VictorJuiz/thesis huggingface dataset:
Elucidating the Mechanism by which KRI-1/CCM1 Regulates Apoptosis Cell Non-Autonomously in Caenorhabditis elegans

Programmed cell death initiated by genotoxic stress requires signalling from surrounding tissues, yet such mechanisms are poorly understood. The C. elegans germline is a powerful model to study cell non-autonomous regulation of apoptosis, since germ cells die in response to DNA damage, and because this death requires regulatory input from the soma. The scaffold protein KRI-1, a homologue of mammalian KRIT1/CCM1, was identified to promote DNA damage-induced germ cell apoptosis from the somatic tissue by an unknown mechanism. I reveal that KRI-1 is required for proper activation of MPK-1/ERK1 in the germline, and genetically up-regulating MPK-1/ERK1 restores germ cell apoptosis in the absence of KRI-1. To determine how KRI-1 signals cell non-autonomously to communicate with MPK-1/ERK1, I conducted a forward genetic screen and identified an ERK5/MAPK pathway and the KLF-3 transcription factor that function downstream of this scaffold. I have shown that like kri-1, mpk-2/erk-5 is expressed in the intestine, as is klf-3, and that over-activation of MPK-2/ERK-5 in this tissue is anti-apoptotic. Furthermore, I found that KRI-1 interacts with K07A9.3/CCM2 and Y45F10D.10/ICAP1, which are required to regulate germ cell apoptosis. RNA sequencing of wild type, kri-1, and kri-1; mpk-2/erk5 mutants, followed by an RNAi screen, identified that the zinc transporter, zipt-2.3/scl39, has a role in regulating germ cell apoptosis. ZIPT-2.3 is expressed in the intestine, and reduced zipt-2.3 expression in the absence of KRI-1 prevents proper zinc storage. This results in suppressed activation of MPK-1/ERK1 and germ cell apoptosis. Therefore, the KRI-1 scaffold protein ensures proper activation of MPK-1/ERK1 and germ cell apoptosis by regulating zinc storage.

Keywords: apoptosis
Caenorhabditis elegans
cell death
cell non-autonomy
germline
zinc
Advisor: Derry, W. Brent
Maternal Critical Illness in Canada: temporal and geographic trends, predictors of outcome, and an examination of the variability in provision of critical care

Objectives: (1) To identify the most appropriate models for use in predicting maternal mortality in pregnant and postpartum women; (2) to establish temporal and geographic trends in maternal morbidity, mortality and admission to intensive care in Canada; (3) to identify factors associated with maternal morbidity and death in Canada; and (4) to explore variation in admission to intensive care among Canadian hospitals for pregnant and postpartum women. Methods: For the first objective, we performed a systematic review of risk prediction models. Objectives two through four were addressed within a series of nationwide population-based observational studies using the database from the Canadian Institute for Health Information. Estimated annual percent change of maternal morbidity, mortality and admission to intensive care were computed with negative-binomial regression models. Multi-level logistic regression models were employed to investigate factors associated with the outcomes. Median odds ratios was used to describe variation in admission to intensive care. Results: The systematic review revealed the Collaborative Integrated Pregnancy High-dependency Estimate of Risk (CIPHER) model and the Maternal Severity Index had very good discrimination and calibration for predicting maternal mortality. The national population-based study identified a stable maternal mortality rate of 6.2 per 100,000 deliveries, but increasing rates of severe maternal morbidity and admission to intensive care with estimated annual percent changes, 1.32% (95% Confidence Interval (CI) 0.60 – 2.04) and 1.83% (95% CI 0.68 – 2.98), respectively. Severe maternal morbidity varied across Canadian regions but was highest in the northern Territories at 22.8 per 1000 deliveries. Extremes of maternal age were associated with severe maternal morbidity and mortality. For two pregnant women with similar characteristics at different hospitals, the median odds of being admitted to ICU was 1.92 in one hospital compared to another, indicating substantial variability in admission patterns to intensive care for pregnant and postpartum women in Canadian hospitals. Conclusions: In Canada, while maternal mortality appears stable, maternal age is increasing over time and is independently associated with severe maternal morbidity. There is substantial regional variation in maternal morbidity and mortality. Finally, there is wide variability in maternal admission to intensive care among hospitals and among provinces in Canada.

Keywords: Intensive Care Unit
Maternal death
Maternal health
Severe maternal morbidity
Temporal and Geographic trend
Variability
Advisor: Fowler, Robert A
It’s Not Simple: Brain Signal Complexity as an Index of Neural Information Processing Described via Music Perception, Complexity and Reward

The dynamic, integrated, network activity that underlies higher cognition produces complex brain signals with information at multiple timescales. The present body of work represents an effort to demonstrate that brain signal complexity can be an indicator of the information integration in the brain that supports cognition and behaviour. Study 1 establishes that magnetoencephalography signal complexity is higher in adult musicians compared to non-musicians. The difference in complexity between groups was largest in a music note perception task, which also showed the largest behavioural difference between groups. Study 2 extends this approach to a longitudinal study of music training in preschool-aged children. Higher electroencephalography signal complexity was observed in a passive music note perception task following training in brain regions typically implicated in music perception (e.g. superior temporal cortex), as well as supramodal regions (precuneus, superior parietal cortex). Therefore, we suggest that network information processing capacity increases with experience to support concomitant increases in behavioural capacity. Studies 3 and 4 examine how the information inherent in music stimuli is represented as neural information, and how this relates to behavioural outcomes. We calculated the complexity of the song and compare it to the complexity of the signals from the listening brain. We found that the information content of brain signals more closely matches that of the auditory environment when participants were attending to the acoustics of the music, compared to when they were attending to their own emotions induced by music listening. Further examination of this emotional effect in Study 4 revealed that music reward is inversely related to the similarity between internal brain and external music complexities. These results suggest that the information content of the environment can be measured in the brain, and the level of neural ‘mirroring’ is related to the type of cognitive processing conducted. We suggest that emotional experiences are associated with the integration of internal thought processes with perceptual input information.

Keywords: brain complexity
information processing
multiscale entropy
music perception
music preferences
reward
Advisor: McIntosh, Anthony R
The Drivers of Mitochondrial DNA Divergences

Mitochondrial phylogeography uses the relationship between matrilineal genealogy and geography to explain speciation, phylogeny and population structure. Several hypotheses on what maintains the parapatric matrilines have been proposed: philopatry, incomplete lineage sorting, vicariance and natural selection on female-linked traits. The small lizard Urosaurus nigricaudus of the peninsula of Baja California, Mexico and southern California, USA has six parapatric matrilines that differ by substantial mtDNA divergence. In this study, I investigate what drives and maintains the deep mtDNA discontinuities in this species. I precisely locate the mtDNA lineage breaks and investigate the presence of physical barriers in those areas. I sequence the entire mtDNA genome and then test the following hypotheses: unrestricted nDNA gene flow occurs across the species; mtDNA divergences correspond to the geological events; and that functional diversifying selection is involved in the maintenance of mtDNA discordances. I use thousands of nDNA SNP loci to test the first and last hypotheses. The time-calibrated genealogy cannot reject the hypothesis that the mtDNA discordances originated due to a series of vicariant events that happened on the peninsula starting in the late Miocene. For millions of years, females have dispersed beyond their place of birth, and yet, they do not cross the mtDNA contact zones. Thus, I reject the hypothesis of female philopatry as an explanation for the mtDNA discontinuities. In the mtDNA contact zones, females from two lineages co-exist in a small area with no barriers forbidding dispersal beyond the mtDNA breaks. The analysis with nDNA SNPs fails to reject the hypothesis of unrestricted nDNA gene flow throughout the peninsula (K=1). Thus, analyses also reject the hypotheses of vicariance and incomplete lineage sorting as explaining the continuing mtDNA discontinuities. Selective pressure analyses point to purifying selection as the evolutionary force acting in the mitogenome of this lizard, thus rejecting the hypothesis that habitat adaptation maintains the mtDNA discontinuities. My results reject most of the proposed hypothesis for the maintenance of mtDNA discontinuities and create exciting opportunities for further investigation on the role of other female-linked traits in the maintenance of mtDNA discontinuities, such as mito-nuclear functional compensation and female behavior.

Keywords: Cytonuclear discordance
Evolution
Female Behavior
Mitochondria
Phylogeography
Advisor: Murphy, Robert W
The Effects of Warming on Aquatic Insects - Individual to Community Responses

Climate change is increasing temperatures globally as well as the frequency and severity of extreme events such as heat waves. Given that the majority of animals on Earth are ectothermic, and therefore physiologically linked to environmental temperatures, it is imperative to predict the impacts of future warming on species. The physiological effects of warming on ectotherms have been studied extensively, yet, species interactions can also be affected by temperature. My thesis assessed how differences in species’ responses to warming affect their interactions and ultimately the structure and dynamics of communities. I first asked if phenological and early developmental responses to warming differed among and within dragonfly species. Warming accelerated growth and developmental rates, however, differences were greater within as opposed to between species in these responses. I also examined whether differences in behavioural responses to warming among species could determine which species became the superior IG predator. Foraging and IGP rates increased with warming but activity level changes were not predictive of the outcome of these interactions. Next, I asked how the interactive effects of warming and predator presence affected prey foraging decisions. Warmer conditions appeared to have a greater impact on prey behaviour that the predator presence, even though the prey’s risk of being eaten increased with temperature. Lastly, I manipulated developmental conditions in pond mesocosms to understand how warming and heat waves affect community structure. Heat waves similarly increased species’ evenness in communities as warming. However, heat waves further boosted survival compared to ambient and warmed conditions, strengthening consumption on primary consumers within these food webs. Together, my thesis demonstrates the importance of understanding complex interactions between species to make more accurate predictions of the effects of future warming on communities.

Keywords: climate warming
community ecology
freshwater
insects
Odonata
trophic webs
Advisor: McCauley, Shannon J
Assessment as Stereotyping: Experiences of Racialized Children and Parents with the Grade 3 EQAO Standardized Testing Preparation and Administration in Ontario

This exploratory qualitative study uses Critical Theory, specifically Critical Race Theory, to examine the subjective experiences of racialized children and parents with the Grade 3 EQAO standardized testing preparation and administration in Ontario, Canada. Standardized testing as a tool for measuring accountability in schools was introduced in 1996 by the Education Quality and Accountability Office (EQAO) which is an arm’s length agency of the Ministry of Education. Each year EQAO assesses students in publicly funded schools in Grades 3, 6, 9, and 10 focusing on numeracy and literacy using criterion-referenced standardized tests to provide an independent gauge of students’ learning and achievement. Data was collected via audio and video recording of semi-structured interviews with eight Grade 3 children and their parent(s). Although there are research studies conducted on EQAO testing, majority has been at the secondary level. Insights from this study contributes to filling in the gap in the field by focusing on EQAO testing in elementary schools and how it impacts racialized children and parents whose voices are often silenced within educational settings due to systemic barriers. Eight findings emerged through focused coding and thematic analysis. Findings indicate the way the Grade 3 EQAO standardized test is prepared for and administered is more harmful than beneficial. The harmful impact of standardized testing is identified under the umbrella term invisible scars and traumatizing effects of standardized testing particularly how EQAO testing marginalizes racialized children and those from lower socio economic backgrounds. Identifying external assessment as stereotyping, it is argued EQAO tests are culturally and racially biased as it promotes a Eurocentric curriculum and way of life privileging white students and those from higher socio-economic status. A shift from equality to an equity approach is recommended to tackle closing the achievement gap. The achievement gap will not be minimized in a sustainable manner without first addressing inequality of opportunity. Education alone, and quality of education, cannot be judged exclusively through standardized tests and their quantifiable indicators. Children have to be viewed as holistic beings with different social, cognitive, emotional, developmental, spiritual and academic needs.

Keywords: accountability
assessment
EQAO
equity
standardized testing
stereotyping
Advisor: Trifonas, Peter P
The Organization and Evolution of Biological Networks in Bacteria - Elucidating Biological Pathways and Complexes Involved in Bacterial Survival and Environmental Adaptation

Bacteria inhabit diverse environmental niches and employ various functional repertoires encoded in their genomes relevant for survival and adaptation. It has long been proposed that gene duplication plays an important role in bacterial adaptation, however systematic experimental study of the functional roles of duplicates in bacteria has been lacking. From decades of small-scale experimental work with the model bacterium, Escherichia coli, our view of the bacterial cell has expanded to encompass the concept of biological networks, a wiring diagram of the cell representing diverse functional associations of genes. To help define these complex functional relationships, large-scale genetic and protein interaction screens have been devised and applied to E. coli, providing datasets for deriving novel and biologically meaningful associations. In this work I present a study of gene duplication in the context of several large-scale biological networks. First (Chapter 2) I investigate two recently published E. coli genetic interaction (GI) networks, and find that duplicates are likely to contribute to increased robustness through epistatic buffering or integration in the context of biological pathways and protein complexes with broad biological roles and DNA damage and repair response pathways. Next (Chapter 3) I further investigate the implications of gene duplication in the context of physical protein interactions, based on a recent mapping of cell-envelope complexes generated for E. coli, revealing several instances where the acquisition of novel physical interactions has likely led to neofunctionalization of duplicates involved in environmental adaptation. Finally (Chapter 4) in a first systematic survey of biofilm secretion machineries, I combine a novel phylogenetic clustering approach and genome proximity networks to identify the impact of duplication on the evolution of operons, as phyla-specific niche adaptations. In summary, this work expands our knowledge of how the rewiring of physical, epistatic, and genomic associations of duplicates has shaped biological pathways in bacteria of adaptive significance.

Keywords: Bacterial Evolution
Biofilms
Biological Networks
Comparative Genomics
Genetic Interactions
Physical Interactions
Advisor: Parkinson, John
New Developments in Transition Metal Alkyl Chemistry

In the first section of this thesis, the synthesis and reactivity of the first reported palladium(IV) aryldiazenido complex is explored, as well as its relevance toward the potential for catalytic coupling cycles based on the Pd(II)/Pd(IV) redox pair. The synthesis was achieved by two-electron oxidation of the anionic palladium(II) complex KPd(Tp*)Me2 (Tp*- = hydridotris(3,5-dimethylpyrazolyl)borate) by an aryldiazonium cation. The resulting Pd(IV) complex could be cleanly isolated in good yields, is stable for weeks as a solid when kept cold, and decays in solution over a period of days at room temperature. The decomposition was studied in great depth by both NMR and EPR spectroscopy and it was determined that one-electron pathways were involved. From the synthesis of the Pd(IV) aryldiazenido complex, side reactions were observed whereby free Tp*- ligand could be modified via hydride abstraction by an aryldiazonium cation to form the elusive tris(pyrazolyl)borane which could be trapped and isolated as its acetone adduct in a Frustrated Lewis-pair type reaction. The resulting compound can act as a bidentate N-donor ligand with unusual axial steric bulk. Addition of a second equivalent of aryldiazonium cation further abstracts a 3,5-dimethylpyrazolide group to form a cationic intermediate which can again be trapped by acetone to form a C2-chiral cation. In the later chapters of this thesis, extensive work towards the synthesis of 1- and 2- adamantyl anion equivalents was explored, as well as their utility in the synthesis of transition metal adamantyl complexes. The development of new reliable synthetic methods to produce adamantyl magnesium and zinc compounds (including the unknown diadamantylzincs) was achieved, producing clean and shelf stable compounds. The applications of these adamantyl anions toward organometallic chemistry was investigated. It was observed that the diadamantylzinc compounds were particularly potent in transmetallation reactions, cleanly producing several new transition metal and main group adamantyl complexes. While compounds containing mercury, gold, bismuth, tungsten, and platinum have now been synthesized, those of particular interest have the potential for C-H bond activation chemistry and could open access to new compound classes of facially trifunctionalized adamantanes.

Keywords: Adamantyl Anions
Adamantyl Metal Complexes
Frustrated Lewis Pair
Organometallic Chemistry
Palladium Coupling
Advisor: Fekl, Ulrich W
Feasibility of Spinal Neuronavigation and Evaluation of Registration and Application Error Modalities Using Optical Topographic Imaging

Intra-operative navigation began with the localization of subsurface structures in cranial neurosurgery using frame-based stereotaxy. Advances in imaging and computing power have led to the development of modern frameless three-dimensional (3D) computer-assisted navigation (CAN), employed across multiple surgical disciplines. In spinal surgery, CAN may guide implant placement, bony decompression and soft-tissue resection. However, adoption of 3D CAN by spinal surgeons has been limited by cumbersome registration protocols, workflow disruption, high capital cost, and questionable quantitative and clinical utility. A novel technique for image-to-patient registration has recently been developed, based on optical topographic imaging (OTI). Whether OTI-based CAN is able to provide accurate intra-operative image-guidance for common spinal procedures, while addressing current limitations of CAN techniques, warrants study. First, we explored the current paradigms of reporting CAN accuracy in the context of spinal procedures, finding that quantitative application accuracy and radiographic screw placement do not correlate. We therefore proposed a combined quantitative and radiographic system of reporting CAN accuracy. Second, we examined the registration workflow and accuracy of OTI-CAN in open posterior thoracolumbar instrumentation, in pre-clinical swine and cadaveric models and subsequently in clinical in-vivo testing. We found that OTI-CAN is comparably accurate to but significantly faster than existing 3D CAN techniques. We subsequently found that OTI-CAN was similarly accurate, with maintained workflow improvements, in minimally-invasive (MIS) thoracolumbar and open cervical approaches. Finally, we explored mechanisms by which current CAN and specifically surface-based registration techniques, including OTI, may fail. We found that navigation error increases with greater working distance to the dynamic reference frame (DRF), and with greater geometric symmetry over the osseous posterior elements. Taken together, this body of work demonstrates that OTI is a feasible technique for spinal CAN, and may alleviate the primary issues plaguing current systems to allow increased adoption into settings where CAN may be most useful.

Keywords: Image guided surgery
Navigation
Spine
Advisor: Yang, Victor XD
Proteome Signatures in Non-Small Cell Lung Cancer

Lung cancer is one of the most common cancers worldwide, and is the top cause of cancer-related death in both men and women. Non-small cell lung cancer (NSCLC) accounts for 85% of lung cancers and is subdivided into two major histological subtypes: adenocarcinoma (ADC) and squamous cell carcinoma (SCC). While the genomic and transcriptomic landscapes of NSCLC ADC and SCC have been well portrayed, the proteome of NSCLC is less characterized although expected to have a pronounced and direct effect on cancer phenotype. In my PhD study, I used mass spectrometry-based quantitative shotgun proteomics approaches to characterize proteome signatures related to NSCLC histological subtypes and patient tumor engraftment, the later of which correlates with prognosis. I first demonstrated that proteomes of human lung ADC and SCC patient tumor-derived xenografts could be resolved and a multi-protein histology signature comprised of various components of the epithelial barrier and metabolism enzymes was identified and validated. The ability of primary NSCLC to engraft in immuno-compromised mice and form a stable patient-derived xenograft is a poor prognosis indicator, suggesting that engraftment selects for aggressive aspects of the cancer phenotype linked to disease progression, which is not understood at a molecular level. I found that proteomes were different between tumors that could or could not engraft, which highlighted a metabolism protein, mitochondrial aconitase 2 (ACO2), as the strongest predictor of engraftment. Consistent with lower ACO2 protein level measured in engrafting tumors, weak ACO2 protein expression level correlated with poor outcome in an independent cohort of NSCLC patients. Furthermore, ectopic expression of ACO2 in a NSCLC cell line suppressed cell proliferation in vitro and in vivo. My work illustrates the power of proteomics approaches to uncover clinically relevant cancer signatures not revealed by genomic and transcriptomic methods and expands our understanding of proteome remodeling in cancers.

Keywords: histology
LC-MS/MS
lung cancer
NSCLC
prognosis
proteomics
Advisor: Moran, Michael F