2A18 Abstracts

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

POSTER PRESENTATIONS – MARCH 31, 2016

Aurora Basinski-Ferris: Application of a simplified Sznajd Model to examine opinion dynamics in a population

Supervisor: Dr. George Dragomir

Sociophysics is an emerging interdisciplinary research field that uses theories and methods developed by physicists as a modelling framework for various social science phenomena. This paper presents the Sznajd model, which is the basis of one of the simplest yet most efficient methods to predict collective human behaviour in a binary opinion society. This model is a variation of the Ising model, which is used in statistical mechanics to study ferromagnetic phase transitions of a system based on the interaction between the neighbouring atomic spins of the system. In both the Ising model and the Sznajd model, individuals are only allowed to have a binary opinion – yes (spin up) or no (spin down).  The Sznajd model is based on social validation –  the model requires that two neighbours share the same opinion to be able to convince individuals around them of their opinion.  Using MATLAB, I apply a two dimensional simplified version of the Sznajd model to track the opinion movement over many time steps in a lattice of individuals with an initial randomly generated distribution of opinions. The results of this simplified model are then analyzed to try to better understand real world binary political opinion systems.

Chimira Andres: The Evolutionary History of Bomb Calorimetry: “Out with the Old and In with the New”

Supervisor: Russ Ellis

The laboratory practice of bomb calorimetry has made many fundamental contributions to the development of laboratory techniques and equipment, specifically in the science of chemistry. Calorimetry was first introduced in the late 1700s through the experiments of Antoine Lavoisier, the “father of modern chemistry”, who estimated the heat produced per unit of carbon dioxide produced. An oxygen bomb calorimeter is a device that measures the quantity of heat produced through the combustion of a sample, with an associated change of state in constant volume. The main focus of this project is to compare and to contrast the experimental results of a historical laboratory procedure using an older model bomb calorimeter with a current laboratory procedure using a modern computer-based bomb calorimeter. By testing samples of different ethanol concentrations as a biofuel, the efficiency of this chemical as a viable source of energy can be determined. When making calorimetric measurements, there is always some level of inaccuracy. The challenge is reducing the level of inaccuracy as much as possible, given the limitations of the testing systems. The goal is to formulate a comparative analysis as to which system, historical or modern w, yields the least error. In this project, the evolution of bomb calorimetry is explored to help establish its role in the progression of chemical equipment and procedures.

 

Mary Bohn: Revealing the secrets of human history: Ancient DNA and skeletal research at McMaster University

Supervisor: Russ Ellis 

The evolutionary history of life on Earth is an extremely complex puzzle that can be approached from an ecological or molecular perspective. Ancient DNA research is rapidly becoming a revolutionary tool to aid research in molecular evolution. By using single primer extension amplification, researchers can now amplify and sequence ancient DNA to test assumptions used in prior reconstructions of evolutionary patterns. Much information regarding past societies can be inferred from sequencing genomes. Studies have shown that significant changes in residence patterns and shifts in ancient DNA sequence can indicate population colonization. However, the methodology behind this field is fraught with technical pitfalls including fragmentation, cross-linking and oxidative damage to the ancient DNA. McMaster University has dedicated substantial resources to create a world leading Ancient DNA Lab with the sole purpose of improving the accuracy of these techniques.  This project aims to define some of the limitations in this field and elaborate on measures currently being undertaken to enhance their accuracy. This will be accomplished through a literary review and personal communication with members of the Ancient DNA lab. If these limitations can be reduced, the field of bioarchaeology is closer than ever to constructing a complete evolutionary history of life.

Jennifer Hanuschak and Chloe Darling: Predator-Prey Coevolution

Supervisor: Russ Ellis 

As Integrated Science is an evolving program, revisions to the curriculum are continuously being done to keep students engaged. This enrichment project looks to add a new lab to the ISCI 2A18 Plant-Animal Interactions (PAIx) module as there is space for an additional lab in the curriculum. Moreover, this project focused on the process of experimental design. Over the course of this project, research was done to gather background information and find experimental inspiration; materials were collected; logistics were discussed and determined; and a protocol was developed, tested with current ISCI 2A18 students, and revised. This project aimed to identify key elements of the design process and their importance. The lab that was developed is a predator-prey simulation which requires students to actively participate in the model system, design a habitat, perform calculations using Microsoft Excel, and analyze how predator and prey populations evolve over several generations. Additionally, concepts of coevolution are illustrated. The feedback received following the trial run of the experiment indicates that this lab will be a valuable addition to the ISCI 2A18 curriculum; its development is an ongoing process and it will continue to evolve after its initiation.

Jonathan Panuelos: Spatial Interactions in Ecological Systems with a Stochastic Lattice Lotka-Volterra Simulation

Supervisors: Dr. Chad Harvey and Dr. George Dragomir

A pioneering and now ubiquitous model in population ecology, the Lotka-Volterra system describes the temporal dynamics of two interacting species as a pair of differential equations. While mathematically elegant, it suffers from being deterministic, demonstrating the periodicity of predator-prey relationships, but little else. Its simplicity prevents more thorough analysis and generalization for more complex ecosystems, calling for a more robust analogue.

The inaccuracies in classical Lotka-Volterra largely stem from its lack of discrete, spatial, and stochastic elements – a more modern model, applying these corrections, is the Stochastic Lattice Lotka-Volterra, which treats the deterministic rates as probabilities applied over a discrete N×N lattice. As the same interactions defined by classical Lotka-Volterra are performed a large number of times, it becomes a Monte Carlo approximation, with probabilities being equivalent to rates at the mean-field limit.

Applying this new model in C, my analysis finds that while it approximates classical Lotka-Volterra, it exhibits more consistency with known ecological theory. In particular, it demonstrates decreasing fluctuation amplitude over time, as well as a bifurcation between the coexistence and extinction states, whereas the classical model implies an inevitable, perfectly periodic, coexistence for any two-species system.

Novel modifications to the simulation provides insight into the spatiotemporal behaviours of different ecosystems, such as species invasiveness and a parity law in trophic interactions. Thus, by applying the Lotka-Volterra model in silica, with the inclusion of discrete, spatial, and stochastic elements, a more accurate and robust model is created, applicable for the study of a wider range of ecosystems.

Jasleen Pahwa: Antibiotic resistance: The growing concern of Staphylococcus aureus

Antibiotic resistance is a growing concern in modern society, as the lives of infected individuals with potentially treatable conditions become threatened. Historically, common infections or minor injuries resulted in the death of many individuals. With the discovery of antibiotics, common infections and diseases became easily curable. However, as certain pathogens were continuously exposed to these antibiotics, they were able to adapt to the medications and develop a tolerance. Today, the rate at which bacteria are becoming resistant to antibiotics is making it nearly impossible to cure certain infections.

Staphylococcus, specifically the class of Staphylococcus aureus (S.aureus), is responsible for many infections ranging from the skin to the respiratory system. The more that S.aureus is exposed to antibiotics, the stronger its resistance becomes. In fact, a certain strain of these bacteria known as methicillin-resistant Staphylococcus aureus (MRSA) is currently resistant to antibiotics. Not only is this strain typically hospital-acquired, but it recently has been suggested that it can also be community-acquired, meaning that it has the ability to infect healthy individuals. Phenomena such as this are prominent in society due to horizontal gene transfer, which allows for this strain of bacteria to release damaging exotoxins into its host, counteracting the response of the immune system.

Without addressing the significance of this issue, humans could be entering a post-antibiotic era in the near future. I aim to present my findings of this topic through a poster representing my research from a literature review.

Dalton Budhram: Sensitivity and Precision of Clinical Queries search filters compared with Cochrane search filters

Supervisor: Dr. Brian Haynes 

Physicians frequently complete literature searches for systematic reviews (SRs) to guide patient care. Exhaustive literature searches for SRs of the health care literature often yield many off target or methodologically poor studies; that is, have low precision (the proportion of retrieved articles that are on target). Clinical Queries (CQs), originally developed to assist clinicians with searches, have high sensitivity (proportion of eligible studies that are retrieved) but also relatively high precision, and may help those doing SRs.

This study compared CQs with Cochrane strategies (CSs) in Cochrane Reviews to determine the more efficient search strategy for health care literature searches. We hypothesize that CQs are as sensitive as CSs, and more precise. Thus, we conducted an analytic survey, with CSs as the gold standard for retrieving included studies, and the sensitivity and precision (positive predictive value) of Cochrane content terms in addition to Cochrane methods filter terms were compared with Cochrane content terms in addition to Clinical Queries maximally sensitive filter (CCQ-S).

Compared with CSs, the average CCQ-S searches in Ovid Medline and Embase retrieved the same proportion of relevant articles (CQ Sensitivity: 84.5%; CS Sensitivity: 82.0%; difference 2.5%, 95% CI -5.77% to 10.77%). Likewise, the precision of both strategies in Ovid Medline and Embase was nearly the same (CQ: 0.26 %; CS 0.29%, difference – 0.03 %, 95% CI (-0.0971% to 0.035%)).

For systematic reviews, the Clinical Queries maximally sensitive filter returns relevant articles in both Ovid Medline and Ovid Embase with equal sensitivity and precision. Thus, either strategy should be used for quick clinical searches and to guide literature searches to enhance patient care.

Erin Smith: The evolutionary effects of ∆9-tetrahydrocannabinol on Cannabis sativa, and human physiology

Supervisor: Dr. Chad Harvey

Humans have consumed Cannabis sativa medically and recreationally, for approximately 5000 years. Throughout this time scientists have strived to enhance its therapeutic capacity. The main psychoactive component of C. sativa, ∆9-tetrahydrocannibinol (THC), has major physiological effects on humans. With increasing knowledge of THC’s effects, scientists will be able to better understand how to maximize its therapeutic potential. THC is a secondary metabolite of C. sativa, which acts as a mechanical and chemical plant defense against herbivores. Within humans, THC interacts with two systems; the central nervous system and the immune system. THC binds to receptors in each system and influences cell growth, and signal propagation. As a result, THC has been a useful therapeutic agent throughout history, and is beginning to be appreciated as a legitimate medical treatment in modern times. The increase in research on THC within the last two decades has improved its role in prevention and treatment of cancer and neurodegenerative diseases. This project is a literature review of primary and secondary research on the existing knowledge of the role of THC in C. sativa and humans. The aim of this project was to determine what the next steps are for determining the activity of THC in the body and how it can benefit humans therapeutically in the future. THC has been an important compound to humans for thousands of years and with continuous advancement in our knowledge of the compound it will continue to maintain this status.

Jamie Maloney: The geological and paleontological history of the Island of Lasair

Supervisor: Dr. Carolyn Eyles 

Over the past 4.6 billion years, geologic processes such as plate tectonics have played a critical role in shaping the Earth. The understanding of these processes is important to the study of geology and the history of the world. The objective of this study is to create a fictional island to demonstrate an understanding of the Earth’s geologic processes from the past, present, and future. The island’s corresponding fossil record, stratigraphy, and geologic structures will provide insight on how to create a timeline of the geologic events that contributed to the formation of the island. A geologic map and cross sections of the island will also be created in order to exhibit the important stages of the evolution of the island. This hypothetical island was formed in the Oligocene Epoch, when a hotspot protruded through the South American Plate. Subsequently, a small island chain was formed through the combined processes of magma formation, eruption, and the continuous movement of the South American Plate eastward over the hotspot. The islands stratigraphy of the island reflects multiple sea level changes overtime along with one major volcanic event during its development. By completing this investigation, a further understanding of environmental changes, geologic regions and geologic processes that are characteristic in island formation can be applied to various fields of science.


Julia Pantaleo: An Investigation of Infrared Spectroscopy Applications in Forensic Analysis

Supervisor: Russ Ellis

Forensic analysis is essential in order to tie people, places, and objects together after a crime has been committed. However, biological evidence is not always found at a crime scene and forensic analysts must rely on other, non-biological evidence in order to develop a suspect pool. In these cases, investigators may employ analysis methods such as infrared (IR) spectroscopy, a tool which has quickly gained merit in the field. IR spectroscopy is a quick, non-destructive analysis method used to identify and characterize compounds recovered from crime scenes. The objective of this study is to investigate the current use of IR spectroscopy in the analysis of forensic evidence and to evaluate the relative effectiveness of this method compared to traditional analysis methods. This was accomplished through a literary review. The results show that IR spectroscopy is primarily used to analyze polymers such as paints and fibres. Paint analysis allows for the identification of binding molecules and pigments, which can be traced back to a specific manufacturer. Fibre analysis allows for the identification of fibre types and treatments done to the fibres such as bleaching or dyeing. Additionally, it was found that IR spectroscopy could be used to analyse compounds such as drugs, inks, and explosives to confirm the results of other analysis methods. Overall, this project will provide insight into modern forensic analysis techniques while emphasizing the importance of effective analysis in crime investigation by applying common laboratory techniques and equipment to a practical setting.

Paige Darville-O’Quinn and Aarani Mathialagan: Pathways of Drug Development: Big Pharmaceuticals versus Mother Nature

Supervisor: Russ Ellis

In modern society, medicinal compounds are ubiquitous and highly integrated into daily life. From mild pain relief to treatment of near-fatal diseases, medicinal drugs improve the quality of life. From the time of ancient civilizations to now, the process of drug discovery has changed extensively: beginning with in the identification and extraction of naturally-occurring ingredients in plant and animal material, to the modern drug development process, which uses advanced technology to screen compounds that have been synthesized in research laboratories.

Our study aims to compare and contrast methodologies of drug discovery and development. It emphasizes differences between therapeutic agents derived from natural compounds, and novel compounds synthesized to target specific ailments. Through communication with experts in the drug discovery and development field, a tour at the McMaster High Throughput Screening laboratory, and literature review, we describe the major changes and advantages of modern and historical drug discovery processes. The historical approach to drug discovery, development and adaptations to the process, the co-existence of natural and synthetic drug treatments, and the future of treatment are discussed.

Jeremy Cooney: Simple Modelling of El Niño as a Chaotic System

Supervisor: Dr. Randall Dumont

El Niño is a weather phenomenon which sees abnormally high surface temperatures in the tropical East Pacific. It is driven by changes in the Walker Cell Circulation and is often preceded by a weakening of the easterly trade winds. The aperiodic nature and complexity of El Niño make it a textbook chaotic system. Rudimentary predictions of El Niño-Southern Oscillation (ENSO) can be achieved by modelling it as a system which shows properties of a Lorenz attractor. In the Vallis Model, three parameters are used in a refined form of the classic Lorenz equations; strength of the trade winds, the temperature difference across the Pacific and the strength of the mid-ocean current are all assumed to sustain ENSO’s irregular oscillatory pattern in isolation from external factors. The model attempts to predict the behaviour of a fluid in convection. Because the ocean and atmosphere are both fluids and because both undergo convection, the Vallis Model can be usefully applied to ENSO. The Vallis model, although crude, gives a good intuition into the dynamics of ENSO. Continued research in this field is invaluable as it may provide new insights into the effects of climate change. Moreover, understanding ENSO may lead to improvements in integrated global weather models and the long range predictive capabilities of weather forecasts.

Anjali Narayanan: Curve-skeletons and their applications in computer aided graphics

Supervisor: Dr. George Dragomir

A Curve-skeleton is a one dimensional representation of a three dimensional object that retains the topology of the object. Curve-skeletons offer an aid to understanding complex three dimensional objects and are used in a wide variety of applied technical fields that involve some form of dynamic geometric modelling or computer aided design, including mechanical engineering, image processing, computer graphics, animation, and other dynamic media environments. In this project, I define and explore properties of curve-skeletons, as well as summarizing their historical origins and development. The greatest challenge in computing curve-skeletons is manipulating their ill-defined mathematical properties and finding the optimal method of producing the curve-skeleton with a set of desired properties. This project focuses on the current usage of curve-skeletons in the field of computer graphics and explains the mathematics of skeletonization based on the medial axis and scale axis transforms. In this project, I use MATLAB as the primary visual software for generating three dimensional models and their associated skeletons. I explore further research directions on the topic of three dimensional curve-skeletons, especially in the context of computer aided graphic design.

ORAL PRESENTATIONS – APRIL 4, 2016

Jordan Aharoni and Sunny Tian: An analysis of the non­indigenous wetland flower Lythrum salicariaand its impact on biodiversity, ecosystems, and human socioeconomics. (15:30-15:45)

Supervisor: Dr. Chad Harvey

Purple loosestrife, or Lythrum salicaria, is an invasive flower that threatens plant and animal diversity in Canadian wetland ecosystems by out­competing existing native species. A widespread issue and danger to biodiversity, purple loosestrife can dominate an area due to highly effective methods of seed dispersal as well as its high tolerance to herbicides and heavy metals contamination. However, these plants hold little nutritional value and cannot be used as nesting material for animals, leading to reduced diversity in the ecosystem. Moreover, they can also clog irrigation canals and degrade the quality of farmland.

In the past, reactive methods have been used to try and diminish the growth of purple loosestrife, such as mowing, burning, and herbicide, but these have largely been ineffective. Therefore, this project aims to develop a deeper understanding of how the species spreads using mapping and trend analysis, with a goal to propose alternative methods for purple loosestrife extermination and prevention.

This study will largely take the form of a written review and meta­analysis of the literature, accompanied by computer generated images. The study will use GIS software to map and model the prevalence of wetlands in certain regions of Canada over time and compare that to any data found on purple loosestrife invasiveness. Data on farmlands and agriculture will also be analyzed to determine if there is a correlation between purple loosestrife spread and changes in the agriculture industry. The results will be used to determine qualitatively and quantitatively the spread and impact of the purple loosestrife on biodiversity and agriculture in Canada.

Aryan Pour-Bahreini: The Legal Implications of Pharmaceuticals (15:45-16:00)

Supervisor: Russ Ellis 

Pharmaceutical drugs have become so common in our lives that we often do not consider the extensive and intricate framework that Health Canada has created to ensure that the products we are consuming are both safe and effective. For every drug produced in Canada, there is an extensive network of judicial guidelines, which must be strictly followed to ensure that the product is both viable and safe. The goal of this research is to expound the legal procedures and organisations involved in the strict regulation of drugs used during both clinical trial stages and post-clinical trial settings. Both the use of primary and secondary sources were used to develop an understanding of Canada’s laws and their application to both pre-and post-clinical trials. A primary source included information obtained from an interview with Dr. Anne Holbrook, who is the current director of the Division of Clinical Pharmacology and Toxicology and one of the most senior drug policy experts in Canada. She was able to provide valuable insight to the interactions between governmental judicial bodies and pharmaceutical researchers. Furthermore, analysis of the current legal framework found in the Food and Drugs Regulations Act yielded extensive insight into regulation of clinical trials from a legal perspective. It is easy to ignore the relatively quiet judicial aspect of drug discovery. However, the continued efforts to ensure that transparent, ethical and legally justifiable clinical work is being conducted represents an important aspect of ensuring appropriate scientific research is carried out in Canada.

Varsha Jayasankar: Identification of Novel Antibacterial Compounds in Curcuma amada (16:00-16:15)

Supervisor: Dr. Chad Harvey

Epidemics of antibiotic-resistant bacteria, such as Clostridium difficile and methicillin-resistantStaphylococcus aureus (MRSA), are frequent in North American hospitals, causing over 30 000 deaths per year in the United States. Similarly, antibiotic-resistant strains of plant pathogenic bacteria such asErwinia amylovora cause over $68 million of annual damages to crops. Sanskrit literature demonstrates the use of Curcuma amada (mango ginger) as an antimicrobial, but this has yet to be substantiated by modern research. With increasing antibiotic resistance becoming an increasing problem, new treatments are constantly being sought out. This project examined the effects of a mango ginger chloroform extract on five bacteria (C. diffcile, MRSA, E. amylovora, Escherchia coli, Xanthomonas campestris), and identified a compound within this extract that has antibacterial properties.  The chloroform extract was tested against the five bacteria using colony forming units (CFU) and Kirby-Bauer (KB) assays, and was proven effective. Using column chromatography, the extract was separated into four fractions with various solvent mixtures, which were subsequently tested using the same assays. Colony counts and zones of inhibition for the CFU and KB assays, respectively, were measured using ImageJ. Statistical analyses of this data was completed using R. Of the four fractions, the fraction separated with methanol and 0.2% acetic acid was the most effective antibacterial.  A novel antibacterial compound was then successfully identified by analyzing this fraction using liquid chromatography/mass spectrometry (LC/MS). This compound has promising applications in antibiotic treatments for patients suffering from infections, in surface sanitation methods in hospitals, and could also be used in organic pesticides for crops.

Joanna Krynski: Analysis and applications of group theory in the study of music tonality (16:15 – 16:30)

Supervisor: Dr. George Dragomir

Western music, music associated with Europe from Medieval times and onwards, strongly relied on tonality until the 20th century. The tonality of a piece of music can be described as the piece’s quality of a fundamental tonal center, or key, that unites a piece. It is what makes music “sound good”. The tonality of a piece is the progression of musically acceptable movements between notes. These acceptable movements can be modeled as acceptable permutations of sets described in group theory. This project explores the use of mathematics, namely the use of natural harmonies or ratios, and concepts in group theory, to define the tonality of music. A literature review is conducted to show the underlying use of ratios and group theory in musical pieces. Additionally, a piece of music (J.S. Bach’s Fugue in C Sharp Minor, BMV 849) is analyzed using concepts from group theory. Finally, I investigate the application of group theory in composition and improvisation of music. Based on preliminary research, there is a strong connection between concepts in group theory and musical tonality, to such an extent that one can use mathematics to create music. Theories in mathematics stretch beyond numbers; abstract ideas like those present in group theory can be applied to many fields with some further investigation.

Connor Nelson: The Use of Trapping Data to Predict Emerald Ash Borer Gallery Density (16:30-16:45)

Supervisor: Dr. Chad Harvey

The Emerald Ash Borer (EAB) (Agrilus planipennis) is a high profile invasive beetle species that feeds on ash trees. With no natural predators in North America, the EAB population remains unregulated, and has caused immense ecological and economic damage in both Canada and the United States. Our most reliable method of determining EAB population density involves removing branches and bark from affected trees in order to observe galleries, causing even more damage to trees that are already under stress. In this study, we assess the value and efficacy of non-destructive sampling methods for estimating EAB densities. Trap capture rates and quantified observational data were directly compared to gallery data, collected from the same trees. A statistical model was constructed to determine the efficacy of non-destructive assessments of gallery density.  The results of this analysis have the potential to predict gallery density of EAB using only non-destructive surveying methods. This will aid tree conservation and increase EAB population density estimates.