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


Lori Minassian – Optimizing the Biochem 3D03 Course

Creating an effective course that promotes learning and retention is an obstacle that many professors face. Though the more traditional route is to format a course with lectures, midterm tests and final examinations, there is growing evidence that this is likely not the most effective way to teach content. This is supported by reports from organizations such as the National Research Council that call for a change in undergraduate education from teaching to learning, specifically in science, mathematics, engineering and technology (SMET). The rationale behind this is that students learn more through active and cooperative learning, including group activity. Many students in the Biochem 3D03 course feel that they are not learning course content effectively. The purpose of the proposed study is to specifically optimize the Biochem 3D03 course to improve learning, mastery and retention of metabolism content. The final result may be that a combination of many of the innovative as well as traditional techniques will be optimal for the specific content of this course. This study has two main methodologies. The first is a review of the literature and governmental programs on the topic of teaching and learning. Once an appropriate amount of studies have been collected, teaching styles will be compared for effectiveness in promoting retention, mastery and understanding of the content. The second methodology is a survey of the students who were enrolled in the course in the Fall 2013 school term. The survey includes questions regarding aspects of the course students enjoyed and found effective and gives students an opportunity to suggest alternative marking schemes and assessments. Results from both methodologies will be combined to form a new course syllabus. To conclude, improving mastery and retention of content in any course is difficult. Active learning techniques might be the key to doing this. This study will aim to optimize the Biochem 3D03 course based on these results.

Alan Zhou – Theories and Applications of Biomedical Techniques: A Cost-Benefit Analysis

In the first half of the 20th century, the discovery of the molecular basis of sickle cell anemia initiated the use of biomedical techniques to study disease. Since then, numerous diseases have been characterized and their mechanisms elucidated, leading to the development of novel treatments. Knowledge of the basic theories behind current biomedical techniques is therefore a prerequisite to deciphering the mechanisms behind the ever-expanding repertoire of disease. In this review, a variety of modern biomedical techniques were studied in the primary literature and review articles, ranging from transfection used in cell biology, to Fluorescence Resonance Energy Transfer (FRET) used in biophysics. Their advantages, disadvantages, and limitations were discussed. Costs, both monetary and temporal, were analyzed to produce a cost-benefit analysis of the techniques. In an effort to glean different perspectives, faculty and students conducting research utilizing these techniques at McMaster University were also interviewed. Studies that utilize these techniques were examined as a backdrop for the discussion of their broad applications. Results demonstrate that decisions of which techniques to use in biomedical research are often influenced by several factors, including specificity, resource availability, and time restraints. While each technique has its own unique applications, all are at the forefront of biomedical research, and an understanding of them is imperative in paving the way for advances in 21st century healthcare.

Adelle Strobel – Modern Protein Crystallography

Crystallography is a century-old interdisciplinary technique used to determine the structure of molecules in a crystalline form. Membrane proteins are often studied as potential drug targets, using crystallography. However, the process to crystalize membrane proteins is arduous because they are macromolecules with flexible 3D-conformations, which can be highly sensitive to the crystallization environmental conditions. These factors lead to limitations in crystal size, causing lower dosage radiation, in turn leading to lower image resolution quality. To best crystallize proteins, one should first optimize crystal formation, and then choose the best imaging technology based on crystal size and quality. A review of the methods used to improve the quality of structural data will be reported. There have been a number of new technologies developed to decrease damage of crystal samples due to the incoming energy — predominantly by increasing beam speed and decreasing its duration. These include cryo-electron microscopy (cryoEM), X-ray free lasers, nanocrystallography, femtosecond X-rays, serial crystallography, and synchrotron radiation. Each imaging modality may give either a high resolution image or a more flexible description of the protein in its natural environment. It has been found that by using serial femtosecond crystallography (SFX) techniques the duration of ionization and thermal energy interaction is much shorter. This creates a higher resolution image for smaller crystals. However, the dose required is much greater, such that serial crystallography has been used in combination with synchrotron radiation and X-ray free-electron lasers. CryoEM or back injection techniques allow the crystals to withstand these higher doses. Furthermore, cryoEM produces images of proteins in their natural state structure but requires multiple crystal data images to record its different conformations. As technology develops, the future of crystallography will progress towards the ability to visualize protein structures as they change conformation over time in adjustable environmental conditions.

Jenin El-Sayes – A Travelling Somatosensory Workshop

Neuroscience is the study of the structure and function of the brain and the nervous system. The somatosensory system is a topic in neuroscience that relates to touch sensations that send signals to the nervous system. To provide a basic understanding of sensory perception and the somatosensory system, an exploratory workshop was designed for students in middle school. It is important to introduce middle school students to neuroscience as it provides the students with an understanding of how they observe and interpret information in the physical world. Neuroscience clearly displays the link between information taken in by the senses, and the perception of that information. Most importantly, neuroscience is not commonly introduced to students until the later years in high school. Through giving students, the opportunity to learn about neuroscience early on, they are able to explore and pursue their scientific interests. This workshop specifically focuses on touch and pain reception. These are a suitable introduction to neuroscience, as they are widely experienced and therefore are very easy to relate to. The concepts of touch and pain reception can be demonstrated using a PowerPoint presentation, followed by an interactive hands-on activity to enhance the learning experience of the students and solidify learning. This workshop outlines concepts such as: the structure and function of neurons; the types of receptors responsible for pain and touch reception: Aβ – fibres, Aδ – fibres, and C fibres; the size and density of receptive fields; and the structure of the somatosensory cortex. Through this design, the student will be able to gain a positive experience when being introduced to science, which will encourage them to pursue their own scientific interests and provide a more positive mindset when learning science.

Madeena Homayoun – Side effects of isotretinoin therapy

The drugs isotretinoin (commonly known as Accutane) and ethinylestradiol cyproterone acetate (commonly known as Diane-35 or Dianette) are both used to treat severe and persistent acne and have both also been linked to deaths in those undergoing treatment. There is currently controversy surrounding the side effects of isotretinoin in society. Depression and suicidal thoughts, gastrointestinal problems, and liver damage are common sources of concern among the public regarding isotretinoin usage. There have been suicides in users of isotretinoin, which has created controversy towards the drug’s effect on mood. Furthermore, the hormonal acne treatment, Diane-35 (a combination of ethinylestradiol and cyproterone acetate) has caused deaths due to venous or pulmonary thromboembolism and was temporarily banned in France in 2013.

The purpose of this review will be to investigate the prevalence of the controversial side effects of the drugs, to investigate the number of deaths related to both drugs, and assess the validity of concerns towards both. The banning and scrutinization of Diane-35 but not isotretinoin by the government will be investigated, in addition to comparatively assessing the harmfulness of both of these compounds. Since isotretinoin has been on the market for over thirty years, and Diane-35 for almost fifteen, recent literature will be investigated on this topic in order to find any new developments that may contradict common knowledge on the drug or provide clarification on unknown links between drugs and side effects. A systematic review will be conducted on literature from the past five years related to adverse effects of isotretinoin through the PubMed MeSH Database – with “adverse effects” as the MeSH Major Topic in regards to isotretinoin. Furthermore, the information on Diane-35 will come from entering “ethinylestradiol cyproterone acetate” into PubMed and searching for results from the past five years as well.

Predicted results include a low prevalence of controversial side effects, and a correlational but non-causal relationship between these side effects and the drug. It is important to understand the true side effects related to these drugs in order to eliminate cultural stigma and misconceptions about usage of isotretinoin and Diane-35 to cure acne. Isotretinoin and Diane-35 have relatively high success rates in eliminating acne and adverse effects must be clear to the public to allow for proper consideration of these drugs as treatments.

Leah Hayward – How the Physical Properties of Sound Propagation in Air Support the Sonar Jamming Hypothesis

The complex predator-prey interaction between echolocating bats and eared moths is a driving force for evolution. Eared moths have evolved the ability to produce ultrasonic clicks as a defense mechanism against bat echolocation. There are two major hypotheses that explain why ultrasonic clicks are used by eared moths: the aposematism hypothesis, and the sonar-jamming hypothesis. Here, evidence for both hypotheses are analyzed through a literature review in an attempt to understand which has more support. Data from various experiments are summarized and used to conclude that there is not enough evidence present in the literature to strongly affirm either hypothesis. However, evidence of counter adaptation in echolocating bat species can be used to support the sonar-jamming hypothesis. Echolocating bats have been shown to shift their frequency range to compensate for the eared moth’s ability to detect their hunting calls. The physical properties of sound propagation through air can be used to support the sonar-jamming hypothesis; atmospheric attenuation affects sounds at higher frequencies, and sounds made at lower intensities decreases the effective hunting distance. Therefore, there must be a strong selective pressure for bats to alter their hunting strategies despite the associated costs. These properties will be presented as evidence for the sonar-jamming hypothesis, and the possibility that the hypotheses are not mutually exclusive will also be explored. The relevance of this study will be demonstrated by looking at how global warming affects sound transmission, and how this can affect bat counter adaptations.

Christina Spinelli – Measuring developmental changes in the auditory cortical oscillatory beta band activity during musical beat processing using EEG

When listening to rhythmic auditory patterns, we are readily able to extract the regularity in the sequence. This allows us to accurately predict the onset of the next beat, which is crucial for our ability to move in synchrony with an auditory rhythm. Recent magnetoencephalography (MEG) research suggests this prediction may be facilitated by oscillatory networks in the brain entraining to the tempo of isochronous auditory sequences. Specifically, the amplitude of induced oscillatory activity in the auditory cortex beta band (15-30 Hz) decreases after each beat and rebounds prior to the onset of the next beat across different tempos. The current study’s objectives were to investigate 1) whether similar results could be found using electroencephalography (EEG), and 2) how this oscillatory activity in the beta band changes with age. Adults and 7.5-year-old children had their EEG recorded while passively listening to isochronous tone sequences at three tempos (390 ms, 585 ms, and 780 ms inter-onset intervals [IOI]). A beta band modulation pattern consistent with the MEG findings was found in the adults’ high beta band (20-25 Hz) across tempo conditions and in the children’s intermediate (585 ms) condition. However, the children did not show a similar response pattern in the fastest (390 ms) and slowest (780 ms) conditions. Thus, the results indicate that EEG can be used to investigate oscillatory beta band networks and that these networks in 7.5-year-olds have not yet fully matured.

Natasha Dovey – What makes bubbles, bubbles?

Those who practice regular hygiene encounter bubbles on a daily basis. Generally composed of the salt of a carboxylic acid, the active component in soap possesses a hydrophobic tail region and a hydrophilic head. As such, the carboxylic acid molecules readily combine in solution to form micelles, usually around fatty, or lipophilic, substances, thus rendering soap an effective cleaning product. The hydrophilic head group rests at the exterior of the sphere, leaving the hydrophobic tail group to surround the lipid substance in a solution or on a surface. The ingredient that aggregates to form these micelles is known as the surfactant. The process of micelle formation in an aqueous solution has positive enthalpy, suggesting that the process is endothermic. As the formation of micelles is also spontaneous, there must also be a positive change in entropy. While this may seem counterintuitive, as the molecules are more ordered while interacting within the micelle, the surrounding solution is left with a greater freedom of movement, corresponding to higher solution disorder. There are various parameters that can be altered to change the sphericity and other physical properties of micelles. Total surface energy is determined by the equation μ = γa + K/a, where μ is the chemical potential at the surface interface, γ is the interfacial energy between the hydrocarbon tails and aqueous solution, a is the surface area occupied by each hydrophilic head, and K is the proportional repulsion constant of the head groups. By setting the derivative of this equation equal to zero the optimal head group area can be solved for, giving ao = (K/γ)1/2. The micelle packing parameter, given by, vc/aolc, where vc is chain volume, ao is optimal head group area, and lc is critical chain length, is a measure micelle curvature. A high packing parameter refers to a more spherical micelle, as it represents a small tail bonded to a large head. Micelles only form above the critical micelle concentration (CMC), which can be viewed as a function of the change of the previously mentioned physical properties. As such, by changing these properties in a theoretical setting, the CMC will be determined. The CMC for soap after the manipulation of common ingredients such as sodium stearate, sodium laurate, and sodium myristate, assuming the surfactant is in an aqueous solution with water. The determination of the CMC also has various practical implications for the formulation of a more effective cleaning solution.

Emma Butcher & Julia Martinko – Crystallization of antibiotic resistant Escherichia coli dihydrofolate reductase.

The widespread application of antibiotics has led to the development of drug resistance in bacterial cells. Resistance may be acquired through a variety of mechanisms such as mutations to the target protein. The effects of these protein mutations can be studied using X-ray crystallography to determine structure-function relationships. One such target protein is dihydrofolate reductase (DHFR), which is required in all cells to catalyze the reduction of dihydrofolate to tetrahydrofolate. Antifolates are a class of drugs used to inhibit DHFR from binding to its substrate. DHFR residues that confer resistance to antifolates have been identified as mutational hot-spots. One such point mutation is the Escherichia coli W30R mutant, which substitutes arginine for the tryptophan at amino acid residue 30 of DHFR. The objective of this study is to express, purify, and crystallize wild type and W30R mutant E. coli DHFR. This will allow for future structure-function analysis of the resistant protein to find novel drug targets.

Cloning was completed using a pET28b plasmid containing the W30R mutant folA gene coding for mutant DHFR in E. coli DH5α. Control reactions were performed using wild type folA. Both the mutant and control were expressed using E. coli BL21 (DE3) and then purified. Low yields of mutant DHFR were obtained, and then characterized using Bradford Assay and SDS-PAGE. Next steps include crystallizing mutant and wild type DHFR using sitting drop crystallization and a salt gradient. If successful, x-ray diffraction will be performed on the crystals to determine the structure of the mutant protein. By structural elucidation and functional analysis of the W30R mutant, new drug targets can be identified to combat antifolate resistance.



Lauren Smith – Phenotypic characteristics of eradicated and persistent Pseudomonas aeruginosa isolates from children with cystic fibrosis

Pseudomonas aeruginosa (P. aeruginosa) is the most common source of respiratory infection in the lungs of cystic fibrosis (CF) patients. Treating first-time P. aeruginosa infections in paediatric CF patients appears to have a 10-40% failure rate. Reasons for this failure rate remain unknown. The goal of the study was to determine whether there are detectable phenotypic differences between persistent and eradicated CF isolates of P. aeruginosa.

A cross-sectional study was conducted during 2011-2012. Subjects included children with CF at the Hospital for Sick Children in Toronto who had incident P. aeruginosa infection (defined as a positive P. aeruginosa sputum culture preceded by at least 1 year of negative cultures). Incident P. aeruginosa isolates were recovered from frozen sputum samples and examined for bacterial phenotypic characteristics including: mucoid status, protease production, swimming motility, twitching motility, and tobramycin MICs. Isolates were categorized as eradicated or persistent based on the subsequent culture result of the first sputum sample obtained following antibiotic treatment. Phenotypic characteristics of persistent and eradicated isolates were compared using a Mann-Whitney statistical test.

Of the 34 patients, 10 (29%) were treated with a 80 mg dose of inhaled tobramycin (tobra) with 2 of those failing eradication (20% tobra failure rate); 23 (68%) were treated with a 300mg dose of tobramycin inhalation solution (TIS), with 3 of those failing eradication (13% TIS failure rate).

The median tobramycin MIC for eradicated isolates was 2 ug/mL (range 2-16 ug/mL) and for persistent isolates, was 2 ug/mL (range 2-64 ug/mL). The persistent isolates appeared to be produce less protease and have less twitching and swimming motility compared to eradicated samples, however this data was not statistically significant. A trend was observed that suggests the mucoid ratings of the persistent isolates were higher than those of the eradicated isolated (p=0.05).

Preliminary data suggests that mucoid P. aeruginosa isolates may be more likely to persist in the CF lung compared to non-mucoid isolates and may provide insight into more effective anti-P. aeruginosa eradication treatments. Additional phenotypic studies including biofilm production of isolates are currently underway.