Below is a list of abstracts by third-year students in the Integrated Science Program:
Ahluwalia, Monish – Using Octave to Model Ra-226 Irradiation and Decay for the Production of Ra-223 in the McMaster Nuclear Reactor (Dr. Adriaan Buijs)
Radium-223 is a medical isotope with applications to cancer treatment. Specifically, it is a short-lived α-emitter, meaning induces targeted cell death through the release of high energy, short-range α-particles. However, the production of this radionuclide requires the irradiation and subsequent decay of Ra-226, a process not previously explored by the McMaster Nuclear Reactor (MNR). We present a mathematical simulation in Octave that seeks to model the pathways Ra-226 can take during the irradiation process. The simulation considers potential by-products including those produced by additional neutron captures and their resulting daughter isotopes. It explores full irradiation and decay chains including minor decay products. Pressure build-up from helium (originating as α-particles) and radon gas is also considered due to the pressurized nature of samples during irradiation. This simulation will provide information to researchers at the MNR to help initiate the production of Ra-223 at the reactor.
AlShenaiber, Leena – An Investigation of Autism Spectrum Disorders (Dr. Sarah Symons)
Autism Spectrum Disorders (ASD) have been thoroughly studied, with a special subset of research which explores the influence of ASD on family, and vice versa. Specifically, many studies have explored the emergence of autistic-like symptoms in the siblings of autistic individuals, the influence of ASD on familial stress and functioning, and family-driven early intervention. However, no study has explored all three topics from a single lens, creating a substantial gap in the literature. The current review will fill in this gap in order to understand the problem and potentially suggest a mediation of the effects of ASD which will improve family functioning. This review will include peer-reviewed North American papers that have been published in the last 10 years. Results show a link between ASD and family, and the potential of family-driven interventions in mediate the effects of ASD and families on one another. This project also has an additional component which explores the prevalence of stereotypes and myths that are viewed as fact by the general public. This topic has been explored before, however, it has not been provided in a clear format for the general public. This project will provide the missing information about the topic in an infographic that will be posted on social media and in government facilities in the community. Overall, this project will fill in areas that have been overlooked in the literature through a thorough review of the literature and an easy to understand infographic.
Balint, Liz – Evaluating Immunotherapies for Peanut Allergy (Dr. Mark Larché)
Peanuts are one of the most common anaphylactic-inducing foods. Currently, there is no effective treatment or existing cure for peanut allergy. Patients with any level of allergy must avoid nut-containing foods for their entire life. Despite these precautions, anaphylaxis can be induced by extremely small amounts of peanut, and accidental ingestion can be fatal.
Researchers are currently investigating various immunotherapies for peanut allergy. These can be categorized as allergen-specific or allergen non-specific. Allergen-specific therapies alter immune responses to allergens while non-specific therapies address allergic symptoms but are not curative. This literature review aims to evaluate the efficacy and safety of allergen-specific immunotherapies for peanut allergy and identify the most feasible therapy for future investigation.
The allergen-specific immunotherapies evaluated include subcutaneous (SCIT), oral (OIT), sublingual (SLIT), epicutaneous (EPIT) and peptide immunotherapy. The injection of peanut in SCIT, while effective, causes many adverse reactions and is unsafe. In OIT, patients ingest small doses of peanut each day, while SLIT involves holding peanut extract under the tongue. Studies have shown that, while SLIT is safer, OIT is more effective at desensitization. Daily application of a peanut patch, EPIT, demonstrates a high efficacy in children with few adverse reactions. Peptide immunotherapy is a new approach, which appears to have a high efficacy and safety profile and may induce tolerance.
Peptide immunotherapy appears to be an ideal candidate for a therapeutic vaccine due to its expected efficacy, safety, and relatively few doses. Further research is needed to thoroughly evaluate peptide immunotherapy for treating peanut allergy.
Barker, Bronwyn – Environmental and Biological Predictors of Gender Dysphoria in Children (Dr J. Ostovich)
Gender dysphoria and transgender representation and knowledge have been growing in the media and in research over the past few decades. Gender dysphoria is the feeling of identifying with a gender other than the one assigned at birth. It is a disorder classified in the Diagnostic and Statistical Manual of Mental Disorders V. The medical field is currently attempting to standardize a procedure for support and transition for pre-pubertal children who are experiencing gender dysphoria. This is because puberty-suppression leads to better psychological outcomes but is not a permanent solution. Although gender identity is thought to be formed by the age of four, knowing how to distinguish between children experiencing child dysphoria temporarily and those for whom the dysphoria persists will help guide families and physicians through deciding treatment options.
This paper aims to identify and analyse any potential predictive factors for persistent gender dysphoria in children. Various databases of scholarly articles were searched using key terms such as “gender dysphoria,” “children,” “transgender,” and “predict*” to find credible sources discussing the development of gender identity and dysphoria in children. Current research suggests that there are multiple influences on the development of discomfort surrounding assigned gender, including intra-uterine hormone exposure, genetics, and childhood home environment. Being aware of factors that contribute to gender dysphoria in childhood and into adulthood can better assist family and physicians in supporting their child.
Bider, Pascale – Investigating Turtle Road Mortality in North America (Dr. Pat Chow-Fraser)
Road networks are a well-known threat to ecosystems and biodiversity. Although they are necessary for human transportation, roads lead to habitat fragmentation, contaminant introduction, invasive species transport, and increased mortality of wildlife. Turtle populations in particular are put at risk by this increased mortality, since individual turtles reach sexual maturity comparatively late and populations have low levels of recruitment. This project sought to compile information on turtle road mortality and present it in a format that is accessible and useful for researchers. To achieve this goal, a literature review was conducted to identify what factors might impact turtle road mortality. Next, several studies that reported rates of turtle mortality were compared. Information relating to each study’s methodologies, surrounding landscape, road infrastructure, and surrounding turtle population was compiled. The results of this comparison emphasized the variability of road mortality rates reported in the literature, as well as highlighted the knowledge gaps that exist in our understanding of North American turtle populations. Furthermore, the present study underscored the need for consistent and standardized techniques for measuring turtle road mortality rates. Ultimately, the information amassed was formatted into tables for future analysis by other researchers, to be used in directing conservation efforts.
Chou, Sommer – Expanding the Antibiotic Resistance Platform to Aid in the Dereplication of Known Antibiotics (Dr. Gerard D. Wright)
The increasing prevalence of antibiotic resistant bacteria has been threatening human health globally for decades. The over-prescription of existing antibiotics, coupled with a lack of novel drug discovery, has amplified the effects that resistant bacteria have on this generation’s healthcare system. The development of new antibacterial compounds is vital to rectify the potential consequences of an antibiotic resistance crisis; however, natural drug discovery is often a long and redundant process due to the rediscovery of known antibiotics. To improve the natural product discovery process, the antibiotic resistance platform (ARP), a collection of genes that encode resistance enzymes, was developed. It allows for efficient screening of potential antibacterial compounds and inhibitors of resistance mechanisms through antibiotic dereplication.
The objective of this project is to expand the ARP through the inclusion of additional resistance genes. The specific focus is the addition of five genes encoding β-lactamase enzymes, which confer resistance to a class of antibiotics called β-lactams. These resistance genes are: blaTEM-30, blaOXA-1, blaOXA-50, blaCTX-M-27, and blaCTX-M-3. The successful inclusion of each gene to the ARP requires the application of a variety of molecular cloning techniques including ligations, transformations, DNA gel electrophoresis, and cell-based drug susceptibility assays. The minimum inhibitory concentration (MIC) of ampicillin for each of the resistance genes was determined and documented with the rest of the β-lactamases that currently exist in the ARP. The versatility of the ARP in antibiotic dereplication and adjuvant discovery necessitate its continued expansion, as it supports humans in the evolutionary arms race against bacteria.
Coles, Victoria – Synthesis of new small molecules that stimulate anti-lung infection defenses (Dr. Jakob Magolan)
The rise of antibiotic resistance represents a global health crisis with the ability to infect millions and increase risks associated with procedures like surgery and chemotherapy. As resistance proliferates through bacterial populations at a rate surpassing the development of new antibiotics, novel strategies must be employed to prevent future epidemics. Pneumonia is a lung infection caused by a variety of different bacteria and represents the leading cause of deaths and hospitalizations among senior citizens. As access to effective antibiotics becomes increasingly limited, the call for novel therapeutic treatments for lung infections like pneumonia grows more urgent.
Working in collaboration with the Bowdish Lab at McMaster University, the goal of this project was to synthesize small molecules that target and induce an antimicrobial response in human respiratory cells. Based on a hit previously identified through a whole-cell assay, a library of fifteen structurally similar compounds were synthesized via peptide coupling. These molecules were analyzed using the software Precepta to make predictions about their solubility, potential off-target effects, and other biologically-relevant properties. Molecules will then be tested in the Bowdish lab for potency relative to the original hit to determine if they display increased antimicrobial activity.
The development of these structural derivatives is an important step in the drug discovery process. By working to enhance the body’s ability to fight off infection, these drugs have the potential to treat diseases like pneumonia while decreasing society’s reliance on antibiotics.
Conant, Amory – Paleowaters: An Analysis of Groundwater Resources Contained in Submerged Ancient Lands (Dr. John Maclachlan)
As the 21st century progresses, the world water crisis continues to grow in severity, with millions affected globally. As a consequence, alternative water resources must be considered in order to meet increasing demand. A potential vast untapped resource is paleowater reservoirs: groundwater trapped in continental shelves that were at least in part emplaced during periods of lowered sea level, when such regions were subaerially exposed. This study conducts a literature review of global submerged paleowaters in order to provide a comprehensive overview of these freshwater deposits. Investigation of methods of emplacement, aquifer structure, salinity levels, accessibility from a physical and legal standpoint, economic viability, and potential impacts is conducted. From this background, groundwater and hydrologic concepts are applied to create a methodology to identify potential regions that experience elevated levels of recharge and freshwater emplacement during lowered sea level periods in the Quaternary. The methodology is subsequently utilized to conduct GIS analysis of several key regions of the world that have been identified as containing paleowater resources. Locations on the seafloor where recharge may have occurred are identified to determine the potential feasibility as a well field. The identification of key locations of potential massive, albeit unrenewable, freshwater resources could provide a significant opportunity for at-risk coastal communities to supplement water supply systems in the near future.
Coppens, Jarod – Limits to Silicon Solar Cell Efficiency due to Free Carrier Absorption (Dr. Rafael Kleiman)
At longer wavelengths, light has a much lower chance of being absorbed in a silicon solar cell. To combat this, different light trapping techniques have been developed that improve absorption by deflecting incoming light at various angles in the cell. At wavelengths near the bandgap of a cell, where light should stop being absorbed, the reflectance observed is lower than 100%. This means some light is still absorbed in the cell. It is unclear to what extent this is caused by absorption in the back-surface contact as opposed to other loss mechanisms such as free carrier absorption (FCA). FCA is when free electrons in the cell absorb photons and turn all the energy into heat as opposed to current.
The goal of this project is to better determine what factors influence cell reflectance at wavelengths near the bandgap. These factors directly influence the efficiency of the solar cell. An optical system has been built that can measure reflected light and the current produced by an illuminated cell. Using cells with different light trapping structures and different intensities of light, we can get a better picture of how these conditions affect efficiency. Furthermore, this project is the first step in developing a system that can accurately measure cell efficiency based on reflectance data. Once completed, our system will also be able to calculate quantum efficiency, the ratio of incoming light entering a cell that produces useable current, which will provide much more detail about solar cell performance.
Craughwell, Meghan – Genetic basis of melanin variation in the human fungal pathogen Cryptococcus neoformans (Dr. J. P Xu)
Cryptococcus neoformans is an opportunistic, human fungal pathogen causing infection, predominantly in immunocompromised individuals. One well-established virulence trait of C. neoformans is the ability to produce the pigment melanin. In comparisons of strains from around the world, a large intra-specific variation in the amount of melanin produced has been found. The LAC1 gene, which encodes for an essential laccase enzyme in the melanin pathway, was recently found to be correlated to variation in melanin production. A further understanding of this pigment would provide further understanding of the progression of cryptococcal infections and may assist in elucidating targets for the treatment of this disease.
This study aims to gain further insight into the genetic basis of the observed variation in melanin through the analysis of progeny from 52 genetic crosses of differing C. neoformans strains, collected from both clinical and environmental settings. Melanin produced by the progeny is quantified through spot densitometry assays and compared to the parental strains. The determined distribution of melanin production is used to predict the number of loci influencing the production of melanin. Since Cryptococcus is a haploid organism, a bimodal distribution would mean a single gene locus, whereas for instance, four different phenotypes would mean two loci. Following phenotypic analysis, genotyping of the progeny at the LAC1 locus is performed and compared to the parental genotypes. The melanin distribution pattern among progeny within and between crosses helps to gain more information about the broad genetic architecture governing melanin production in C. neoformans.
Daniel, Tanya – Aquaponics: A life cycle assessment of its sustainability and feasibility (Dr. Jurek Kolasa)
Due to population growth, urban expansion has escalated resulting in an increased demand for food. Since food is typically produced in rural areas, there are environmental costs to growing and transporting the produce to populated regions. By cultivating food within the city perimeter, natural spaces are preserved from farmland development. To ensure that detrimental ecological consequences from importing food products are mitigated, a proposed solution is to integrate aquaponics in urban communities. This diversification of food production also aids in local food security.
Aquaponics is the combination of two self-sustaining production systems: aquaculture and hydroponics. Aquaculture techniques are used to farm fish while a hydroponics system grows leafy vegetables in soilless surroundings. Thus, these food products are available to be cultivated and consumed by local citizens.
The primary research objective is to examine aquaponics as a viable system for urban food production. Thus, a life cycle assessment considering financial and environmental costs to run an aquaponics system was conducted to evaluate its sustainability from multiple perspectives.
Overall, it is crucial that informed opinions about the feasibility of aquaponics are communicated with government officials and policy makers before these sustainable practices are implemented into eco-friendly cities.
Doan, Alexi – Epidemiology of Fear: Investigating Societal Responses to Pathogenic Invasion (Dr. Chad Harvey)
Deadly epidemics have punctuated human history. The social environment associated with epidemics often elicits secondary ‘epidemics’ of fear, stigmatization, and moralization. If not properly addressed, these secondary epidemics pose a theoretical threat to public order. Hence, it is vital to develop policy specifically designed to anticipate and quell human responses to epidemics. In order to predict how societies will respond to future epidemics, it is necessary to critically analyze historical records of disease presented in media discourse. As such, a total of 216 examples of media discourse pertaining to three major historical epidemics—the second cholera epidemic (1831-1833), HIV/AIDS (1981-1983), and the West African Ebola Outbreak (WAEO) (2014-2015)—were collected in the form of newspaper articles, and twitter ‘tweets’. The type of language used was then categorized by valence. It was noted that media discourse pertaining to the HIV/AIDS pandemic was frequently inflammatory towards marginalized groups, and was associated with negative valence more often than news discourse for the other two case studies. There was also a stark disparity between valence levels for social media and news discourse; social media discourse was more often associated with negative valence than all other news discourse. This could be because, anecdotally, language used by social media was far more flippant and even tended towards fearmongering in some instances. In all, fatal disease has—and always—will be part of human society, which makes past responses an untapped resource to inform future endeavors to develop effective response policies.
Fraschetti, Ariana – Optical Vortices in Random Wave Interference (Dr. Duncan O’Dell)
Wave interference is a phenomenon most notably demonstrated by Thomas Young’s double-slit experiment in 1801, in which two combining wave sources produced a distinguishable interference pattern. Further studies by Nye and Berry in 1974 explored the resulting interference patterns and dislocations created when combining multiple optical waves. One particular dislocation they studied was an optical vortex: a singularity in a two-dimensional optical field where the phase of the wave at that point takes on all possible values, thus appearing as a point of destructive interference. These vortices are noted in optical fields, seen in all plane wave interference patterns of three or more interacting waves, and are manipulated in laboratory settings for experimental applications. For instance, vortices may be used to trap and move charged particles in optical tweezers, and vortices are a key component in stimulated emission depletion (STED) microscopy. In this study, plane waves of randomized parameters including phase and amplitude are combined to create interference patterns in one and two dimensions. Using the software Mathematica, the interference patterns are simulated and graphed to identify the presence of vortices, and their corresponding distribution in space is analyzed. The aim of this simulation is to delve into the properties and characteristics of the wave-nature of light, explaining the physics behind how and why optical vortices occur. As various types of plane waves are seen interfering in numerous natural phenomena, this simulation can give further insight into how one may manipulate them for a wide variety of applications and studies.
Garnett, Jacqueline – A Comparative Phylogenetic Analysis of Accessory Gland Evolution in Fishes (Dr. Sigal Balshine)
Sperm competition arises when two or more males compete to fertilize a female’s eggs; this phenomenon puts an evolutionary pressure on males to develop adaptations that will increase their reproductive success. It is thought that one such adaptation is the development of accessory glands, which are secondary sexual organs that assist in sperm production and storage. Accessory glands can be found across a wide variety of taxa, but their phylogenetic origin is largely unknown. Within fishes, only a relatively small number of species have accessory glands. I employed a discrete comparative phylogenetic analysis to analyze the evolutionary history of accessory glands in teleost fish species (Teleostei), based on a previously published phylogeny for fishes by Rabosky et al. (2013). The presence or absence of accessory glands was identified in 107 families; this information was compared to their evolutionary histories to determine the number of times that accessory glands independently evolved across the studied lineages. Future studies may expand upon these results to elucidate the phylogenetic relationship between accessory glands, mating systems, and the presence of alternative reproductive tactics. Furthermore, the predicted relationship between sperm competition and the evolution of accessory glands can then be explicitly tested. This work will shed light on the types of selective forces that lead to the evolution of accessory glands and help to create a more complete understanding of how fish and other vertebrates respond to selective pressures on their reproductive success.
Graham, Katie – Identifying a low complexity domain within residues 1-197 of Ataxin-1 (Dr. Ray Truant)
Spinocerebellar ataxia type 1 (SCA1) is one of nine polyglutamine (polyQ) diseases, which are characterized by the expansion of CAG, an unstable trinucleotide within the coding region of the gene. The causative protein for SCA1, Ataxin-1 (ATXN1), is a nuclear protein with unknown normal function, despite the understanding of the ability of the mutated protein to cause degeneration of Purkinje cells in the cerebellar cortex. ATXN1 has been shown to aggregate in nuclear inclusions, a process essential for SCA1 pathogenesis. The ability of ATXN1 to form nuclear aggregates implies the presence of a low complexity domain (LCD), although an LCD has not been characterized within the protein.
Present research has primarily focused on regions following the CAG tract, however no studies have analyzed the 197 amino acids preceding this expansion. This study aims to characterize an LCD within the first 197 residues of ATXN1. Polymerase chain reactions and recombinant technology were used to isolate, amplify, and insert seven specific ATXN1 fragments into a green fluorescently tagged plasmid, which was then transfected into RPE1 cells for imaging. The latter experiment assessed the ability of the ATXN1 fragments to form nuclear aggregates based on visual aggregation of fluorescent signals to regions in the nucleus, resulting in the identification of an LCD. Due to the high concentration of cytosine and guanine in the fragments, they were not obtained in high enough yields for transfection, and thus further research is needed to characterize an LCD in Ataxin-1.
Greenblat, Leeor – Transmission and Reflection of a Quantum Particle for the Potential (Dr. Walter Craig)
The potential term in the Schrödinger equation describes the environment in which a quantum particle propagates. Two commonly studied potentials are the rectangular barrier and well. In this report, the Schrödinger equation is solved for a potential barrier/well with height 1/ and width . Various properties of the resulting wave functions are examined, including the transmission and reflection coefficients as well as the scattering matrix for the scattering states. Bound states are also examined, including how the number of bound states depends on geometry of the potential. The spatial components of the wave functions are generated by solving the time independent Schrödinger equation. The transmission and reflection coefficients are then calculated by ensuring continuity of the zeroth and first derivative of the wave function at the edges of the potential. The resulting functions are then examined to determine energy values for which transmission is optimized. Additionally, an proof is used to show the potential barrier approaches the delta function as approaches zero.
We find that the transmission coefficient for the potential barrier is dependent on both the width, height, and energy of the travelling wave. Furthermore, a correspondence between the putative values of the transmission coefficient for the delta function and the calculated values are demonstrated.
These results contribute to our understanding of potential barriers/wells by predicting transmission coefficients when a trade-off exists between the width and height of a potential. Furthermore, they provide an alternative method of finding wave functions for the delta potential.
Houpt, Noah – Foraging Behaviours and Distribution of Four Avian predators of the Plainfin Midshipman (Porichthys notatus) (James Quinn and Sigal Balshine)
Acquiring resources is necessary for survival and reproduction in all known forms of life. When important resources are transiently available, the pressure to acquire them in an efficient way is even stronger due to time constraints, but this is poorly understood. The plainfin midshipman (Porichthys notatus) is a species of intertidally breeding fish which serves as a seasonally and diurnally transient resource for four avian piscivore species along the Pacific coast of North America. Descriptions of the foraging strategies employed by these predators to capture midshipman would provide insight into how predators take advantage of transiently available resources. The behaviours employed by bald eagles (Haliaeetus leucocephalus), glaucous-winged gulls (Larus glaucescens), great blue herons (Ardea herodias), and northwestern crows (Corvus caurinus) to capture and consume plainfin midshipman are described here. Additionally, bird census data are provided to describe how the distribution of these four predators relates to the availability of the midshipman fish. I found that bald eagles and great blue herons showed significantly higher abundance when the tide was receding than when it was incoming. Additionally, I found that glaucous-winged gull abundance in the intertidal zone decreased over time throughout the midshipman breeding season. The behavioural descriptions provide insight into the foraging strategies employed by four avian piscivores to take advantage of the transiently available resource of the midshipman fish. The bird census data provide some evidence that bald eagles, great blue herons, and glaucous-winged gulls distribute themselves spatio-temporally to take advantage of the transiently available midshipman fish.
Johnstone, Graham – Superconductivity in Heavy Fermion URu2Si2 (Dr. Graeme Luke)
The superconducting state of a material is characterized by the transmission of electric current with no resistance. This is a tantalizing prospect for developing novel electronics. It is also an exhibition of quantum mechanics on a macroscopic scale. The superconducting heavy fermion metal URu2Si2 has gained popularity over the past 30 years for its 17.5K transition into what is referred to as the “hidden order” phase. This order parameter is not well understood, but it is evidenced by jumps in thermodynamic properties such as heat capacity at the phase transition. Characterizing the hidden order will reveal properties of metals and the superconducting state. This project explores the literature surrounding superconductivity research and URu2Si2 experiments. The objective of this project was to synthesize single crystal URu2Si2 specimens and apply different annealing procedures. The purpose of annealing is to remove impurities in the crystal, thereby increasing the temperature at which it enters the superconducting phase. A single crystal URu2Si2 sample was grown in a tri-arc furnace then separated into 3 pieces. One of these pieces was annealed at 700°C, one at 800°C, and the last at 900°C. Once annealed the magnetic susceptibility of the samples was determined using SQUID magnetometry. This result predicts the superconducting phase transition temperature. Impurities in URu2Si2 samples can reduce the critical temperature. As such, developing an annealing procedure to achieve a higher and more precise values for this temperature is an asset for reducing error in future studies involving this material.
Kawamoto, Cory – Determining the Effects of administration of BD584, dosage of BD584 and route of administration of BD584 on immune function (Dr. Mahony)
The immune system is a complex system that protects an organism against foreign pathogens. There are four main isotypes of antibodies, which include IgA, IgG, IgM, IgE. Vaccinations stimulate the immune system to produce antibodies.
In this study, the effects of BD584, dosage and vaccination route on immune function will be determined. Five groups of mice are injected with BD584 over a 7 day period. Group 1 is administered BD584 intranasally at an exponentially increasing dose. Group 2 is administered BD584 subcutaneously at an exponentially increasing dose. Group 3 is administered BD584 inranasally at a constant dose. Group 4 is administered BD584 subcutaneously at a constant dose. Group 5 is administered PBS intranasally. Serum was collected on study day 14 and IgG, IgG2a, IgA were determined using an Enzyme Linked Immunosorbent Assay (ELISA). Antigen kinetics has an effect on the magnitude and quality of the long term immunity. This study will explore the effects of regulating antigen exposure and adjuvant kinetics on vaccine potency.
Kim, Noel – Research Proposal: Does Atypical Visual Sensory Processing in ASD Affect the Use of Visual Supports at School? (Dr. Nikol Piskuric)
Autism spectrum disorders (ASDs) are neurobiological disorders of early brain development that are increasingly prevalent in Canada. Traditionally, research on ASD has focused on the social, communicative, and cognitive aspects of the disorder; however, recent research highlights atypical sensory processing in ASD. Regarding visual processing, individuals with ASD are often described as ‘seeing the trees, but not the forest’. These impairments in global visual processing may lead to learning difficulties, necessitating the use of alternative teaching strategies in the classroom. Therefore, this research proposal aims to investigate whether mouse models of ASD display atypical visual processing, and how this may affect their learning abilities. Given that the neural computations involved in sensory processing are generally conserved between rodents and humans, if mouse models of ASD express deficits in visual processing, then their learning in response to visual stimuli may be impaired. Furthermore, these mouse models can be investigated for potential neural mechanisms underlying atypical visual processing, namely impaired GABAergic signaling. By understanding how atypical visual processing affects learning in mice, this study can help inform teaching practices in Canadian classrooms. Accordingly, in a parallel research project, I will assess the present strategies used by Ontario educators to teach students with ASD and provide recommendations for future strategies that are informed by current neuroscience research. This information will be presented in a poster targeted toward educators in the Hamilton community. As a whole, this project investigates the neuroscience of ASD, while bridging the communication gap between scientists and educators.
Koniar, Helena – Mobility of Bicoid Morphogen in Fly Embryos (Dr. Cecile Fradin)
The Bicoid (Bcd) morphogen is critical for early development in the fruit fly Drosophila melanogaster. Morphogens are proteins that form concentration gradients in embryos and developing tissues to affect cell differentiation in a concentration-dependent manner. Bcd proteins form an exponential concentration gradient with maximum concentrations at the anterior pole of the embryo, decreasing towards the posterior pole. Understanding the mechanism behind the establishment of Bcd’s concentration gradient is fundamental in comprehending the precision and robustness of its transcriptional response. The Synthesis Diffusion Degradation (SDD) model is the simplest and most widely considered model for the establishment of the Bcd gradient. This project aims to measure the diffusion coefficient of Bcd to support the diffusion aspect of the SDD model. Fluorescence correlation spectroscopy (FCS) is a powerful technique capable of single molecule sensitivity to obtain information on dynamic processes in physiological conditions. We used FCS to measure the diffusion coefficient of Bcd in live fly embryos. The diffusion coefficient was measured in the cytoplasm and in nuclei of the embryos to determine if the diffusion coefficient is constant throughout the embryo. A constant diffusion coefficient suggests that Bcd diffuses by simple unhindered diffusion while a spatially varying coefficient suggests that more complex diffusion or transport phenomena are at play. Diffusion plays an important role in biological systems especially in the dynamic processes of protein interactions. Our measurements of the diffusion coefficient of Bicoid are made possible by the application of key concepts from the world of physics and allow us to better understand complex cellular processes.
Lefebvre, Michèle – Depressive thinking and its implication in inclusive fitness optimization in complex situations (Dr. Paul Andrews and Sarah Goegan)
Inclusive fitness theory posits that natural selection favours individuals behaving in ways that maximize their inclusive fitness. As humans are complex social species, the path to optimizing inclusive fitness is not always simple and may involve making trade-offs between direct means of reproduction (e.g., having children) and indirect means (e.g., supporting biological siblings) or sacrificing important resources (e.g., social support, safety, social standing). As a result, humans have likely evolved mechanisms to assist in the analysis of complex, fitness-related problems and choose solutions that optimize their inclusive fitness. The Analytical Rumination Hypothesis suggests that when the problem is complex and evolutionarily relevant, depression, in particular rumination, may represent one such mechanism. An exploratory literature review was conducted to evaluate the hypothesis that, under certain circumstances, depressive thinking facilitates weighing the relative costs and benefits of a difficult decision to abandon direct reproductive pursuits in order to promote inclusive fitness. Literature examining the potentially adaptive function of depressive thinking was reviewed, and a model outlining the form of this mechanism is presented. Additionally, behaviours involving trade-offs between direct and indirect fitness, such as suicide, were reviewed to gain further insight into their implications in this model. This paper presents an intersection between evolutionary theory and clinical psychology and adds to the body of literature that is attempting to find an ultimate explanation for depression. A better understanding of the function of depressive thinking can help delineate normative from pathological processes and aid in improving early intervention and treatment practices to support those who are experiencing depression.
Liu, Aileen – Synthesizing Liposomes Using Reverse-Phase Evaporation to Deliver Antibiotics at Controlled Rate to Target Biofilm (Dr. Zeinab Hosseini-Doust)
Bacteria, such as Staphylococcus aureus, tend to adhere to and colonize on the surfaces of implanted devices, then secrete biofilm as a stress response. Biofilm is an extracellular matrix that serves as a form of resistance as it shields bacteria from interacting with antibiotics and host immune cells, therefore permitting bacteria to proliferate. Nosocomial infections caused by biofilm formation can lead to severe chronic infections that are challenging to prevent and treat, as they contain different properties than planktonic bacteria. This study aims to synthesize liposomes, a type of nanoparticles with a lipid shell and a hydrophilic core, that can target biofilm and release antibiotics to the bacterial colonies at a controlled rate. Liposomes with a high drug loading efficiency and carry a uniform size between 100 nm to 300 nm will be successful in eliminating biofilm. The liposomes were synthesized using the reverse-phase evaporation method and evaluated variations in lipid chain length, drug size, and drug-to-lipid ratio to determine the combination of factors that yield the ideal drug carrier for biofilm infections. Lipids DPPC, DSPC, or soy lecithin with cholesterol were used to generate the lipid layer and vancomycin or crystal violet were loaded as cargo using drug-to-lipid ratios of 1:10. Properties including size and delivery rate were measured. Liposomes made with soy lecithin and cholesterol loading vancomycin displayed the best results due to the integrity of the phospholipid membrane. Liposomes synthesized using this protocol can be further developed to target and eliminate S. aureus biofilm infections.
Loukiantchenko, Elsie – Inkjet printing of conductive nanocellulose inks for flexible electronics (Dr. Emily Cranston)
Cellulose nanocrystals (CNCs) are rod-shaped nanoparticles extracted from renewable natural resources. They possess impressive mechanical and rheological properties, are non-toxic and biodegradable, and have many potential applications. In combination with conductive nanoparticles, CNCs can be used in inks to print conductive circuits for transparent electronics. The CNCs colloidally stabilize the conductive nanoparticles and improve the “printability” of the inks. This project aims to produce, characterize, and optimize CNC-based inks, and to use them to print transparent conductive patterns.
CNCs will be prepared through sulfuric acid hydrolysis of pure cotton. Five inks will be tested: (1) CNCs only, (2) CNCs with silver nanoparticles synthesized in situ (3) CNCs mixed with silver nanoparticles, (4) CNCs mixed with carbon nanotubes (CNTs), and (5) CNTs only. The concentrations of CNCs and conductive nanoparticles in the inks will be optimized in order to print transparent interconnected rings, taking advantage of the coffee ring effect. In particular, the surface tension of the inks, their printability, and coffee ring thickness and transparency will be optimized. This will be characterized using polarized optical microscopy and atomic force microscopy. Ultraviolet-visible spectrophotometry will be used to determine the transparency of the patterns.
It is hoped that an optimized concentration will be formulated for all 5 inks. Following that, further research will be done to determine which of the inks will offer the best conductivity. This research is an important step towards creating sustainable printable circuits. Additionally, these inks have many potential applications, especially in the growing field of flexible technology.
Macklai, Sabrina – Method Validation of a MSI-CE-MS Analytical Strategy for the Systematic Surveillance of Drugs of Abuse (DoA) (Dr. Philip Britz-McKibbin)
As the opioid crisis continues to rapidly increase in Canada, it is imperative to have a reliable and fast technique to identify and quantify drugs of abuse (DoA). The current gold standard for the screening of DoA involves a two-tiered approach: 1) detection of DoA through an immunoassay test followed by 2) confirmatory identification and quantification via liquid chromatography-mass spectrometry (LC-MS/MS). Immunoassays, however, are prone to bias whilst also being unable to detect new designer drugs. Herein, a novel non-targeted, high-throughput approach for DoA screening was proposed by multi-segment injection–capillary electrophoresis–mass spectrometry (MSI-CE-MS). In order to confirm the effectiveness of this approach, 218 morning urine specimens were collected from clinically depressed in-patients at St. Joseph’s Healthcare Hamilton hospital and screened via the gold standard and MSI-CE-MS with full-scan data acquisition using an 84 drug panel containing five major classes of drugs and their metabolites. It was determined that only 25% of immunoassays were able to accurately detect DoA and, of that, less than 10% were able to detect all DoA present in the sample. It was also observed that the sensitivity of immunoassays is reliant on the class of drug being screened, with less sensitivity for benzodiazepine detection. Immunoassays were also unable to detect synthetic urine specimens that contained creatinine, a common urinary metabolite used by manufacturers to evade positive screening tests. These results confirm that immunoassays are a poor primary test for DoA screening and should be replaced by the more reliable MSI-CE-MS approach.
MacLean, Connor – Evaluating Science Communication Within the Faculty of Science (Dr. Maureen MacDonald)
An investigation of the effectiveness of the current science communication structure between undergraduate students and staff in the Faculty of Science at McMaster University was conducted. Science communication can consist of the promotion of academic resources, support services, volunteer opportunities, career opportunities, events within the faculty, research showcases, and more. This investigation resulted in proposed recommendations to refine the structure of the Faculty, allowing for more of a collaborative student focus. Students are presented with a wealth of information about careers, research, academics, and extracurricular activities on a variety of independent platforms, each implementing different methods of advertising this information to students, if at all. Faculty members have conceded that there is a lack of consideration regarding how students would like this information to be provided to them and to what extent. This study aims to research the cause of this issue of communication and identify methods by which it can be improved for all students and faculty members. Current strategies for science communication have been identified and evaluated from a student perspective. Qualitative and quantitative information was collected through student surveys and interviews with faculty members and administration. The goal is to understand science communication and outline necessary actions to improve it based off of gathered information.
Martin, Sonya – Fluorescent Methods for the study of Bicoid’s DNA Binding Domain (Dr. Cecile Fradin)
Morphogens are molecules that can aid in cell differentiation, an important process for embryo development. In the Drosophila melanogaster embryo, the Bicoid (Bcd) protein acts as a morphogen and forms an exponential concentration gradient along the anterior-posterior axis. Bicoid exerts its effect by acting as a transcription factor for important marker genes involved in pattern development in D. melanogaster. The goal of this project is to develop a fluorescent mutant of the DNA binding domain, or homeodomain, of Bcd to use in future single particle detection experiments to better understand the Bcd – DNA interaction.
Two fluorescent labelling strategies were reviewed. The first option considered was to use the green fluorescent protein (GFP). Some of the previous successful cloning and purification methods to obtain a Bcd-GFP protein fusion were reviewed. The second option considered was to attach an organic fluorophore to a cysteine in the protein. However, a point mutant to the Bcd homeodomain is needed because the wild type protein does not contain cysteine. The structure of the Bcd homeodomain was examined and possible positions for the mutation, that avoid disrupting the structure of Bcd, were proposed.
In the end, labeling the protein with a bright organic fluorophore was judged to be both more straightforward and more likely to result in a strongly fluorescent functional Bcd. Obtaining the fluorescent protein will aid in future experimentations to better understand the properties of Bcd’s DNA binding domain. This research can then be applied to better understanding Bcd’s role in embryo development.
Norman, Bryce – Quantum Dynamics of a Bose-Einstein Condensate (Dr. Duncan O’Dell)
Singularities are important for indicating when approximate quantum mechanical theories break down and a more in depth theory must be used. One particular singularity of interest are vortices, points around which the value of a closed path changes by 2π. The point at the center of the vortex takes on all possible values so the value goes to zero. A Bose-Einstein condensate in a double-well potential is a system in which quantum vortex singularities can arise. Bose-Einstein condensates are a state of matter in which a collection of bosons occupy the same quantum state. Systems involving this state of matter are of interest because they allow microscopic quantum phenomena, such as matter interference, to become macroscopic. The vortices that arise in this double-well system are quantized, as the phase difference of the system can only take on specific values. By investigating the dynamics of a set of bosons in a double well potential, a better understanding of these quantum vortices can be obtained. To investigate this system, the Hamiltonian is written in Fock space (number difference space) and analytically reduced to a set of coupled differential equations. Python is used to numerically integrate the differential equations that arise from the system and obtain solutions. Using this method, the behavior of quantum vortices within this system is investigated to understand why they arise and what processes cause them to appear. This will allow for a better understanding Bose-Einstein condensates which are a candidate for use in quantum computing.
Pavic, Sarah – An Investigation of Opioid Use and Poisoning in Hamilton and at McMaster University (Dr. Nikol Piskuric)
For the past two decades, Canada has been experiencing an opioid epidemic. During this period, rates of opioid misuse have risen, resulting in rapidly increasing rates of opioid-related poisoning and death. The opioid epidemic continues to persist in Ontario, including Hamilton. In Ontario, the use of nonmedical prescription opioids among the general adult population started to decline in 2010, but began to rise significantly in 2015. In Hamilton, the prevalence of opioid related deaths has been above the provincial average since 2005, and last year it more than doubled the provincial average. Many universities in Ontario have implemented strategies to address the opioid epidemic. These include distributing posters on opioid awareness and training campus police and emergency teams to administer naloxone, a life-saving medication used to reverse opioid poisoning. In contrast, McMaster University has not yet made significant attempts to address the opioid epidemic. This report describes the need for collecting drug use data from McMaster students by evaluating factors that contribute to substance use among students. Accordingly, I outline a plan for collecting these data on campus through a university-wide survey with the intention of establishing a permanent drug use database to provide a system for campus services (e.g., the Student Wellness Centre) to collect these data in the future. I also propose an opioid awareness and naloxone training workshop for McMaster students. Ultimately, this project aims to determine ways to increase awareness of opioid use and improve services on campus that address opioid use.
Saunders, Jacob – Synthesis and Characterization of Starch Nanoparticle Hydrogels (Dr. Todd Hoare)
Hydrophilic polymer gels (hydrogels) have extremely useful properties with respect to chemical and biomedical engineering. Nanoparticle hydrogels, in which nanoscale particles function as building blocks, can offer increased functional diversity and controllable release kinetics. Starch nanoparticles are hypothesized to be advantageous building blocks for biomedical hydrogels due to their cytocompatibility and functionalizability. Starch nanoparticles were functionalized with aldehyde and hydrazide groups to enable cross-linking through hydrazone chemistry, which can be performed rapidly under physiological conditions to facilitate in situ gelation following injection. Aldehyde functionalization was achieved utilizing sodium periodate to break the carbon-carbon bond between the adjacent hydroxyl groups via oxidation. Hydrazide functionalization was achieved by taking the aldehyde-functionalized nanoparticles and reacting them with a large excess of adipic acid dihydrazide followed by reductive amination. Four degrees of substitution (D.S.) were synthesized (0.05, 0.10, 0.25, 0.40) and analyzed with proton nuclear magnetic resonance spectroscopy to determine that the correct structures were attained. The gels were synthesized at five different concentrations (5, 7.5, 10, 25, and 35 wt%). Gelation times were measured directly using rheometry, providing information on their mechanical properties in the form of storage and loss moduli. The 0.25 D.S. appears to be the most promising with a gelation time of 114 seconds whereas the other degrees experienced difficulty in either gelation or dissolution in water. With the successful gelation of a pure SNP hydrogel, continued investigation of the gel properties such as mechanical strength, may open an exciting new realm of possibilities for biodegradable, optimizable drug delivery systems.
Sharpe, Isobel – A Systematic Review and Meta-Analysis on the Effects of Vitamin D Supplementation in a Healthy Adolescent Population (Dr. Forough Farrokhyar)
Vitamin D is a prohormone essential to a variety physiological processes, including calcium absorption and bone formation. Vitamin D deficiency (VDD), measured through levels of serum 25-hydroxyvitamin D (25(OH)D), is prevalent in adolescents worldwide. VDD is associated with various health problems including cancer, diabetes, multiple sclerosis, and some psychiatric disorders. Additionally, VDD is associated with rickets, a disease specific to children and adolescents which causes bone deformation and reduced growth. Currently, there are few policies aimed at combating VDD. Due to the negative impacts of VDD on health, it is important to assess the effects of vitamin D supplementation on serum 25(OH)D levels, which will subsequently inform global health policy. The goal of this study is to determine the effects of vitamin D supplementation interventions on serum 25(OH)D levels and various health outcomes in a healthy adolescent population. This systematic review and meta-analysis includes healthy adolescents aged 10-18, the data for which was collected from an ongoing project. To obtain the highest standard of evidence possible, only randomized controlled trials were used. The baseline characteristics of the data will be summarized, then the data will be stratified and analyzed using a random effects model. It is predicted that levels of serum 25(OH)D will change based on vitamin D dosage, and that this effect may differ over season, latitude, and baseline serum 25(OH)D levels. Overall, this information can be used to help determine optimal doses for vitamin D supplementation in adolescents with VDD, providing a useful resource for policy makers.
Smith, Jeneva – Exploring the Effects of Emotional Dysregulation and Interoceptive Deficits in Patients with Binge Eating Disorder (BED) and Bulimia Nervosa (BN) (Dr. Iris Balodis)
Bulimia nervosa (BN) and binge eating disorder (BED) affect millions of Canadians. Up to a third of those who receive treatment relapse, indicating a need for more effective treatments. Recent literature has demonstrated a connection between eating disorder severity and emotional dysregulation (ED) and interoceptive deficits (ID), suggesting their potential as treatment targets. This study examined the relationship between interoceptive deficits and emotional dysregulation with treatment outcome in BN and BED groups. This retrospective research analyzed treatment records collected at the Eating Disorders Clinic at St. Joseph’s Healthcare Hamilton, where the participants (n=100) attended a 25 week long out-patient treatment program. The patients’ ED and ID scores were examined at the beginning of treatment using the Eating Disorders Inventory-3 and bingeing behaviour was monitored weekly using checklists. An ANOVA tested group differences in ID and ED and treatment outcome. A mixed model analysis tested for changes in bingeing behaviour across the treatment in BN and BED groups. Based on previous studies, it was hypothesized that the BN and BED groups will have similar rates of ID, but the BN group will report significantly higher rates of ED. In the BED group, we anticipate no relationship between treatment outcome and ID and ED scores; in the BN group, we hypothesize that higher ED scores will relate to poorer treatment outcome. This research can inform clinicians on how ID and ED may play a role in treatment outcome for people with BN and BED, potentially leading to more effective treatments.
Sreerangan, Pooja – Changing Perceptions of Nutrition Over Time Through The Canada Food Guide (Dr. Chad Harvey)
Nutrition and dieting is more prominent and vital than ever. The Canada Food Guide is a staple in Canadian nutrition decision-making. The Canadian government first released a food guide during World War II to acknowledge food rationing whilst preventing nutritional deficiencies and improving the overall health of Canadians. As scientific research focusing on general health and nutrition advanced and food production evolved, the concept of dieting popularized. This led to changes in perceptions of what is a healthy diet, resulting in revision of the food guide over time. Eating Well with Canada’s Food Guide, as it is known today, remains an important resource for Canadians making healthy diet choices.
The purpose of this study was to review how the perception of a nutritious diet has changed since 1977 centering upon the Canada Food Guide. This study was divided according to the four food guides released since 1977. The rationale for modifications to these four food guides were assessed, and compared, using relevant scientific publications and popular media of the time. The results of this review can be used by researchers and students to learn how and why our understanding of nutrition has evolved over time.
Stewart, Jack – How Planetary Formation and Migration Influences Their Ability to Support Prebiotic Life (Dr. Sarah Symons)
The solar system we live in is seemingly unique in so much as we have not yet discovered systems with similar features or characteristics. However, this does not mean analogous systems are impossible, as many studies have run computational models simulating the production of similar systems. Although, the majority of these studies seem to agree that we are the exception rather than the rule, both in terms of type and arrangement of the planets. The aim of this literature review is to evaluate how planetary formation and subsequent migration can lead to the development of the solar system like that we see today. It will emphasize the effect that the migration of giant planets had on its composition, the subsequent effect this had on the delivery of biomolecules, and ability of planets to support the development of these molecules. This review evaluates the current research and connects the links between these events. Furthermore, it highlights where the current areas of interest and study are, and what the most impactful studies have been. Finally, it shows what the competing theories surrounding this topic are and what the consensus of the wider scientific community is.
Swing, Megan – Determining the Extent of the Barron River Tectonic Window (Dr. Alan Dickin)
The Grenville Province is the youngest component of the Canadian Shield which spans across Ontario and into northern Quebec. The province is known for its high-grade metamorphism that occurred during a major orogeny, or crustal deformation event, caused by a continental collision approximately one billion years ago. The Grenville orogeny allowed younger continental crust in the southeast to be thrust over older crust to the northwest forming a layered structure. After the thrusting event the crust underwent significant erosion, resulting in an intricate structural pattern containing tectonic ‘windows’ that reveal older crust. A final event that created additional complexity was the Ottawa Graben, which was a rifting event that occurred 600 million years ago. These events have made the Grenville province difficult to map, which poses challenges towards determining the smaller scale structure as well as the potential for earthquakes.
This study explores an outcrop known as the Barron River, located near the Ottawa river where the Grenville Orogeny thrusts and Ottawa Graben faults interact. Rocks taken from this region confirm its structural complexity as samples have been found to contain older rock than surrounding areas, suggesting the presence of a tectonic window. Using Sm-Nd isotope dating, the model ages of the remaining samples can be determined, allowing for greater understanding of the nature of this structure. By estimating the extent of the Barron River window, we can uncover the result of major processes throughout history that have allowed the formation of the Grenville province as it is seen today.
Takahashi, Monica – EYE-MAC Project: Providing vision screening tests to children around Hamilton (Dr. Kourosh Sabri)
Poor vision can have numerous effects of varying severity on an individual. It has been shown to increase one’s chance of developing a mental health issue, such as anxiety or depression and in contrast, it can decrease one’s academic achievements and socio-economic status. There are also several eye conditions, such as amblyopia, that could result in permanent blindness, if not caught early. Unfortunately, there exists a lack of public awareness regarding the importance of vision screening, so most children do not get screened. This is exacerbated in rural areas as there is a lack of access to eye physicians.
As a part of the McMaster Paediatric Eye Research Group (McPERG), I will be sent to elementary schools around Hamilton to perform vision screening tests on children between the ages of 4 and 14, and I will assess their visual acuity and stereoacuity. Children who do not pass these tests will be contacted and referred to a partnering ophthalmologist. I created a form that the children will bring with them to the ophthalmologist so that we can assess our efficacy as vision screeners by comparing the scores that the doctors gave the students to the scores that we gave them.
Through my participation in this ongoing study, I hope to gain a better understanding into clinical research as I will be partaking in all aspects of the study. These include the initial contact with the school, distributing and collecting consent and assent forms, performing the vision screening tests, entering the data, and contacting families for follow ups.
Tam, Audrey – Investigating the Effects of Aging and Collinearity on Contour Integration (Dr. Patrick Bennett)
An essential component of object perception involves the detection and discrimination of contours. Studies have shown that contour perception depends significantly on several stimulus factors, such as the alignment of contour elements, and that the effects of these stimulus variables change with healthy aging. However, the neural mechanisms that underlie age differences are not well understood. The present study explores the impact of aging and contour element alignment on contour discrimination by comparing behavioural and neurophysiological measures in younger and older adults.
Electroencephalography (EEG) activity in both age groups was examined during a contour perception task. Participants were presented with a visual stimulus consisting of a spiral-shaped contour embedded among distracters. The contour consisted of multiple, oriented elements, and the alignment of these elements was manipulated between trials to vary contour salience. Contour discrimination ability was assessed by requiring subjects to locate the tail of a spiral contour on each trial. The behavioural data collected to date are consistent with previous findings and show that i) contour discrimination was affected by element alignment; and ii) was generally worse in older adults. Preliminary EEG analyses have also revealed age differences in both the timing and topography of the neural signals evoked by the contour stimulus. Further analyses will examine whether these differences in brain activity correlate to the differences observed in performance. Overall, results suggest that the neural processes underlying contour integration change with age, which may impact our perception of the world around us.
Tweedle, Adam – Contrast Between High and Low Density Monospecific Stands of Garlic Mustard Proposal (Dr. Susan Dudley)
Garlic Mustard (Alliaria petiolata) is a unique plant species that has invaded and spread throughout the Eastern United States and Canada. Originating from Eurasia, they are a biennial species, which requires two years of growth to reach maturity. They are dominant in the understory of forests, creating a monoculture in their non-native environment. The aim of this study is to determine where biomass is allocated in Garlic Mustard and whether leaf area, leaf development, root mass or other morphological traits are related in plant biomass allocation. The study will be conducted at the McMaster Forest, sampling paired quadrants along a transect. At each paired site, one of the two sites will then be randomly selected and will have individual plants removed to simulate a low-density environment. Light intensity, air temperature, leaf temperature, and photosynthetic activity will be measured. Baseline measurements will be made at each site before plant removal to account for any changes made due to the removal of the Garlic Mustard. It is hypothesized that Garlic Mustard biomass allocation will cause individuals with a large leaf area to have a small root mass, while individuals who have a low leaf area, leaf development, will have a large root mass in comparison. The findings of this research would allow for conservation authorities to determine the most effective treatment method when removing Garlic Mustard, an understanding of morphological traits as well as integrated management options.
Vitali, Elias – Quenching Radii for X-Ray Bright and Faint Galaxy Groups (Dr. Laura Parker)
Galaxies live in a variety of environments, from isolated regions to clusters containing thousands of galaxies. Observed galaxy properties vary across these environments and by studying how these properties correlate with environment we can constrain galaxy evolution mechanisms. A correlation has been shown between the star formation rate (SFR) of galaxies and their distance from the center of their host group, but it is not clear which physical mechanism(s) are driving this trend. Previous work shows that some properties of galaxies (SFR, morphology) are sensitive to the X-ray luminosity of their host environment. In this work we explore these relationships further with a large sample of X-ray bright and faint galaxy clusters from the Sloan Digital Sky Survey (SDSS). We constrain the radius within clusters where SFR ceases, or is quenched in astronomy parlance. We define a quenching radius – the distance from the center of a cluster at which a certain fraction of galaxies are quenched. Through examination of data from the SDSS catalogue, we explore various definitions for quenching radius and investigate its relationship with galaxy stellar mass, cluster halo mass, and x-ray luminosity. The quenched fraction of galaxies which have high stellar mass () show little to no dependence on location within the cluster whereas low to intermediate mass () galaxies are more greatly affected. Different galaxy transformation mechanisms should manifest at different radii; these results provide insight on the mechanisms behind galaxy evolution in large clusters and ultimately help answer big questions about galaxy formation.
Wynn, Gabriella – Developing microfluidic devices for the immobilization of biomolecules inside micro-scale channels for biosensor fabrication (Dr. Tohid Didar)
Microfluidic devices are a novel technology aimed towards miniaturizing scientific processes. These devices have the capability of integrating several laboratory functions on a micro-scale at a lower cost and with less waste than traditional instruments. Microfluidic devices are used for a variety of experiments, ranging from portable diagnostics to the development of artificial organs. Surface functionalization on microfluidic devices allows for the immobilization of biomolecules to detect ions, bacteria, and other biomolecules. This study investigates the bio-functionalization of microfluidic devices for DNA detection. To create these microfluidic devices, different surfaces were functionalized to allow for the binding of organic compounds to the inorganic surfaces. As a control, fluorescent labeled DNA was immobilized on the surfaces. After confirming efficient covalent attachment to the control surfaces, single- stranded DNA was printed onto various surfaces. To run the detection on the DNA modified surfaces, fluorescent labeled complementary DNA was then added to the surfaces and analyzed using fluorescence microscopy to confirm successful hybridization. An integrated microfluidic DNA detection device will then be created with the bio-functionalized surfaces. The final goal of the project is to create a platform that reduces non-specific binding while maximizing the attachment of specific biomolecules. Furthermore, these microfluidic devices will allow for faster and more efficient detection of molecules, such as antibodies or enzymes, in biological samples.
Yachouh, Josh – Student Track Record for Innovative and Valuable Experiences (STRIVE): Investigating an Opportunity to Empower McMaster Students Through the Use of Co-Curricular Records
Increasingly, post-secondary institutions have been discussing the importance of recognizing activities that students are involved in both inside and outside of the classroom. This has resulted in institutions implementing mechanisms to track the experiences of students that extend beyond academic accomplishments such as grades and scholarships), these systems have been referred to as Co-Curricular Records (CCR). This report, grounded in a literature review, commented on the ability for McMaster University to accommodate such a system and the usefulness it would have on encouraging students to develop and reflect on the broad skills they have learned throughout their undergraduate careers. Initial obstacles the University may encounter may be: distinguishing between visible and invisible involvement opportunities, creating a shift in campus culture to engage with relevant programming, and keeping a record of the hundreds of volunteer and co-curricular opportunities on campus. These challenges can all be combatted through proper administrative support, cross-faculty communication, and newly created workshops to support intentional involvement. These obstacles and recommendations are further discussed in the article. Although extensive research presents employers as willing to review CCRs, student and faculty surveys are yet to be conducted on campus. Crucial next steps in this project are collecting campus voices to assess the culture surrounding this new system and then assess methods to most comfortably introduce CCRs to McMaster.
Yeung, Jonas – Integration of polyaniline wire sensor in microfluidic devices for biosensors (Dr. Ravi Selvaganapathy)
Biosensors have attracted a considerable amount of attention due to their applications in clinical and environmental settings. For instance, glucose meters are biosensors used among diabetic patients to monitor blood glucose levels. Hence, there is an increased need for creating biosensors that are more affordable with improved efficacy. There have been significant efforts integrating microfluidic systems with biosensors. Microfluidics devices allow the manipulation of small amounts of fluids, with microchannels serving as small pipes. These devices have the ability to mimic repetitive laboratory methods in a miniaturized system. Advantages include a reduction in the sample, energy, reagent consumption, and waste production. The aim of this project is to integrate wire sensing technology into a microfluidic device. The benefits would be higher sensitivity due to the increased surface area and the possibility of detecting multiple parameters simultaneously. Two biosensor and microfluidic concepts were investigated in this study. First, palladium wires were oxidized to create palladium oxide electrodes that are known to have pH sensing properties. The wire’s open circuit potential was tested with a Ag/Cl reference electrode from pH levels ranging from 3 to 8. A calibration curve for the wires were plotted and gave an average slope of around -40 mV/pH, which is near the predicted value of -50 mV/pH given by the Nernst equation. Secondly, the wires were integrated in a microfluidic device to detect pH with a small volume of solution. Therefore, this device demonstrates the innovative approach of integrating biosensing technology into microfluidic devices.
Yu, Brian – Mechanisms of Phosphate Use Efficiency in Eutrema (Dr. Elizabeth Weretilnyk)
Soil phosphate levels are frequently limit crop productivity. Furthermore, crops are unable to take up much of the phosphate supplied by fertilizers. In addition, rock phosphate, the natural resource that phosphate is derived from, is being rapidly depleted. As such, there is merit to identifying and employing a plant model that is able to thrive under low nutrient conditions in order to discover biochemical pathways and genes responsible for high phosphate use efficiency.
The Yukon ecotype of Eutrema salsugineum has been shown to be extremely hardy with respect to low phosphate, salt, cold, and pathogenic agents; however, the mechanisms, biochemical pathways, and genes responsible for its high stress tolerance remain undetermined. To this end, Eutrema was grown at different phosphate regimes and extracted for intercellular fluid.
Phosphatase activity of these fluids was assayed using a p-nitrophenyl phosphate hydrolysis assay and compared to activities from remaining leaf tissue and cell-free extracts. Determining where phosphatase activity is heavily localized to in Eutrema is valuable, as its phosphate recycling efficiency may include phosphate recovery from fluids. The intercellular fluids were also assayed for cytoplasmic markers which ensured the extraction didn’t include extraneous tissue damage. The inorganic phosphate contents of plant tissues were also analyzed to observe where phosphate is being preferentially partitioned.
Zhang, Nicole – Short Interspersed Nuclear Element Bov- tA HEL17 Evolution in Artiodactyl Order (Dr. Brian Golding)
Transposons are known as “jumping genes”, a special class of DNA sequence that can replicate or relocate itself within the genome. It can cause nonsense mutations that affect an organism’s vitality and is tightly regulated in germ cells. Once it is inserted into a sequence, it is unlikely to get completely deleted and can accumulate mutations. Therefore, it provides a good marker for timing evolution events. Short interspersed nuclear elements (SINE) belong to Class I retro- transposons that lack replication machinery genes. The evolution of a group that share SINE elements can often be revealed by analyzing the difference between the elements present in the genome. Bov-tA is a SINE element that emerged after the Pecora speciation event in the Artiodactyl order. It is a tRNA derived SINE element and has two domains of consensus sequences. To unmask the evolution of Bov-tA SINE element within the Artiodactyl group, the Bov-tA subfamily element HEL17 and its flanking sequences in the 10 species whose whole genome sequence were available were found using NCBI blastn program with a e-value less than 1e-30. The longest sequence of HEL17 from each species are aligned to each other using MUSCLE then to generate a tree via Monte Carlo Markov Chain analysis (MCMC). By comparing the sequences, we found homology between the Bov-tA HEL17 phylogenetic tree and the consensus tree, and the abnormal location of the giraffe SINE element in the group suggests a translocation event that have likely contributed to the SINE element segmentation.