Faculty of Science

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The Faculty of Science (FSCI) provides students with the tools needed to adapt to future developments in the scientific path of their choice. Areas of study include applied & industrial mathematics, chemistry, integrative neuroscience, forensic science, computer science and physics.

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Webcasting Made Interactive: Persistent Chat for Text Dialogue During and About Learning Events
(Springer, 2007) Ronald, Baecker; Fono, David; Blume, Lillian; Collins, Christopher; Couto, Delia
This paper presents a “persistent chat” extension to the ePresence Interactive Media webcasting infrastructure to support real-time commenting on and discussing of issues that arise during a learning event, followed by ongoing asynchronous dialogue about these issues while viewing the archives after the event. We report encouraging results of a field study of use of the system by students and a teaching assistant in a computer science class on communication skills, which encouraged students to review, think critically about, and improve their public speaking abilities.
Mass transport in the cathode electrode of a molten carbonate fuel cell
(2009-04-01) Findlay, Justin Earl; Berg, Peter
A molten carbonate fuel cell (MCFC) is an electro-chemical energy conversion technology that runs on natural gas and employs a molten salt electrolyte. In order to keep the electrolyte in this state, the cell must be kept at a temperature above 500 C, eliminating the need for precious metals as the catalyst. There has been only a limited amount of research on modelling the transport processes inside this device, mainly due to its limited ability for mobile applications. In this thesis, three one-dimensional models of a MCFC are presented based on different types of diffusion and convection. Comparisons between models are performed so as to assess their validity. Regarding ion transport, it is shown that there exists a limiting case for ion migration across the cathode that depends on the conductivity for the liquid potential. Finally, an optimization of the diffusivity across the cathode is carried out in an attempt to increase the cell performance and its longevity.
A "Communication Skills for Computer Scientists" Course
(ACM, 2009-07) Blume, Lil; Baecker, Ronald; Collins, Christopher; Donohue, Aran
This paper describes "Communication Skills for Computer Scientists," a novel undergraduate course at the University of Toronto. We describe in detail the three major instructional streams of the course: writing, speaking, and interpersonal communications. We present a novel approach to teaching writing, interactive multimedia web technology to teach public speaking, and specific interpersonal skills training as the integral parts of the course. We contribute a detailed description of the curriculum and report measures of success, both quantitative data and reactions from students in their own words.
Biochemical alteration of gravesoils between season and soil type
(2009-07-01) Benninger, Laura; Forbes, Shari; Carter, David
Decomposition chemistry refers to the biochemical degradation processes which occur in soft tissue as decomposition proceeds. This study aims to investigate the relationship between the release of decomposition fluids into contrasting soil environments and their potential correlation with the presence of a decomposing carcass. Soil from two different carcass decomposition trials was utilized to determine if seasonal and soil variation altered the soils reaction to a carcass. The reaction was determined by investigating the soil available phosphorus, extractable lipid-phosphate, pH, moisture and fatty acid content. A significant increase in the relative concentration of extractable lipid-phosphate, soil available phosphorus, and fatty acid content was identified, confirming the flux in the microbial biomass in the soil. Contrary to these nutrients, there were no notable changes in the soil pH and moisture content. The findings of this study were able to highlight the future forensic potential of these techniques and demonstrate a need for further research.
Molecular characterization of GABA receptor subunits from the parasitic nematode Haemonchus contortus
(2009-08-01) Siddiqui, Salma; Forrester, Sean; Bonetta, Dario
Haemonchus contortus is a parasitic nematode that is controlled by several nematocides which target ion channels. We have identified two H. contortus ion channel genes, Hcounc- 49B and C that encode two GABA-gated chloride channel subunits. Electrophysiological analysis shows that the Hco-UNC-49B subunit forms a functional homomeric channel in Xenopus laevis oocytes that produces a robust response to GABA and is highly sensitive to picrotoxin. In contrast, Hco-UNC-49C alone does not respond to GABA but can assemble with Hco-UNC-49B to form a heteromeric channel with an increased sensitivity to GABA and a lower sensitivity to picrotoxin. To investigate the subunit requirements for high agonist sensitivity, we generated cross-assembled channels by co-expressing the H. contortus subunits with UNC-49 subunits from the nematode Caenorhabditis elegans (Cel-UNC-49). Co-expressing the Cel-UNC-49B with Hco- UNC-49C produced a heteromeric channel with a low sensitivity to GABA. In contrast, co-expressing Hco-UNC-49B with Cel-UNC-49C produced a heteromeric channel that was highly sensitive to GABA. These results suggest that the Hco-UNC-49B subunit is the key determinant for the high agonist sensitivity of heteromeric channels.
Growth, survivability, and reproductive effects of pulse-dosed endosulfan on jordanella floridae (florida flagfish) over one complete life-cycle
(2009-08-01) Beyger, Lindsay Alexandra; Holdway, Douglas
Endosulfan is a commonly used organochlorine in Durham Region, Ontario Canada which has known toxic effects on non-target organisms including fish. This research investigated the effects of endosulfan on Florida flagfish (Jordanella floridae), using both continuous and pulse-exposure. The 96 hour continuous exposure LC50 in larval flagfish was 4.35 μg/L; sub-lethal observations included hyperactivity, convulsions, and some axis malformation. The effects of a 4 hour endosulfan pulse-exposure on 7-8 day-old larval growth, reproduction, and survivability were investigated over one full life-cycle. The 4 hour pulse-exposure LC50 value for larval flagfish was 49.7 μg/L; there were no growth or reproductive effects of endosulfan pulse-exposure up to the highest exposure concentration of 10 μg/L. Thus, the life-cycle 4-h pulse-exposure no observed effect concentration (NOEC) and lowest observed effect concentration (LOEC) were 3.2 and 10 μg/L endosulfan, respectively, due to significantly higher mortality.
Immunomodulatory effects of dietary fibre supplementation: effects on cytokine and antibody production and lymphocyte population profiles
(2009-08-01) Gannon, Mark; Green-Johnson, Julia
Gastrointestinal microflora has been shown to have a bi-directional relationship with the host immune system. A variety of fermentable carbohydrate polymers largely pass through the small intestine, providing fermentable substrates for gut microflora. Dietary fibre supplementation may provide a strategy for manipulating the intestinal bacterial profile, changing the interaction with the mucosal immune system, thereby modulating the host immune system. We used a BBc rat animal model to evaluate the effects of oat bran and wheat bran dietary fibre on the immune system. Previous collaborative efforts have shown that these dietary fibres can change the intestinal microflora, with wheat bran fibre showing a greater ability to influence colonic microbial community diversity. We have shown that dietary wheat bran fibre led to reduced IL-4 levels in the liver and T lymphocyte numbers in the Mesenteric Lymph Node and may be involved in reduced IgA levels in the cecal contents. In addition, IgA in the cecal contents was decreased while MLN B cell numbers increased in response to dietary wheat bran fibre. It was observed that neither wheat bran or oat bran treatments exerted any pro-inflammatory effects, with oat bran actually improving antioxidant status. These results suggest that both oat and wheat bran fibre treatments induce changes in the intestinal microflora, and that the microflora changes due to wheat fibre are associated with immunomodulatory effects on the host. This type of dietary fibre supplementation could ultimately provide a potential strategy for promoting health through microflora-associated effects on the immune system.
Chronic toxicity of phthalates, biphenol and a Canadian bottled water stored under different light regimes using the Cnidarian Hydra Viridissima©
(2009-08-01) Ganeshakumar, Mathumai; Holdway, Douglas
There is general concern whether human exposure to selected Canadian bottled waters and the chemicals which may leach from them, could potentially cause deleterious effects. This research was designed to determine whether exposures to bottled water and plastic leachates caused toxicity to the freshwater Cnidarian Hydra viridissima (green hydra). Three chemicals used in the production of polycarbonate and polyethylene plastics, bisphenol A (BPA) and two phthalate esters: dibutyl phthalate (DBP) and bis (2- ethylhexyl) phthalate (DEHP) along with one type of commercial bottled water were investigated. One brand of bottled water was analyzed over four months (stored in light and dark conditions) along with lab water similarly stored in glass, polycarbonate and polyethylene bottles. Following 2, 4, 8 and 16 weeks in each of the two treatments, hydra bioassays were conducted. Chronic toxicity tests were also conducted on the two phthalates and BPA. The chronic toxicity tests showed that BPA caused effects on hydra morphology and population at low doses and DBP and DEHP both showed signs of hormesis.
Chronic effects of single intra-peritoneal injection of endosulfan on rainbow trout (Oncorhynchus mykiss) and field observations of caged rainbow in Oshawa Creek
(2009-08-01) Armour, Jeffrey Andrew; Holdway, Douglas; Bonetta, Dario
The organochlorine pesticide endosulfan has been shown to be highly toxic to fish and there is some evidence to support that it may act as an endocrine disrupting chemical. Juvenile rainbow trout (Oncorhynchus mykiss) were caged at 4 sites in Oshawa Creek during the fall and spring of 2008 and 2009 while another group was intra-peritoneal injected in the laboratory with varying concentrations (ppm) of endosulfan. Plasma vitellogenin (VTG) levels, liver ethoxyresorufin-O-deethylase (EROD), citrate synthase (CS), lactate dehydrogenase (LDH), and brain acetylcholine esterase (AChE) (caged fish only) enzymatic activities were measured. Trout injected with endosulfan experienced an increase of the anaerobic (LDH activity) and a decrease of the aerobic (CS activity) metabolic pathways, while male VTG levels increased. Since it was a singular injection, VTG results have to be confirmed. Fall caged trout showed increased EROD activity and inhibited AChE activity while those caged in the spring experienced an unexpected exposure to the lampricide 3-Trifluoro-Methyl-4-Nitro-Phenol (TFM) which disrupted metabolic parameters (inhibited CS and increased LDH activity). Both fall and spring caged trout experienced no induction of VTG activity. Further research is needed since the spring exposure was altered due to the unplanned TFM treatment and thus did not represent a valid temporal replicate.
Dynamical effects in crystalline solid state systems: theory of temperature dependent optical response of bulk gaAs and vibrational modification of C(111) 2 x 1 Surface in Comparison to Experiment
(2009-08-01) Teatro, Timothy A.V.; Chkrebtii, Anatoli
This thesis presents a new theoretical formalism which incorporates dynamical effects in atomistic electronic structure and related calculations. This research, fundamental by nature, brings about a deeper understanding of the dynamical processes in a range of materials. This establishes technologically important correlation with experimentally measured macroscopic properties and materials characterization. This method—the first of its kind—is a natural and long overdue extension of customary adiabatically separated time-independent electronic structure methods. It accounts explicitly for atomic motion due to thermal and zero-point vibration. The approach developed requires no direct treatment of time dependence in the quantum mechanical calculations, making the method widely applicable utilizing currently available electronic structure and ab-initio molecular dynamics software. The formalism is extensively applied and demonstrated for the linear optical response of bulk gallium arsenide and electronic structure of the C(111) 2 x 1 surface. Both cases are complimented by comparison of key observables to experimental data which may be used to judge the quality of the results. The results are found to be in good agreement with experimental data, with most exceptions being readily explainable and well understood.
Characterization of carbon nanotubes grown by chemical vapour deposition
(2009-08-01) Ahmed, Muhammad Shafiq; Gaspari, Franco; Smith, William
Carbon nanotubes (CNTs), discovered by Ijima in 1991, are one of the allotropes of carbon, and can be described as cylinders of graphene sheet capped by hemifullerenes. CNTs have excellent electrical, mechanical, thermal and optical properties and very small size. Due to their unique properties and small size, CNTs have a great potential for use in electronics, medical applications, field emission devices (displays,scanning and electronprobes/microscopes) and reinforced composites. CNTs can be grown by different methods from a number of carbon sources such as graphite, CO,C2H4, CH4 and camphor. Under certain conditions, a metallic catalyst is used to initiate the growth. The three main methods used to grow CNTs are: Arc-discharge, laser ablation (LA) and chemical vapour deposition (CVD). In the present work CNTs were grown from a mixture of camphor (C10H16O) and ferrocene (C10H10Fe) using Chemical Vapour Deposition (CVD) and argon was used as a carrier gas. The iron particles from ferrocene acted as catalysts for growth. The substrates used for the growth of CNTs were crystalline Si and SiO2 (Quartz) placed in a quartz tube in a horizontal furnace. Several parameters have been found to affect the CNT growth process. The effects of three parameters: growth temperature, carrier gas (Ar) flow rate and catalyst concentration were investigated in the present work in order to optimize the growth conditions with a simple and economical CVD setup. The samples were characterized using electron microscopy (EM), thermogravimetirc analysis (TGA), Raman and FTIR spectroscopy techniques. It was found that the quality and yield of the CNTs were best at 800°C growth temperature, 80sccm flow rate and 4% catalyst concentration.
The regulation of RANK and RANKL mRNA expression through activation of the JAK2/STAT5a pathway in human breast cancer cell lines ©
(2009-09-01) Praetorius, Lisa J.; Jones-Taggart, Holly; Sanchez, Otto
The receptor activator of nuclear factor-kB (RANK) and its ligand, RANKL has have been implicated as an important link between breast cancer and metastasis to bone because of their ability to activate intracellular signal cascades leading to altered cancer cell behaviour and bone breakdown. The JAK/STAT5a cell signaling pathway is also crucial to breast biology and is involved in transcriptional regulation of many genes. The objective of this study is to determine if RANKL mRNA expression is regulated through the JAK/STAT5a pathway by stimulating human breast cancer cell lines, MCF-7 and MDA-MB-231, with prolactin (PRL), epidermal growth factor (EGF) and heregulin-beta1 (HRG-1), all known to activate STAT5a and play a role in breast cancer progression. This study shows that RANKL expression is upregulated by PRL, EGF and HRG-1, and that PRL and HRG-1 regulate transcription through the JAK/STAT5a pathway.
Immunomodulatory effects of lactic acid bacteria on human intestinal epithelial cells and macrophages in the context of a pro-inflammatory challenge
(2009-09-01) Cooper, William; Forrester, Sean; Strap, Janice
Immunomodulatory effects of lactic acid bacteria vary with strain and may vary with growth phase and medium. The ability of different lactobacilli strains (Lactobacillus helveticus R0052, L. rhamnosus R0011, L. rhamnosus GG) at different growth phases to modulate macrophage and intestinal epithelial cell cytokine production following a pro-inflammatory challenge was examined. Modulation of cytokine production by human macrophage cell lines (U-937) and intestinal epithelial cells (HT-29) induced by Tumor Necrosis Factor α was assayed by ELISA for interleukin-8 (IL-8). Granulocyte-macrophage colony stimulating factor (GM-CSF) production was assayed by ELISA in the HT-29 cell line. Strain-dependent differences were observed in the ability of viable bacteria and spent de Mann-Rogosa- Sharpe (MRS) broths from log versus stationary growth phase in HT-29 and U-937 cells. Overall, variation in the immunomodulatory activity of these lactic acid bacteria and spent broths reflects not only strain variation but potentially also differences in growth phase and substrate.
Diffusion in inhomogenous media
(2009-10-30) Bandola, Nicolas; Lewis, Gregory
This project considers the diffusion of water molecules through a cellular medium in which the cells are modeled by square compartments placed symmetrically in a square domain. We assume the diffusion process is governed by the 2D diffusion equations and the solution is provided by implementing the Crank-Nicolson scheme. These results are verified and illustrated to agree well with the finite element method using the Comsol Multiphysics package. The model is used to compute the values of the apparent diffusion coefficient, (ADC) which is a measure that is derived from diffusion weighted MRI data and can be used to identify, e.g., regions of ischemia in the brain. With our model, it is possible to examine how the value of the apparent diffusion coefficient is affected whenever the extracellular space is varied. We observe that the average distance that the water molecules travel in a definite time is highly dependent on the geometrical properties of the cellular media.
On the integration of Computational Fluid Dynamics (CFD) simulations with Monte Carlo (MC) radiation transport analysis
(2009-12-01) Ali, Fawaz; Waller, Ed
Numerous scenarios exist whereby radioactive particulates are transported between spatially separated points of interest. An example of this phenomenon is, in the aftermath of a Radiological Dispersal Device (RDD) detonation, the resuspension of radioactive particulates from the resultant fallout field. Quantifying the spatial distribution of radioactive particulates allow for the calculation of potential radiation doses that can be incurred from exposure to such particulates. Presently, there are no simulation techniques that link radioactive particulate transport with subsequent radiation field determination and so this thesis develops a coupled Computational Fluid Dynamics (CFD) and Monte Carlo (MC) Radiation Transport approach to this problem. Via particulate injections, the CFD simulation defines the spatial distribution of radioactive particulates and this distribution is then employed by the MC Radiation Transport simulation to characterize the resultant radiation field. GAMBIT/FLUENT are employed for the CFD simulations while MCNPX is used for the MC Radiation Transport simulations.
Stability of heroin metabolites and oxycodone in rat hair and liver during decomposition
(2010-01-01) Tse, Galiena W.; Forbes, Shari L.; Kelly, Tamsin
The aim of this study was to investigate the influence of soft tissue decomposition on the stability of drugs incorporated in hair antemortem. Two burial trials were conducted: in the first trial, rats were administered oxycodone over five days; in the second trial, rats were administered heroin over nine days then drug abstinent for another nine days. After each respective treatment the rats were sacrificed and buried in controlled burial microcosms. Concentrations of oxycodone and selected metabolites or the metabolites of heroin; 6-monoacetylmorphine and morphine, incorporated within rat hair and liver were measured before and during the decomposition process. Oxycodone was analysed in hair and liver samples, while morphine and 6-monoacetylmorphine were analysed in hair samples by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Oxycodone concentrations in both hair and liver decreased as the interment period and decomposition of the carcasses progressed. 6-Monoacetylmorphine was not detected in any hair samples collected from the exhumed carcasses.
Synthesis and characterization of purely sulphonated and composite membranes for high temperature fuel cells
(2010-04-01) De Almeida, Nicole E.; Easton, Brad
Fuel cell technologies have developed high interest due to their ability to provide energy in an environmentally friendly method. Proton exchange membrane fuel cells (PEM-FCs) require a PEM for use, where the most accepted PEM used today is Nafion. Nafion is ideal due to its chemical durability and high proton conductivity however it is highly expensive and limited to 80˚C during operation. To target these issues two methods have been developed. One was to synthesize a new membrane material to replace Nafion based upon sulphonated polysiloxanes and the other was to improve Nafion by synthesizing a composite. Both of these methods involved the sulphonated silane 2-4-chlorosulphonylphenethyltrimethoxysilane. Methods to characterize membranes to observe their properties compared to Nafion were thermogravimetric analysis (TGA), Fourier transmission infrared spectroscopy (FT-IR), electrochemical impedance spectroscopy (used to determine proton conductivity) and fuel cell performance.
Transport-theory-equivalent diffusion coefficients for node-homogenized neutron diffusion problems in CANDU lattices
(2010-04-01) Patel, Amin; Nichita, Eleodor M.
Calculation of the neutron flux in a nuclear reactor core is ideally performed by solving the neutron transport equation for a detailed-geometry model using several tens of energy groups. However, performing such detailed calculations for an entire core is prohibitively expensive from a computational perspective. Full-core neutronic calculations for CANDU reactors are therefore performed customarily using two-energy-group diffusion theory (no angular dependence) for a node-homogenized reactor model. The work presented here is concerned with reducing the loss in accuracy entailed when going from Transport to Diffusion. To this end a new method of calculating the diffusion coefficient was developed, based on equating the neutron balance equation expressed by the transport equation with the neutron balance equation expressed by the diffusion equation. The technique is tested on a simple twelve-node model and is shown to produce transport-like accuracy without the associated computational effort.
Pure culture and metagenomic approaches to investigate cellulose and xylan degradation
(2010-04-01) Ng, Sita; Strap, Janice; Bonetta, Dario
Lignocellulose is composed of lignin, hemicellulose, and cellulose. Lignocellulose waste is a sustainable and renewable resource available for use in biotechnological applications. Efficient enzyme production and enzymes with high catalytic activity are needed for the use of lignocellulose. The study of cellulases and xylanases that degrade cellulose and xylan into constituent monosaccharides is required to advance industrial application of these enzymes. The use of a traditional pure culture approach to discover and characterize cellulases and xylanases from novel actinomycete isolates and the use of metagenomics to uncover previously unidentified cellulase genes was undertaken. Actinomycetes were cultivated from soil samples and the isolate with the best cellulase and xylanase activity was subjected to strain improvement through protoplast fusion. Enhanced enzymatic activity was found in one fusant. Differential release of sugars from xylan was observed through gas chromatographic analysis between the parental and fusant cultures. Genome shuffling was observed in 16S rRNA genes after protoplast fusion. Finally, one putative endo-β-1,4-glucanase was discovered in a metagenomic library created from cellulose-enriched potting soil.
Applications and numerical investigation of differential-algebraic equations
(2010-05-01) Milton, David Ian Murray; Berg, Peter; Staley, Mark
Differential-algebraic equations (DAEs) result in many areas of science and engineer- ing. In this thesis, numerical methods for solving DAEs are compared for two prob- lems, energy-economic models and traffic flow models. An energy-economic model is presented based on the Hubbert model of oil production and is extended to include economic factors for the first time. Using numerical methods to simulate the DAE model, the resulting graphs break the symmetry of the traditional Hubbert curve. For the traffic flow models, a numerical method is developed to solve the steady-state flow pattern including the linearly unstable regime, i.e. solutions which cannot be found with an initial value solver.

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