Papers by Christopher Yip
1.Pancreatic islets respond metabolically to glucose by closing KATP channels resulting in Ca2+-i... more 1.Pancreatic islets respond metabolically to glucose by closing KATP channels resulting in Ca2+-influx and insulin secretion. Previous work showed that the importance of glycolytic flux in triggering insulin secretion. However, it is unclear whether the triggered (‘first phase’) secretion is further amplified by Ca2+-stimulation of mitochondrial NADH production and/or oxidative phosphorylation (OxPhos). To tease apart the metabolism of first phase glucose-stimulated insulin secretion, we designed an islet-on-a-chip microfluidic device to simultaneously measure O2-consumption rate (OCR) and Ca2+-activity of individual islets with high temporal resolution. We used finite element analysis to optimize the placement of sensor in optically clear microwells on a thin glass coverslip. The microfluidic channels were subsequently fabricated using O2-impermeable plastic to limit outside-in diffusion and push islets in the device against the microsensor. We validated our device using living mou...
Biochemical Pharmacology, 2021
Clostridioides difficile infections (CDI) are the leading cause of nosocomial antibiotic-associat... more Clostridioides difficile infections (CDI) are the leading cause of nosocomial antibiotic-associated diarrhea. C. difficile produces dormant spores that serve as infectious agents. Bile salts in the gastrointestinal tract signal spores to germinate into toxin-producing cells. As spore germination is required for CDI onset, anti-germination compounds may serve as prophylactics. CamSA, a synthetic bile salt, was previously shown to inhibit C. difficile spore germination in vitro and in vivo. Unexpectedly, a single dose of CamSA was sufficient to offer multi-day protection from CDI in mice without any observable toxicity. To study this intriguing protection pattern, we examined the pharmacokinetic parameters of CamSA. CamSA was stable to the gut of antibiotic-treated mice but was extensively degraded by the microbiota of non-antibiotic-treated animals. Our data also suggest that CamSA's systemic absorption is minimal since it is retained primarily in the intestinal lumen and liver. CamSA shows weak interactions with CYP3A4, a P450 hepatic isozyme involved in drug metabolism and bile salt modification. Like other bile salts, CamSA seems to undergo enterohepatic circulation. We hypothesize that the cycling of CamSA between the liver and intestines serves as a slow-release mechanism that allows CamSA to be retained in the gastrointestinal tract for days. This model explains how a single CamSA dose can prevent murine CDI even though spores are present in the animal's intestine for up to four days post-challenge.
Microscopy Research and Technique, 2021
BioRXiv-non-peer reviewed preprint ABSTRACT. Fluorescence standards allow for quality control and... more BioRXiv-non-peer reviewed preprint ABSTRACT. Fluorescence standards allow for quality control and for the comparison of data sets across instruments and laboratories in applications of quantitative fluorescence. For example, users of microscopy core facilities expect a homogenous and time-invariant illumination and a uniform detection sensitivity, which are prerequisites for quantitative imaging analysis, particle tracking or fluorometric pH or Ca 2+-concentration measurements. Similarly, confirming the three-dimensional (3-D) resolution of optical sectioning microscopes prior to volumetric reconstructions calls for a regular calibration with a standardised point source. Typically, the test samples required for such calibration measurements are different ones, and they depend much on the very microscope technique used. Also, the ever-increasing choice among these techniques increases the demand for comparison and metrology across instruments. Here, we advocate and demonstrate the multiple uses of a surprisingly versatile and simple 3-D test sample that can complement existing and much more expensive calibration samples: simple commercial tissue paper labelled with a fluorescent highlighter pen. We provide relevant sample characteristics and show examples ranging from the sub-µm to cm scale, acquired on epifluorescence, confocal, image scanning, two-photon (2P) and light-sheet microscopes.
mBio, 2021
Entamoeba histolytica is a leading parasitic cause of death in developing countries, and our effo... more Entamoeba histolytica is a leading parasitic cause of death in developing countries, and our efforts are focused on defining the molecular basis of RNA interference (RNAi) gene regulation in this parasite. The Entamoeba RNAi pathway effectively silences a subset of endogenous genes and has also been harnessed as a gene silencing tool to study gene function in this organism.
Journal of medicinal chemistry, Jan 9, 2018
Clostridium difficile infections (CDI), particularly those caused by the BI/NAP1/027 epidemic str... more Clostridium difficile infections (CDI), particularly those caused by the BI/NAP1/027 epidemic strains, are challenging to treat. One method to address this disease is to prevent the development of CDI by inhibiting the germination of C. difficile spores. Previous studies have identified cholic amide m-sulfonic acid, CamSA, as an inhibitor of spore germination. However, CamSA is inactive against the hypervirulent strain R20291. To circumvent this problem, a series of cholic acid amides were synthesized and tested against R20291. The best compound in the series was the simple phenyl amide analogue which possessed an IC value of 1.8 μM, more than 225 times as potent as the natural germination inhibitor, chenodeoxycholate. This is the most potent inhibitor of C. difficile spore germination described to date. QSAR and molecular modeling analysis demonstrated that increases in hydrophobicity and decreases in partial charge or polar surface area were correlated with increases in potency.
Scientific reports, Apr 10, 2017
Class I hydrophobins are functional amyloids secreted by fungi. They self-assemble into organized... more Class I hydrophobins are functional amyloids secreted by fungi. They self-assemble into organized films at interfaces producing structures that include cellular adhesion points and hydrophobic coatings. Here, we present the first structure and solution properties of a unique Class I protein sequence of Basidiomycota origin: the Schizophyllum commune hydrophobin SC16 (hyd1). While the core β-barrel structure and disulphide bridging characteristic of the hydrophobin family are conserved, its surface properties and secondary structure elements are reminiscent of both Class I and II hydrophobins. Sequence analyses of hydrophobins from 215 fungal species suggest this structure is largely applicable to a high-identity Basidiomycota Class I subdivision (IB). To validate this prediction, structural analysis of a comparatively distinct Class IB sequence from a different fungal order, namely the Phanerochaete carnosa PcaHyd1, indicates secondary structure properties similar to that of SC16. T...
Medical Instruments and Devices, 2015
Biophysical Journal, 2014
the ToxR/TcpP/toxT protein-DNA complex important in early pathogenesis. In addition to elucidatin... more the ToxR/TcpP/toxT protein-DNA complex important in early pathogenesis. In addition to elucidating the regulatory pathway of V. cholerae, the impact of this work will be to further provide a general model for outermembrane-bound transcription control in bacteria and nuclear-membranebound transcription in eukaryotic cells.
Pharmaceutical Research, 2007
Polymeric membranes containing pH-sensitive nano-hydrogels and glucose oxidase were found to exhi... more Polymeric membranes containing pH-sensitive nano-hydrogels and glucose oxidase were found to exhibit glucose-responsive insulin release. To verify that this glucose-responsiveness stemmed from the decrease in the internal pH of the membranes, we determined the spatial and temporal pH profiles inside the composite membranes in situ for the first time. A pH-sensitive fluorescent dye and an inert internal reference was incorporated in the membranes consisting of poly(N-isopropylacrylamide-co-methacrylic acid) nanoparticles in a polymer matrix, with or without glucose oxidase and catalase. The fluorescence intensity versus time was measured by laser scanning confocal microscopy. The intensity ratios of the two fluorescent dyes were used to determine the internal pH profiles of the membranes in buffer solutions of various pH or glucose levels. The internal pH was found to be lower than the external pH of buffer solutions. The pH decreased with an increase in glucose concentration, incubation time and the distance towards the center of the membranes due to the relative rates of glucose oxidation and solute diffusion. The results provided direct experimental evidence of acidic internal pH that inversely related to external glucose concentration in an external medium of constant neutral pH.
Cell, 2005
Phagosomes were traditionally thought to originate from an invagination and scission of the plasm... more Phagosomes were traditionally thought to originate from an invagination and scission of the plasma membrane to form a distinct intracellular vacuole. An alternative model implicating the endoplasmic reticulum (ER) as a major component of nascent and maturing phagosomes was recently proposed (Gagnon et al., 2002). To reconcile these seemingly disparate hypotheses, we used a combination of biochemical, fluorescence imaging, and electron microscopy techniques to quantitatively and dynamically assess the contribution of the plasmalemma and of the ER to phagosome formation and maturation. We could not verify even a transient physical continuity between the ER and the plasma membrane, nor were we able to detect a significant contribution of the ER to forming or maturing phagosomes in either macrophages or dendritic cells. Instead, our data indicate that the plasma membrane is the main constituent of nascent
Blood Coagulation & Fibrinolysis, 2007
Thrombosis is a major complication of central venous access devices, its incidence depending on m... more Thrombosis is a major complication of central venous access devices, its incidence depending on material, diameter, tip position, and tip surface. Catheters are usually cut to the appropriate length for accurate positioning. Cutting is not recommended, however, as rough surfaces can serve as a nidus for thrombosis. The present study was performed to assess the roughness of catheter tips provided by various manufacturers versus the roughness once cut and handled. Three types of catheters (Hickman, Port-a-Cath, and Per Q Cath) were cut by scissors, iris scissors, or scalpel, and were handled with debakey forceps, a needle driver, adson with teeth or adson without teeth, to determine the damage created on the catheter. The uncut manufactured tip was compared as a control. Scanning electron microscopy was used for imaging of all samples, and roughness was quantified by atomic force microscopy for the cutting methods. Qualitative results by scanning electron microscopy showed that scalpel-cut and manufactured ends appeared smoother relative to those cut with scissors or iris scissors. This complemented the roughness analysis by atomic force microscopy. Catheters handled by debakey forceps and adsons with teeth showed most roughness, visible as deep holes or a grainy surface when observed by high-magnification scanning electron microscopy. Overall, the smoothest result was produced by scalpel, followed by the manufactured end, scissors, and iris scissors. Handling should be minimized, and use of adsons with teeth, needle drivers and debakey forceps should be avoided, as they can leave permanent damage. Adsons without teeth appeared the least damaging. Blood Coagul Fibrinolysis 18:531-536 ß 2007 Lippincott Williams & Wilkins.
Biotechnology and Bioengineering, 2003
Implanting recombinant cells encapsulated in alginate microcapsules to secrete therapeutic protei... more Implanting recombinant cells encapsulated in alginate microcapsules to secrete therapeutic proteins has been proven clinically effective in treating several murine models of human diseases. However, once implanted, these microcapsules cannot be assessed without invasive surgery. We now report the preparation and characterization of a novel ferrofluid to render these microcapsules visible with magnetic resonance imaging (MRI). The ferrofluid was prepared as a colloidal iron oxide stabilized in water by alginate. The presence of iron particles in the ferrofluid was verified with chemical titration, dynamic light scattering, and magnetization measurement. The microcapsules fabricated with various concentrations of the ferrofluid in the core, or on the surface of alginate microcapsules, or both, all produced microcapsules with smooth surfaces as shown with light and scanning electron microscopy. However, at the nanoscale level, as revealed with atomic force microscopy, the ferrofluid-fabricated microcapsules demonstrated increased granularity, particularly when the ferrofluid was used to laminate the surface. From the force spectroscopy measurements, these modified microcapsules showed increasing surface rigidity in the following order: traditional alginate < ferrofluid in the core < ferrofluid on the surface. Although the mechanical stability of low-concentration ferrofluid (0.1%) microcapsules was reduced, increasing concentrations, up to 20%, were able to improve stability. When these ferrofluid microcapsules were examined with MRI, their T 2 relaxation time was reduced, thereby producing increased contrast readily detectable with MRI, whereas the traditional alginate microcapsules showed no difference when compared with water. In conclusion, such ferrofluidenhanced alginate is suitable for fabricating microcapsules that offer the potential for in vivo tracking of implanted microcapsules without invasive surgery.
Biophysical Journal, 2010
dimerization of the receptor-ligand complex and then oligomerization. Past research, through pred... more dimerization of the receptor-ligand complex and then oligomerization. Past research, through predominantly biochemical methods, have concluded that EphA2 signaling depends on the degrees of multimerization of the proteins and the topology of the ligand presentation. However, clustering mechanisms of EphA2 proteins are not well understood because these signaling molecules function in the cell membrane, which is an environment that is difficult to characterize and manipulate. Our hypothesis is that the multi-scale organization of EphA2 in the cell membrane regulates its biochemical function. To mimic the cell-cell junction, we use a supported lipid bilayer -cell membrane hybrid system. Breast cancer cells presenting EphA2 are cultured on a fluid lipid bilayer consisting of ligand fusion proteins, which can stably interact with a subset of capturing lipids within the bilayer. This interaction allows us to control the protein density, precisely image it, and maintain molecular mobility so ligand-induced receptor clustering can occur. Receptor cluster size is varied by changing the cluster size and degrees of oligomerization of its ligand. On the nanometer length scale, antibodies are used to cross link monomeric forms of ligand fusion proteins and thereby vary the degrees of oligomerization. On the micrometer scale, patterned chromium substrates are used to segregate ligands into corrals of variable cluster sizes. Our results suggest that the spatial organization of receptor plays a role in orchestrating the cascade of signaling switches.
Biomacromolecules, 2004
To elucidate the mechanism of stimuli-responsive permeability and to optimize the design, the nan... more To elucidate the mechanism of stimuli-responsive permeability and to optimize the design, the nanostructure of polymeric composite membranes, developed in our laboratory, was characterized. The membranes were prepared to contain various amounts of stimuli-responsive nanoparticles of poly(N-isopropylacrylamide-co-methacrylic acid), with or without polyelectrolyte coating. Scanning electron microscopy and X-ray photoelectron spectroscopy were used respectively to examine the morphology and surface chemical composition, whereas atomic force microscopy and laser scanning confocal microscopy were employed to characterize the in situ surface and internal structure of the membranes in aqueous media of various pHs. The porous structure was evidenced in the presence of the nanoparticles. The surface content of the nanoparticles increased with increasing particle concentration while the polyelectrolyte coating was nearly undetectable. AFM images revealed that the particles in the membranes shrank with a concomitant increase in pore size as the buffer pH decreased. LSCM results indicated that particles were distributed through the membrane as interconnected clusters.
Annals of the New York Academy of Sciences, 2002
Annals of the New York Academy of Sciences, 2002
The clinical performance characteristics of artificial organs, engineered living tissues, and cel... more The clinical performance characteristics of artificial organs, engineered living tissues, and cell-based therapies are inherently tied to the structural and functional analysis of material components at molecular, cellular, and tissue-length scales. This mandates a consideration of static and dynamic materials analysis in both twoand three-dimensions, as well as under both model and physiologically relevant systems. If we are to develop innovative biomaterials for use in reparative medicine, we must identify the key structure–property parameters that describe the in situ physical situation. In order to effect these measurements, we need to develop the appropriate instrumentation and techniques that can measure these properties or attributes over a wide range of dimensional length scales. Ideally these instruments will adopt an integrated strategy such that the measurements are performed in real-time, in situ, and under nominally physiologically realistic conditions. Designing new biomaterials requires careful consideration of the necessary biorelevant structure–function–property relationships. However, more than simply identifying the physical or chemical parameters—strength, frictional characteristics, chemical inertness / reactivity—we may need to also consider the following:
Journal of Physics: Conference Series, 2010
ABSTRACT Welcome to the Proceedings for HPCS2010! HPCS (High Performance Computing Symposium) is ... more ABSTRACT Welcome to the Proceedings for HPCS2010! HPCS (High Performance Computing Symposium) is Canada&#39;s foremost HPC conference - a multidisciplinary conference where computational researchers from all disciplines in industry and academia, computer scientists, and vendors exchange new tools, techniques and interesting results in and for HPC computational research. HPCS2010, the 24th in the series, took place at the University of Toronto, 5-9 June. We are very pleased with the range and depth of excellent work that was presented at this year&#39;s High Performance Computing Symposium. The work that follows is a collection of papers presented by authors from institutions in five countries, covering topics ranging from squeezing every last cycle out of a single GPU to the design of an entire data centre, and almost everything in between. We particularly encourage you to look through the &#39;Award Winners&#39; section, where works are presented by junior and student researchers which were awarded prizes for being amongst the best work presented at HPCS2010. Enjoy the excellent research that follows, and we look forward to seeing you in Montreal for HPCS2011! Jonathan Dursi, for all of members of the Scientific Organizing Committee of HPCS2010.
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Papers by Christopher Yip