4A12 Abstracts 2015

Below is a list of thesis abstracts by fourth-year students in the Integrated Science Program:

THESIS PRESENTATIONS – MARCH 30, 2015

Ben Windeler – Modelling the impact of extreme weather events on terrestrial vegetation ecosystems.

Supervisor: Dr. Altaf Arain
Extreme weather events, heat waves and droughts in particular, can have devastating impacts on terrestrial vegetation ecosystems. The frequency and intensity of extreme weather events are expected to increase in the foreseeable future, with unpredictable impacts on carbon dioxide (CO2) levels, food security, and ecosystems. In order to better understand these impacts, it is essential to first quantify the effect they have on the accuracy of terrestrial ecosystem models (TEMs), which are our best tool for predicting future impacts. Here a new version of CLASS-CTEM (the coupled Canadian Land Surface Scheme and Canadian Terrestrial Ecosystem Model) was developed to incorporate nitrogen cycling algorithms. The model was run with meteorological data collected from three coniferous forest sites from Canada and the USA to analyze carbon dynamics over recent time periods. The accuracy of the new model was quantified and validated by its efficiency index (EI), which compares model outputs to in situ observations.

In addition to validating the new version of CLASS-CTEM, the effects of temperature and precipitation extremes were analyzed by identifying notable events in the historical datasets. Model accuracy was significantly impaired by dry precipitation extremes and hot temperature extremes. A further change in soil water extraction processes was made to mitigate these problems. Following, a sensitivity analysis was performed to further elucidate the role of precipitation and temperature as controls on carbon dynamics. Increases in average temperature and precipitation variability based on future climate scenarios reduced the ability of forest ecosystems to sequester carbon.

Sarah McPherson – Investigating the relationship between shield size and social interactions in the pukeko (Porphyrio melanotus melanotus).

Supervisor: Dr. Jim Quin
Within animal communication, signals represent the method through which information is conveyed from the sender to the receiver. Badges of status are a type of signal that indicates an individual’s dominance status and/or fighting ability and are relatively cost-free to produce. Therefore, badges of status are disputed in signal theory, as the source of their reliability is unknown. It has been hypothesized that social costs in the form of agonistic interactions between a dishonest signaler and other group members may maintain the reliability, or honesty, of badges of status. In a previous study, Dey et al. (2014) found that experimentally reducing the badge of status (shield) of the pukeko caused an increase in the amount of aggression received by the manipulated bird, and ultimately caused a decrease in true shield size. Here, the source of the increased aggression, whether from more dominant or more subordinate birds, was investigated by scoring behavioural interactions from the videos taken in the aforementioned study. In terms of aggressive behaviour, there was no increase in attacks but there was an increase in amount of challenges; however there was no source-specific increase. There was also a trend of a decrease in submissive behaviour received by the manipulated bird post-treatment, and the decrease appeared to originate from the subordinate birds. This study provides more research into an aspect of honest signalling and dominance hierarchies in social animals, thus providing more insight into a topic that plays a central role in animal societies.

Reference:
Dey, C.J., Dale, J., and Quinn, J.S., 2014. Manipulating the appearance of a badge of status causes changes in true badge expression. Proceedings of the Royal Society B: Biological Sciences, 281(1775), p.20132680.

Alexander Shephard – Fever: evidence of adaptation for the coordination of the immune system to fight pathogens.

Supervisor: Dr. Paul Andrews
Fever, the elevation of core body temperature by behavioral or physiological means, is one of the most salient aspects of human sickness. Other researchers have claimed that fever is an evolved adaptation, but these arguments have been based on weak evidentiary standards. The purpose of this research is to apply the strong epistemological framework of evolutionary biology to the question of whether fever is an evolved adaptation.

To determine if a trait is an evolved adaptation, one carries out a design analysis of the trait. A design analysis involves deconstructing the trait to figure out how its components interact. As more is understood about how these individual components operate together, one can begin to form a conceptual blueprint of how the trait operates and what it does. If the trait shows evidence of highly non-random organization or coordination all directed towards promoting a unique effect, then this effect is called the trait’s function. Only then can an inference of adaptation be made about the trait, since natural selection is the only known natural process that can generate a high degree of biological non-randomness.

In this project, a design analysis is applied to fever to build an epistemologically strong argument to answer the question of whether there is adaptation in the immune system for being coordinated by febrile temperatures. To address this, we look for evidence that the immune system is non-randomly coordinated by fever, and whether this coordination is so non-random that these effects could not have arisen due to chance.

Mackenzie Richardson – Thermally cleavable carbonate linkages designed for use in conjugated polymer-suspended carbon nanotubes.

Supervisor: Dr. Alex Adronov
The use of carbon nanotubes as organic thin film transistors would allow for the development of a wide array of low-cost, flexible, carbon-neutral electronics. Currently, carbon nanotubes are suspended into organic solutions using conjugated polymers, functionalized with alkyl side chains to improve solubility. The presence of these side chains causes increased internanotube junction distance, raising the overall resistance. Controlled removal of these alkyl side chains via pyrolysis should allow for thin nanotube films to be made with overall lower sheet resistances. A synthetic strategy for creating conjugated polymers with thermally labile carbonate linkages was developed and investigated. The use of carbonyldiimidazole as a phosgene equivalent allowed for the facile creation of a library of organic carbonates. Thermogravimetric analysis of early model compounds provided insufficient data as to thermally lability of the carbonate, so larger model compounds were necessarily envisioned and synthetically planned. Although fully functionalized model compounds and conjugated polymers were not achieved, this work provides a useful starting point for the ultimate design and implementation of carbonate functionalized conjugated polymers. Ultimately, the work shows that alkyl substituents of conjugated polymers can be attached easily using imidazole carbamate intermediates.

Alexandra Kasper – The effects of viscosity on the swimming dynamics of C. elegans.

Supervisor: Dr. Kari Dalnoki-Veress
The millimeter-sized nematode Caenorhabditis elegans is a model organism in biology and an ideal system for exploring the response of an undulatory swimmer to changes in its environment. Like other organisms that exhibit undulatory motion such as snakes and spermatozoa, C. elegans is capable of moving in and on a variety of complex media including: gels, wet granular materials like soils, and fluids with a wide range of viscosities. Investigating the ways in which this simple organism adjusts its motion to suit its environment can address important questions in the fields of motor control, fluid dynamics, the development of undulatory robots, and gait modulation in response to a changing environment.

This research uses the micropipette deflection technique to characterize the swimming of C. elegans. In these experiments, a nematode is held by the tail via suction applied to the micropipette and filmed with a high speed camera. Image analysis is used to track both deflections of the micropipette and the motion of the nematode. By force-calibrating the micropipettes, the deflection can be used to directly measure the propulsive and lateral forces experienced by the nematode throughout its swimming cycle. We find that C. elegans reduces both its swimming frequency and amplitude as viscosity increases. Furthermore, the forces of the system increase with increased viscosity; however, despite changes in its swimming pattern, the nematode maintains a constant power output. Finally, comparison with previous work indicates that gait modulation due to physical confinement and environmental viscosity are indistinguishable.

Jesse Bettencourt – The beautiful geometry of aperiodic tessellations.

Supervisor: Dr. Miroslav Lovric
This presentation will provide historical background and introduce foundational concepts to the study of plane tessellations, or tilings. Characterization of tessellations, including symmetries and periodicity, will provide context to the primary research goals of the project: the investigation of geometric features of non-periodic plane tessellations. Non-periodic tessellations are compelling mathematical objects that feature apparent self-similar geometric structure, but lack translational symmetry. The presentation will discuss the discovery of the most famous non-periodic tessellations: the Penrose tiling. Due to their aperiodicity, these tesellations cannot be sequentially constructed algorithmically, as one would tile a bathroom floor one tile after the last. Instead, the tiling is constructed through a set of substitution rules, called inflation and deflation. The Penrose tiling deflation rules make significant use of the Golden Ratio and produce aesthetically captivating patterns when iterated. These patterns will be presented at this talk, including a brief discussion of the Mathematica code written to generate these tessellations. Further, different features of the tessellation will also be illustrated through Mathematica graphics, including patterns which inhibit translational symmetry, illustrating the unified relationship between all Penrose tilings, and geodesic paths along the tilings. The goals of this project are exploratory and this presentation will focus mostly on discussion of graphical results requiring minimal mathematics background. “I am interested in mathematics only as a creative art… Beauty is the first test: there is no permanent place in this world for ugly mathematics.” – G. H. Hardy

Myles Marin – Exploring the Mandelbrot set.

Supervisor: Dr. Miroslav Lovric
Purpose: Since 1980, the Mandelbrot set has become the focal point for numerous studies involving natural phenomena. The Mandelbrot set has presented new means of understanding challenges involved in complex non-linear systems and has made them more accessible. This work took hold of an opportunity to break down theoretical proofs and computational construction of the Mandelbrot set for the greater accessibility and understanding of undergraduate students. Furthermore, original research on Mandelbrot set area has been conducted since little literature was dedicated to the subject.

Approach: Construct and investigate the Mandelbrot set via the technical-computing language MATLAB. An n-by-n pixelated grid is constructed with vectors and MATLAB function meshgrid[,], from which each pixel represents a complex number. Each pixel is then coloured black if it does not escape to infinity after it undergoes a certain number of iterations, predetermined in the program. A complex plane is then overlaid to plot the orbits of specific points on the set.

Outcomes: Arrival at a comprehensive review of boundedness, compactness, and simply connectedness as introduction to the paper entirely based on undergraduate-level mathematics. Following, an exploration of Mandelbrot set point orbits and area calculations using computer software.

Research limitations: MATLAB operated on laptop computer software; additional computing power was not available.

THESIS PRESENTATIONS – MARCH 31, 2015

Pratik Samant – pH-dependent molecular diodes.

Supervisor: Dr. Randy Dumont
A working molecular wire is a promising candidate in the context of creating various different circuit elements involved in the construction of quantum computers. To this end, it is important to look for candidate molecules that can function as numerous types of circuit elements. In this thesis, a molecular diode was looked for using a self-consistent approach. Electronic properties of molecules were analyzed be protonating and deprotonating said molecule, in the hopes of identifying a pH-dependent molecular switch or diode. The primary structure of analyzed molecules was that of a polyene chain with a separate polyene antenna group attached to the main chain. At the end of the antenna was a carboxylic acid group which could be protonated and deprotonated as needed. The Fermi levels of the two leads, as well as the position of lead contact, could be varied, and limitless permutations of these variables exist. Candidate molecules for molecular switches were also screened. A molecular diode and switch were found and their molecular properties analyzed. A follow-up study could be done in which this system is analyzed non-perturbatively.

John Buchanan – A computational study of molecular conduction in redox pairs.

Supervisor: Dr. Randy Dumont
At the microscopic boundary of electronics, the study of molecular electronic devices (MEDs) explores the transport of electrons at the scale of atoms and molecules. Although experimentation on MEDs has been accomplished, a theory of molecular conduction has not been forthcoming for quantum chemists and physicists. Investigations are being made into the electronic structure of covalently-bonded molecules and the transport of electrons through these structures, using quantum mechanical models and perturbative methods.

A model of a molecule can be constructed using the Hückel theory of molecular orbitals. This picture of the delocalized π-system of a molecule captures the relevant electronic structure for the transport of electrons from one point on the molecule to another (where input and output electrodes may be attached). In particular, this model suffices to determine a Hamiltonian for the π-system of a conjugated hydrocarbon and to derive its energy levels, albeit only to a qualitative level of accuracy.

Applying this Hamiltonian to a 1st-order perturbation – representing the gradual appearance of a potential difference across the molecule – the study modelled the conductive behavior of certain molecules in MATLAB. This project sought to identify hydrocarbons that exhibited conductive behavior under the above model, with the goal of comparing conduction in different oxidation states. Differences in conduction might make the molecule suitable for a molecular switch, molecular diode, or other MED in future attempts to create functioning molecular devices. A major outcome of this research was the creation of a categorized list of candidate molecules for such devices.

Mary Kate MacDonald – Analysing stress in undergraduate science students: effects of gender and pedagogical strategies.

Supervisor: Dr. Chad Harvey and Dr. Debbie Nifakis
Undergraduate students often experience high degrees of stress due to the transition to a more independent life, and the high volume of academic demands and evaluations associated with university. This stress is frequently correlated with illnesses, both physical and psychological in nature. Specific to students, high levels of stress often result in a decrease in academic success. In order to address the issue of student stress, it is paramount to identify student populations that experience augmented stress levels in addition to the potential causes. Recent developments of novel and unconventional undergraduate science pedagogies and teaching environments means that there is a need to understand how these varying environments affect the perceived stress of science undergraduate students. Specific to this project, the Integrated Science program at McMaster University, which employs a problem-based and small group learning style, contrasts with the more traditional large-scale, lecture-based teaching styles of the Life Sciences Program. Additionally, as stress can be related to personality as well as environment, it is important to determine if certain personality types are attracted more so to different learning environments and if certain personality traits affect the perception of stress. To address this comparison, I employed an online survey to male and female students in the Life Sciences and Integrated Science programs in order to quantify the potential differences in their perceived stress, personality traits, and pedagogical preferences. Student stress did not vary by program, yet did by gender with male students perceiving their stress to be lower than female students. Contrary to expected trends, male students were more conscientious than female students. Overall, the majority of students recorded stress levels that indicate high risk of stress-induced health concerns. This research suggests that greater efforts to reduce stress for all students and to make the academic environment less stressful for female undergraduate science students are needed.

Rebecca DiPucchio – Synthesis of antiparasitic quinolines for the potential treatment of latent toxoplasmosis and malaria.

Supervisor: Dr. James McNulty
Co-authors: Carla Brown, James McNulty
Effectively managing parasitic diseases such as malaria and toxoplasmosis requires synthesizing lead compounds with potent activity to warrant further testing. These parasitic diseases are popular research targets because they are very prevalent, with latent toxoplasmosis affecting one third of North Americans. With this goal in mind, quinolines represent an important class of bioactive compounds that are attractive due to their potential in disease treatment. Expansive literature exists to describe quinoline synthesis, with methodology ranging from the acid-catalyzed Friedlander synthesis to Povarov-type cyclizations or modern transition-metal catalyzed options. Not all substitution patterns are equally well-established, the most common being quinolines substituted at position 2 on the pyridine ring. Previous work in the McNulty group published the synthesis and in vitrotesting results for a series of 4-arylquinoline-2-carboxylate esters. The proposed target of these compounds is the cytochrome bc1 complex that exists in both Plasmodium falciparum and Toxoplasma gondii, parasites responsible for malaria and toxoplasmosis respectively. These quinolines can be generated via a multicomponent reaction of anilines and akylnes with ethyl glyoxylate. This project built upon previous results and generated multiple new sets of novel quinolines for testing against T. gondii by modifying the ester bond and alkyne substituents based on promising structure-activity analysis (SAR) for literature compounds with the same target. Entirely new substitution patterns are now being explored: 3-arylquinolines. Challenges associated with generating 3,4 substituted quinolines via a selection of isatins and enolizable aldehydes as well as biological testing results for all series of compounds will be discussed.

Hanna Stewart – Red blood cell assay quantitating plasmalogen concentration to diagnose peroxisome disorders.

Supervisor: Dr. Murray Potter and Dr. Philip Britz-McKibbin
Peroxisomal disorders are rare genetic diseases characterized by single enzyme defects or failure of peroxisomal biosynthesis affecting multiple peroxisome functions including plasmalogen biosynthesis. Biochemical screening is typically done by very long chain fatty acids (VLCFAs) and phytanic acid (PA) analysis by GC-MS. However, this approach cannot detect single enzyme defects of plasmalogen biosynthesis. We have developed a GC-MS method for plasmalogen quantitation to complement existing testing of VLCFAs and PA.

Lipid extraction of a whole blood was followed by derivatization with methanolic HCl to produce dimethyl acetal (DMA) derivatives of the plasmalogens and fatty acid methyl esters (FAMEs). C16 and C18 molecules were analysed using an Agilent 240 ion trap GC-MS using a with 15m x 0.25mm column and EI+ ionisation. C16:0, C18:0 FAME and C16:0, C18:0 DMA standards were used to construct calibration curves. The method was found to be linear for all analytes: C16 FAME 5-5200µM (R2=0.96); C18 FAME 20-3200µM (R2=0.95); C16 DMA 0-300µM (R2=0.93); C18 DMA 0-470µM (R2=0.94). Reference intervals (95% percentile) were established for each analyte and ratios of DMA/FAME using anonymized core lab samples: C16 FAME 150-6500µM; C18 FAME 80-2900µM; C16 DMA 5-850µM; C18 DMA 10-750µM; C16 DMA/FAME 0.03-0.17; C18 DMA/FAME 0.05-0.29. Total imprecision of C16 DMA/FAME was 28.3% CV.

While no true positive patient samples were available for testing, the S/N ratio of C16 DMA was greater than 10:1 at levels comparable to the reported levels of affected patients in literature, theoretically allowing detection. Further evaluation is required.

Kira Moor – Predicting fluid retention in porous media.

Supervisor: Dr. James E. Smith
An increase in awareness of the adverse environmental effects of agricultural, industrial, and urban activities has created a rise in concern for groundwater and subsurface contamination. In order to understand the existing state of groundwater, the water table, and the infiltration of any contaminant, it is important to be able to predict the hydraulic properties of the subsurface. This can be done in two ways: through regional pumping techniques or using sediment data and pedotransfer functions. This project provides an alternative to costly pumping techniques by using grain size data to offer reasonable predictions of water content, effective saturation, and saturated and unsaturated conductivity. Using ROSETTA software and a series of hydraulic equations (van Genuchten, Maulem, Kozeny-Carman), these hydraulic properties can be modelled for water. In this project those hydraulic properties have been extended to include potential contaminants such as TCE and PCE. From these predictions, both the infiltration of water and potential contaminants can be modeled for a given area. This was shown by the application of these techniques to a set of borehole logs from the Geeorgetown region. Upon entering a new sediment layer, the water content can drastically change. This illustrates the effect of the capillary barrier. The goal of this paper is to bridge the gap between hydrogeology and sedimentology, and to provide an easy and cost effective approach for estimating the hydraulic properties in a study area.

Melissa Ling – Impaired macrophage function with age.

Supervisor: Dr. Dawn Bowdish
Elderly individuals display increased susceptibility to microbial infections and chronic inflammatory diseases. To combat pathology and improve quality of life, it is important to understand how and why age-associated immune dysfunction occurs. Macrophages are key inflammatory innate immune cells that act as first-line defenders against pathogens and influence the development of adaptive immunity. With age, these phagocytes undergo changes that affect their antimicrobial defenses and inflammatory response. Nitric oxide, metabolized from L-arginine, is one such defense mechanism macrophages use that may be impaired with age. Understanding if and how nitric oxide dysfunction occurs in the elderly will allow for better prevention and control of age-associated diseases. In this project, bone marrow-derived macrophages from young (6-8 week) and old (18 month) C57BL/6 mice were grown in the presence and absence of L-arginine. Cytokine analysis using an IL-6 and TNFα enzyme-linked immunosorbent assay was performed to examine changes in cytokine response to stimulation (LPS 100ng/mL) between conditions. Killing ability of macrophages with and without the presence of L-arginine was also measured. Understanding age-related macrophage dysfunction is important in understanding infectious and chronic diseases that occur with age so that effective therapeutic strategies to restore innate immune function can be developed.

 Jared Valdron – Of wealth, well-being and work: the origins of monetary attitudes and their influence on workplace behaviours.

Supervisor: Dr. Aaron Schat
Employers often offer opportunities, such as incentives, in hopes of increasing employee motivation and productivity, but the success of such incentives varies significantly. Some of this variation could reasonably originate from how much employees associate wealth with happiness, which itself could vary across contexts. It was hypothesized that people in a home context would have a stronger implicit association between wealth and happiness than those in work or neutral contexts, and that implicit attitudes towards money would be a stronger predictor of work-related behaviours than explicit attitudes. 200 full-time employed participants completed one of three priming tasks (Work, Home, or Neutral), an Implicit Association Test (IAT) with Wealth and Happiness, and questions regarding work-related decisions, direct explicit monetary attitudes, and physical location. The priming and physical location conditions were then compared with respect to implicit attitudes, and implicit and explicit attitudes were compared with respect to predictive power for the work-related behaviours. The obtained results were unsupportive of our primary hypotheses of the contextual malleability of implicit attitudes, and the superior ability of implicit attitudes to predict work-related behaviours. However, it was found that explicit attitudes have significant ability to predict work-related behaviours, but only when those behaviours had distinct financial components. These findings provide key insights into how employees make work-related decisions, which is critical information for employers. A potential application of these results is the tailoring of incentives to specific departments in an organization that vary in their monetary attitudes.

THESIS PRESENTATIONS – APRIL 6, 2015

Stephanie Taylor – Benthic Habitat Preferences of Inia geoffrensis and Sotalia fluviatilis in the Samiria River, Pacaya-Samiria National Reserve, Peru.

Supervisor: Dr. Chad Harvey
For the past five years, the Amazon River basin has undergone dramatic changes resulting from climate change. To determine the effects of climate change on ecosystems within this area some studies have used river dolphins, Inia geoffrensis and Sotalia fluviatilis, as indicators of aquatic health. However, this method has proven difficult given that both species are currently classified as data deficient by the International Union for Conservation of Nature (IUCN). Gathering more data on I. geoffrensis and S. fluviatilis will aid the IUCN in their classification and help understand how the dolphins may react to climate change. This study investigates the benthic habitat preferences of I. geoffrensis and S. fluviatilis. For two months, boat surveys went out twice a day in four different habitat types on the Samiria River in Peru. During each survey, data was collected each time a new individual or group was sighted. Benthic habitat was based on depth, debris size and vegetation size. A significant correlation was found between the debris size and the habitat I. geoffrensis was observed in, but analysis of data for both species showed only a significant correlation between dolphin sightings and debris size. Behaviour had no significant effects on benthic habitat preference. This new information on I. geoffrensis can help shed light on why they move from area to area and how climate change may affect their movements.

Adelle Strobel – Interactions connecting metabolic pathways in plant stress of Eutrema salsugineum and herbivore colour change in Myzus persicae.

Supervisor: Dr. Elizabeth Weretilnyk and Dr. Chad Harvey
Eutrema salsugineum, a model extremophile plant species, may have the ability to produce specialized metabolites to defend against herbivores. However, the agricultural pest Myzus persicae may have acquired counteradaptation traits that enable it to convert harmful specialized plant metabolites into pigments. In order to understand this plant-herbivore interaction further, the cause of colour change in a population of M. persicae was explored. Soil sulfur conditions were manipulated to potentially alter plant resource allocation, specialized metabolite production, and M. persicae colour phenotype. The proposed interconnecting metabolic pathways from E. salsugineum to M. persicae were tested via two different perspectives. Firstly, aphid population and qualitative plant health measurements were analyzed using a mixed, generalized linear model for repeated measures. Secondly, methods were explored to test the suitable metabolite markers, glucosinolate content in E. salsugineum and carotenoid composition in M. persicae, as these chemicals will be useful to demonstrate metabolic pathway connections between plant and insect species. These approaches will be needed to determine whether chemicals produced during plant stress impact herbivore phenotypes, metabolomes, and transcriptomes. The application of identifying the mechanism of colour change in M. persicae could lead to improvements in integrated pest management.

Eric Turner – Vortices in the diffraction pattern of an atomic beam.

Supervisor: Dr. Duncan O’Dell
When we diffract light through slits we see interference patterns. Likewise, when we diffract an atomic beam through a standing wave of light we see an interference pattern. The particular pattern we see from this atomic beam diffraction is called a cusp. A cusp is the most general pattern created by the focusing of light since it describes imperfect focusing. Within this cusp structure are singularities called vortices. The vortex structure comes from positions of undefined phase in Fock space. We aim to explore similarities and differences between a continuous and a discrete case in the vortex structure’s semiclassical limit. To do this we will be performing our analysis and simulation of the diffraction using Mathematica. Implementing a tool called the “path of least phase” we were able to locate vortices in the discrete case. The vortex pattern in the discrete case matched well with the continuous case for the semiclassical limit. As we move towards the more quantum regime vortex pairs begin to disappear due to beam width and vortex-antivortex pair separation distances. This is due to the pair separation distance being constant in the discrete case but varying with the square root of the distance into the cusp for the continuous case. We also find that these vortices tend to sit on saddle points of the adjacent beams. This research has applications in photolithography, which is currently limited to the wavelength of light, whereas atomic wavelengths can reach smaller values.

Lori Minassian – Identifying key regulatory proteins involved in activation of SPI-2 genes in Salmonella enterica sv. Typhimurium.

Supervisor: Dr. Brian Coombes
Salmonellae enterica is a group of enteric Gram-negative bacteria that infect a wide range of warm-blooded animals, usually through consumption of contaminated food or water. The availability of genetic tools, animal models, and cell lines appropriate for in vitro studies have made Salmonella an extremely important model for bacterial pathogenesis. Salmonella infection is dependent on a set of genes encoded by two horizontally acquired Salmonella Pathogenicity Islands (SPI), SPI-1 and -2. Once Salmonella has infected the host cell, it uses genes within SPI-2 to survive and replicate in macrophages and achieve systemic infection. Genetic regulation of SPI-2 is controlled by a number of two-component systems that can detect intracellular signals and cause activation of SPI-2 genes. Once the pathogen is engulfed by immune cells, it is exposed to a number of host defense mechanisms, with reactive oxygen species (ROS) being one of the first. Since ROS are one of the first immune responses Salmonella faces once phagocytosed, they could be an important signal for induction of intracellular survival genes. We exposed wild-type Salmonella and mutants for each of the signaling components to ROS and checked for activation of SPI-2 genes. Our results show that SPI-2 is activated in response to ROS, and is thus sensing the presence of ROS as a signal for intracellular localization. In addition, ΔssrA, ΔssrB and ΔslyA regulatory mutants have a reduced ability to activate SPI-2 genes upon exposure to ROS, indicating that these components may be necessary for detecting ROS. These data provide intriguing insights into mechanisms pathogens use to avoid host immune responses.

Matt Galli – Student perceptions of Level I blended learning science courses at McMaster University.

Supervisor: Dr. Chad Harvey
Blended learning (BL), a combination of online video modules and face-to-face (F2F) instruction, was implemented in Level I Science at McMaster University to increase learner control and in-class engagement. The current blended courses offered are PSYCH 1X03 and 1XX3, BIOLOGY 1A03, and CHEM 1A03. Additional blended courses for chemistry, mathematics, and physics are being planned. An online survey was designed to quantify student global perceptions of BL, course-specific perceptions (PSYCH 1X03, BIOLOGY 1A03, CHEM 1A03), and to gauge receptiveness of plans for future blended courses. The survey was disseminated via the PSYCH 1X03, CHEM 1A03, and BIOLOGY 1A03 Avenue to Learn webpages.

Participants thought BL increased personal control over learning, required more self-discipline, and increased workload. Students in just PSYCH 1X03 had positive opinions of BL relative to students in just BIOLOGY 1A03, CHEM 1A03, or BIOLOGY 1A03 and CHEM 1A03. Students felt one to two BL courses per semester are ideal. For PSYCH 1X03, BIOLOGY 1A03, and CHEM 1A03, participants found it easier to maintain focus during F2F course components relative to online video modules. Students rated the usefulness of the online modules in helping to learn course material for PSYCH 1X03 higher relative to both BIOLOGY 1A03 and CHEM 1A03. Having a blended format slightly reduced stress levels associated with PSYCH 1X03 relative to BIOLOGY 1A03 and CHEM 1A03 where the blended format slightly increased stress. Perceptions of suitability for BL varied between disciplines. Participants felt BL is most suited towards theory/concept-heavy disciplines relative to calculation/problem solving-heavy disciplines.

Kerri Kosziwka – Feeding ecology of crown-of-thorns starfish (Acanthaster planci) in Hoga Island, Indonesia.

Supervisor: Dr. Chad Harvey
Coral reef ecosystems are depleting at an alarming rate. The main structural components of these reefs are hard corals, which provide food and shelter to many diverse organisms. Global coral cover is declining due to reef-building corals becoming targeted by disease and corallivores. One corallivore, Acanthaster planciexists at a low density on Hoga Island reefs within Wakatobi Marine National Park, Indonesia. High density outbreaks of A. planci can be extremely detrimental to reef ecosystems as these organisms have a high fecundity, minimal predators, and no interspecific competition allowing them to be highly successful while decimating coral populations. Although Hoga Island currently hosts a low-density population of A. planci it is important to understand all aspects of their feeding ecology in order to form management strategies against potential outbreaks. Hoga Island reefs have extremely high levels of coral diversity and by extension vast food resources for A. planci. In the summer of 2014, coral abundance and diversity data along with observed feeding data for A. planci were collected through daily snorkels across three sites along Hoga Island’s home reef. Chi-squared analysis has shown a feeding preference towards the coral genus Porites in its massive morphology across the three sites. In addition, size of A. planci individuals showed no significance in determining which coral they preferred. This research currently shows that A. planci have a preference for massive Porites. The available literature shows several different genera preferences (Acropora spp. being the most preferred); meaning preference could be specific to global position.

Harrison Martin – Scaling relationships of rib-and-furrow structures in modern and ancient dunes and bars in rivers.

Supervisor: Dr. Janok Bhattacharya
A common problem in the interpretation of fluvial paleoenvironments is the estimation of river scales and properties using stratigraphic features such as the sedimentary structures associated with dunes and bar bedforms. A scaling relationship between the furrow width of duneforms in plan-view and features of the bars or rivers in which they appear could aid in the interpretation of the sizes, shapes, and paleohydraulic parameters of ancient fluvial systems using rib-and-furrow measurements of preserved features. Modern, high-resolution remote sensing satellite data is available via Google Earth and is of sufficient quality to allow individual dunes to be resolved. In a previous study, no relationship was found between furrow widths and river widths in two modern rivers. This study adds data from three additional rivers and integrates USGS river flow data for rivers within the USA and other hydrologic data for rivers elsewhere. This allows for the investigation of scaling relationships between dune widths and bar widths, river widths, flow depths, and river discharges. These results suggest that duneforms, as commonly measured, have a furrow width which scales to the width of the bar upon which they are formed until they achieve a maximum scale, at which point they “sub-divide” and split into multiple furrows. This suggests that the dune furrow widths are equal to the cross-flow wavelength of the sinuous crest of a hither-to unnamed “dune-row” which appears to be an elementary unit of the bar form. In addition, the duneforms observed in measurements of the ancient record are of a smaller, unit scale which is unobserved in the modern satellite data. The scaling relationship between bar widths and river widths was also investigated. For the rivers studied, the ratio between bar width and river width remains approximately constant for fully developed unit bars but scales linearly for partially developed unit bars. This suggests that variations in this ratio along the length of a bar might be used to identify contacts between unit bars in a compound point-bar.

Chuqiao Huang – The development of growth faults containing planar bedding within the Notom Delta Ferron Sandstone of Utah.

Supervisor: Dr. Janok Bhattacharya
Growth faults are synsedimentary listric faults which form on underwater slopes with high sediment supply; that is to say, they have a high dip at the surface which decreases with depth, and form as large masses of sand collapse into unstable, unconsolidated muddy sediment. The large regional scale growth faults on passive continental margins are of economic interest due to their potential to form sealed hydrocarbon reservoirs. Such growth faults are also inaccessible and as such, their study is limited to seismic analysis and core data. Since many structural features are similar at different scales, an in-depth understanding of growth faults at the outcrop scale may be applied to less accessible regional scale growth faults. This study focuses on a series of growth faults containing planar bedding within parasequence 6 of the Notom Delta Ferron Sandstone in Utah. Two composite and one vertical measured section(s) were created in order to determine the depositional environments of growth and pre-growth strata. A gigapan was generated to determine the order of depositional, faulting, and deformation events. The results of this study may then be extrapolated to answer some larger scale-questions:

  1. Are small deltaic growth faults linked to their stratigraphic position in a clastic wedge?
  2. Are growth faults limited to river-dominated deltas?

THESIS PRESENTATIONS – APRIL 7, 2015

Christina Spinelli – Measuring adaptive cognitive changes during human pregnancy and the post-partum period.

Supervisor: Dr. Mel Rutherford
Co-authors: Marla Anderson and Mel Rutherford
During pregnancy, many women self-report experiencing a decline in cognitive function, namely lapses in memory, reduced concentration, and impaired coordination. This decline is colloquially known as “baby brain”. However, previous attempts to use objective means to document these cognitive deficits have led to equivocal results. Furthermore, it is uncertain if there is a general or a specific decline in cognitive function. Previous research suggests certain deficits in the latter half of the pregnancy, while others have found no differences, despite using a battery of similar cognitive tasks. The objective of the current project was to conduct a longitudinal study comparing pregnant and non-pregnant women from early pregnancy to the post-partum period on two full-scale IQ tests. The Wechsler Adult Intelligence Scale (3rd Ed.) and the Stanford-Binet Intelligence Scales (5th Ed.) were used to measure memory, executive processing, and general cognitive processes. Participants attended four testing sessions occurring approximately 12 weeks apart and the standardized test administered in each session was alternated. Repeated measures ANOVA on Full Scale, Performance, and Verbal IQ scores indicated no general decline in cognitive functioning during pregnancy. However, significant differences were found during the post-partum period on Full Scale and Performance IQ scores. Trends were found on examination of specific subscales where mathematical reasoning appeared to be compromised during pregnancy while deficits in abstract reasoning and working memory were indicated in the post-partum period.

Rebekah Ingram – Investigation of the biodegradation of toluene and ethanol using δ13C signatures of microorganism phospholipid fatty acids.

Supervisor: Dr. Greg Slater
Petroleum hydrocarbons are some of the most common groundwater contaminants. In gasoline, petroleum hydrocarbons are joined by a fuel oxygenate, and the use of ethanol for this purpose is increasing. In conventional fuels in Canada, the ethanol content can be as high as 10% of the fuel volume. An important component of natural attenuation of contaminants is in situ biodegradation. Ethanol is a more energetically favourable compound for microorganisms to utilize as a carbon source than the more complex petroleum hydrocarbons and is therefore expected to be preferentially biodegraded. This may inhibit biodegradation of the petroleum hydrocarbons, allowing them to be transported further distances following a fuel spill. This study addresses the question of preferential degradation of ethanol by combining δ13C signatures with the age-old expression: “You are what you eat”. The δ13C signatures of phospholipid fatty acids formed by microorganisms will be similar to that of their carbon source and thus can be used to elucidate what carbon source they were using. To investigate this experimentally, microorganisms were grown in several bottles containing water-saturated sand with the addition of toluene (representing petroleum hydrocarbons found in a fuel) and ethanol in a 9:1 ratio to simulate the addition of an ethanol containing fuel to a groundwater system. The phospholipid fatty acids created by the microorganisms were extracted and analyzed. The δ13C signatures of the microorganisms were compared to that of toluene (δ13C = -25 to -32 ‰) and ethanol (δ13C = -10 to -14 ‰) to determine if preferential biodegradation of ethanol occurred in the hope of better understanding the influence the presence of ethanol may have on the behaviour of petroleum hydrocarbons released concurrently. While the occurrence of toluene degradation was clearly observed within some of the microcosms, preferential degradation of ethanol was not observed in this experiment.

Lori vandenEnden – Microbial carbon sources and cycling during oil sands tailing reclamation via end pit lakes.

Supervisor: Dr. Greg Slater
The oil sands deposits of Northern Alberta are economically important for Canada; with total reserves estimated to be greater that 170 billion barrels, the oil sands represent over 30% of Canadian crude oil production. However, there are environmental concerns associated with oil extraction that must be considered. The surface mining process disturbs large areas of land and the chemical extraction of the oil produces both solid (fluid fine tailing; FFT) and liquid wastes (oil sands process water; OSPW) both of which are enriched in heavy metals and organic compounds. The mining companies must comply with a zero-discharge policy; none of this waste can be released from the mine lease. Additionally, the provincial regulations require that the land be returned to a usable condition at the completion of mining activities.

One proposed remediation strategy is the construction of end pit lakes (EPLs), by filling the bottom of a mine pit with FFT and capping it with OSPW. It is unknown if these engineered lakes will fill the same ecosystem function as natural lakes. In a natural aquatic system, microbial life is an important contributor to the cycling of elements, transforming them into forms that can be utilized by species at higher trophic levels. Therefore, the structure and size of the microbial communities in an aquatic system is a good indicator of the ecosystem functioning. This will be achieved by measuring changes in the phospholipid fatty acid (PLFA) distribution, which reflect changes in community composition and are a direct indicator of live biomass.

EPL microcosms were constructed in the lab and sampled bi-weekly for 12 weeks. Tailings were collected at each sampling point from each of an endemic system (biotic) and an irradiated system (abiotic control), repeated in triplicate. The total water column biomass was collected via biofilm units deployed for 12 weeks. Fatty acid profiles were obtained by extraction and analysis with gas chromatography-mass spectrometry and gas chromatography-isotope ratio mass spectrometry. Temporal changes in both the fatty acid profile and carbon isotope ratios will be presented and discussed in terms of ecosystem health and potential oil sands remediation.

Rebecca Englert – A regional study of the Quaternary geology of the Niagara Peninsula.

Supervisor: Dr. Carolyn Eyles
In Southern Ontario, glacial deposits derive from the Wisconsin glaciation (110 – 10 Ka) and make up a significant component of the surficial geology. During this period the Laurentide Ice Sheet traversed and eroded Paleozoic bedrock, depositing a complex stratigraphy of glacial till, glaciolacustrine, and glaciofluvial unconsolidated sediment. The Ontario Ministry of the Environment Water Well database is one of the most abundant sources of subsurface data in Ontario; however, its use for geologic investigations has been limited by its inconsistent descriptions and poor resolution of lithologic units. This study uses water well data, in combination with borehole data and field observations, to examine Quaternary glacial deposits over the Niagara Peninsula. Water well record geologic descriptors were classified using tools created in ArcGIS 10.2 and inputted into a geologic modeling software package, Rockworks 2006. A bedrock topography model was created by interpolation between bedrock contacts, identifying a series of bedrock valleys between the Niagara and Onondaga Escarpments. Glacial deposits were also analyzed to determine trends across the study area and examine the distribution of sand and gravel units. Overburden sediments and bedrock relief were compared to investigate the potential influence of bedrock topography on glacial processes. This study describes a method of examining a region using a publicly available, spatially extensive dataset that could form the basis for future investigations or be applied to other areas. In addition, further understanding of the control of bedrock on glacial stratigraphy is critical for predictive modeling and the search for potential overburden aquifers.

David Yun – Perceptions regarding the communication of scientific research to non-specialist audiences.

Supervisor: Dr. Carolyn Eyles and Dr. Sarah Symons
There is currently a systemic disconnect between science researchers and the non-specialist public concerning a number of science-based societal issues, including childhood vaccinations, genetically modified foods, and climate change. This disconnect needs to be addressed for non-specialists, including policy-makers, to make better informed decisions concerning scientific issues. At McMaster University, President Patrick Deane identified community engagement as a priority in his 2011 Forward with Integrity letter. The purpose of the present study is to assess the measures being taken by science professors at McMaster to communicate scientific information to non-specialist audiences, while also proposing recommendations for McMaster to improve its science outreach. An online questionnaire was administered to professors within the Faculty of Science at McMaster to quantify current science communication efforts, incentives and limitations to the outreach process, and opinions on its relevance. One-on-one interviews were also conducted to allow professors to elaborate on their online responses and to gain a qualitative understanding of attitudes held by McMaster researchers. Results indicate that there are too few incentives for science professors to communicate in ways that are accessible to the public. Professors were generally passive about public communication. A public outreach organizer within the Faculty of Science could mediate these concerns. If McMaster’s goal is to increase public outreach efforts, measures to incentivize and facilitate this process need to be introduced. Furthermore, the efficacy of such communication efforts could be improved by shifting more emphasis to scientific methodology, rather than strictly discussing results.

Victoria Balkwill Tweedie – Temperature dependence of acid-liberated COfrom carbonate minerals: application to stable isotope geochemistry.

Supervisor: Dr. Sang-Tae Kim
Stable isotope geochemistry studies the relative abundance of stable isotopes of an element in geologic materials. The ratio between the stable oxygen isotopes oxygen-18 (18O) and oxygen-16 (16O) harvested from carbonate minerals in ice cores and geologic layers, for example, provide insight into the feature’s formation temperature. The relative abundance of 18O and 16O are altered in a process called isotopic fractionation. To measure the isotopic signature of oxygen in a carbonate mineral, it is reacted with phosphoric acid, and the signature of the oxygen within the product carbon dioxide ( δ18OCO2 (acid)) is measured. Since the reactant carbonate has three oxygen molecules (ex. CaCO3) and the acid-liberated carbon dioxide (CO2) has only two, the measured value does not account for all of the oxygen in the original carbonate mineral. Instead a fractionation factor is used to account for this discrepancy. Numerous studies suggest that this fractionation factor varies by carbonate mineralogy and the temperature of the phosphoric acid reaction. Current literature shows great variation in the temperature dependences for a single carbonate mineral (ex. calcite). Measurements of δ18O in stable isotope geochemistry are very sensitive and require incredibly precise acid fractionation factors to yield the most accurate result. Therefore this research project (1) characterized the influence of reaction temperature on the oxygen isotopic composition of acid-liberated carbon dioxide from a variety of different carbonate minerals, and (2) compared the output values of Dual Inlet (DI) and Continuous Flow (CF) Isotope Ratio Mass Spectrometer (IRMS) techniques to enhance the precision of future measurements ofδ18OCO2 (acid). Both DI- and CF-IRMS techniques were applied to a variety of different carbonate minerals at 25 and 50°C and data collected was used to determine temperature dependence slopes for each mineral. The slopes were compared to those in the literature values to provide a better understanding of the temperature dependence of each mineral. This research enhances the precision of future work involving the fractionation of oxygen in acid-liberated carbon dioxide for future applications in fields such as paleoclimatology.

Daniella Pryke

Supervisor: Dr. Sarah Glen
Abstract not available.

Phil Lauman – Investigating the link between critical thinking and understanding of evolutionary theory in undergraduate students.

Supervisor: Dr. Sarah Symons
In the information age, many aspects of the modern lifestyle are becoming increasingly complex and Critical Thinking (CT) skills are often required to navigate these challenges. Moreover, since the internet makes most factual information accessible at the push of a button, it is clear that an ability to understand and think critically is rapidly replacing rote memorization in terms of practical importance to society. As such, it is imperative that education systems be modified to address this new requirement. Several course topics have been shown to correlate strongly with CT skills, and previous research has clearly demonstrated that an infusion approach to CT-development, in which teaching mechanisms designed to develop CT are infused into courses dealing with these select topics, is much more effective than direct approaches to CT- development in terms of documented increases in both specialized and generalizable CT skills.

Evolutionary theory is an important academic topic and requires elements of CT for full comprehension, suggesting a link that could be exploited in the development of infusion-based course modules in which evolutionary theory is used to develop generalizable CT skills. To verify the existence of this link, we developed an optional, anonymous online survey consisting of four sections, which assess acceptance of evolutionary theorydisposition towards scientific thinkingcritical thinking skills, and understanding of evolutionary theory, and circulated this survey via e-mail to the undergraduate population of McMaster University. Our results indicate strong correlations between understanding of evolutionary theory and critical thinking skills (p = 0.0003) as well as between understanding of evolutionary theory and acceptance of evolutionary theory (p = 0.0007) and disposition to scientific thinking (p = 0.0004). These results confirm the existence of a link between CT skills and an understanding of evolutionary theory, which may be used to design course modules that use evolutionary theory to develop generalizable CT skills.