Chemistry, Department of

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Mouse Organ-Specific Proteins and Functions

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2021-12-08
Abstract: 

Organ-specific proteins (OSPs) possess great medical potential both in clinics and in biomedical research. Applications of them—such as alanine transaminase, aspartate transaminase, and troponins—in clinics have raised certain concerns of their organ specificity. The dynamics and diversity of protein expression in heterogeneous human populations are well known, yet their effects on OSPs are less addressed. Here, we used mice as a model and implemented a breadth study to examine the panorgan proteome for potential variations in organ specificity in different genetic backgrounds. Using reasonable resources, we generated panorgan proteomes of four in-bred mouse strains. The results revealed a large diversity that was more profound among OSPs than among proteomes overall. We defined a robustness score to quantify such variation and derived three sets of OSPs with different stringencies. In the meantime, we found that the enriched biological functions of OSPs are also organ-specific and are sensitive and useful to assess the quality of OSPs. We hope our breadth study can open doors to explore the molecular diversity and dynamics of organ specificity at the protein level. 

Document type: 
Article
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General Chemistry Education in a Pandemic

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2021-07-12
Abstract: 

With the start of the Covid-19 pandemic and the decision to close post-secondary schools to in-person teaching, an opportunity was presented to examine the challenges, benefits and ability to pivot to an online teaching environment, both from the student and instructor perspectives. In the Summer 2020 semester at Simon Fraser University, Chemistry 121 (General Chemistry and Laboratory I) ran for the first time as an online course. In this paper, we will explore the experience of developing and running the course.

Document type: 
Article
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Maximizing Student Learning Through the Use of Demonstrations

Author: 
Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2021-09-16
Abstract: 

As society becomes more technologically complex, post-secondary institutions have responded by incorporating science-based courses in the non-science curriculum. As chemist, we are often called upon to teach these courses and explain complex concepts to learners with limited science background. An effective method to engage students with the material is using demonstrations. In this study, we examine the use of science-based demonstration in our third-year science course for non-science students.

Document type: 
Article

Enabling a High-Throughput Characterization of Microscale Interfaces within Coated Cathode Particles

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2021-09-10
Abstract: 

Lithium ion batteries represent an emerging field. The development of battery materials could benefit from quick techniques that enable atomic-level diagnostics. High performance cathodes, such as high-voltage spinel, often require coatings to protect against the destructive electrochemical environments at the particle-to-electrolyte interface. The preparations of these coating are still in the early phases of development, and their analytical inspection by high resolution scanning and transmission electron microscopy (HR-S/TEM) techniques presents a significant challenge due to the microscale dimensions of cathode particles. In this work, a high throughput ultramicrotome technique was assessed for the characterization of the particle to coating interface. The ultramicrotome technique enabled the rapid preparation of cross-sections with a thickness of 126 ± 66 nm as determined by electron energy loss spectroscopy (EELS) measurements. Cathode particles composed of high-voltage spinel, LiNi0.5Mn1.5O4 (LNMO), coated with lithium niobate (LiNbO3) were synthesized and cross-sections were inspected using HR-S/TEM techniques. These ultra-thin cross-sections enabled the ability to obtain nanoscale information regarding the composition and crystallinity of the particle-to-coating interface over lateral areas of >1 µm. Accessible correlations between the electrochemical performance of the LiNbO3 coated LNMO particles and the HR-S/TEM results were enabled by the high-throughput method. Discharge capacity measurements were acquired over a series of 100 electrochemical cycles for both the LiNbO3 coated and the as-prepared LNMO particles. The limitations of the ultramicrotome technique are also discussed herein with respect to the coating morphology and the procedure for guidance toward technique optimization. The rapid preparation of ultra-thin cross-sections can assist the advancement of protective coatings on the surfaces of cathode particles for an efficient characterization of bulk-to-surface interfaces.

Document type: 
Article

Contact Transfer of Engineered Nanomaterials in the Workplace

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2021-08-18
Abstract: 

This study investigates the potential spread of cadmium selenide quantum dots in laboratory environments through contact of gloves with simulated dry spills on laboratory countertops. Secondary transfer of quantum dots from the contaminated gloves to other substrates was initiated by contact of the gloves with different materials found in the laboratory. Transfer of quantum dots to these substrates was qualitatively evaluated by inspection under ultraviolet illumination. This secondary contact resulted in the delivery of quantum dots to all the evaluated substrates. The amount of quantum dots transferred was quantified by elemental analysis. The residue containing quantum dots picked up by the glove was transferred to at least seven additional sections of the pristine substrate through a series of sequential contacts. These results demonstrate the potential for contact transfer as a pathway for spreading nanomaterials throughout the workplace, and that 7-day-old dried spills are susceptible to the propagation of nanomaterials by contact transfer. As research and commercialization of engineered nanomaterials increase worldwide, it is necessary to establish safe practices to protect workers from the potential for chronic exposure to potentially hazardous materials. Similar experimental procedures to those described herein can be adopted by industries or regulatory agencies to guide the development of their nanomaterial safety programmes.

Document type: 
Article
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Tuning the Surface Chemistry of Second-Harmonic-Active Lithium Niobate Nanoprobes Using a Silanol–Alcohol Condensation Reaction

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2021-06-15
Abstract: 

The surface functionalization of nanoparticles (NPs) is of a great interest for improving the use of NPs in, for example, therapeutic and diagnostic applications. The conjugation of specific molecules with NPs through the formation of covalent linkages is often sought to provide a high degree of colloidal stability and biocompatibility, as well as to provide functional groups for further bioconjugation. Nanoparticles of lithium niobate (LiNbO3) have been explored for use in second harmonic generation (SHG) based bioimaging, expanding the applications of SHG based microscopy techniques. The efficient use of SHG active LiNbO3 NPs as probes will, however, require the functionalization of their surfaces with molecular reagents such as polyethylene glycol and fluorescent molecules to enhance their colloidal and chemical stability, and to enable a correlative imaging platform. Herein, we demonstrate the surface functionalization of LiNbO3 NPs through the covalent attachment of alcohol-based reagents through a silanol-alcohol condensation reaction. Alcohol-based reagents are widely available and can have a range of terminal functional groups such as carboxylic acids, amines, and aldehydes. Attaching these molecules to NPs through the silanol-alcohol condensation reaction could diversify the reagents available to modify NPs, but this reaction pathway must first be established as a viable route to modifying NPs. This study focuses on the attachment of a linear alcohol functionalized with carboxylic acid and its use as a reactive group to further tune the surface chemistry of LiNbO3 NPs. These carboxylic acid groups were reacted to covalently attach other molecules to the NPs using copper-free click chemistry. This derivatization of the NPs provided a means to covalently attach polyethylene glycols and fluorescent probes to the NPs, reducing NP aggregation and enabling multimodal tracking of SHG nanoprobes, respectively. This extension of the silanol-alcohol condensation reaction to functionalizing the surfaces of LiNbO3 NPs can be extended to other types of nanoprobes for use in bioimaging, biosensing, and photodynamic therapies.

Document type: 
Article

Tandem Bioorthogonal Labeling Uncovers Endogenous Cotranslationally O-GlcNAc Modified Nascent Proteins

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2020-09-01
Abstract: 

Hundreds of nuclear, cytoplasmic, and mitochondrial proteins within multicellular eukaryotes have hydroxyl groups of specific serine and threonine residues modified by the monosaccharide N-acetylglucosamine (GlcNAc). This modification, known as O-GlcNAc, has emerged as a central regulator of both cell physiology and human health. A key emerging function of O-GlcNAc appears to be to regulate cellular protein homeostasis. We previously showed, using overexpressed model proteins, that O-GlcNAc modification can occur cotranslationally and that this process prevents premature degradation of such nascent polypeptide chains. Here, we use tandem metabolic engineering strategies to label endogenously occurring nascent polypeptide chains within cells using O-propargyl-puromycin (OPP) and target the specific subset of nascent chains that are cotranslationally glycosylated with O-GlcNAc by metabolic saccharide engineering using tetra-O-acetyl-2-N-azidoacetyl-2-deoxy-d-galactopyranose (Ac4GalNAz). Using various combinations of sequential chemoselective ligation strategies, we go on to tag these analytes with a series of labels, allowing us to define conditions that enable their robust labeling. Two-step enrichment of these glycosylated nascent chains, combined with shotgun proteomics, allows us to identify a set of endogenous cotranslationally O-GlcNAc modified proteins. Using alternative targeted methods, we examine three of these identified proteins and further validate their cotranslational O-GlcNAcylation. These findings detail strategies to enable isolation and identification of extremely low abundance endogenous analytes present within complex protein mixtures. Moreover, this work opens the way to studies directed at understanding the roles of O-GlcNAc and other cotranslational protein modifications and should stimulate an improved understanding of the role of O-GlcNAc in cytoplasmic protein quality control and proteostasis.

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Article
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4-Phenylnaphtho[2,3-c]furan-1(3H)-one, 9-Phenylnaphtho[2,3-c]furan-1(3H)-one and 3a,4-Dihydro-9-phenylnaphtho[2,3-c]furan-1(3H)-one Crystal Structures

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2021-07-23
Abstract: 

The crystal structures are reported for two unsubstituted arylnaphthalene lactones, 4-phenylnaphtho[2,3-c]furan-1(3H)-one (2), 9-phenylnaphtho[2,3-c]furan-1(3H)-one (3) and a non-aromatic dihydro arylnaphthene lactone, 3a,4-dihydro-9-phenylnaphtho[2,3-c]furan-1(3H)-one (5). There are only minor differences in the geometrical parameters of these structures. However, in certain cases, both isomers of arylnaphthalene lactones (termed Type I and Type II) were found in the same asymmetric unit cell.

Document type: 
Article
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Metabolism of Vertebrate Amino Sugars with N-Glycolyl Groups: INTRACELLULAR β-O-LINKED N-GLYCOLYLGLUCOSAMINE (GlcNGc), UDP-GlcNGc, AND THE BIOCHEMICAL AND STRUCTURAL RATIONALE FOR THE SUBSTRATE TOLERANCE OF β-O-LINKED β-N-ACETYLGLUCOSAMINIDASE

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2012-08-17
Abstract: 

TheO-GlcNAcmodificationinvolvestheattachmentofsingle-O-linkedN-acetylglucosamine residues to serine and threo-nine residues of nucleocytoplasmic proteins. Interestingly, pre-vious biochemical and structural studies have shown thatO-GlcNAcase (OGA), the enzyme that removesO-GlcNAc fromproteins, has an active site pocket that tolerates variousN-acylgroups in addition to theN-acetyl group of GlcNAc. Theremarkable sequence and structural conservation of residuescomprising this pocket suggest functional importance. Wehypothesized this pocket enables processing of metabolic vari-ants ofO-GlcNAc that could be formed due to inaccuracy withinthe metabolic machinery of the hexosamine biosynthetic path-way. In the accompanying paper (Bergfeld, A. K., Pearce, O. M.,Diaz, S. L.,Pham, T., and Varki, A. (2012)J. Biol. Chem.287,28865–28881),N-glycolylglucosamine (GlcNGc) wasshown to be acatabolite of NeuNGc. Here, we show that the hexosamine sal-vage pathway can convert GlcNGc to UDP-GlcNGc, which isthen used to modify proteins withO-GlcNGc. The kinetics of incorporation and removal ofO-GlcNGc in cells occur in adynamic manner on a time frame similar to that ofO-GlcNAc.Enzymatic activity ofO-GlcNAcase (OGA) toward a GlcNGcglycoside reveals OGA can process glycolyl-containing sub-strates fairly efficiently. A bacterial homolog (BtGH84) of OGA,from a human gut symbiont, also processesO-GlcNGc sub-strates, and the structure of this enzyme bound to a GlcNGc-derived species reveals the molecular basis for tolerance andbinding of GlcNGc. Together, these results demonstrate thatanalogs of GlcNAc, such as GlcNGc, are metabolically viablespecies and that the conserved active site pocket of OGA likelyevolved to enable processing of mis-incorporated analogs ofO-GlcNAc and thereby prevent their accumulation. Such plas-ticity in carbohydrate processing enzymes may be a generalfeature arising from inaccuracy in hexosamine metabolicpathways.

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Article
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Insights into O-Linked N-Acetylglucosamine ([0-9]O-GlcNAc) Processing and Dynamics through Kinetic Analysis of O-GlcNAc Transferase and O-GlcNAcase Activity on Protein Substrates*

Peer reviewed: 
Yes, item is peer reviewed.
Date created: 
2012-05-01
Abstract: 

Cellular O-linked N-acetylglucosamine (O-GlcNAc) levels are modulated by two enzymes: uridine diphosphate-N-acetyl-D-glucosamine:polypeptidyltransferase (OGT) and O-GlcNAcase (OGA). To quantitatively address the activity of these enzymes on protein substrates, we generated five structurally diverse proteins in both unmodified and O-GlcNAc-modified states. We found a remarkably invariant upper limit for k(cat)/K(m) values for human OGA (hOGA)-catalyzed processing of these modified proteins, which suggests that hOGA processing is driven by the GlcNAc moiety and is independent of the protein. Human OGT (hOGT) activity ranged more widely, by up to 15-fold, suggesting that hOGT is the senior partner in fine tuning protein O-GlcNAc levels. This was supported by the observation that K(m,app) values for UDP-GlcNAc varied considerably (from 1 μM to over 20 μM), depending on the protein substrate, suggesting that some OGT substrates will be nutrient-responsive, whereas others are constitutively modified. The ratios of k(cat)/K(m) values obtained from hOGT and hOGA kinetic studies enable a prediction of the dynamic equilibrium position of O-GlcNAc levels that can be recapitulated in vitro and suggest the relative O-GlcNAc stoichiometries of target proteins in the absence of other factors. We show that changes in the specific activities of hOGT and hOGA measured in vitro on calcium/calmodulin-dependent kinase IV (CaMKIV) and its pseudophosphorylated form can account for previously reported changes in CaMKIV O-GlcNAc levels observed in cells. These studies provide kinetic evidence for the interplay between O-GlcNAc and phosphorylation on proteins and indicate that these effects can be mediated by changes in hOGT and hOGA kinetic activity.

Document type: 
Article
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Supervisor(s): 
Canadian Institutes of Health Research (CIHR)
Natural Sciences and Engineering Research Council of Canada (NSERC)