145 research outputs found
International year of older persons: Mentoring research project
No full textA report, by Judith MacCallum and Susan Beltman, Murdoch University, that identifies models of good practice of mentoring in school settings. The report looks at issues associated with the implementation of mentoring programs in school settings and key recommendations for consideration by Australian schools and education systems
Design and Synthesis of a New Family of Amphiphilic beta-Cyclodextrin Liquid Crystals.
No full textThe field of liquid crystals has fascinated scientists since 1888 when a molecule of cholesteryl benzoate exhibited two different melting points. It corresponds to a state of matter between the isotropic liquid and the crystalline solid-state. Since then, the field has grown, and liquid crystal-based materials have become an important component of our lives. Cyclodextrin (CD) are polyhydroxylated macrocycles containing 6-8 units of beta-D-glucopyranose units linked together via a series of alpha-1,4-glycosidic linkages. The formed macrocycles are shaped like a truncated cone that combines two hydrophilic surfaces and a hydrophobic cavity that can be used to form inclusion complexes with different organic molecules. Our group has been developing chemistries to modify the two hydrophilic surfaces of CDs by a variety of chemical methodologies to generate amphiphilic molecules capable of self-assembling into liquid crystalline mesophases. This thesis focuses on the synthesis a new family of amphiphilic CDs for liquid crystal research. These CD-derivatives can be easily obtained via polyesterification at one of the hydrophilic faces with hydrophobic aliphatic chains and installation of functionalized oligoethylene glycols at the other surface via the copper(I)-catalyzed Huigsen 1,3-dipolar cycloaddition. These novel amphiphilic CD derivatives have been characterized by polarized optical microscopy, thermogravimetric analysis and differential scanning calorimetry
Computer Simulation of Biomolecular Systems of Interest in Bionanotechnology
No full textBiomolecules, including lipids and enzymes, are of special interest in biotechnology and nano-medicine applications. A knowledge of structure, dynamics, and function of these biomolecular systems is required for development and improvement of drugs and drug delivery systems. Computer simulation, as a complementary technique to experiments, could assist in such an understanding by providing atomistic details on the molecular systems. In this thesis, molecular dynamics (MD) simulation technique was used to study three molecular systems of interest in biotechnological applications: 1) Lamellar phases composed of zwitterionic and ionizable cationic lipids, 2) inverted hexagonal (HII) phases composed of cone-shaped lipids, and 3) a membrane enzyme called CTP:phosphocholine cytidylyltransferase (CCT). First, lipid bilayers composed of POPC and DLin-KC2-DMA (also known as KC2) ionizable cationic lipids were studied as a function of pH, temperature, and mixing ratio. Simulations suggest that neutral KC2 are segregated in the presence of POPC. This segregation was proposed to affect both the internal structure and drug release efficacy of lipid nanoparticles containing KC2. Next, DOPE and POPE HII phases were constructed, simulated, and their structural properties as a function of hydration level and temperature were studied using MD simulations. HII systems are usually challenging to study experimentally, especially at low hydration regimes. Our findings suggest that MD simulation could successfully reproduce structural properties of HII phase in a good agreement with experimental data. Furthermore, a computational protocol for construction of HII molecular systems equivalent to the corresponding HII systems in experiments was proposed. Finally, the auto-inhibition and activation mechanism of CCT enzyme upon attachment or detachment of two autoinhibitory helices was studied. Attachment of autoinhibitory helices were shown to affect the dynamics and consequently the catalytic function of the CCT enzyme. Accordingly, a novel two-part autoinhibition mechanism for CCT enzyme was proposed
Rheometric Properties of Liquid Elemental Sulfur and the Modifying Effects of Hydrogen Sulfide
No full textTransportation and handling of molten sulfur is inherently complex due to the unique rheological behavior of sulfur at differing temperatures. Upon melting at 115 °C, sulfur's viscosity remains close to 10 × 10-3 Pa∙s until reaching T > 160 °C, the λ-transition region, where the viscosity dramatically increases to a maximum of ca. 93000 × 10-3 Pa∙s at 187 °C. This research reports and examines the modifying effects of hydrogen sulfide (H2S) within liquid sulfur due to its relevance and association within prominent industrial processes, e.g., Claus sulfur recovery or sulfuric acid production. Using the experimental data from this study, a semi-empirical correlation model was produced based on the reptation model of Cates to estimate the impact of H2S on liquid sulfur’s viscosity as a function of temperature. The correlation model yields a final fit value of R2 = 0.9983. Also within this work, previous studies on the non-Newtonian rheometric properties of liquid elemental sulfur are revisited and discussed. Past misinterpretation of apparent behavior is attributed to instrumental artifacts. Additionally, this research examines experimental evidence for the relaxation behavior of liquid sulfur through the use of oscillation-based measurement
Gout Biosensor: Towards the development of a peptide-based diagnostic for crystal arthropathies and Amplifying Graduate Student Perspectives on Supervision and Satisfaction at the University of Calgary
No full textThis thesis primarily investigates the use of fluorescently labelled crystal-targeting peptides to develop a gout biosensor to improve the diagnostics of crystal arthropathies. Additionally, Chapter 7 examines survey responses from a secondary research project exploring graduate student experiences related to supervision and satisfaction within NSERC disciplines at the University of Calgary. With the growing prevalence of gout, there is an increasing need for accurate, cost-effective, and automated diagnostic methods to distinguish between monosodium urate (MSU) crystals, which cause gout, and calcium pyrophosphate dihydrate (CPPD) crystals, responsible for pseudogout. The current gold-standard diagnostic approach, compensated polarized light microscopy, is limited by its dependence on operator skill and lack of automation. To address these challenges, the study employed a multifaceted strategy involving phage display, peptide synthesis, microscopy, flow cytometry, and computational modelling to identify peptides capable of differentiating between MSU and CPPD crystals. Initial phage display efforts were hindered by high background binding of the phage, leading to the unexpected discovery of an interaction between MSU crystals and the major coat protein of the bacteriophage. This finding laid the groundwork for enhancing peptide binding to MSU crystals. While the identified peptides demonstrated strong binding to MSU crystals, specificity remained a challenge due to similar binding observed with CPPD crystals. An Alizarin Red S counterstain was introduced to improve differentiation, distinguishing CPPD crystals without affecting MSU crystals in microscopy studies. However, when flow cytometry was explored as a high-throughput tool, we encountered challenges with dye compatibility. Although 84% accuracy was achieved in classifying individual crystals through logistic regression of peptide-bound crystal data, issues with dye stability and clinical sample complexity indicate further refinement is needed before clinical implementation. The second project focused on graduate students' supervisory and program experiences in NSERC disciplines at the University of Calgary. Data from the 2022 and 2023 Graduate Student Experience Surveys indicated overall satisfaction with supervisory support and communication but highlighted ongoing issues with inadequate funding and mental health challenges despite available institutional resources. These findings highlight areas where enhanced supervisor support and training could better meet evolving student needs
Synthesis and Biological Evaluation of Heterobifunctional Small Molecules for Proteasome-Mediated Protein Degradation of Myeloid Cell Leukemia 1 (MCL1)
No full textProtein–protein interactions (PPIs) have emerged as significant targets for therapeutic development, owing to their critical nature in diverse biological processes. However, these kinds of protein interactions are difficult to perturb using traditional medicinal chemistry strategies. This has given rise to the development of a new method of addressing disease related proteins known as targeted protein degradation (TPD). TPD employs heterobifunctional small molecules which are capable of recruiting the cell’s natural recycling machinery, the ubiquitin proteasome system (UPS), and inducing proximity between this natural degradation machinery and a protein of interest (POI) to promote proteasomal degradation of the protein into its amino acid subunits. An ideal PPI-based target is the anti-apoptotic protein myeloid cell leukemia 1 (MCL1), a critical prosurvival factor in cancers such as multiple myeloma (MM) where MCL1 levels directly correlate to disease progression. Current strategies for halting the antiapoptotic properties of MCL1 revolve around inhibiting its sequestration of proapoptotic factors. Existing inhibitors disrupt endogenous regulatory proteins; however, this strategy leads to an increase of MCL1 protein expression, a detrimental effect for several diseases. MCL1 has also been a challenging biological target to inhibit due to the prolific on-target cardiotoxicity associated with global MCL1 inhibition or knockdown.This work showcases the development of the first in class heterobifunctional small molecules capable of selectively targeting MCL1 through TPD methodology, leading to successful degradation. A synthesis program was embarked upon where chemical probes and cellular assay-guided structure activity relationship (SAR) studies motivated the optimization of these degrader compounds. We have confirmed the involvement of the E3 ubiquitin ligase CUL4A–DDB1 cereblon (CRBN) ubiquitination pathway through rigorous UPS checkpoint validation, making these MCL1 degraders a first step toward a new class of antiapoptotic B-cell lymphoma 2 (BCL2) family protein degraders
Investigating Direct Heteroarylation Reactivity in the Synthesis of π-Conjugated Materials for use in Organic Solar Cells
No full textThis thesis is focused on applying direct heteroarylation as an efficient synthetic route to access new π-conjugated molecular materials for use in organic solar cells. Chapter one introduces π-conjugated materials, organic solar cells, and design considerations in the development of sustainable and efficient methods towards accessing high-performance materials. Chapter two introduces a novel π-conjugated building block, indoloquinoxaline, which is available from inexpensive starting materials and can be accessed from a modular and high yielding synthesis. Its materials’ properties are investigated through its incorporation as a terminal unit in three different molecular constructs (1-3) using Stille couplings and the more economical direct heteroarylation coupling. Building directly from this work, chapter three focuses on the use of the indoloquinoxaline building block and its fluorinated derivative to access a series of π-extended squaraine dyes (4-7) via Sonogashira and direct heteroarylation couplings expanding the substrate scope of the latter more versatile and atom-economical cross-coupling. Chapter four applies the synthetic methods developed in chapters two and three and extends these principles to the design and synthesis of an asymmetric π-conjugated molecular structure combining the organic dyes, perylene diimide, diketopyrrolopyrrole, and indoloquinoxaline in a linear fashion via direct heteroarylation (8). The asymmetric compound 8 is exploited for its low energy absorption as a non-fullerene acceptor in organic solar devices. Adapting the synthetic protocols from chapter four, chapter five explores the incorporation and effect of a rylene building block new to organic electronics, N-(alkyl)benzothioxanthene- 3,4-dicarboximide (BTXI), on materials properties in order to learn more about its potential use in organic electronic applications (9-11). The three molecular semiconductors (9-11) are compared and evaluated in organic thin-film transistors and organic solar cells. Chapter six concludes this thesis detailing unprecedented direct heteroarylation reactivity which is uncovered and exploited in order to access a novel tetrameric perylene diimide (12) non-fullerene acceptor for organic solar cell applications
Design, Synthesis and Evaluation of Novel Pannexin 1 Channel Modulators
No full textPannexin 1 (Panx1) channels are transmembrane proteins that release ATP and play an important role in intercellular communication. They are widely expressed in somatic and nervous system tissues, and their activity has been associated with many pathologies including stroke, epilepsy, addiction, inflammation and chronic pain. While there are a variety of known Panx1 inhibitors, there is a dearth of sufficiently potent and selective drugs targeting Panx1, and relatively little is known about the mechanism of channel inhibition. Structure-activity relationship (SAR) studies can provide information about the critical functional groups controlling substrate activity and lead to the development of more potent inhibitors. This thesis outlines the importance of Panx1 channels as a potential therapeutic target and describes the synthesis, SAR and evaluation of novel inhibitors based on biological assays. In silico modeling was also used to identify compounds from the ZINC database with similar pharmacophore characteristics to known Panx1 inhibitors. The compounds developed over the course of study may have potential as novel drugs for the relief of multiple important pathologies. Provisional patent protection for this work is currently being pursued
Elucidating the Interplay Between Lipids and Membrane Proteins Using Multiscale Computer Simulations
No full textBiological membranes are complex cellular structures formed by a large number of different lipid types, that also contain a variety of bound proteins, carbohydrates, and other molecules. The detailed orchestration of all these elements has been a major focus of scientific research during the last 5 decades. Computer-based methods, such as molecular dynamics (MD) simulations, have proven to be a valuable approach in addressing many of the details of lipid organization and membrane protein activity. I used MD simulations at both atomistic and coarse-grained level of detail to study the number of way lipids and proteins interact and their possible functional ramifications. In part of my work, I studied the interaction of G Protein-Coupled Receptors (GPCRs) with lipids at a family-wide level. Plenty of other computational studies had shown specific lipid-protein interactions for a handful of GPCRs but with quite different outcomes on their number, location, and lipid identity. In my work, I simulated 28 different GPCR structures and showed that they are distinguished by a unique interaction profile with membrane lipids. I provided a comprehensive analysis of simulation results with available crystallographic data. I also studied the lipid-protein interaction profile of AMPA receptors and cyclooxygenases (mainly COX-1), showing that they both form specific interactions with lipids, but do so in a quite different fashion. AMPA receptors interact specifically with diacylglycerol lipids, whereas COX-1 enzymes do so indiscriminately with glycerophospholipids, cholesterol, and fatty acids, but at different levels of interaction strength. Using atomistic simulations, we show the binding pathway of arachidonic acid to COX-1 and identify a series of arginine residues that guide it toward the hydrophobic cavity of the enzyme. As part of my work, I also developed a webserver that automates the analysis and visualization of lipid-protein interactions from MD simulations allowing for the creation of automated pipelines to study lipid-protein interactions in the future. Lastly, I provide a short review of some of the main challenges facing the field along with possible solutions going forward. My work expands our understanding of lipid-protein interactions
Advancing Techniques of Structural Mass Spectrometry for Integrative Structural Modelling
No full textProteins are the fundamental functional units underlying all cellular activities. Protein function emerges from structure. To understand cellular activity and the diseases that arise from protein dysfunction we require knowledge of protein structure and structural dynamics. The toolbox offered by mass spectrometry (MS) allows a wide range of perspectives on protein structure, enabled by the application of chemical reagents that can encode structural properties. Improvements in the performance of labelling chemistries in turn can enhance the data returned and the structural models that are ultimately produced. Photogenerated carbenes are one such high-performance chemistry that offer unbiased sampling of protein structure at timescales relevant to protein dynamics. On the other hand, no single method can offer the breadth of data necessary to produce a comprehensive model of protein structure and dynamics—protein systems span broad spatial and temporal scales that exceed the scope of any single technique. To resolve large and complex protein systems, the integration of multiple data sets from orthogonal techniques is necessary. Here, I evaluate and advance structural MS methods with the goal of improving the accuracy and precision of structural models produced by MS-driven integrative structural modelling. Of particular interest is the application of carbene-based crosslinking and covalent labelling reagents which are shown to produce data with greater sequence coverage and improved accuracy in representing the equilibrated conformational state. Novel analytical software routines are developed to overcome the complications that arise from the labelling of proteins with a non-specific chemistry such as ambiguity in localizing modifications. Structural models are produced with integrative modelling workflows, including the development of a novel modelling restraint based on crosslinking and hydrogen/deuterium exchange data. MS-driven integrative modelling is demonstrated on multiple systems, including large complexes and systems with substantial disorder
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