Science (Faculty of)http://hdl.handle.net/10012/99362024-03-29T06:56:42Z2024-03-29T06:56:42ZEvolution of the Laurentide Ice Sheet in north-central Ontario from subglacial sedimentsTaves, Robinhttp://hdl.handle.net/10012/203942024-03-13T02:31:01Z2024-03-12T00:00:00ZEvolution of the Laurentide Ice Sheet in north-central Ontario from subglacial sediments
Taves, Robin
Till stratigraphic analysis of 10 sediment bluffs near Ogoki Post in the Hudson and James Bay Lowlands.
2024-03-12T00:00:00ZArylbenzamide and Arylcarboxamide Derivatives as Modulators of Amyloid-Beta AggregationZhao, Yushenghttp://hdl.handle.net/10012/203922024-03-12T02:30:54Z2024-03-11T00:00:00ZArylbenzamide and Arylcarboxamide Derivatives as Modulators of Amyloid-Beta Aggregation
Zhao, Yusheng
Alzheimer’s disease (AD) is a complex neurodegenerative disease with increasing incidence and prevalence globally. The current AD therapies based on small molecules offer only symptomatic relief and are not curative therapies. The recently launched anti-amyloid monoclonal antibodies hold promise although these are new to the market and their long-term benefits and potential disease-modifying effects are unknown. The global increases in the aging population and increasing life span mandate the need to understand the mechanisms of AD and discover effective and safe therapies. Over the past several decades, few hypotheses have been proposed to explain the pathophysiology of AD, among which the amyloid beta (Aβ) cascade is now considered as one of the initiating factors that drives the progression and other pathological factors of AD. The aggregation of Aβ into oligomers and fibrils together with its downstream signaling pathway are neurotoxic. Thus, small molecule modulators that could reduce the overall toxic burden of Aβ aggregates are thought to be beneficial in treating AD.
In this thesis, a library of 72 small molecule derivatives were designed based on the chemical structure of chalcone and curcumin, two bioactive natural compounds that are able to modulate Aβ aggregation and reduce their neurotoxicity. The derivatives reported in this thesis encompass four different templates, namely, N-benzyl (Chapter 2), N-phenethyl (Chapter 3), N-benzyloxy (Chapter 4), and N-phenyl (Chapter 5) benzamide and carboxamides. These compounds were synthesized by coupling the amine substrates with either acid halides or carboxylic acids to obtain the target compounds in 72-93.6% yields. A number of biophysical and biochemical experiments were carried out to determine the ability of these small molecules to modulate the aggregation properties of Aβ42. The experiments carried out include i) thioflavin T based fluorescence aggregation kinetics experiments; ii) transmission electron microscopy studies; iii) 8-anilino-1-naphthalenesulfonic acid based fluorescence spectroscopy; iv) antioxidant assay by fluorescence spectroscopy; iv) cell viability studies in mouse hippocampal HT22 neuronal cells and Aβ42-induced neurotoxicity assay; v) fluorescence microscopy studies to assess the neurotoxicity using Proteostat dye, and vi) computational modelling studies to determine the interactions of small molecules with Aβ42 aggregates. From this library, 51 aggregation inhibitors were identified (inhibition of Aβ42 ranging from 7-53.1% at 25 µM). These derivatives were able to provide significant neuroprotection from Aβ42-induced cytotoxicity in mouse hippocampal HT22 cells (cell viability ranging from 80.8-96.8% versus 38.7% for Aβ42-treated control). Molecular docking studies indicate that these derivatives were able to interact with the hydrophobic domains of the Aβ42 oligomer and fibril through hydrophobic interactions. In a striking and unusual finding, 8 derivatives were identified as Aβ42 aggregation promotors with the ability to promote the aggregation by 1.2-5.1 folds. Two lead promotors 14b (N-benzylbenzofuran-2-carboxamide) and 14c (N-benzylbenzo[b]thiophene-2-carboxamide) were identified. These two compounds were able to rescue HT22 cells from Aβ42-induced cytotoxicity (cell viability 73.8% and 73.9% for 14b and 14c versus 19.7% for Aβ42-treated control). These two compounds have the ability to increase the surface hydrophobicity of Aβ42 aggregates and promote fibrillogenesis. Molecular docking studies suggested that Aβ42 aggregates might undergo conformational change upon binding and thus transit to much more stable and less toxic/nontoxic fibrils. Further structure-activity relationship study indicated that the hydroxy- and methoxy-disubstituted phenyl moiety was required to possess Aβ42 inhibition activity, where the presence of bicyclic aromatic rings such as benzofuran and benzothiophene, and 4-methoxyphenyl moiety is required for pro-aggregation activity. The results show that these benzamides and carboxamides possessing N-benzyl, N-phenethyl, N-benzyloxy, and N-phenyl templates hold promise in the design and development of novel small molecules as Aβ42 aggregation modulators. Remarkably 14b (N-benzylbenzofuran-2-carboxamide) and 14c (N-benzylbenzo[b]thiophene-2-carboxamide) were able to accelerate Aβ42 aggregation and remodel the aggregation pathway to form less toxic/nontoxic aggregates suggesting their application as novel chemical tools to understand the mechanisms of Aβ42 aggregation cascade.
2024-03-11T00:00:00ZEnvironmental DNA barcoding as a method of amphibian species detection compared to conventional monitoring techniques in southern Ontario vernal poolsZamora, Cailynhttp://hdl.handle.net/10012/203782024-03-07T03:30:58Z2024-03-06T00:00:00ZEnvironmental DNA barcoding as a method of amphibian species detection compared to conventional monitoring techniques in southern Ontario vernal pools
Zamora, Cailyn
Ongoing monitoring is vital for the conservation of amphibian species and is conducted through conventional auditory and visual surveys. A molecular method, termed environmental DNA (eDNA) barcoding, may offer a more sensitive method of species detection that negates the need for direct species observation. The research aims of this thesis were to conduct a comparative analysis of eDNA barcoding versus conventional (audio/visual) species detection methods for six amphibian species in southern Ontario. I hypothesized that eDNA barcoding would offer equal or greater species presence detections compared to the conventional methods. Conventional surveys and eDNA collections were conducted in three vernal pools from April-July 2019 in collaboration with rare Charitable Research Reserve (Cambridge, ON). Conventional methods included collection of daily audio files from acoustic song meters and weekly/biweekly visual encounter surveys. Audio data was analyzed using Kaleidoscope Pro. Alongside conventional surveys, duplicate water samples containing eDNA were collected at multiple sampling locations around three vernal pools. After water collection, eDNA was concentrated by filtration, extracted, and quality controlled. eDNA samples were processed using optimized eDNA barcoding assays using quantitative PCR. Comparative analysis between conventional methods and eDNA barcoding contradicts a one-size-fits-all model of amphibian monitoring. eDNA barcoding offered a reliable and effective method of species detection for five of the target amphibians especially for obligate vernal pool breeding species, however this method failed to accurately detect the spring peeper despite detections by passive acoustic surveys. I propose using eDNA barcoding alongside a conventional method of species detection to optimize detections across a spatiotemporal scale, however, this should be catered to the target species of interest. Future studies could implement a multi-year study as well as a comparison of eDNA barcoding to metabarcoding for Ontario amphibian species. eDNA barcoding offers a new method of species detection that could aid in ongoing amphibian monitoring and therefore conservation efforts of the declining taxa.
2024-03-06T00:00:00ZDevelopment and biomedical applications of solid phase micro-extraction (bio-SPME) chemical biopsy devicesJiang, Runshan (Will)http://hdl.handle.net/10012/203542024-02-23T03:30:55Z2024-02-22T00:00:00ZDevelopment and biomedical applications of solid phase micro-extraction (bio-SPME) chemical biopsy devices
Jiang, Runshan (Will)
Micro-sampling is a vital component in modern diagnostics and
personalized medicine. In vivo SPME is a novel branch of biomedical
applications of SPME (Bio-SPME) that offers unique advantages complementary
to existing in vivo micro-sampling techniques such as micro tissue biopsy and
microdialysis. When coupled with powerful modern detection methods, such as
mass spectrometry, the minimally invasiveness and convenient sample-cleanup
of in vivo chemical biopsy SPME enable the rapid analysis of exogenous and
endogenous analytes from a biological system in vivo. In vivo SPME has seen
success in numerous clinical applications from therapeutic drug monitoring (TDM)
to untargeted metabolomic/lipidomic fingerprinting. While the scope of theoretical
considerations extends deep into the realm of complex physical chemistry, bio-
SPME and in vivo SPME can still be executed by medical personnel with limited
theoretical knowledge as long as a few key experimental parameters are
controlled, such as extraction time. Chapter 2 details the fabrication of a novel
recessed SPME chemical biopsy probe and a push-pull microsyringe sampling
device. Compared to conventional in vivo sampling tools, the latest devices offer
superior physical robustness with a convenient chemical sorbent that does not
require solvent activation. Such devices have been successfully implemented in
human in vivo studies which are also included in this chapter. Chapter 3
presents a proof-of-concept study showing the importance of non-destructive
sampling (ie. in vivo SPME) in untargeted metabolomics using ovine lung tissue
as a model coupled with a commercial metabolomics kit. Chapter 4 is another
proof-of-concept study which explores the applicability of bio-SPME in
proteomics which was thought to be impossible. Various sample preparation and
device fabrication strategies such as protein digestion and porous coating were
employed to achieve protein identification in clinical SARS-CoV-2 patient saliva
samples. Chapter 5 of the thesis addresses some of the flaws with previous in
vivo applications of SPME, provides strategies to overcome them, and
showcases numerous clinical in vivo applications with the improved calibration
strategies. In short, this thesis work offers a comprehensive strategy for various
in vivo and ex vivo bio-SPME applications.
2024-02-22T00:00:00Z