VictorJuiz/thesis huggingface dataset:
Regulation of Telomerase by DNA and Protein Interactions
Keywords: telomeres
telomerase
senescence
DNA binding domain
processivity
reverse transcriptase

In most eukaryotes, chromosomes ends are protected by telomeres which are formed by repetitive DNA, specialized binding proteins, and higher order structures. Telomeres become shorter following replication due to the positioning and degradation of terminal RNA primers, as well as resection by nucleases. Extensive telomere shortening over many cell cycles elicits a DNA damage checkpoint that culminates in senescence or, in the absence of tumor suppressor pathways, apoptosis. These effects block the expansion of cells with unstable genomes, but can also precipitate disease in tissues that rely on regeneration for function. In many unicellular eukaryotes and proliferative human cells including cancer cells, telomeres can be maintained by the telomerase reverse transcriptase (TERT) and its associated RNA (TR). The elongation of telomeric DNA by telomerase depends on the telomerase essential N-terminal (TEN) and C terminal reverse transcriptase (RT) domains. We found that human TEN interacted with single-stranded telomeric DNA and restored function, in trans, to an hTERT mutant lacking hTEN. Telomerase required hTEN residues for activity, telomere maintenance, and extension of cellular replicative lifespan. Two inactive hTERT variants bearing mutations in TEN and RT domains, respectively, cooperated to regenerate telomerase activity in vitro. hTEN interacted with several regions of hTERT suggesting that dimerization may occur via TEN-TERT interactions. The in vivo defect of certain hTEN mutants may involve an inability to interact with factors that recruit the enzyme to the telomere and/or stimulate activity. Human homologs of the S. cerevisiae recruitment factor Est1 interacted with telomerase in a species-specific manner. The TPR domain of hEST1A interacted with the N-terminus of hTERT. The TPR domain of ScEst1 was required for telomere length maintenance by telomerase, and, paradoxically, also negatively regulated telomere length. In preliminary experiments, hTERT interacted with hPOT1/hTPP1. This interaction may stimulate the elongation of telomeres by telomerase. The DNA and protein interactions described herein expand our knowledge of telomerase and present new targets for the manipulation of telomerase function in human disease.
Ontario Colleges in the Digital Age: Understanding the Student Experience, Perceptions and Attitudes of Online Learning at one Ontario College
Keywords: Online learning
student perspective

The global economy is undergoing drastic upheavals as Canada enters the 21st century. The key driver of this transformation is the emergence of the digital age. The digital age is impacting all facets of Canadian society, including postsecondary education. The integration of educational technologies into curriculum is spawning a new form of learning commonly referred to as online learning. Online learning has the potential to radically alter the manner in which knowledge is taught and learned in Canadian higher education. This mixed-methods study utilized both quantitative and qualitative data collection methods. The qualitative phase (n = 16) was developed and built upon the development and analysis of the quantitative phase (n = 279), which is based on Chickering and Gamson’s (1987) Seven Principles for Good Practice in Undergraduate Education, permitting the researcher to probe more deeply into the college students’ attitudes and perceptions of their online learning experience. The participating students represented most of the programs offered by this college. After the data analysis and interpretations of the findings, several themes emerged. The participants in the online questionnaire were satisfied with their online learning experiences at this one Ontario college. The participants cited the convenience, flexibility and the ability to control their learning as major benefits associated with online learning. Although the students who participated in the online questionnaire were satisfied with their online learning experiences, the quantitative and qualitative findings of this study provide compelling evidence that, as a matter of preference, students would chose a face-to-face / hybrid course over an online course. The participants in the semi-structured interviews repeatedly discussed how the interaction and physical contact between faculty and student, and between students enhanced the learning experiences, which contributed to their academic success. The socialization that occurred in the classroom was also a contributing factor for the preference for face-to-face / hybrid instruction. The results of this study may inform and guide college leadership and faculty about the complexities associated with implementing an online learning strategy at their college. Implications of the conclusions are presented and discussed on how they may impact Ontario’s colleges.
Touching the Future: Educators and the Law
Keywords: Educational Law
Beginning Teachers
Ethical Standards
Legal Boundaries

Teachers are perceived by society and in law to be in a position of trust. As a result of the daily interaction with their students, educators have the opportunity to be influential and they are expected to behave in a responsible, ethical and moral manner. Being viewed as a moral compass of society is a significant responsibility and the implications of such a statement are substantial upon not only teachers but also impact on teacher education programs. This study investigates how educational law impacts on beginning teachers in light of the many legal and ethical boundaries that educators will experience throughout their career. The literature review discusses the delicate balance between an educator’s mission and the requirement to follow policies and procedures; documented court cases, which have an impact on educators; and, finally, the educational law component within the teacher education framework. Six participants were interviewed in this study of which two are teachers in their first three years of teaching, two recent graduates, a principal and an official with a teacher union who is a member from the Counseling department. All four of the teachers completed a two-year initial teacher education program. In addition, the principal is a member of the Partnership Advisory Council of the program. Maintaining the delicate balance between an educator’s mission and the law will continue to be a challenge. The direct and indirect statutory rules and regulations which impact on the education system and the supporting landmark court case decisions clearly bring to question the level of preparedness of teacher candidates and indicate a need to examine the role teacher education programs play in preparing future teachers. The major themes include the impact of educational law on the professional and personal lives of beginning teachers, the role of initial teacher education programs, and the legal enablers and barriers for educators. The key findings for each of the themes are discussed. Educators find themselves in a very complex role. The teacher education programs in Ontario need to examine the importance of including meaningful and insightful dialogue about the legal and ethical aspects of being a teacher.
Biotic filters in fungal endophyte community assembly
Keywords: fungal endophytes
Fusarium

My work focuses on the community ecology of symbioses, specifically of fungal endophytes and their hosts. This thesis describes how plant defense compounds and a seed endophyte influence community structure of maize fungal endophytes. Maize produces benzoxazinoids (BXs), compounds toxic to microbes and insects. I assessed the influence of three factors on endophyte communities: host BX production, host neighbor identity and presence of a BX-detoxifying endophyte, Fusarium verticillioides (FV). To determine the influence of BXs on communities, two BX-producing (BX+) and one BX-nonproducing (BX–) genotype were planted in Ridgetown and Harrow, Ontario (triculture). Fungi were isolated and tested for tolerance to 2-benzoxazolinone (BOA), a toxic BX byproduct. Species and functional diversity (community distribution of BOA tolerance levels) was calculated. In seedling roots and mature leaves, the community proportion with low BOA tolerance was greater in BX– than BX+ plants. Fusarium abundance was up to 35 times higher in mature leaves of BX+ than BX– plants. Next, to assess the effect of host neighbor identity on communities, BX– monocultures were planted, and communities from BX– plants in monoculture and triculture compared. Monoculture root communities had higher species diversity than those in triculture. In vitro experiments were conducted to evaluate the influence of BOA on endophyte species interactions. FV facilitated species with lower BOA tolerance in the presence of BOA. Finally, fields were planted with a BX+ and BX– genotype in Ontario, Canada and Georgia, USA. Seed was inoculated with FV (FV+) or sterilized (FV–). FV abundance was highest in BX+FV+ plants, and Fusarium abundance was greater in BX+ than BX– plants in mature leaves. In Georgia, BX+FV+ communities in below ground tissue had lower abundance of BOA sensitive species than BX+FV–. Overall, results suggest that BXs are a habitat filter that increased colonization by horizontally transmitted and seed-born Fusarium species. This invokes the hypothesis that selective breeding for enhanced BX concentrations increased abundance of Fusarium species in maize. The in vitro study indicated that FV could facilitate other species. In contrast, field results suggest that FV interacts competitively with community members, a trait enhanced in the presence of BXs.
Methodological Examination of Screening Prenatal Exposure to Alcohol and Illicit Substances
Keywords: screening
alcohol
pregnancy
illicit substances

Fetal alcohol spectrum disorder (FASD) is the leading non-genetic cause of brain damage. In an effort to reduce alcohol-exposed pregnancies, steps are needed to identify at risk women as early as possible so that appropriate intervention can occur. The objective of this dissertation was to examine screening methods validated in identifying pregnant women at risk for consuming alcohol and illicit drugs during pregnancy. A systematic review identified three main approaches including maternal self-report, use of standardized questionnaires and detection via biological markers. Since most screening tools were developed in alcoholic women, it was important to examine performance in problem drinkers. Alcohol screening tools (ASQ), currently the best method of predicting prenatal problem drinking, were not effective in a cohort representative of problem drinkers. ASQ performance improved minimally, using higher thresholds, but not enough to be used alone. Provider’s knowledge of complexities inherent in women under their care is an important component in screening. As illicit drug use is an important predictor of problem drinking, identifying maternal risk factors associated with substance use was necessary. Increased rates of STD’s, untreated psychiatric disorders, binge drinking and heavy smoking were all identified as predictors of prenatal methamphetamine (MA) use. These factors, combined with high rates of unplanned pregnancies have serious adverse implications for the fetus. The most widely used method to screen for illicit substance use is based on a practice-based approach that relies heavily on maternal self-report. Most providers do not ask about alcohol and substance use in the absence of a high index of suspicion due to the assumption that patient will deny use. But evidence suggests that maternal account can be accurate in a supportive environment. The last study examines the agreement between self-reported data, in comparison to illicit drug use based on positive hair test results. A reasonable agreement between the two approaches of identification demonstrates that maternal self-report can be reliable in women who are motivated enough to seek prenatal care. No single approach is sufficient to effectively identify at risk women. However, combining two or more methods will improve screening and help reduce the number of alcohol-exposed pregnancies.
Chemical Kinetic Modeling of Biofuel Combustion
Keywords: biofuel
combustion modeling

Bioalcohols, such as bioethanol and biobutanol, are suitable replacements for gasoline, while biodiesel can replace petroleum diesel. Improving biofuel engine performance requires understanding its fundamental combustion properties and the pathways of combustion. This study's contribution is experimentally validated chemical kinetic combustion mechanisms for biobutanol and biodiesel. Fundamental combustion data and chemical kinetic mechanisms are presented and discussed to improve our understanding of biofuel combustion. The net environmental impact of biobutanol (i.e., n-butanol) has not been studied extensively, so this study first assesses the sustainability of n-butanol derived from corn. The results indicate that technical advances in fuel production are required before commercializing biobutanol. The primary contribution of this research is new experimental data and a novel chemical kinetic mechanism for n-butanol combustion. The results indicate that under the given experimental conditions, n-butanol is consumed primarily via abstraction of hydrogen atoms to produce fuel radical molecules, which subsequently decompose to smaller hydrocarbon and oxygenated species. The hydroxyl moiety in n-butanol results in the direct production of the oxygenated species such as butanal, acetaldehyde, and formaldehyde. The formation of these compounds sequesters carbon from forming soot precursors, but they may introduce other adverse environmental and health effects. Biodiesel is a mixture of long chain fatty acid methyl esters derived from fats and oils. This research study presents high quality experimental data for one large fatty acid methyl ester, methyl decanoate, and models its combustion using an improved skeletal mechanism. The results indicate that methyl decanoate is consumed via abstraction of hydrogen atoms to produce fuel radicals, which ultimately lead to the production of alkenes. The ester moiety in methyl decanoate leads to the formation of low molecular weight oxygenated compounds such as carbon monoxide, formaldehyde, and ketene, thereby reducing the production of soot precursors. The study concludes that the oxygenated molecules in biofuels follow similar combustion pathways to the hydrocarbons in petroleum fuels. The oxygenated moiety's ability to sequester carbon from forming soot precursors is highlighted. However, the direct formation of oxygenated hydrocarbons warrants further investigation into the environmental and health impacts of practical biofuel combustion systems.
Liquefaction of Early Age Cemented Paste Backfill
Keywords: Monotonic and Cyclic Liquefaction
cemented paste backfill
Mining-induced seismicity
Silt-sized tailings

Modern mines require systems that quickly deliver backfill to support the rock mass surrounding underground openings. Cemented Paste Backfill (CPB) is one such backfilling method, but concerns have been raised about CPB’s liquefaction susceptibility especially when the material has just been placed, and if it is exposed to earthquakes or large mining induced seismic events. Conventional geotechnical earthquake engineering for surface structures is now relatively advanced and well accepted, and so the objective of this thesis is to consider how that framework might be extended to assess the liquefaction potential of CPB. Seismic records were analyzed for earthquakes and for large mining induced events. Important seismological trends were consistent for rockbursts and earthquakes when the signals were recorded at distances as proximate as one kilometre, suggesting that the conventional earthquake engineering approach might plausibly be adapted for such design situations. For production blasts and for more proximate locations to rockbursts, much higher frequencies dominate and therefore new design methods may be required. Monotonic triaxial tests conducted on normally consolidated uncemented mine tailings demonstrated that the material is initially contractive up to a phase transition point, beyond which dilation occurs. Most importantly the material never exhibits unstable strain softening behaviour in compression, and only temporary or limited liquefaction in extension. The addition of 3% binder results in initial sample void ratios that are even higher than their uncemented counterparts, and yet the material friction is slightly enhanced when tested at 4 hours cure. These results suggest that the flow liquefaction phenomenon commonly associate with undrained loose sand fills will not occur with paste backfill. Cyclic triaxial test results analyzed in terms of number of cycles to failure for a given cyclic stress ratio exhibited a trend consistent with previous tests on similar materials. However, the addition of 3% binder and testing at 4 hours cure resulted in an order of magnitude larger number of cycles to failure – a surprising and dramatic increase, suggesting good resistance of the material to cyclic mobility. Future research is recommended to build on these results and develop more robust methods for liquefaction assessment of CPB.
Functional Partitioning of the Human Lumbar Multifidus: An Analysis of Muscle Architecture, Nerve and Fiber Type Distribution using a Novel 3D in Situ Approach
Keywords: lumbar multifidus
muscle architecture
3D modeling
fiber type distribution
innervation
morphology

Muscle architecture, innervation pattern and fiber type distribution of lumbar multifidus (LMT) throughout its volume was quantified. Musculotendinous (n=10) and neural components (n=3) were dissected and digitized from thirteen embalmed cadaveric specimens. The data were imported into Autodesk® Maya® 2008 to generate 3D neuromuscular models of each specimen. Architectural parameters (fiber bundle length, FBL; fiber bundle angle, FBA; tendon length) were quantified from the models using customized software. The medial branch of the posterior rami (L1-L5) was traced through LMT to determine its distribution. Using immunohistochemistry, Type I/II muscle fibers were identified in 29 muscle biopsies from one fresh frozen specimen. The total area and number of each cell type was calculated using Visiopharm® (image analysis software). Architectural and fiber type data were analyzed using ANOVA with Tukey’s post-hoc test (p ≤ 0.05). From L1-L4, LMT had three architecturally distinct regions: superficial, intermediate and deep. At L5, intermediate LMT was absent. Mean FBL decreased significantly from superficial (5.8 ± 1.6cm) to deep regions (2.9 ± 1.1cm) as did volume (superficial, 5.6 ± 2.3ml; deep, 0.7 ± 0.3ml). In contrast, mean FBA increased from superficial to deep. The medial branch of the posterior ramus (L1-L5) supplied the five bands of LMT. Each medial branch in turn divided to supply the deep, intermediate and superficial regions separately. The area occupied by Type I fibers was significantly less (p< 0.01) in the deep (56%) compared with the superficial regions (75%). Based on architecture and morphology, superficial LMT with the longest FBL and relatively small FBA is well designed for torque production and controlling the lumbar lordosis. Intermediate LMT with significantly longer FBL compared with the deep region and with its caudal to cranial line of action may help to control intersegmental stability. Furthermore, the absence of intermediate LMT at L5 and may contribute to the higher incidence of instability observed at the lumbosacral junction. Deep LMT with its short FBL, large FBA and proximity to the axis of spinal rotation may function to provide proprioceptive input to the CNS rather than a primary stabilizer of the lumbar spine.
Buoyant Plumes with Inertial and Chemical Reaction-driven Forcing
Keywords: Fluid Dynamics
Chemo-hydrodynamics
Buoyancy-driven flow
Plumes

Plumes are formed when a continuous buoyant forcing is supplied at a localized source. Buoyancy can be created by either a heat flux, a compositional difference between the fluid coming from the source and its surroundings, or a combination of both. In this thesis, two types of laminar plumes with different forcing mechanisms were investigated: forced plumes and autocatalytic plumes. The forced plumes were compositionally buoyant and were injected with inertial forcing into a fluid filled tank. The autocatalytic plumes were produced without mechanical forcing by buoyancy that was entirely the consequence of a nonlinear chemical reaction -- the iodate-arsenous acid (IAA) reaction. This reaction propagates as a reacting front and produces buoyancy by its exothermicity, and by the compositional difference between the reactant and product. Both the forced and autocatalytic plumes were examined in starting and steady states. The starting, or transient, state of the plume occurs when it initially rises through a fluid and develops a plume head on top of a trailing conduit. The steady state emerges after the plume head has risen to the top of a fluid filled tank leaving only a persistent conduit. Plume behaviour was studied through experimentation, simulation, and by using simple theoretical analysis. We performed the first ever study of plumes as they crossed over the transition between buoyancy-driven to momentum-driven flow. Regardless of the driving mechanism, forced plumes were found to exhibit a single power law relationship that explains their ascent velocity. However, the morphology of the plume heads was found to depend on the dominating driving mechanism. Confined heads were produced by buoyancy-driven plumes, and dispersed heads by momentum-driven plumes. Autocatalytic plumes were found to have rich dynamics that are a consequence of the interplay between fluid flow and chemical reaction. These plumes produced accelerating heads that detached from the conduit, forming free vortex rings. A second-generation head would then develop at the point of detachment. The detachment process for plumes was sensitively dependent on small fluctuations in their initial formation. In some cases, head detachment could occur multiple times for a single experimental run, thereby producing several generations of autocatalytic vortex rings. Head detachment was reproduced and studied using autocatalytic plume simulations. Autocatalytic flame balls, a phenomenon closely related to autocatalytic plumes, were also simulated. Flame balls were found to have three dynamical regimes. Below a critical radius, the smallest flame balls experienced front death. Above this radius, they formed elongating, reacting tails. The largest flame balls formed filamentary tails unable to sustain a reaction.