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

John Taehun Kim -The Role of Antioxidants on Management of Type 2 Diabetes Mellitus

Diabetes mellitus is one of the leading causes of mortality in Canada, claiming over 7,000 lives per year. Prevalence rates of type 2 diabetes are increasing rapidly. Diabetes is a chronic disease characterized by a sustained increase in blood glucose levels. Vitamins and minerals play an important role in regulating glucose metabolism and can alter the development and progression of many chronic diseases. Deficiencies of these key micronutrients may contribute to the development of diabetes. This review article investigates the therapeutic role of antioxidants (vitamins A, C, E, carotenoids, and glutathione) in type 2 diabetes. Although dietary recommendations exist for the normal healthy population, there are no current nutritional guidelines specifically for those with diabetes. Thus, the information compiled in this project may be used to establish more effective and healthy lifestyle interventions and dietary recommendations for diabetic individuals.

Sarah Drohan -Comparison of Temporal Disease Dynamics in New York City

Mathematical models are indispensable tools for understanding infectious disease dynamics. In the field of epidemiology, controlled experiments are not always feasible and thus mathematical analysis may be the only way to investigate disease spread and management. These models can also help us interpret historical epidemiological data, the results of which may provide information about how to prevent further disease spread in the present day. Historical records of disease incidence have been acquired from New York City for the period of 1958 to 1976. Using the data for chickenpox, rubella, measles, mumps, scarlet fever, and whooping cough, the mechanisms of disease spread can begin to be investigated. The data for these diseases is likely to provide an accurate picture of the disease dynamics since each is easily diagnosed. Due to the large size of New York City and thus the large sample size of the data, the mechanics of disease transmission should be clear, and amenable to fitting with models. Descriptive statistical analyses such as spectral density and wavelet analysis will be applied to the time series. This will allow for the identification of potential differences and similarities and the possible medical, historical, and societal causes relevant to disease transmission. Compartmental epidemiological models may also be fitted to the data which may aid in the understanding of the dynamics of infection spread. This preparatory work will serve as a background for a more intensive analysis of the associated differential equations to be conducted in the summer of 2013.

Rebecca Englert and Rebekah Ingram – Create an Island

Plate tectonics has played a critical role in shaping the face of the Earth, including the formation of mountain ranges and opening of ocean basins. These events are recorded by rocks and fossils, which allow reconstruction of Earth’s paleoenvironmental and tectonic history. This study involved the creation of an island in a conceptual framework to understand past, present, and future plate tectonics on Earth, and to demonstrate the geologic structures and stratigraphic record produced during the development of the island. The fictional island was formed in the Mid Paleozoic to the Early Mesozoic eras at an oceanic-oceanic plate margin, became sutured onto Gondwana during the creation of the supercontinent Pangea, then eventually rifted from Gondwana due to a hot spot. The study includes a timeline of geologic events that contributed to the formation of the island, and outlines the island’s corresponding rocks, fossils, and geologic structures. A geologic map and various cross-sections of the island record important stages of island evolution. The island stratigraphy reflects sea level changes, orogenic events, volcanism, and plate movements that occurred during its theoretical construction. In addition to a poster, a three-dimensional physical model will be present to allow visualization of the surface physiography of the island. The investigation of island formation ties together processes responsible for shaping the Earth by drawing on knowledge from various areas of Earth Science including plate tectonics, sediment deposition, orogeny, environmental changes, and fossilization. These relationships can be used to further understand many geologic regions on Earth, and can be applied practically in the field.

Dusan Vukmirovic – The Development of an Undergraduate Biophysics Lab

The Department of Biophysics is a recent addition to McMaster University’s Faculty of Science and is also a new concentration offered in the Integrated Science (iSci) Program. It allows students to make connections between physics and biology that contribute to the interdisciplinary approach to learning many science programs are introducing to universities. However, the exposure that first year iSci undergraduate students have to this field, in either the disciplines of biology or physics of the iSci curriculum, is at a minimum. Since biophysics is a discipline that has a significant emphasis on experimental lab work, the development of an undergraduate biophysics lab would be the most effective way to bring biophysical concepts to students and would also serve to familiarize them with this topic. This project serves to develop a lab that would tailor to a first year undergraduate iSci student and provide the basic understanding of a particular concept in biophysics – the ear as a frequency analyzer. The lab requires that students understand the basic structure function relationship of the auditory system through mathematical representation of the outer, middle, and inner ear as well as their respective roles in sound recognition. Additionally, the lab requires construction of fletcher munson curves to demonstrate the principle of equal loudness and the overall frequency response of the auditory system. This has particular importance in hearing sensitivity tests, which provides a direct application of biophysics. The learning objectives consist of the following questions: What is biophysics? What are the various fields in biophysics? What are the applications of biophysics research? The lab protocol, budget and constraints are also taken into consideration.

Thilakshan Arulesan -Use of Agent Based modelling to simulate Game Theory Scenarios

Game theory is a relatively recent mathematical field that analyzes strategic decision making in games. A ‘game’ is defined as a problem in which there are one or more players, a set of strategies from which the players may choose, and payoffs for each player depending on their own choice of strategy and the choices of all other players. The ideas of conflict/compromise that arise in game theory can be used as a model for human interactions, and for this reason game theory is relevant to fields such as economics, social psychology, and climate change science. Computer software, specifically agent-based modelling, can be used to enhance the analysis of game theory problems. Agent-based computer modeling involves programming the actions of several autonomous objects (known as ‘agents’), and placing these agents in the same environment where they may interact with one another according to a set of rules. This study will analyse an agent-based model of a general game theory scenario, in which the players of the game are the agents and their interaction is in the form of games. From this model, it will be demonstrated that agent-based models of game theory scenarios will generally agree with the principles developed by game theorists. This study seeks to demonstrate how past techniques used to understand game-theory can be enhanced through the use of agent based modelling. From this, further adaptations of the model can be made to simulate real-life problems in economics, social psychology, and climate change that could not be solved analytically.

Philip Lauman -Effects of Point Mutations on Nevirapine Antiretroviral Treatment of HIV

Acquired Immunodeficiency Syndrome (AIDS) is a global pandemic spread by Human Immunodeficiency Virus (HIV), and is currently the fourth leading cause of death worldwide. Consequently, a number of drugs which interfere with the life-cycle of HIV have been developed in an attempt to slow viral infection and proliferation. One of the most important targets of these drugs is reverse transcriptase (RT), an enzyme responsible for the conversion of viral RNA to DNA, which is subsequently used to infect the cell. Although drugs such as nevirapine are initially effective in allosterically inhibiting the catalytic action of RT, HIV has a characteristic lack of molecular proofreading mechanisms, which results in a very high rate of mutation and consequent resistance to treatment. It is therefore necessary to constantly develop new drugs to combat AIDS. This process is greatly simplified by understanding how common mutations cause resistance to previously-utilized drugs. In this study, several strains of HIV-1 expressing common mutations in the RT-gene are compared to the wild-type strain using the molecular modelling and simulation programs MVM and ZMM. MVM is used to generate models of the mutant strains from an available crystal structure image of the wild-type strain, while ZMM simulates the interaction between the enzyme strains and the medical inhibitor nevirapine. These investigations will illustrate how common mutations cause changes in enzyme-inhibitor affinity, and thus viral resistance, through altered steric and electrostatic interactions. This information will prove useful towards the synthesis of a new drug, to which common HIV-1 mutations do not confer resistance.

Kaian Unwalla -Sensory Dominance: Why does one sense dominate others?

It is a common belief that one’s senses provide a veridical account of the surrounding world. However, it has been shown that when the senses receive conflicting information, the surroundings are often misinterpreted. By understanding why senses dominate, it may be possible to more accurately predict the dominating sense in new situations and this knowledge can then be applied to various situations, such as the media to increase the realism of special effect, or to increase realism of virtual realities. Several theories have been proposed to explain this occurrence. Two such theories are modality appropriateness and optimal integration. The first submits that the sense providing the most reliable unimodal information will dominate multisensory integration, while the second proposes that as information from one sense is degraded, another will dominate in a statistically optimal fashion. In order to better understand why a specific sense dominates, a review of past literature involving vision, audition, and touch was conducted. The situations ranged from simple tasks, such as determining how many taps were presented to a finger, to more complex situations involving the rubber hand illusion. The results suggest that vision dominates in spatial tasks, audition for temporal tasks, and touch for texture judgments, but only if the information is reliable. The findings support a combination of the two aforementioned theories. The sense best suited for a task will dominate, but if that information is made less reliable, thus reducing its proficiency, then another will dominate.

Rodrigo Narro Perez -A thermal investigation of surface water-groundwater interactions in Silver Creek, Georgetown, Ontario

In areas where the source of potable water comes from aquifers it is important to understand the interaction between the groundwater and any surface water bodies as the amount of water being pumped may impact the surface water systems. The use of temperature as a conservative tracer to measure groundwater-surface water interaction has grown in the last decade. Water flow models can be built with the knowledge that surface water is susceptible to air temperature changes, especially during the summer and winter when the contrast between groundwater temperature, which is almost constant yearlong, is substantial and measurable. The town of Georgetown, Ontario receives its potable from aquifers deposited in the Quaternary period. Due to an expected increase in population higher water pumping rates are expected. It is important to full understand the interaction between groundwater and the urban fluvial system of Silver Creek, which runs through the center of the town. The use of streambed temperature measurements is one of the many ways in which the interaction between groundwater and surface water is being assessed. This independent project has two main components. First, a comprehensive literature review has been done to understand the theory behind the use of temperature as a proxy to water flow. An understanding of the available models will be explained, with the selection of the most applicable for this study. The practical component of this study is the building and trial of the temperature measuring instrument in which the process will be explained. Lastly, if time permits, preliminary analysis will be shown from data gathered by the instrument during March.

Angela Huynh -Heterologous Production and Characterization of hSRCR1

Since ancient times, organisms have used the innate immune system to protect themselves from invading pathogens. Macrophages help facilitate this function by recognizing, internalizing, and destroying harmful substances. Found on macrophages are scavenger receptors which have a broad binding specificity that is used to discriminate between self and non-self substances. One specific receptor, the macrophage receptor with collagenous region (MARCO), plays a critical role in protecting organisms against airborne pathogens. Like other receptors in the same class, it was believed to only bind polyanions, but it has been recently found that the SRCR domain of MARCO also binds bacterial ligands. However, no specific ligand has been identified. To search for possible MARCO-binding bacterial ligands, we have expressed and purified recombinant variants of MARCO containing the SRCR domain. Furthermore, these constructs have been shown to specifically bind to Streptococcus pneumonia, one of many nasopharynx infections known for causing meningitis, sepsis, and pneumonia. By having these constructs, further studies can be pursued to identify specific ligands, determine the structure of this region of MARCO, and define which region of MARCO binds to what type of ligand: polyanions vs. bacterial ligands. Our work sets the foundation to look for MARCO-binding bacterial ligands. Future work will include the structure determination of this fragment of MARCO bound to its bacterial ligands in order to elucidate how the interaction occurs at the molecular level. In the long term, the molecular, biochemical and structural characterization of these interactions can be exploited to develop vaccines against nasopharynx infections.

David McDonough -Aesthetic and Usability Considerations for a Summer Camp Website

Arts and Science and Integrated Science, two highly reputable honours bachelor programs coming out of McMaster University, have joined forces to create FUSION: An Integrated Arts and Science Experience. FUSION is a summer camp running in mid-July 2013 on McMaster campus that provides Grade 7 and 8 students an opportunity to learn about the arts and sciences in the context of real-world, integrated topics. As part of the initial stages of the camp, a website is being developed to advertise and reach a wide demographic. This project looks to develop a website such that feelings of security and safety are conveyed to parents of potential campers, and feelings of fun and excitement are conveyed to participants. A number of design aspects are considered in an attempt to evoke certain feelings in different population groups. Simplicity, symmetry, human imagery, typography and colour are some aspects of a website that can be developed with a target audience in mind. The FUSION website’s main goal is to be divided into two separate sections – one for parents and guardians, and one for participants. This will allow aesthetics to differ between the two sections and different design psychology methods to be utilized. The efficacy of design aspects will be evaluated by simple questionnaire with members of the target age demographics [pending ethics approval].

Myles Marin -Exercise Intensity on the Enzymatic Profile of Fat Oxidation

Carbohydrates and fatty acids provide major oxidative fuel sources for athletes and sedentary subjects. Research has shown variable exercise intensity influences oxidative fuel source. Recent propositions have suggested the implementation of exercise training targeted at 40% to 55% of maximum oxygen consumption (FATmax) in weight management programs because this exercise intensity has proven to be effective in maximising the ratio of fat oxidation for a given energy expenditure. Other studies have demonstrated that exercise intensity at 100% maximum oxygen consumption increased energy expenditure, ascribable to carbohydrate oxidation, resulting in a greater absolute amount of fat oxidized. There are also reports describing the interspersion of high intensity exercise intervals within exercise at FATmax offers an increased energy expenditure without compromising the benefits of maximum fat oxidation. Hence, an understanding of the substrate mechanisms involved in fat oxidation at different exercise intensities is important. The objective of this meta-analysis is to show the acting enzymatic profiles involved at various exercise intensities to refine conclusions drawn by the current literature.