Biochemistry, Biophysics, and Structural Biology Commons^™

Synthesis And Characterization Of Cr-Znga2o4 And Eu-Ca3(Po4)2 Composite, Benjamin Hulme

Undergraduate Student Research Internships Conference

No abstract provided.

Global Regulation Of Mirna And Mrna Homeostasis By Terminal Uridylyltransferases Tent3a/B, Pengcheng Zhang

Electronic Thesis and Dissertation Repository

The terminal nucleotidyltransferases TENT3A and TENT3B (TENT3A/B) regulate microRNA (miRNA) and messenger RNA (mRNA) stability by 3' end uridylation, leading to degradation by the U-specific exonuclease DIS3L2. Uridylation dependent decay is thought to be a highly specific process, and the prevalence and impact of this pathway on the transcriptome is unexplored. I investigate the prevalence of uridylation dependent decay by transcriptionally profiling HEK 293T cells lacking TENT3A/B. I found while TENT3A/B target a variety of miRNAs, the let-7 family of miRNAs were the most impacted (increased) in TENT3A/B deleted cells. Consequently, let-7 mRNA targets are decreased in abundance in TENT3A/B …

The Effect Of Breathing Patterns Common To Competitive Swimming On Gas Exchange And Muscle Deoxygenation During Heavy-Intensity Fartlek Exercise, Kevin J. Grossman

Electronic Thesis and Dissertation Repository

The purpose of this study was to compare the respiratory and muscle deoxygenation (HHb) responses of regulated breathing versus free-breathing, during continuous exercise (CONLD) and intermittent 5s breath holds (BH) (CONLD-BH), intermittent 5s sprint (FLK) and combined 5s BH and sprint (FLK-BH) followed by 25s of free-breathing. Oxygen uptake(V̇O₂)was unchanged between CONLD (2.12±0.35L/min) and CONLD-BH (2.15±0.42L/min; p=0.116), and FLK (2.24±0.40L/min) and FLK-BH (2.20±0.45L/min; p=0.861). Δ[Hb_tot]: CONLD (3.3±1.6µM) > CONLD-BH (-2.5±1.2µM; ∆177%; p<0.001), but unchanged between FLK (2.0±1.6µM) and FLK-BH (0.82±1.4µM; p=0.979). Δ[HHb]: CONLD (7.3±1.8µM) > CONLD-BH (7.0±2.0µM; ∆4%; p=0.011), and FLK (6.7±1.8µM) < FLK-BH (8.7±2.4µM; p<0.001). It is suggested that the unchanged V̇O₂ between CONLD and CONLD-BH was supported by increased deoxygenation, reflected by decreased ∆[Hb_tot] and blunted …

Biochemistry Of Trehalose Accumulation In The Spring Field Cricket, Gryllus Veletis, Alyssa R. Stephens

Electronic Thesis and Dissertation Repository

The freeze tolerant spring field cricket, Gryllus veletis, accumulates trehalose in the blood and tissues during cold acclimation. Trehalose is the main blood sugar in insects, thus its blood concentration is tightly regulated, and trehalose is readily metabolized. How do crickets modify their metabolism to accumulate trehalose in their hemolymph and tissues? I hypothesized that trehalose production, transport, and consumption were modified during the cold acclimation to facilitate trehalose accumulation. Trehalose and the trehalose-specific transporter, TRET-1, are distributed among all tissues, and trehalose accumulates in the hemolymph, fat body, Malpighian tubules, and gut. Trehalose production increases during cold acclimation …

The Hydrophobic Residues In Amino Terminal Domains Of Cx46 And Cx50 Are Important For Their Gap Junction Channel Ion Permeation And Gating, Roa'a Jaradat

Electronic Thesis and Dissertation Repository

Connexins are ubiquitous transmembrane proteins that assemble to form intercellular channels, called gap junctions (GJs). The amino terminal (NT) domain and residues within this domain have been shown to be important for both V_j-gating and single channel conductance (γ_j) of several GJs including Cx46 and Cx50. High-resolution structures of Cx46 and Cx50 GJs were recently resolved showing that NT domain folds into the inner pore where hydrophobic residues are packed against M1/2 domains stabilizing open-state conformation. We studied functional properties of GJs formed by several point variants at NT (Cx46 L10I, N13E, A14V, Q15N and Cx50 …

Kinetic And Structural Influences Of Acetylation On Ubiquitin Processing, Rachel E. Lacoursiere

Electronic Thesis and Dissertation Repository

Ubiquitin (Ub) is a small modifying protein abundant in cells where it serves numerous regulatory roles including immune signaling, transcriptional regulation, and proteostasis. To exert its function, Ub covalently interacts with a series of E1, E2, and E3 enzymes before final substrate modification. Dysregulation of Ub signaling has implications in human maladies such as cancer, autoimmune disorders, and neurodegenerative diseases. In these diseases and associated in cellulo models, modifications to Ub serve an additional role in Ub regulation. Post-translational modifications like acetylation or phosphorylation modulate protein-protein interactions and Ub signaling. To understand how acetylation of Ub alters the central E2 …

Illuminating Transfer Rna Variants As Genetic Modifiers In Models Of Human Disease, Jeremy T. Lant

Electronic Thesis and Dissertation Repository

Transfer RNAs (tRNAs) physically link the genetic code to an amino acid sequence, by recruiting amino acids to three-nucleotide codons in messenger RNAs. To ensure that the genetic code is translated as intended, tRNAs must be accurately aminoacylated and faithfully recognize codons in the ribosome during protein synthesis. Given the critical function of tRNAs, it has often been assumed that mutations in human tRNA genes would be either lethal to cells or not significantly impair tRNA function. My goal was to rigorously test this assumption in mammalian cell models, prompted by the recent discovery of unprecedented variation in human tRNA …

Radiation Exposure Determination In A Secure, Cloudbased Online Environment, Ben C. Shirley, Eliseos J. Mucaki, Joan H.M. Knoll, Peter Rogan

Biochemistry Publications

Rapid sample processing and interpretation of estimated exposures will be critical for triaging exposed individuals after a major radiation incident. The dicentric chromosome (DC) assay assesses absorbed radiation using metaphase cells from blood. The Automated Dicentric Chromosome Identifier and Dose Estimator System (ADCI) identifies DCs and determines radiation doses. This study aimed to broaden accessibility and speed of this system, while protecting data and software integrity. ADCI Online is a secure web-streaming platform accessible worldwide from local servers. Cloud-based systems containing data and software are separated until they are linked for radiation exposure estimation. Dose estimates are identical to ADCI …

Likely Community Transmission Of Covid-19 Infections Between Neighboring, Persistent Hotspots In Ontario, Canada, Ben C. Shirley, Eliseos J. Mucaki, Peter Rogan

Biochemistry Publications

Introduction: This study aimed to produce community-level geo-spatial mapping of confirmed COVID-19 cases in Ontario Canada in near real-time to support decision-making. This was accomplished by area-to-area geostatistical analysis, space-time integration, and spatial interpolation of COVID-19 positive individuals.
Methods: COVID-19 cases and locations were curated for geostatistical analyses from March 2020 through June 2021, corresponding to the first, second, and third waves of infections. Daily cases were aggregated according to designated forward sortation area (FSA), and postal codes (PC) in municipal regions Hamilton, Kitchener/Waterloo, London, Ottawa, Toronto, and Windsor/Essex county. Hotspots were identified with area-to-area tests including Getis-Ord Gi*, Global …

Elucidating The Structural And Dynamical Properties Of The Intrinsically Disordered Protein Nrf2 Using Molecular Dynamics Simulations, Megan Nicole Chang

Electronic Thesis and Dissertation Repository

The nuclear factor erythroid 2-related factor 2 (Nrf2) protein is a critical transcription factor for activating the antioxidant response pathway, a primary defense mechanism against disproportionate levels of oxidants in the cell, via the upregulation of cytoprotective genes. Notably, aberrant activation of Nrf2 in cancer cells increases their resistance to chemotherapy, rendering the treatment ineffective. The focus was to uncover the conformational landscape of Nrf2’s Neh4 and Neh5 domains, which participate in crucial interactions for complete transcriptional activation. Since Nrf2 is an intrinsically disordered protein (IDP), molecular dynamics simulations were employed to capture its dynamic nature and conformational heterogeneity. The …

Investigating The Role Of Pkc And Its Mechanisms In Regulation Of Igf-I Bioavailability In Fetal Growth Restriction, Allan W. Chen

Electronic Thesis and Dissertation Repository

Fetal growth restriction (FGR) is associated with decreased nutrient availability and reduced insulin-like growth factor (IGF)-I bioavailability via increased IGF binding protein (IGFBP)-1 phosphorylation. While protein kinase C (PKC) is implicated in IGFBP-1 hyperphosphorylation in nutrient deprivation, the mechanisms remain unclear. I hypothesized that the interaction of PKCα with protein kinase CK2β and activation of PKCα under leucine deprivation (L0) mediate fetal hepatic IGFBP-1 hyperphosphorylation. Parallel Reaction Monitoring Mass Spectrometry (PRM-MS) followed by PKCα knockdown demonstrated the PKCα isoform interacts with IGFBP-1 and CK2β under L0. Pharmacological PKCα activation with phorbol 12-myristate 13-acetate (PMA) increased whereas inhibition with bisindolylmaleimide II …

The Study Of The Structure And Dynamics Of Parkin Activation, Elaine Aisha Freeman

Electronic Thesis and Dissertation Repository

Parkin is an RBR E3 ubiquitin ligase that has been implicated in both sporadic and familial Parkinson’s disease. Upon mitochondrial damage, parkin is activated step-wise to recruit and ligate ubiquitin to a substrate on the outer mitochondrial membrane. Disruption of this activation and ligation cascade is hypothesized to result in neuronal death related to Parkinson’s disease.

While structures of parkin for a number of these activation states exist, it is important to note they are not of full-length human parkin. These structures are often truncated and come from various non-human species to eliminate important, yet hard to quantify structural elements. …

Improved Radiation Expression Profiling In Blood By Sequential Application Of Sensitive And Specific Gene Signatures, Eliseos J. Mucaki, Ben C. Shirley, Peter K. Rogan

Biochemistry Publications

Purpose. Combinations of expressed genes can discriminate radiation-exposed from normal control blood samples by machine learning based signatures (with 8 to 20% misclassification rates). These signatures can quantify therapeutically-relevant as well as accidental radiation exposures. The prodromal symptoms of Acute Radiation Syndrome (ARS) overlap those present in Influenza and Dengue Fever infections. Surprisingly, these human radiation signatures misclassified gene expression profiles of virally infected samples as false positive exposures. The present study investigates these and other confounders, and then mitigates their impact on signature accuracy.

Methods. This study investigated recall by previous and novel radiation signatures independently derived …

Validation Of Arterial Spin Labeling For Longitudinal Monitoring And Differential Diagnosis Of Frontotemporal Dementia, Tracy Ssali

Electronic Thesis and Dissertation Repository

Frontotemporal dementia (FTD) is a devastating neurodegenerative disease characterized by a rapid decline in behavioural, language, and motor abilities. Advances in the understanding of FTD genetics and pathophysiology, and the subsequent development of novel disease modifying treatments have highlighted the need for tools to assess their efficacy. While structural magnetic resonance imaging (MRI) and functional imaging with ¹⁸F-flurodeoxyglucose (FDG) positron emission tomography (PET) are used for clinical diagnosis, structural changes are subtle at the early stages and PET imaging is expensive and access limited. Given the coupling of cerebral blood flow (CBF) to energy metabolism, an attractive alternative is …

Phase Imaging For Reducing Macrovascular Signal Contributions In High-Resolution Fmri, Olivia W. Stanley

Electronic Thesis and Dissertation Repository

High resolution functional MRI allows for the investigation of neural activity within the cortical sheet. One consideration in high resolution fMRI is the choice of which sequence to use during imaging, as all methods come with sensitivity and specificity tradeoffs. The most used fMRI sequence is gradient-echo echo planar imaging (GE-EPI) which has the highest sensitivity but is not specific to microvasculature. GE-EPI results in a signal with pial vessel bias which increases complexity of performing studies targeted at structures within the cortex. This work seeks to explore the use of MRI phase signal as a macrovascular filter to correct …

Exogenous Surfactant As A Delivery Vehicle For Intrapulmonary Therapeutics, Brandon J. Baer

Electronic Thesis and Dissertation Repository

As an organ system, the lung has unique advantages and disadvantages for direct drug delivery. Its contact with the external environment allows for the airways to be easily accessible to intrapulmonary delivery. However, its complex structure, which divides into more narrow airways with each branch, can make direct delivery to the remote alveoli challenging. The objective of this thesis was to overcome this issue by using exogenous surfactant, a lipoprotein complex used to treat neonatal respiratory distress syndrome, as a carrier for pulmonary therapeutics. It was hypothesized that therapeutics administered with a surfactant vehicle would display enhanced delivery to the …

Development Of 3d Bioartificial Human Tissue Models Of Periprosthetic Shoulder Joint Infection, Tony B. Huang

Electronic Thesis and Dissertation Repository

Periprosthetic joint infection (PJI) is a devastating and costly post-surgical complication that is not well understood due to the scarcity of physiologically representative experimental models. This thesis outlines the development of two 3D bioartificial human tissue models designed to study the cellular and biochemical interactions between primary fibroblasts from the shoulder capsule (SC) and infectious microorganisms. Using the Fibroblast-Bacteria Co-culture in 3D Collagen model, we demonstrated a global gene repression of metabolic and homeostatic processes in SC fibroblasts following 48 hours of co-culture with Cutibacterium acnes – the most common microbial cause of PJI in the shoulder. These cellular changes …

A Quantitative Assessment Of Hemodynamic And Histological Parameters In The Mdx Mouse Model, Sarah Hakim

Electronic Thesis and Dissertation Repository

Duchenne muscular dystrophy (DMD) is one of the most commonly inherited musculoskeletal disorders affecting 1 in 3500 boys worldwide. The disorder is due to a lack of functional dystrophin protein, which, in turn, results in a loss of cell membrane integrity in skeletal, cardiac muscle and the brain leading to changes in perfusion. As such, within DMD tissue, necrosis is commonly observed, and it has been previously hypothesized that this may be due to a reduction in regional blood supply. Here, we aim to measure hemodynamic changes during disease progression in DMD (Mdx/Utrn+/+) mice, using dynamic contrast enhanced …

Assessing Selective Plasmids For Bradyrhizobium Sp. Doa9 And Mesorhizobium Loti, Aiden J. Wilcox, Rebecca Meaney, Bogumil Karas

Undergraduate Student Research Internships Conference

No abstract provided.

Effect Of Carbon Monoxide Releasing Molecule 3 (Corm - 3) On Platelet Adhesion To Human Brain Microvascular Endothelial Cells, Najat S. El-Farra

Undergraduate Student Research Internships Conference

Sepsis is characterized by the widespread inflammation of the body. Systemic inflammation activates and recruits inflammatory cells (e.g., leukocytes) and platelets to the affected organs.

During these inflammatory conditions, human brain microvascular endothelial cells (hBMEC) and platelets both upregulate adhesive molecules rendering platelets to adhere to hBMEC.

Although carbon monoxide is thought of as a toxic molecule to many, previous work shows its anti-inflammatory properties. Evidence has shown carbon monoxide-releasing molecules (e.g., CORM-3; that release small, non-toxic amounts of CO) can combat the effects of severe inflammation in several in vivo animal model.

In this current study, we are looking …

Understanding The Role Of Rhamm In Tumor Load– Mediated Tumor Invasiveness Of Triple Negative Breast Cancer, Ashwin Sritharan, Britney Messam

Undergraduate Student Research Internships Conference

1.Compare the levels of proliferation between RHAMM+/+ and RHAMM -/- MDA-MB-231 spheroids as determined by ki67 and Caspase 3 signaling 2.Compare levels of RHAMM, CD44, Has2, and p-ERK activation between RHAMM+/+ and RHAMM -/- MDA-MB-231 spheroids

Fine-Scale Morphological Divergence Of Wing Trait Variables In Highly Fragmented Populations Of The Bog Copper Butterfly (Lycaena Epixanthe), Jessica L. T. Jeong

Undergraduate Student Research Internships Conference

Habitat fragmentation can adversely affect animal and plant species through subdividing their natural habitats into smaller, more isolated patches. Oftentimes, these isolated groups are subject to reduced dispersal and gene flow, leading to genetic divergence and, consequently, morphological divergence among populations. This study aims to quantify the morphological divergence of the bog copper butterfly, Lycaena epixanthe, between nine isolated bog sites in Algonquin Provincial Park, Ontario, via seven quantitative morphological traits in their wing pattern. Statistical analyses demonstrate significant differences in wing trait measurements between populations. As bog coppers are small, weak fliers with a strict host-plant dependency, it …

The Cofactor Specificity Of Nqo2, Shujun Dong

Undergraduate Student Research Internships Conference

NQO1 and NQO2 are closely related quinone reductases, which are FAD-linked enzymes that catalyze the 2-electron reduction of quinones. Whereas NQO1 has a well-defined role in cellular detoxification of quinones, NQO2’s function is less clear; it uses the conventional cofactors NADH/NADPH inefficiently compared to smaller nicotinamide cofactors, which are often present in low cellular amounts. This unique cofactor specificity suggests that NQO2 may have non-enzymatic functions, such as a role in intracellular signalling.

The goals of this research project include: 1) examining whether cofactor specificity is conserved in amniote NQO2 enzymes and 2) re-constructing ancient enzymes along the evolutionary pathway …

Investigating Stop Codon Readthrough In Saccharomyces Cerevisiae, Amy Kwon

Undergraduate Student Research Internships Conference

Stop codon readthrough occurs via genetic and epigenetic mechanisms, resulting in a longer polypeptide chain at the C-terminus. Although these readthroughs may seem like an error made by translational mechanisms, evidence from yeast suggests that stop codon readthrough has an impact on various cellular processes. Readthrough has the potential to create genetic diversity, similar to RNA splicing, mRNA editing, and protein modification. The diversity created by translational readthrough may result in a beneficial change in phenotype, and thus have a role in evolution and adaptability. Translational readthrough is observed in organisms such as yeast and E. coli but may also …

Synthesis Of Nucleotide Prodrugs As Potential Antiviral Agents, Mohammed Attaelmanan

Undergraduate Student Research Internships Conference

No abstract provided.

Investigating Dha Levels In Rat Brain Tissues In Relation To Maternal Thc Exposure Using Maldi-Ims, Aleksandra (Ola) Doktor

Undergraduate Student Research Internships Conference

This research focuses on investigating whether maternal exposure to THC (tetrahydrocannabinol) has an effect on lowering DHA (Docosahexaenoic Acid) levels in female and male offspring, and if an omega-3 rich diet, containing DHA, is able to recover DHA levels following a THC caused deficiency. To study this, DHA levels in rat brain tissues from 21-Day-Old offspring were compared across four different groups of maternal rats, vehicle rats with a controlled diet (veh/ct), vehicle rats with an omega-3 rich diet (veh/n3), THC treated rats with a controlled diet (thc/ct), and THC treated rats with an omega-3 rich diet (thc/n3) using MALDI-IMS …

Exploring Sensitivity And Resolution For Cell Tracking With Magnetic Particle Imaging: The Effects Of Cell Proliferation And Intracellular Nanoparticle Relaxation, Maryam A. Berih, Olivia C. Sehl, Paula J. Foster

Undergraduate Student Research Internships Conference

Magnetic particle imaging (MPI) is an emerging modality that directly detects SPIOs.our first aim is to quantify the dilution of SPIOs in breast cancer cells in vitro using MPI. MPI signal is generated from a combination of Néel (internal rotation of magnetization) and Brownian (physical rotation of nanoparticle) relaxation. Brownian relaxation of SPIO is influenced by the nanoparticle’s surroundings and we hypothesize this may have implications for detecting partially immobilized intracellular SPIOs. A second aim is to determine how MPI signal and resolution change when SPIOs are intracellular (live cells) compared to free SPIOs (lysed cells).

A reduction in MPI …

Characterizing The Structural, Biophysical And Functional Effects Of S-Glutathionylation On Stim1 Ca2+ Sensing, Christian Michael Sirko

Electronic Thesis and Dissertation Repository

Stromal interaction molecule 1 (STIM1) is an endo/sarcoplasmic reticulum (ER/SR) calcium (Ca²⁺) sensing protein that initiates cytoplasmic Ca²⁺ influx via store-operated calcium entry (SOCE). STIM1, in conjunction with Orai, a plasma membrane (PM) protein, function as mediators of SOCE through the formation of calcium-release activated calcium (CRAC) channels. S-Glutathionylation of STIM1 at Cys56 has been shown to evoke constitutive Ca²⁺ entry in DT40 cells, however no studies have carefully investigated the biophysical and structural effects of this covalent modification to the luminal domain, which are critical for understanding the molecular mechanism underlying the regulation of …

The Regulation Of Pannexin1 And Pannexin2 In The Skin In Health And Disease, Rafael E. Sanchez Pupo

Electronic Thesis and Dissertation Repository

Pannexins (PANX1, 2, 3) are a family of channel-forming glycoproteins that mediate intracellular and paracrine signaling. In contrast to PANX2, PANX1 has been extensively investigated in the skin, modulating cell differentiation, wound healing, and melanoma development. PANX1 and PANX2 can co-exist in the same cell and form mixed channels where their glycosylation seems to regulate their intermixing. N-glycosylation and caspase cleavage have been proposed as modulators of the function of PANX1, but their effects on PANX2 are unknown. We explored the PANX2 expression in mouse skin and showed that a Panx2 splice variant (PANX2-202) is continuously expressed throughout aging skin. …

Mapping Ku70 Protein Interactions Using Proximity-Dependent Biotin Identification, Sanna Abbasi

Electronic Thesis and Dissertation Repository

The Ku heterodimer, composed of subunits Ku70 and Ku80, is a highly abundant protein complex, known for its affinity for double-stranded DNA ends. Accordingly, Ku is most well-studied for repairing double-stranded DNA breaks through the non-homologous end-joining (NHEJ) DNA repair pathway. Aside from NHEJ, Ku has also been implicated and studied in various other cellular processes including V(D)J recombination and telomere maintenance.

Numerous protein interactions have been mapped to the C-terminal region of Ku70, although few have been mapped to its N-terminal von Willebrand A-like (vWA) domain. Here, we used the high-throughput proteomic technique, proximity-dependent biotin identification (BioID, BioID2) to …