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


Katherine Woodstock – The role of C-reactive protein as a risk marker for acute myocardial infarction: a systematic review.

Supervisor: Russ Ellis
In order to better assess cardiovascular disease risk, significant research has been conducted on C-reactive protein (CRP) as an alternative risk marker. Elevated CRP levels can indicate heightened arterial inflammation, and therefore increased risk of cardiovascular disease. It has been found that populations of lower socioeconomic status have higher CRP levels overall, partially due to chronic stress and other health issues that are disproportionately prevalent. Therefore, linking CRP levels to cardiovascular disease risk would help explain the higher incidence of cardiovascular disease in people of lower socioeconomic status. The aim of this systematic review was to determine the current consensus on the viability of CRP as a cardiovascular disease risk marker. Specifically, the association between CRP levels and acute myocardial infarction (AMI) incidence was assessed. A systematic review of PubMed was conducted to identify all retrospective, case-controlled studies assessing the role of CRP as an AMI risk marker. Only articles where measured CRP levels were effective as a proxy for preinfarction levels were included for analysis. It was found that AMI patient groups had elevated CRP levels more frequently than control groups (Odds Ratio>1). This indicates that elevated CRP levels are likely to indicate AMI risk. This study suggests that heightened CRP levels indicate increased cardiovascular disease risk, supporting its potential as a mediator of the relationship between socioeconomic status and cardiovascular disease. CRP is potentially applicable as a general risk marker for AMI, as well as in creating more targeted interventions to address disparity in cardiovascular disease incidence.

Julia Martinko – Expression of targets of the peripheral serotonin system in human and rat liver cells.

Supervisor: Dr. Alison Holloway
The liver plays a central role in energy homeostasis as an important regulator for both glucose and lipid metabolism. Dysregulation of energy homeostasis in the liver can lead to diseases such as obesity, diabetes, and fatty liver disease. Peripheral serotonin synthesized in the gastrointestinal cells acts on the liver to regulate glucose and lipid homeostasis. Key targets of the peripheral serotonergic system include tryptophan hydroxylase I, serotonin transporter, and serotonin receptors 1A, 2A, 2B, and 2C. Studies in the central nervous system demonstrate that disruption of serotonergic signalling by environmental contaminants such as pesticides has biologically relevant consequences. A similar disruption of the peripheral serotonin system in the liver may cause an imbalance in energy homeostasis leading to metabolic disease, however this has not yet been studied. The goal of this project is to determine the level of expression of these targets in the liver of rats and humans, to develop an animal model for use in these studies. RNA was obtained from McA-RH7777 rat hepatoma cells and Hep G2 human hepatocellular carcinoma cells. Reverse transcription was performed to generate cDNA, and quantitative realtime polymerase chain reaction was completed to determine the expression of the targets discussed above. These results will show the expression of these targets in each cell type, which will facilitate the development of a rat model which can be translated to humans. Future research will elucidate the role of the peripheral serotonergic system on metabolism in the liver, and further understanding of how environmental contaminants are associated with metabolic disease.

Kira Innes – Dust in the centre of supergiant elliptical galaxies.

Supervisor: Dr. Robert Cockcroft and Dr. Bill Harris
Supergiant elliptical galaxies are the largest existing galaxies in nature. These objects are thought to have grown through the accretion of smaller satellite galaxies. Such accretion events can leave behind traces of small particles in the form of dust, which accrete to the centre of the galaxy more slowly than the majority of the satellite galaxy. By examining the centres of such galaxies, any dust that remains can be studied. The dust properties of 17 supergiant elliptical galaxies imaged with the Advanced Camera for Surveys of the Hubble Space Telescope in the B- and I-bands are examined. Dust is observed in 12 of 17 galaxies, 4 in the form of disks or spirals, 5 in the form of lanes, and 3 with irregular dust patterns. Through comparing models of the galactic light to the original image, we can isolate the light that is blocked by the dust features. The light blocked by the dust can be compared to characteristics of the dust features such as ellipticity, radius, and position angle, to give a more thorough understanding of the dust features. By examining dust patterns in the centres of such galaxies we hope to gain a better understanding of how merger events occur.

Conserved Hunter software by understanding the mechanism behind promoter regions.

Supervisor: Dr. Jonathon Stone
The objective of this project is to enhance the Promoter Regulatory Conserved (PoRC) Hunter software, a new computational tool that is being developed by Dr. Jonathon Stone’s lab. This tool is a promoter search program that utilizes a novel algorithm, whose main objective is to determine the most likely sequence within a gene that acts as a promoter. In order to accomplish this objective, the software identifies the section in the sequence that contains the highest quantity of non-random motifs, referred most commonly as core promoter elements. Even though, other promoter search programs that have already been developed, there are many inherent difficulties in promoter recognition, such as the high probability that a short motif can occur just by chance. PoRC Hunter manages these difficulties better than other existing programs. In order to enhance this program, I will first write a literature review on promoter regions and the promoter searching software, that have already been released. After I complete this, I will develop a feature that will improve PoRC Hunter. With this feature, I will try to generate a new pattern that will encompass the diversity of promoter regions more efficiently. If I do not find a method to accomplish this goal, I will develop a graphic interface that makes the software more appealing and user friendly. In the event that I have some time leftover, I will look into the algorithm behind the software and I will attempt to improve upon it. Developing a new feature for this software, will help researchers identify and analyze regulatory regions more effectively, in genes whose mechanism is poorly understood.

Vincent So – Characterization of the two human CDP-diacylglycerol synthase isoforms using bioinformatic tools.

Supervisor: Dr. Richard Epand
CDP-Diacylglycerol Synthase (CDS) is a critical enzyme that catalyzes the formation of CDP-diacylglycerol (CDP-DAG) from phosphatidic acid (PA). CDS plays a key role in the synthesis of several phospholipids including phosphatidylinositol (PI) through the PIcycle. There are two mammalian isoforms, CDS1 and CDS2. Of the two isoforms, only CDS2 exhibits acyl chain specificity for its lipid substrate, specifically 1-stearoyl-2- arachidonoyl-phosphatidic acid. Arachidonic acid is a biomolecule, which can be liberated from PI cycle intermediates and can have a pro-inflammatory role. In addition, arachidonic acid has been suggested to have a role in cancer and cell proliferation, making enzymes that enrich phospholipids with arachidonoyl moieties an important area of study. This project aims to use bioinformatics tools to analyze the key differences between the isoforms of CDS. Although the enzymes exhibit sequence similarities, there are key differences that may explain differences in function. Bioinformatic tools have also predicted that the isoforms have varying structural components, post-translational modifications (phosphorylation sites), and sites of protein expression. Preliminary results suggests that CDS1 and CDS2 undergo different post-translation modifications and that perhaps CDS2 might be more tightly regulated and CDS1 might be more of a constitutive enzyme. This suggests that each isoform may play a different role within the cell and may be subject to independent regulation and localization. It is therefore important to study the enzymes that exhibit acyl chain specificity (specifically for arachidonoyl moieties), such as CDS2, in hopes of elucidating the mechanisms behind PI synthesis that are important in cancer and cell proliferation.

Robert Rawlins – TBA.

Supervisor: TBA
Coming soon.

Andrew Valente – Lichen algae desiccation tolerance and relations to photosynthetic protein mobility.

Supervisor: Dr. Cecile Fradin
Photosynthetic organisms are subjected to many stresses including osmotic and high light stress (excessive light energy). Water is necessary in proper functioning of the photosynthetic proteins which harvest light energy. Under dehydrated conditions, the photosynthetic proteins can become damaged if the absorbed light energy cannot be dissipated safely. The algae occurring as the photobiont in lichen have developed photoprotection mechanisms allowing themselves to safely dissipate the excess light energy. Mechanisms include energy spillover from the less robust PSII protein to the hardy PSI protein, physical shading by changes in the lichen structure, and quenching by other molecules in the chloroplast. The tolerance of the algae has been shown to be dependent upon the rate of desiccation though the exact mechanisms behind this dependence are unclear.

As such it is important that a more complete picture of the dynamics of photosynthetic proteins be developed. Here, fluorescence techniques including fluorescence correlation spectroscopy and fluorescence recovery after photobleaching are used to determine the mobility of photosynthetic proteins. The employment of these techniques allows for the rate of diffusion of the PSII protein to be approximated and compared under different cell conditions. From the data and 3-dimensional reconstructions of the chloroplast, it is apparent that the diffusion is more complex than simple 2-dimensional diffusion, with some of the protein being bound or immobile while a subset of the population is free to diffuse. It is concluded that further investigation is required for a full understanding of PSII diffusion to be made and suggestions will be made for future work.

Julia Higgins – Effectiveness of online learning resources for the reinforcement of undergraduate education.

Supervisor: Dr. Jason Brodeur
Within postsecondary educational institutions, the vast majority of students rely on online teaching resources to help with their understanding. Online learning tools are becoming more prevalent in the classrooms, and it is important to understand what makes these tools beneficial. The aim of this project to create a practical learning website for 3D printers which uses pedagogical research as a basis for content displayed, and how this content is displayed. 3D printers are becoming more popular in many industrial and educational settings. They have the potential to greatly benefit undergraduate students by reinforcing their understanding of many scientific concepts that may be hard to communicate orally. An online database for the 3D printers will be created, with topics such as a step-by-step guide on how to use the printers, resources for model prototypes, and user troubleshooting. However, in order for this to become a practical means of further education, the website must be able to teach the students in an effective way. By creating this pedagogically reinforced website to help students learning, it will be able to determined what learning tools worked well and which need improvement.

Liming Chen and Geneva Neal – Improving resources for teaching the behaviour of van der Waals gas.

Supervisor: Dr. Randy Dumont
Current simulations used to enhance student understanding of thermodynamic processes tend to focus only on ideal gases and lack a connection between macro- and microscopic behaviour. This project involved the creation of a new learning resource for undergraduate students studying thermodynamics at McMaster University. The purpose of this resource is to improve student understanding of the macro- and microscopic behaviour of a van der Waals gas, as well as a heat engine as it undergoes isochoric, isobaric, isothermal, and adiabatic processes. This resource aims to provide a more realistic visual understanding for students in thermodynamics. Self-paced student activities were developed using best-practices from the pedagogical literature and focus on conceptual understanding of thermodynamic processes, particularly those necessary for the operation of heat engines. These activities will accompany a computer simulation currently being developed by Dr. Dumont which will allow students to manipulate the variables in the program and observe the different outcomes of the thermodynamic system in both microscopic and macroscopic points of view. These variables include different gases and their masses, mass of the piston, temperature and pressure. The activities are designed to proactively target common misconceptions and disentangle the appearance of the unified behaviour of the gas at a macroscopic level with the stochastic processes occurring between individual particles. Ultimately, this activity provides a bridge between the abstract mathematical relationships taught in class and the actual behaviour of the systems studied.


Bianca Bantoto – Suicidal ideation and behavior among methadone maintenance patients: identifying and evaluating risk factors.

Supervisor: Dr. Zena Samaan
The misuse of prescription opioids within Canada has risen at an alarming rate. Extensive prescription of pain medications, combined with their highly addictive nature, has propelled an increase in the non-medical use of opioids and a consequent surge in health problems. Methadone maintenance treatment (MMT) is the most widely used treatment for opioid dependence, and has been associated with lower mortality, illicit opioid use, criminal activity, and health care costs. As enrollment in MMT programs continues to grow alongside rising rates of opioid dependence, the more pressing the need to investigate the psychiatric and medical comorbidities of MMT patients.

Suicide risk, which is associated with drug dependence, is a particular concern. The principal objective of this study is to investigate the characteristics of MMT patients reporting suicidal ideation and behavior. This multi-centre study recruited patients (n=409) receiving methadone as a treatment for opioid dependence between May 2013 and March 2015 from ten methadone clinics across Southern Ontario. Demographic information, medical history, methadone dose, methadone treatment duration, and psychiatric assessment were obtained using structured interviews. This data was then analyzed using a descriptive statistical summary and a multivariable logistic regression model created in STATA 12.

As the population of MMT patients continues to increase, the identification of risk factors influencing suicidal behavior in this population is imperative in order to take appropriate action in monitoring suicide risk. By recognizing these risk factors, suicide risk may be better assessed, and as such, steps may be taken in preventing suicide among MMT patients.

Nick Luymes – Resource partitioning of overwintering tree-foraging birds at the McMaster Conservation Corridor.

Supervisor: Dr. Chad Harvey
The optimal foraging behaviour of overwintering birds is a topic that has not yet been examined in the McMaster Conservation Corridor. As one of the goals for the Corridor is to act as a model system for other urban forests, research into the ecological interactions associated with these behaviours is needed for a more complete understanding of the overall ecosystem functions. The present study focussed on understanding the effects that multiple species of coexisting birds had on species specific foraging behaviours. In doing so the goal was to learn whether or not the birds were partitioning the available resources as a strategy to avoid competition. To test for the presence of resource partitioning, observational methods will be used to determine the foraging locations of resident bird species in the different habitat types of the Corridor. The observational data will be analysed to determine (1) if there are preferences in habitat, tree species and location on tree; and (2) if these preferences differ between birds. If significant differences are found, it will show that the birds are using the available resources in different ways, which will provide evidence for the existence of resource partitioning. A better understanding of the foraging behaviour of resident birds at the Corridor will contribute to greater insight into the intricate processes involved in urban forests. These processes are important for groups that are looking to conserve urban forests for the many benefits they provide including mental health improvement and air purification.

Emma Butcher – Is accelerated artherosclerosis a microvascular complication of diabetes?

Supervisor: Dr. Geoff Werstuck
Atherosclerosis is an accumulation of plaque on the walls of large arteries. These plaques can occlude arteries and carry high risk of rupture, leading to aberrant blood clotting, heart attack, and stroke. Atherosclerosis-mediated cardiovascular disease is the leading cause of death worldwide, but its prevalence is particularly high in individuals with diabetes. It is believed that hyperglycemia damages the walls of arteries, exacerbating atherosclerosis and risk of cardiovascular disease. Diabetes is also known to cause abnormal angiogenesis in very small blood vessels, or microvessels. It is possible that changes in the microvessels that feed the walls of large arteries, known as the vasa vasorum, may accelerate the development of plaques by causing decreased perfusion. The objective of this project is to determine whether diabetes causes changes in the density of vasa vasorum, which would designate atherosclerosis as a microvascular complication of diabetes. Human coronary arteries have been collected from individuals with and without diabetes from the Hamilton General Hospital morgue. The vasa vasorum was stained immunohistochemically for von Willebrand factor, a coagulant factor that is secreted from arterial walls. Inverted fluorescence microscopy and NIS-Element software were used to visualize and quantify the density of vasa vasorum. Researchers were kept blind as to whether samples originated from individuals with diabetes until study completion. Results have yet to be analyzed. Correlation between diabetes and lower density of vasa vasorum will provide strong evidence that accelerated atherosclerosis is a microvascular complication of diabetes, opening new options for prevention and treatment of cardiovascular disease.

Braedan Huras – White-tailed deer habitat preference in McMaster Forest.

Supervisor: Dr. Chad Harvey
The McMaster Forest has been the focus of many plant-centred studies, but the animal inhabitants have been much less researched. White-tailed deer are a large ungulate species that occupy the McMaster Forest and studying their foraging habits and population ecology can provide information about ungulate impacts in urban forests. The McMaster Forest is split into many different habitats, each with their own vegetation composition. This study aims to find a correlation between habitat and where white-tailed deer prefer to forage and rest. In order to reach this goal, field transects were completed to count the number of faecal pellet groups and bed-down spots in each surveyed habitat. These transects stretched from one end of the habitat to the other and were about 75m apart. However, some habitats were difficult to survey due to extreme slopes or other restricting factors. After data collection, statistical analysis using ANOVA tests will be performed to determine if habitat preference is significant. This will provide useful information about ungulate population ecology impacts in urban forests, specifically deer behaviour in the presence of human influence. This type of study can also provide information about the population size, leading to an understanding of whether or not the area is overpopulated or underpopulated so that human action may be taken to restore local biodiversity. While analysis has yet to be completed, the results so far do appear to indicate some sort of habitat preference. In conclusion, this research will provide important information regarding ungulate population ecology in urban forests and can be applied to other urban forests in Ontario as well as future studies in the McMaster Forest.

Aaron Goldberg – Quantum catastrophes: investigating the singularities in a system of bosons in a double well.

Supervisor: Dr. Duncan O’Dell
Singularities are important in any theory, as they indicate the situations in which the theory breaks down. It has been shown that the stable singularities of any gradient map, or any theory described by the extremization of some quantity, must belong to a certain finite set of geometric structures known as catastrophes. Quantum mechanics is an example of a gradient map, and so it is imperative to discover the circumstances that necessitate a more sophisticated level of theory. The system we study here is a set of bosons in a double well potential. In the mean-field limit in Fock space, the Hamiltonian for this system is analogous to that of a pendulum; however, it has been shown that the mean-field treatment yields “cusp catastrophe” singularities. By analytically reducing the full Hamiltonian to a set of coupled partial difference equations, we use MATLAB to both solve this system of equations and numerically diagonalize the Hamiltonian, both of which resolve the cusp catastrophes. We use these two methods to investigate the structural stability of the cusp catastrophes. It has also been theorized that this system will undergo a dynamical phase transition in crossing the mean-field Hamiltonian’s separatrix, analogous to the pendulum completing full revolutions. We intend to fully characterize this transition, by applying the two methods to further investigate the effect of temporally varying the barrier between the two wells. The results from this study will be used to answer the fundamental question of where certain theories of quantum mechanics are inadequate.

Jessica Kun – Characterization of STAT3-inhibitor complexes.

Supervisor: Dr. Alba Guarné
Cancer is one of the most common causes of death worldwide. Research into causes, prevention and treatment are being done, with one of the most prevalent therapies being direct targeting through the use of chemotherapeutics. A promising target for such therapy is STAT3. The signal transducer and activator of transcription (STAT) family of proteins are important for cell proliferation and survival. They are activated through an extracellular growth signal that triggers a signaling cascade resulting in the dimerization and translocation of the STAT proteins into the nucleus to bind to promoter regulatory elements. In cells that function normally, this pathway is highly regulated; however, various extrinsic factors can result in unusual activation of STAT proteins leading to a higher incidence of dysregulated growth and survival of damaged cells, a hallmark of cancer. Recent research has indicated that specific targeting of STAT3 to prevent dimerization can alleviate unusual activation and work as treatment against tumors. Several inhibitors have been created, tested, and optimized for inhibitory activity. The objective of this project is to determine how the inhibitor specifically binds to the protein. In order to do this, we will be determining an X-ray crystal structure of several inhibitor-protein complexes. By studying the specific binding region in the complex it can be understood in detail and inhibitors can be further optimized. Targeting STAT3 with optimized inhibitors is a promising route for cancer therapy.

Aakash Shaw – Demonstrating the safety of an oncolytic vaccine for HPV cancers.

Supervisor: Dr. Brian Lichty
High-risk strains of the human papillomavirus (HPV) are the cause of 90% of cervical cancers and as recently established, 25% of head and neck cancers. These cancers express major HPV proteins, E6 and E7, which are responsible for degrading tumour suppressors p53 and pRb respectively and thus contribute to tumour development. Tumours comprised of E6/E7 can be targeted via engineered oncolytic viruses; inactivated viruses which express mutated E6/E7 proteins in order to stimulate an immune response against HPV-derived cancers. This study attempted to determine the degree of oncogenicity associated with mutated E6/E7 proteins in order to validate their use in therapeutics. Lipofectamine DNA transfections were performed to transfect mutated E6/E7 into carcinomic alveolar epithelial cells (A549). A549 cells were ideal for this test because they express specific amounts of p53 and pRb and these levels provide an indication of the activity of mutated E6/E7. A Western blot was conducted to measure levels of p53 and pRb in both groups. The transfected proteins should be unable to degrade p53 and pRb due to mutated interaction sites on E6/E7 and thus it is anticipated that both groups should show similar levels of the tumour suppressors. The findings of this study would confirm the degree of oncogenicity for mutated E6/E7 and provide verification for the use of mutated E6/E7 in viral oncolytic therapeutics. The implications of this study will be significant for improving the treatment and prognosis for HPV-derived cancers.

Suvin Chandula Fernando – The feasibility for neutron tomography in the McMaster Nuclear Reactor.

Supervisor: Dr. Nicholas Bock
There aren’t many quality sources of neutrons in the world. With this in mind, The McMaster Nuclear Reactor (MNR) is a valuable resource with three beam ports, each providing a high quality beam of thermal neutrons (0.01 eV – 0.5 eV) ideal for neutron radiography. Currently two of these beam ports (BP1 and BP2) are used to conduct two-dimensional neutron radiography. This independent project investigates the feasibility of implementing a three-dimensional neutron tomography system for the remaining Beam Port 3 of the McMaster Nuclear Reactor. MATLAB was used to model the neutron beam and its interaction with a standardized “phantom”, to simulate theoretical images created by the proposed system. This involved taking multiple 2D projections of the phantom at varying angles and reconstructing the three-dimensional image using back-filtered projection. Since the detectors of the system collect count data, image noise was simulated using a Poisson distribution. While conducting the maximum number of projections (180) resulted in the image with the least noise, it also required the most time to produce. The efficiency of the system was maximized by conducting multiple trials to determine the minimum projections required to produce an image with reasonable contrast and signal-to-noise ratio.

Neutron radiography is crucial for industrial purposes, exposing the internal structures of metal bodies that can’t be penetrated by x-rays. Neutron tomography can improve neutron radiography and can introduce similar benefits to industrial imaging as Computed Tomography (CT scans) did to x-ray radiography in medical imaging.

Nicole Yokubynas – Investigation of prenatal nutrient restriction on accelerated ovarian follicle recruitment in the PI3K/Akt signalling pathway.

Supervisor: Dr. Deborah Sloboda
Developmental programming induced by poor prenatal nutrition causes decreased ovarian follicle numbers, resulting in early ovarian aging (EOA) and decreased fertility. This presents a risk to the female offspring of women who do not comply with nutritional requirements during pregnancy. Recent findings have confirmed that prenatal nutrient restriction (UN) in rats resulted in a significant decrease in antral follicles with an insignificant difference in the primordial follicle count in adult offspring, suggesting that EOA may be dependent on accelerated primordial follicle recruitment. Primordial follicle recruitment is regulated through the PI3K/Akt pathway. The quantity of fundamental proteins involved in this pathway were analyzed in order to determine if this pathway is differentially regulated in nutrient restricted offspring. Ovarian tissues of offspring at p4, p27, and p60 days postnatal age from female rats fed a control diet (100% standard chow ad-lib during pregnancy and lactation) and an UN diet (50% control diet during pregnancy, 100% control diet during lactation) were used for analysis. Tissues were stained for immunopositive phosphorylated Akt, phosphorylated FOXO3a, c-kit receptor, AMH and the AMHRII receptor to localize and determine ovarian protein levels in the PI3K/Akt pathway. Preliminary results indicate localization of phosphorylated Akt and FOXO3a in the oocyte, c-kit receptor on the oocyte membrane, and of AMH in the ovarian granulosa cells. Additionally, increased immunohistochemical staining of pAkt in UN p4 and p27 ovaries, and increased phosphorylated FOXO3a in UN p27 and p60 was observed. These initial results suggest an upregulation of proteins in the PI3K/Akt pathway in UN neonates, supporting the hypothesis of accelerated follicle recruitment in nutrient restricted subjects as a mechanism of EOA.

Relevant Sources
Bernal, A.B. et al., 2010. Maternal undernutrition significantly impacts ovarian follicle number and increases ovarian oxidative stress in adult rat offspring. PloS One, 5(12), p.e15558.

Nickolas Goncharenko – Developing a protocol for the high throughput synthesis of hydrogels for use in in vitro assays .

Supervisor: Dr. Ryan Wylie
Hydrogels are a class of polymers which dramatically expand in water. Ideally, hydrogels which are stable at physiological conditions (7.4 pH, 37°C, hydrophilic etc.) are beneficial in many fields including implants, stem cell support, drug delivery and cell migration. This is because hydrogels mimic the extracellular matrix (ECM) at physiological conditions. One of the best polymers for this purpose is poly-ethylene glycol (PEG), as it is both inert and non-toxic, but can be functionalized with moieties to change its chemical and physical properties.

To date, hydrogels have been synthesized as one or two variants at a time. By synthesizing gels in 150 μl volumes, the gels can be synthesized in high throughput, so many different gels can be tested at the same time. Ideally the gel is synthesized in high yield with few free moieties. Washing, if required, complicates high throughput assays, as free moieties would invalidate the results.

To see if high-throughput synthesis of hydrogels is possible, a method of PEG hydrogel synthesis by click chemistry reported by Pritchard et al. has been modified and its ability to incorporate moieties has been tested. PEG gels functionalized with SAMSA-fluorescein were equilibrated with phosphate-buffered saline (PBS). Based on fluorescence readings from the fluorophore in the PBS solution the percentage of free moieties was determined. The percentage of free moieties after washing was highly dependant on the weight percentage (%wt.) of the gel, with higher weight percentage having the highest fluorophore retention.

Rui Xu – The biophysical theory of the bolalipid membrane.

Supervisor: Dr. An-Chang Shi
The application of theoretical and computational techniques to the study of biological membranes has proven useful for understanding fundamental properties of bilayer membranes. One such technique, originally applied to the study of polymers, is Self-Consistent Field Theory (SCFT). In this study, we use SCFT to investigate the stabilizing effect of bolalipids in biological membranes. Bolalipids are found in the membranes of Archaea living in extreme environments. We model lipids as block copolymers, forming self-assembled bilayer membranes in flat and curved geometries. We investigate the effects of lipid composition, specifically phospholipid versus bolalipid, on physical and mechanical properties of the membrane, such as bending moduli, line, and surface tension. These properties can be combined into the Helfrich bending energy, a measure of the elasticity of an open lipid membrane. It is expected that the bolalipid membrane will have a higher Helfrich bending energy than the phospholipid membrane, due to a reduction in conformational degrees of freedom associated with the bolalipid. The study of the Helfrich bending energy will advance the understanding of whether the bolalipid membrane allows Archaea to survive in extreme environments. Molecular dynamics simulations suggest that these membranes have greater rigidity than their phospholipid counterparts. However, analytical studies of bolalipid membranes disagree with these findings. This study is the first to apply SCFT to bolalipid membranes, and should solve this disagreement between molecular dynamics and analytical calculations. If increased bolalipid membrane rigidity is confirmed, bolalipids may hold promise in drug microencapsulation.

Katie Maloney – Investigating the applications of Google Earth in first year Earth and Environmental Science courses.

Supervisor: Dr. Carolyn Eyles
Undergraduate students often find visualizing Earth Science topics to be a challenging process. A geographic information system that is accessible and easy to use can be an asset to help students visualize and conceptualize ideas that are introduced in class. To investigate the practicality of implementing Google Earth in first year Earth and Environmental Science courses three virtual “tours” were created focusing on a variety of curriculum-based topics, including plate tectonics, volcanoes, and glaciers. Professors can embed Google Earth tours within their lectures to clarify how concepts fit together and relate to geographic locations on the Earth. Other applications of these tours could include an audio script to enable the material to be presented as an on-line activity or activities could be designed based on data collection through the software. The results of this study will be applicable to other disciplinary areas where students would benefit from enhanced understanding of the spatial distribution of phenomena.

Shawn Kurian – Investigating the involvement of the Greceptor in regulating guanosine’s trophic effects.

Supervisor: Dr. Shucui Jiang
Millions of people across the globe suffer from spinal cord injury (SCI), stroke, and neurodegenerative diseases. Studies have demonstrated that following SCI or disease, extracellular guanosine exhibits many neuroprotective effects. Further research suggests that guanosine exerts its trophic effects by binding to its own cell-surface receptor, the G1 receptor. This experiment will provide additional support for the involvement of the G1 receptor in regulating guanosine’s trophic effects, including its effects on cell morphology, apoptosis, and survival. Following apoptosis and guanosine administration in transfected and non-transfected (with the G1 receptor) Drosophila Schneider 2 (S2) cells, a light microscope will be used to compare the cell density, viability, and number of survived cells. Additionally, using a confocal microscope, images of the cells will be captured to compare their sizes and morphology. Altogether, three treatment methods will be used for each cell type: guanosine, guanosine vehicle, and a control. The overarching hypothesis is that having received guanosine treatment; the transfected S2 cells will show significantly reduced apoptosis. As such, they will appear healthier: denser, and larger in size and number. Furthermore, transfected S2 cells from guanosine vehicle and control treatments will show results similar to non-transfected S2 cells and appear less healthy: most of the cells will have undergone apoptosis with a significant decrease in size and density. This experiment will contribute to the literature by providing concrete visual evidence of guanosine’s anti-apoptotic effects. It will also provide further support for the involvement of a specific cell-surface receptor in regulating guanosine’s trophic effects.

Lauren Oldfield – Hawaiian experiential course proposal.

Supervisor: Dr. Carolyn Eyles
“For the things we have to learn before we can do them, we learn by doing them” (Aristotle) and what better way to learn about the Hawaiian Islands than through a hands-on experience? This presentation will describe a proposal for an experiential course to be run through McMaster University for science students. The itinerary, course evaluations, logistics of the trip, and accommodations are all addressed. The proposed experiential learning course would take on many facets of scientific learning through a hands-on, interdisciplinary approach. The course will span subjects such as geology, ecology, marine biology, and topics such as the introduction of foreign species into the island ecosystem, volcanic activity of the islands, the balance between people and nature, renewable energy and resources of the island, as well as Hawaiian history and culture. Students will learn and utilize skills pertaining to fieldwork methods and analysis. The aim of this course is to allow students to garner skills across all areas of science and to gain in-depth understanding of a unique island environmental system. Students will explore Oahu and the Island of Hawaii (Big Island) over the course of approximately 12 days and will visit numerous points of educational interest, including: Volcanoes National Park, home of the infamous Kilauea Volcano; Hanauma Bay, a secluded bay allowing access to the marine ecosystem; Diamond Head Crater, an extinct volcanic vent; and Pearl Harbour, home of the historic WWII naval base. Student evaluation will be based upon a pre-trip assignment, a presentation whilst in Hawaii, a final project, a field notebook evaluation, and an oral exam.

Daim Sardar – Biocuration and antibiotic resistance: analyzing the 16S rRNA of Escherichia coli to detect potential antibiotic resistant mutations.

Supervisor: Dr. Andrew McArthur
Antibiotic resistance acquired by infectious bacteria is an increasingly evolving threat in the world today. Although classical microbiology techniques that study both antibiotics and antibiotic resistant elements are vital to this field, bioinformatics and the genome revolution are providing new avenues through which to explore this issue. Bioinformatics is an invaluable tool in the field of antibiotic research that bridges the gap between biomedical research and clinical healthcare. The Comprehensive Antibiotic Resistance Database (CARD) developed at McMaster University aims to unify data in this field into a single, accessible tool. By using this database, the objective is to analyze an Escherichia coli genome dataset provided by the National Microbiology Laboratory for evidence of antibiotic resistant mutations. For this research, mutations in the 16S rRNA of the small ribosomal subunit will be analyzed. Currently in the CARD, there are no data available for mutations in this subunit. The first part of the project was to design an ontology structure to provide an organizational framework for loading 16S mutation data into the database. An ontology of biological terminology is a system that models concepts and the relationships between them. By working alongside programmers, the structure was curated into the CARD, along with the mutation data. After this reference data was incorporated, sequence analysis using the Resistance Gene Identifier tool of the CARD will be used to analyze the E. coli genome data to identify potential mutations against any antibiotic. Determining the role of the 16S rRNA in antibiotic resistant strains of E. coli will provide valuable information for both diagnostic testing and future studies.

Michael Gill – Analyzing financial networks in the National Banking Era.

Supervisor: Dr. Matheus Grasselli
In September 2008, the default of the massive financial firm Lehman Brothers sent ripples through international markets. The crises that followed cost thousands of people their homes and jobs, while economies across the globe were sent into a recession. The inability of financial regulators to predict or control such large-scale problems demonstrated an incomplete understanding of how default and illiquidity spread through financial networks. A large reason for this lies in the opaque nature of contemporary financial networks.

By studying simpler systems, however, we may be able to obtain a better understanding of current networks. This project aims to explore the qualities associated with one such system: the National Banking Era. Specifically, I will explore the qualitative and quantitative traits of the banking crises in this era, which spanned from 1863 to 1913 in the US. This includes examining trends in aggregate balance sheets, determining detailed accounts of the real crises that occurred in the period, assessing statistical properties of the network, and examining the results of shocks modelled through MatLab.

Assessment of the literature suggests 1893 as an ideal test year, but even here there is limited evidence of bank default. This aligns with preliminary testing, which demonstrates that the model is resistant to default cascades. Instead, history suggests that illiquidity cascades will be observed following a shock to the model in any crisis year. Finding this would suggest that illiquidity has a much greater role to play in bank crises that default.


Heather Fice – Transforming the development of inquiry skills: quantifying inquiry-based learning skills in chemistry and chemical biology students.

Supervisor: Dr. Pippa Lock
In recent years, there has been a shift in pedagogical research to begin examining the development of different learning skills within science. Problem-based learning and critical thinking have been thoroughly examined; however inquiry-based learning (IBL), specifically in the realm of chemistry, is an area that is not yet present in the literature. IBL hinges on students’ inherent curiosity. There are eight main skills associated with IBL: accountability for one’s own learning, oral communication, written communication, ability to access primary literature, ability to critically analyze primary literature, ability to develop an experimental method, ability to critically analyze an experimental method, and ability to develop a research question. Student perceptions of IBL skill development, based on those specific eight skills, have been observed through online mixed-methods surveys that analyze many sources of IBL skill development.

Additionally, an instrument will be developed to quantitatively assess students’ IBL skill development. This instrument will consist of a question set and an associated rubric. This will be developed with the use of pedagogical literature as well as data from in-person interviews with inquiry teaching professors. Understanding the relationship between student perceptions of, and quantitative values for, IBL skill development may provide valuable insight into the benefit of learning experiences available to students. As courses and programs are refined, this may allow more beneficial opportunities to be incorporated into their learning experience. It is expected that this research will reveal a relationship between student perceptions of IBL skill development and a quantitative assessment of that development. This research is specifically relevant to course development in Chemistry and Chemical Biology, and can potentially be transferred to developing or assessing inquiry in other disciplines.


Alexandra Garbe – Acute flaccid paralysis in Canadian children: evaluation of etiological factors and response to therapy.

Supervisor: Dr. Kevin Jones
During the fall of 2014, an unusually high number of children in North America were reported to have acute flaccid paralysis (AFP) with anterior myelitis. AFP is the sudden onset of weakness or paralysis in the muscle, and anterior myelitis is inflammation or lesions in the gray matter of the spinal cord. AFP with anterior myelitis is typically associated with viral myelitis, including poliomyelitis, which is caused by poliovirus. These reports coincided with an outbreak of respiratory illnesses caused by enterovirusD68 (EV-D68), which is being investigated as a potential cause. This project is part of a national collaborative study designed to determine the etiology, clinical presentation, neurological findings, optimal treatment, and outcomes of this disease. A systematic literature review was conducted and identified similar reports that had inclusion criteria related to our study. This literature was used to establish a databank to compare our cases against, in order to help identify patterns and explain the etiology. Specifically, we will be comparing the cases of four patients with AFP and anterior myelitis during July – October 2014 from the McMaster Children’s Hospital to this databank. This study aims to determine the causes of these cases, whether that includes EV-D68 or not, identify the best treatments, and predict the outcomes. We expect to find that the causes of these cases are heterogeneous, and not limited to a single pathogen. Additionally, this cohort can be used to establish a foundation of knowledge and data for future studies. AFP is a serious syndrome, and it is important to continue studying this disease and its many causes, in order to properly treat or prevent it.

Amy Jenne – CHEM 1AA3 student perceptions of blended learning in CHEM 1A03, and how this compares to instructor perceptions.

Supervisor: Dr. David Brock and Dr. Pippa Lock
This past summer, the chemistry course CHEM 1A03 at McMaster University transitioned into a blended learning environment. Blended learning is a method of teaching that combines online learning with face-to-face time. Students are provided the required content through the use of online modules, and class time is used for practice problems, demonstrations, and questions from students. Current research in this area has shown that blended learning is beneficial for students in terms of higher grades, lower dropout rates, and for long-term retention of information. Few researchers studying this topic have looked at student or professor perceptions, especially in chemistry. Therefore, this project is focussed on addressing this gap. A survey, with ethics approval, polled students who are currently enrolled in CHEM 1AA3 about their perceptions of CHEM 1A03 instruction compared to the traditional instruction used in CHEM 1AA3. This survey had separate questions for students who experienced the blended version and students who took the course at an earlier point. Interviews with CHEM 1A03 instructors were also conducted to determine how they perceive the implementation of blended learning. It is expected that students will overall prefer the blended learning method to the traditional methods of lecturing due to the increased freedom to learn on their own time. It is expected that professors will also prefer the benefits of blended learning to traditional methods, due to its increased impact on students. The survey and interviews will be used as an aid to transition CHEM 1AA3 to a blended learning format as well as refine the blended CHEM 1A03 course.

Natasha Dovey – Cancer stem cells: evidence, caveats, and areas in which research is lacking.

Supervisor: Dr. Sheila Singh
The cancer stem cell (CSC) has caught the interest of researchers across many fields. A paper published in 1994 by Dr. John Dick and associates described a small subset of cells able to initiate human acute myeloid leukemia after transplantation into severe combined immune-deficient mice. While the cancer stem cell hypothesis rooted in this paper was thought only to apply to non-solid tumours, CSCs have been found to exist in some solid tumours, including glioblastomas and medulloblastomas. Research in the field of CSCs is crucial to expand the base of knowledge with regard to the existence of CSCs in tumours other than those of the blood and brain. As well, it will be critical in the advancement of chemotherapeutic agents with regard to better targeting these drugs to achieve total tumour population elimination. A literature review of both primary and secondary research on the current base of knowledge of CSCs will be used to answer the following questions: how can chemotherapeutics be better developed in order to target the cancer stem cell population in tumours to mitigate the possibility for relapse, what are the hallmarks of a cancer stem cell, both at the intercellular and intracellular levels, and how can they be used to confirm or deny the probability for their existence in a tumour, and what techniques are the most effective at isolating populations of CSCs, and finally, what improvements could be made?

Mankeeran Dhanoa – Characterization of endothelial cells derived from human induced pluripotent stem cells (iPSCs).

Supervisor: Dr. Eva Szabo
Endothelial cells comprise the inner lining of blood vessels within the body and play an essential role in the exchange of waste, nutrients and monocytes between the tissues and the vascular apparatus. The successful differentiation of endothelial cells from induced pluripotent stem cells (iPSCs) has provided a novel opportunity to study pathogenesis specific to these cells, specifically endothelial dysfunction in the development of early onset coronary artery disease (EOCAD). Endothelial dysfunction is a pathological state of impairment of endothelial cells, often inflicted by lifestyle-related risk factors such as obesity, hypercholesteremia, and diabetes. The absence of these risk factors in EOCAD patients suggests that endothelial dysfunction may instead be driven by genetics. In order to determine this, an in vitro model of endothelial dysfunction is needed. An investigation of this nature can be accomplished using endothelial cells derived from iPSCs generated through viral reprogramming of mononuclear cells from blood samples of EOCAD patients. Using reverse transcriptase qPCR, this project aims to characterize and monitor the differentiation of endothelial cells from iPSCs. By detecting transcriptional changes throughout differentiation, it can be determined whether endothelial cells derived from iPSCs in vitro can indeed serve as a model for endothelial cells in vivo. It is anticipated that the transcriptional profile of these endothelial cells will resemble human umbilical vein-derived endothelial cells. The applications of these findings can prompt further investigations into genetic mutations underlying EOCAD, while contributing to the limited body of knowledge surrounding the mechanisms of endothelial dysfunction to improve clinical outcomes.

Nicole Lindsay-Mosher – Investigating the immunogenesis of heparin-induced thrombocytopenia.

Supervisor: Dr. Ishac Nazi
Heparin-induced thrombocytopenia (HIT) is a severe immunological drug reaction that can occur in patients treated with the anticoagulant heparin. Individuals with HIT develop antibodies against complexes of platelet factor 4 (PF4) and heparin, resulting in blood clotting and low platelet levels. It is still unclear why heparin induces drastic immunological responses in some individuals while most patients tolerate it without problems, although recent studies have suggested that pre-existing immunity to PF4/heparin may play an important role in the development of HIT. This study investigates the presence of anti-PF4/heparin-producing B cells in healthy donors and HIT patients. Peripheral mononuclear blood cells (PBMCs) from each sample group were either stimulated for 6 days to induce antibody production or were incubated for 6 days without stimulants. Interleukin-2 (IL-2) and the polyclonal B cell activator R848 were used as memory B cell stimulants. Enzyme-linked immunospot (ELISPOT) assays were used to detect antibody-producing B cells, while antibody concentration was measuring using an enzyme immunoassay (EIA). B cells producing IgM antibodies against PF4/heparin were identified in some but not all healthy donors, while B cells producing IgG antibodies against PF4/heparin were identified in HIT patients. Stimulation with R848 and IL-2 increased anti-PF4/heparin production in PBMCs from healthy donors but not in HIT PBMCs. These results indicate that anti-PF4/heparin-secreting B cells exist in some healthy individuals prior to heparin exposure, and therefore B cell memory could play an important role in HIT. Greater understanding of this process could aid in the prevention and treatment of this disease.

Andrew Valente – The nanoscale structure of bone as determined by TEM.

Supervisor: Dr. Henry Schwarcz
Co-author: Henry Schwarcz
Bone is a composite tissue that supports our everyday activities. The structural characteristics of bone vital to our wellbeing arise from not only the properties of the individual components, primarily mineral and collagen fibrils, but how they are organized and interact. The structure and composition of the composite at the nanoscale is still highly debated and necessary to better understand bone health. The study presented strives to better characterize the bone structure by introducing and using careful techniques designed to minimize the risk of artifacts while allowing for the material to be investigated at the needed resolution.

The mineral of bone can be described as a hydroxyapatite-like crystalline material found as microscopic flakes only a few nanometers thick arranged into larger mineral structures (MSs). Characterization of these larger structures is difficult in whole bone, so it is advantageous to remove the collagen to view how the mineral on its own is arranged. Prior studies using bleach or hydrazine to remove the collagen yielded single flake-like crystals. In thin sections it is noted however that the flakes are typically found stacked on the outside of the collagen fibrils. Using ethylenediamine to remove collagen and preserve these arrangements of flakes or MSs, the properties of the flakes and how they are organized could be studied. Our research has found that the mineral isolated from collagen can produce much larger structures than described previously (over 300 nm) and that our methods have no significant impact on the mineral of bone.

Alan Zhou – CpG methylation as a mechanism of inflammaging.

Supervisor: Dr. Dawn Bowdish
Inflammaging, defined as an age-associated increase in pro-inflammatory cytokines, is implicated in age-related immune dysregulation and health complications including chronic illnesses and frailty. Since inflammation has been associated with methylation status, CpG methylation has been proposed as a mechanism behind inflammaging. Specifically, CpG methylation in promoter regions of pro-inflammatory cytokines is thought to control cytokine expression. However, there is little evidence in the literature to support this. The aim of this study was therefore to identify age-related CpG methylation changes in the promoters of proinflammatory cytokines TNF and IL-6, and to correlate these with changes in serum cytokine levels. To accomplish this, we extracted DNA from young adults (age 19-45, n=56), community-dwelling elderly (CDE, age 60-80, n=50), and nursing home elderly (NHE, age 75-100, n=35). We then used Bisulfite Sequencing and Polymerase Chain Reaction (PCR) to compare methylation status of the TNF and IL-6 promoters between the three cohorts. Results were correlated with previous serum cytokine data from the same three cohorts. Since NHE are the most frail and chronically ill cohort, we hypothesize that they will display the most hypomethylation and the highest serum levels of TNF and IL-6. Conversely, we expect that as the healthiest cohort, young adults will have the least hypomethylation and the lowest serum levels of the pro-inflammatory cytokines. These results would indicate an associative relationship between CpG methylation status and inflammaging. By establishing this connection, we shed light on the role of epigenetic modifications in impaired immune function and declining health in the elderly.

Yachun Cao – TBA.

Supervisor: TBA
Coming soon.

Laura Hogg – Modelling human microbiome succession using NetLogo.

Supervisor: Dr. Jennifer Stearns and Dr. Michael Surette
Over the past couple of decades, microbiologists have turned their attention to the plethora of bacterial populations that make up the human microbiome. The variety and breadth of these bacterial species, particularly those in the gut, are strongly correlated with human health. Population fluctuations do occur in the adult gut; however, the system is generally quite stable. In contrast, dramatic variations in microbial composition occur as the microbiome is established in infancy. For this reason many scientists suspect that the early diversification of the gut has the potential to affect disease susceptibility much later in life. Mode of delivery, breastfeeding, and antibiotic exposure are factors with a known impact on microbiome development. An individual-based model (IBM) was created using NetLogo to describe the impact of these different factors on bacterial succession in the infant gut. This model was calibrated using “gold standard” (naturally-born, breastfed, antibiotic­-free) data from a longitudinal study monitoring a cohort of infants over the span of several months. Stool samples were collected at 3 days, 10 days, 6 weeks, and 12 weeks and 16S rRNA sequences were used to identify bacterial phylogenies present in these samples. The inputs in the calibrated model were manipulated and the resultant outputs analyzed to find causal relationships in the system. The initial bacterial populations present were found to be the most important factor in determining final population structure. This research is particularly relevant when considering possible long term effects of birthing method (cesarean section as opposed to natural birth), as this is when inoculation of the gut first occurs.

Nathaniel Smith – Building simple lab gadgets.

Supervisor: Dr. Deda Gillespie
For cell and synaptic physiology, special gadgets can make certain tasks easier. Physiologists often want to deliver dyes or genetic material to single cells without piercing the cell. Physiologists may also want to deliver picoliter volumes of a drug to tissue in a precisely-timed manner. The first problem can be solved by an electroporator, which is a machine that uses voltage steps at the cell membrane to temporarily create small pores for delivery of a reagent. The second can be solved by another machine called a picospritzer, which allows the user to program the opening of a valve, thus releasing compressed air on carefully timed intervals. While these devices are straightforward in concept, they can be quite costly to buy. Our task was to build a functional single-cell electroporator and a functional picospritzer that could be used easily in the lab.

To begin, we used analogue electronic components on a breadboard to interpret and test model circuit diagrams. Second, we used CadSoft Eagle software to produce the digital code for the final product: a printed circuit board (PCB). McMaster’s Institute of Electrical and Electronics Engineers (IEEE) provided the service of processing the code and etching the circuit onto a PCB. Finally, we soldered the electroporator and picospritzer PCBs into plastic boxes, so they could be used safely in the lab. This project is a good example of the integration of physics (electronics) and neurophysiology.

Derek Hambly – Exploring the geologic evolution of southern Ontario.

Supervisor: Dr. Carolyn Eyles
The impetus for discovery is imagination. Sadly however, instilling the necessary desire to learn into school-aged youth is an ever-increasing challenge. In today’s society of instant gratification and constant technological distraction there is little cause to look around at the world around us and simply wonder. The evolution of Earth is a process that does not occupy chapters of high-school science textbooks, nor does this topic merit direct media coverage. Therefore, teaching this topic to high-school students involves assuming no prior background knowledge. From this platform, developing a medium from which to teach the geologic processes that have shaped the planet is challenging. I have sought to do this by creating two detailed maps with accompanying reports that depict and describe the geology of the landmasses that became Ontario. This informational tool has been directed towards grade 9 and 10 students in Ontario high-schools as a supplementary educational aid for science. The primary objective is to demonstrate that there is a sufficient degree of content to warrant the inclusion of the evolution of Earth and the geologic process involved, as a unit in science at the secondary level. These maps have been compiled from a collection of data from geologic databases and provincial water and mining resources which, when conglomerated into detailed maps, showcase the rich history of our province that predates human history.

Drake Lee – Simulating the synthesis of amphiphiles in meteorite parent bodies.

Supervisor: Dr. Ralph Pudritz
Amphiphiles are extremely important in the origins of life as they can spontaneously form vesicles in water. A substantial number of these molecules were likely brought to Earth on meteorites during the Late Heavy Bombardment period. Meteorites are broken-up pieces of larger bodies called planetesimals. The cores of planetesimals in the protoplanetary disks of solar systems are often heated above 100 degrees Celsius for millions of years by radioactive materials in their interior. This provides ideal conditions for the formation of a whole suite of organic molecules. In order to account for the importance of these molecules in the origins of life on Earth it is vital that we understand how they are formed. This work aims to begin investigating the mechanism for which amphiphiles are formed inside planetesimals. First, a literature review of the organics found in meteorites, specifically monocarboxylic acids was performed. These, unlike the phospholipids largely used today, are the most likely molecules to have been used to form a membrane in early life. The Fischer-Tropsch type reaction is then investigated as the mechanism of formation using a computational software which aims to minimize Gibbs free energy. The conditions for each petrological class of meteorite will be entered into the simulation, and specific abundances of carboxylic acids will be obtained by minimizing Gibbs free energy. Comparing our theoretical carboxylic acid abundances to the actual organics found in real meteorite samples will begin to demonstrate if Fischer-Tropsch type reactions could be responsible for the synthesis of carboxylic acids in planetesimals.

Lauren Smith – Measuring the magnetic moments of M. magneticum using birefringence methods.

Supervisor: Dr. Cecile Fradin
AMB-1 Magnetospirillum magneticum is an aquatic, Gram-negative anaerobic species of bacteria possessing ferromagnetic magnetosome structures that allow the cell to align itself with the earth’s magnetic field. The main focus of this project is to determine whether the magnetotaxis of M. magneticum is due to active or passive sensing of an external field. Finding an answer to this question will provide insight into the functionality of the unique magnetic organelles, which may have future applications in the medical and biotechnology fields.

Quantitative optic experiments were done on both live and dead bacteria to compare the prevalence of active and passive sensing in a magnetic field. It is hypothesized that living bacteria aligning more precisely with the magnetic field will be an indication of active sensing, while dead bacteria aligning more precisely with the field will suggest a passive sensing process. For each experiment, the strength of the magnetic field was varied in order to investigate if and how the field strength plays a role in the importance of active vs. passive magnetotaxis. In accordance with the Faraday effect, it is expected that the intensity of a laser beam passing through a sample in a magnetic field will result in a change in polarization of the light, which was measured and used to calculate the birefringent index of M. magneticum in that field. This birefringent index is related to the magnetic moment of the cells, and will provide an indication of how well the bacteria are able to align with the propagated magnetic field.


Jonathan Ho – Folate synthesis pathway of the Streptococcus milleri Group.

Supervisor: Dr. Michael Surette
The Streptococcus milleri group (SMG) is a group of opportunistic pathogens that are part of the normal human gastrointestinal and respiratory microbiota. When pathogenic, the SMG has been shown to be the causative agent of solid liver and brain abscesses, and has also been implicated in the pulmonary exacerbation of cystic fibrosis patients. The SMG are innately resistant to sulfonamides because they lack the target enzyme dihydropteroate synthase (folP), an enzyme in the folate synthesis pathway. As folate is an essential molecule that is implicated in DNA and RNA synthesis, the absence of this enzyme suggests that the SMG use an alternative and currently unknown pathway to synthesize folate. We hope to identify the folate synthesis pathway of the SMG, and to identify the alternative enzymes used to catalyze the reactions. Using the Joint Genome Institute’s Integrated Microbial Genomes online genomic database, the gene neighborhoods of folate synthesis enzymes in the sulfonamide sensitive Streptococcus agalactiaeand Streptococcus pneumonia will be compared with those of Streptococcus intermedius, a member of the SMG. While the absence of dihydropteroate synthase in S. intermedius has been well-defined in scientific literature, our comparative studies have identified 3 other enzymes that are also absent in the folate synthesis pathway of S. intermedius, but are present in other Streptococcus species. The investigation of sulfonamide resistance in the SMG is of prime importance to the current antibiotic resistance crisis. Few treatment modalities remain for resistant bacteria, and as the SMG have a high incidence of horizontal gene transfer with other streptococci, sulfonamide-resistant folate synthesis may soon become prevalent.

Leah Hayward – The effect of altitude ancestry on aerobic metabolism plasticity in the deer mouse (Peromyscus maniculatus).

Supervisor: Dr. Grant McClelland
Heat production, or thermogenesis, is an important homeostatic mechanism that allows mammals to accommodate for environmental stressors, such as low temperature. Small free-ranging homeotherms, such as the deer mouse (Peromyscus maniculatus), must endure both cold and hypoxic conditions at high altitudes, which has interesting implications for their thermoregulatory systems. The goal of this study is to determine the effect that altitude ancestry has on the plasticity of aerobic metabolism in P. maniculatus. This will be accomplished by determining the roles thermal conductance and nonshivering thermogenesis play in thermoregulation by measuring fur length and the surface area of brown adipose tissue (BAT)—an important thermogenic effector tissue. The animals in this experiment are F1 progeny of two different populations of deer mice, highland and lowland. There are four treatment groups: 1) warm normoxic, the control; 2) warm hypoxic; 3) cold normoxic; and 4) cold hypoxic. Ten F1 progeny from each population will be acclimated to each of the four treatment groups, and measurements of BAT surface area and hair length will be determined. It is expected that when both populations are acclimated to chronic cold conditions, the surface area of the BAT deposit will increase to allow for more heat production. When hypoxia is introduced, it is expected that the mice native to highland populations will maintain a large BAT deposit despite limited oxygen availability. The lowland native population will need an alternative mechanism to maintain body temperature, such as increased hair length. By measuring the components of non-shivering thermogenesis and thermal conductance in the control and acclimated groups, the precise effect of the naturally occurring high altitude stressors, hypoxia and cold, can be elucidated.