burwell Briggs., 2002) underscoring their value for developmental research. Using a novel statistical framework, dynamic structural equation modeling (DSEM), interaction processes such as reciprocity and intrapersonal and interpersonal flexibility were examined during a 5-minute conflict resolution task on a sequential basis. Successful interactions among siblings require a certain degree of behavioural flexibility. In this study, siblings engaged in a “tit-for-tat” interaction dynamic, whereby they matched one another’s behaviour from one moment to another. Siblings who demonstrate more flexibility were more constructive in their approach to conflict resolution. However, this behaviour was moderated by the dyadic composition, because as the power differentials increases between siblings (i.e., increasing age disparities between siblings), the more dominant partner (older sibling) behaved less flexibly towards their younger sibling.
Perceptions of end-of-life communication in older adults with advanced heart failure and their family caregivers
Keywords: end-of-life care
end-of-life communication
geriatrics
heart failure
older adults
qualitative

In advanced heart failure, end-of-life communication can be integral to one’s understanding of illness and preparation for the end-of-life. In older adults with heart failure, end-of-life communication is challenged by an uncertain illness trajectory, the risk of mortality, and the presence of multimorbidity and frailty, which all underscore the need for earlier communication. In this qualitative study of older adults with advanced heart failure and their caregivers, most participants had a limited understanding of illness and did not understand the consequences of serious illness. In this context, four challenges of end-of-life communication were identified: trivializing illness, positivity in late-life, discomfort in having end-of-life discussions, and reluctance to engage despite need. The findings highlight the need to address understanding of illness for patients and caregivers to perceive the need to discuss end-of-life care and emphasize the importance of engaging in end-of-life communication as an iterative process earlier in advanced illness.
Teacher Presence Pedagogy, a thematic interview discussion about online learning
Keywords: Asynchronous discussion
Community of Inquiry
Knowledge building
Online learning
Teacher presence

This paper examines drivers of online instruction methods, through thematic open-ended interviews with 10 graduate-level faculty, active in online and blended learning courses in a major Canadian public university. The research forms a bounded case study of ten instructors who teach online courses using a web-based environment, PeppeR. The research question motivating this study is: How do online instructors describe the processes and activities they try to nurture in online courses, and what sort of decisions and methods do they use? Educators are conscientious about being stakeholders, giving concrete examples, and offering suggestions that are meaningful. Findings highlight detailed responses from educators which emphasize design and organization, facilitating discourse, and direct instruction in a computer-mediated environment. Ideas around effective online teaching presence echo in the pedagogy of stakeholders in an environment of engaged learners and faculty.