Below is a list of abstracts by fourth-year students in the Integrated Science Program:
Julianne Bagg – Synthesis of Brushite and Hydroxyapatite for Oxygen Isotope Fractionation Studies
Calcium phosphates are important compounds as they are involved in many interdisciplinary studies that take place in the fields of chemistry, biology, and geology. One of the most ubiquitous forms of calcium phosphate is hydroxyapatite (Ca10(PO4)6(OH)2). Much research has been done on the oxygen isotope relationship between the phosphate in apatite and water; however very little has been done on the oxygen isotope relationship between carbonate-bearing apatite and water. It is important to understand the oxygen isotope systematics in the hydroxyapatite carbonate-water system, expressed through an oxygen isotope fractionation equation, since this allows for an understanding of formation temperatures of apatite containing minerals, such as teeth. Various conditions for synthesizing hydroxyapatite were examined, starting from the procedure developed by Lecuyer et al. (2010), in order to determine the optimum conditions for formation. Crystals produced were characterized using x-ray diffraction techniques, to determine mineralogy and crystal structure. Preliminary results have revealed that brushite, a precursor to hydroxyapatite, as well as a mixture of various calcium phosphates including hydroxyapatite were produced. An understanding of the conditions necessary to produce brushite and hydroxyapatite will be developed. Using this information, minerals produced can be analyzed in terms of their isotopic composition using a stable isotope ratio mass spectrometer. As the minerals would be synthesized at different temperatures, a temperature-dependent relationship could be investigated. This type of relationship can be used to study the formation temperature of biogenic samples.
Darren Fernandes and Dr. Ralph Pudritz – Amino Acid Synthesis in Pre-Biotic Solar System
The abiotic synthesis of biological compounds is an important open question in astrobiology. The famous Miller-Urey experiment demonstrated that amino acids can form from reducing gasses, such as those released from hydrothermal vents. Furthermore, carbonaceous meteorites have been shown to have significant quantities of amino acids. In light of these discoveries, it is believed that amino acids both formed on Earth around hydrothermal vents, and were brought by carbonaceous meteorites. Nevertheless, the mechanisms behind amino acid synthesis in both hydrothermal vents and meteorites are still not fully understood. Using equilibrium thermodynamics, we created a model that can predict amino acid concentrations in both systems. Parent bodies in the early solar system would have gathered large amounts of water, HCN, ammonia and aldehydes all of which were abundant in the early solar media. These chemicals would have then reacted via the Strecker mechanisms to create the amino acids we see in meteorites today. Hydrothermal vents also feature a similar mechanism where HCN is produced by the BMA process. We assess which system, meteorites or hydrothermal vents, was better at synthesizing amino acids. This has various implications for the development of early life, the genetic code and the MSL.
Prateek Gupta – Spatial and Morphological Analysis of Glacially Eroded Landforms (P-forms) at Whitefish Falls, Ontario
Analysis of glacially eroded landforms, particularly of their morphology and spatial distribution can provide valuable information about past subglacial conditions. However, the precise mechanism of formation of many erosional landforms and the factors controlling their distribution are still poorly understood. This study provides detailed morphological and spatial analyses of a collection of small-scale sculpted landforms known as p-forms. Qualitative analysis was conducted on twelve 20m by 20m study-areas of exposed argillitic bedrock near Whitefish Falls, Ontario. This Proterozoic bedrock of the Gowganda Formation eroded by the Laurentide Ice Sheet hosts several glacially eroded features. Detailed sketches and photographs were taken of p-form systems and relevant micro-scale features. Particular attention was given to ice flow direction by means of measuring glacial striae, as well as the directionality and shape of each individual p-form. Morphological analysis was used to identify complex p-form features such as convergent, divergent, and nested structures. Spatial analysis showed relationships between the organization of p-forms across study areas and presented relationships between p-forms to ice-flow and relative topography. P-forms were seen to develop on the flanks of bedrock highs and lows, suggesting erosion in regions of flow dynamic change. Taken together with existing theoretical models describing ice and fluid dynamics, schematic models of p-form development are evaluated and discussed. This investigation can facilitate improving predictive models used for a range of environmental and mineral exploration purposes.
Nicholas Pun – Macrofungal Diversity of Southwestern China
Fungal diversity is a key component of overall biodiversity. Fungi are involved in many key ecosystem processes like nutrient cycling, decomposition and are part of key interactions with plants and animals. Among the diverse groups of fungi, mushrooms are the most conspicuous and the most extensively surveyed group of fungi. However, relatively little is known about mushroom diversity in many parts of the world, including tropical and subtropical Asia. This study aims to sample to macrofungal diversity of the Ailao mountains in Yunnan, China using the ITS barcode region as a species identifier as well as to identify any the fine-scale spatial patterns of mushrooms in this area. Over 300 samples of mushrooms were collected and likely comprise only a portion of the fungal diversity in this area.
Dora Rosati – Mathematical model of coupled neural oscillators: A possible explanation for consonance perception in music
A combination of two musical notes (an interval) is termed consonant if it is perceived as pleasant and dissonant if it is perceived as unpleasant. Despite being a fundamental concept in music cognition, the neural mechanisms behind consonance perception are not understood. It has long been acknowledged that the degree of consonance associated with a musical interval appears to be related to the degree of simplicity of the integer frequency ratio associated with this interval. However, the reason for this correlation is largely unknown. Recently, the theory of mutual coupling between integrate-and-fire neural oscillators has been used to construct a system of differential equations that models consonance perception in the human brain. This model shows that for two neural oscillators firing in response to pairs of pure tones, the range of frequencies for which they fire at a fixed ratio (or mode-lock) corresponds directly to the degree of consonance of the pure tone pairs. It has subsequently been shown that the ordering of mode-locked states by stability depends on the degree of coupling between neurons. This mode-locking is also greatly reduced upon introduction of neural noise. In this study, the model is expanded to respond to pairs of complex tones, which constitute more realistic stimuli. The effects of this modification on mode-locking between neural oscillators are observed, and the implications for whether this theory is a plausible explanation for consonance perception are discussed.
Emily Taylor – The role of FMRP in the proliferative capacity of neural progenitor cells
Fragile X Syndrome (FXS) is the most common cause of inherited intellectual disability. FXS is caused by a CGG trinucleotide expansion in the 5’ UTR of the FMR1 gene, which results in the loss of the fragile X mental retardation protein (FMRP). FMRP has been implicated in neurogenesis, including the process of proliferation of neural progenitor cells (NPCs). The expression of intrinsic proliferation markers, Nestin and SOX2, in both wild type (WT) and Fmr1-knockout (KO) mice was studied. Neurospheres were generated from hippocampal cells and cultured for 5 and 8 day time periods, and stained for Nestin and SOX2 using immunocytochemistry. It is hypothesized that a larger number of NPCs will stain positively for both Nestin and SOX2 in KO mice as compared to the WT, indicating an increase in proliferative capacity in the absence of FMRP. This abnormal neurogenesis may contribute to the cognitive impairments seen in individuals with FXS, especially in the hippocampus as it is implicated in the processes of learning and memory. This will provide a greater understanding of the role that FMRP has in the neurogenesis of neural progenitor cells, contributing to the development of treatments for FXS.
Michelle Zhu – The effects of familiar amyotrophic lateral sclerosis-inducing mutations of the human profilin1 protein and their interactions with the huntingtin protein.
Neurodegenerative diseases are illnesses characterized by the progressive death of neurons and loss of neuronal functions. Amyotrophic lateral sclerosis (ALS) and Huntington’s disease (HD) are two such diseases. ALS is a result of motor neuron degeneration, while HD results largely from the degeneration of the efferent medium spiny-sized neurons in the striatum. HD is hereditary and caused by a mutation in the huntingtin protein. In contrast, hereditary or familial ALS (FALS) accounts for only 10% of all ALS cases and genetic causations are not yet identified for all the FALS cases. This study examines four human profilin1 (PFN1) protein mutations found to cause FALS: C71G, M114T, E117G, and G118V. Different neurodegenerative diseases often have overlapping mechanistic pathways. The interactions between the FALS-inducing PFN1 mutants and the huntingtin protein are examined in this study. The goal is to examine protein mutations in FALS in a HD context to determine potential commonality between the two diseases. The PFN1 mutant proteins are studied in a mouse striatal cellular model of HD with humanized exon 1 of the huntingtin protein. All PFN1 proteins were fused to a cyan fluorescent protein at the C-terminus. This allowed for visualization of protein localization when excited by light at 440nm. Mutant PFN1 protein aggregates did not recruit endogenous huntingtin. The overexpression of the mutant PFN1 was more toxic to the cells than the wild type. The mutants also affected the structure of the cytoskeleton.
Rachel Charney – The Population Dynamics of the Round Goby in Clean and Contaminated Areas of Hamilton Harbor
The round goby (Neogobius melanostomus) is an invasive fish species found throughout the Laurentian Great Lakes, including Hamilton Harbour. We monitored and sampled the round goby in areas with clean sediment and contaminated sediment through Hamilton for the past eleven years (2002 – 2012). Here, we present an update on previous analyses (Young et al., 2010) of round goby population dynamics as they relate to these sampling sites. We found that a higher proportion of round goby males living in areas with contaminated sediment are reproductive than round goby males living in areas with clean sediment. Round goby living in areas with contaminated sediment are also longer than round goby living in areas with clean sediment. Length has been decreasing over time, while body condition has been increasing over time. Additionally, the parental mating tactic is more prevalent than the sneaker mating tactic for reproductive males. An understanding of the population dynamics of Hamilton Harbor round gobies can help with efforts to protect indigenous fauna.
James Boudreau – Identification and characterization of hypH, a putative alpha-ketoglutarate semialdehyde dehydrogenase in Sinorhizobium meliloti
Hydroxyproline is a common modified amino acid in plant and animal cells. Its availability in soil and root cell exudates makes it a potentially significant source of carbon and nitrogen for certain bacteria. Hydroxyproline catabolism has been identified in the nitrogen-fixing legume endosymbiont Sinorhizobium meliloti, and a previously hypothesized pathway is in the process of being characterized. In the putative pathway, an isomer of hydroxyproline is converted over the course of four enzymatic reactions to a-ketoglutarate (KG), an important intermediate in the citric acid cycle. This project investigates the final step in this pathway, the conversion of a-ketoglutarate semialdehyde (KGSA) to KG, by studying hypH, a gene in the hydroxyproline catabolism cluster, which is hypothesized to code for an a-ketoglutarate semialdehyde dehydrogenase (KGSADH). hypH mutant strains retain their ability to grow with hydroxyproline as a sole carbon and nitrogen source due to the activity of another KGSADH, coded by araE. This project demonstrates that strains lacking functional copies of both hypH and araE show negligible ability to grow with hydroxyproline and that complementation of the double deletion mutant with a functional hypH copy rescues the hydroxyproline catabolism phenotype. Purified HypH enzyme is expected to convert KGSA to KG in vitro when NADP+ is present, producing a measurable change in absorption at 340nm. The absorbance change has been observed and the substrate and product of this reaction will be analyzed using mass-spectrometry in future.
Helen Guo – Invisibility Cloaking by Coordinate Transformation
The study and realization of invisibility cloaks is a fairly recent endeavour. Currently, one of the most common approaches is the coordinate transformation method, wherein the theory of transformation optics and the technology of metamaterials are used to design an electromagnetic device capable of manipulating light waves to create the illusion of invisibility. Mathematically, this technique can be implemented by a suitable coordinate transformation of the macroscopic Maxwell’s equations. Due to the covariance properties of these equations, the transformation requires that only the permittivity and permeability tensors of the cloaking material be altered. This project aims to numerically verify the coordinate transformation method applied to an elementary model of a cylindrical cloak. The model was chosen based on previously proposed methods that were derived from the study of transformation optics. All numerical computations were programmed and executed using MATLAB, and the results provide a detailed and comprehensive overview of the mathematical process involved in the design of a simple invisibility cloak. This innovative field of research has a vast array of potential applications, which can be extended to other areas of research such as acoustics, environmental science, and quantum mechanics, as well as perceptions of science fiction.
Emily Kramer, Barbara Fenesi, Joseph Kim – Multimedia learning and individual differences: Removing split-attention in multimedia instruction mediates the effects of working memory capacity
Multimedia instruction is generally defined as an instructional presentation that uses both verbal information and visual information. Understanding how individuals process information from different multimedia presentation designs is critically important to improve instructional design and increase learning efficiency. This study examines how individual differences in working memory capacity influence learning from different multimedia designs. Participants’ verbal working memory was measured, and then they watched a presentation in one of two multimedia design conditions: complementary or split attention. Both conditions used relevant images and narration. The conditions differed in that the complementary design used minimal on-screen text while the split attention design used verbatim on-screen text synchronized with the narration. Learning outcomes were measured with a test containing both simple recall questions and more complex questions that required transfer of knowledge. Individuals with high working memory capacity were found to perform equally well on both types of questions in both presentation conditions. Individuals with low working memory capacity were found to perform equally on recall questions in both conditions, but performed significantly worse on the transfer questions in the split-attention condition. Performance on transfer questions in the complementary condition was equal for both low and high working memory capacity individuals. These findings support the theory that a low working memory capacity individual has fewer attentional resources that can be overloaded in the context of redundant information. However, these results also show that the performance of low working memory capacity individuals can equal the performance of high working memory capacity individuals if multimedia design principles are effectively applied.
Lauren Yamasaki – A model for the evolution of antibiotic resistant bacteria
The evolution of antibiotic resistance in bacteria is a serious concern in the field of healthcare. Infections caused by these resistant bacteria often spread in hospitals, where the individuals at risk of being infected may have compromised immune systems and deteriorated health, making an infection potentially life-threatening. In order to better understand how antibiotic resistance develops, and how to prevent or minimize the effects of an outbreak of antibiotic-resistant bacteria, mathematical models can be used. This research aims to build on a previously constructed model which describes the development of resistance to multiple antibiotics. By adding to previous research, a more accurate description of the infection dynamics is found. The previously constructed model was changed by including an additional path to developing antibiotic resistance. Using modeling software, the adjusted model was tested to see the impact of the modifications. The new model predicts that the number of infections caused by multiply resistant bacteria will be higher than originally predicted, which follows from biological reasoning as well.
Krista Stemmler – A study of men’s preferences in female vocal attractiveness in relation to fertility during the menstrual cycle
This study examines whether women’s voices are rated as more attractive when they are fertile compared to when they are not fertile, and consequently the influence of vocal cues to fertility on men’s mating decisions. This was carried out by presenting vocal stimuli that has been collected from different women, thus allowing for a comparison of between-subject stimuli. The testing provides insight into whether men can pick up on women’s cues of ovulation in a setting with multiple females, and whether these cues make an impact on mating decisions. Male participants were presented with voice recording pairs from which they made a decision between one woman’s voice recording from the fertile phase, and a different woman’s voice recording from the non-fertile phase. The men were asked to choose the voice they found more attractive. Previous experiments on the vocal cues of fertility have shown slight preferences for vocal stimuli recorded at high fertility, but not all researchers have been able to replicate these results. The inability to replicate this preference indicates that these cues are not very robust, even when using within-subject stimuli comparisons. Therefore, vocal cues that indicate fertility may go unnoticed when using a between-subjects comparison method. Resultantly, the current hypothesis is that women’s vocal fluctuations across the menstrual cycle are not robust enough so as to affect men’s preferences when they must choose between the stimuli of two different women. Thus, I predict that men will choose the more attractive woman regardless of her fertility status.
Yohan Yee – Dynamics and Thermalization of Quantum Systems
Statistical mechanics provides a description of thermalization—the relaxation of observables to an equilibrium independent of initial conditions—in classical systems. Quantum systems are not afforded this convenience; the initial state that a quantum system is started in affects its long time equilibrium dynamics. Furthermore, the constraints of the system govern the equilibrium state to which the system (classical or quantum) tends. In this talk, I will describe the dynamics of quantum systems and relate this to the study of thermalization. Using a generic system consisting of bosons in a double well potential (by itself, a system that does not thermalize), I will present theoretical findings that relate to the ultimate goal of better understanding thermalization in quantum systems. More specifically, I will compare the equilibrium dynamics of the system of bosons with the predictions of the generalized Gibbs ensemble (a statistical ensemble of quantum systems under constraints of the system). The aforementioned system of bosons in a double well is a powerful tool in the study of quantum mechanics. From a theoretical standpoint, analogies can be made to the well known classical pendulum, allowing for a deeper mathematical understanding of this system. Such a system can also be realized in the laboratory with finely tuned parameters, providing a means to test fundamental quantum mechanics. In the context of thermalization, this research allows for a better understanding of the role of constraints in the path to thermal equilibrium, possibly allowing for the engineering of “unthermalizable” states with applications in quantum information.
Samantha Esteves – Ecosystem Stability Based on the Functional Classification of Rock Pool Invertebrates
Feeding trials were conducted at the Discovery Bay Marine lab to determine zooplankton feeding preferences. This information, combined with past literature and isotopic analysis, was used to classify rock pool invertebrates into one of five functional groups: water column feeders, benthic feeders, deposit feeders, large predators, and small predators. Functional groups were determined based on food source, method, and location of feeding. Functional groupings were used as a measure of biodiversity from which ecosystem stability was calculated. Functional group stability was compared to stability calculations for aggregate number of species. This may provide a new way in which to determine the diversity of an aquatic community and result in a more accurate understanding of how biodiversity influences the stability of a system.
Adam N. Pantaleo – Lithium and Magnesium Complexes of an Extremely Bulky Pincer Ligand
The study of metal-alkane complexes, which feature alkane ligands coordinated to a metal centre, is an emerging field in organometallic chemistry that is both fundamentally relevant and carries practical applications. In particular, metal-alkane complexes are relevant to C–H bond activation, a transformation that has the potential to convert unreactive hydrocarbons into more valuable and synthetically useful molecules. The Emslie group at McMaster University has recently synthesized several metal-alkane complexes of the form [K2(XAT)(RCH3)] (a). Given the ability of [K2(XAT)] to coordinate alkanes, the syntheses of neutral dilithium and dicationic dimagnesium analogues of this system were attempted with the goal of further understanding the nature of metal-alkane interactions. This thesis reports the synthesis of the trilithium n-butyl derivative [Li3(XAT)(C4H9)] (b), which was unexpectedly obtained in very high purity by reaction of the pro-ligand [H2(XAT)] with n-butyllithium. This product was characterized using NMR spectroscopy, elemental analysis, and single-crystal X-ray diffraction. Also reported in this thesis are attempted syntheses of two magnesium derivatives formed by salt metathesis between [K2(XAT)] and MgI2. The reaction initially forms a new product, which is then slowly converted into a second product by reaction with excess MgI2. Although attempts to completely separate the two products were unsuccessful, the second product could be isolated in approximately 90% purity. This research led to the discovery of a unique lithium(XAT) alkyl complex and also demonstrated the feasibility of synthesizing magnesium(XAT) derivatives. Future work will focus on isolating the magnesium derivatives and probing their propensity to interact with alkanes.
Solomon Barkley – Measuring non-thermal stochastic effects in the statistical mechanics of magnetotactic bacteria
Magnetotactic bacteria (MTB) synthesize magnetosomes, unique organelles that contain magnetite crystals and rotate the cell to align it with local magnetic fields. In order to investigate the presence of non-thermal stochasticity in MTB orientation, the magnetic moment of a population of Magnetospirillum magneticum was measured using six different techniques. Five of these were developed for this study and rely on analysis of MTB motion. Orientation of MTB has been previously considered physically equivalent to atoms in a paramagnetic material. Three of the techniques used to measure MTB magnetic moment here – angle distribution, trajectory dispersion, and orientation correlation – rely on the assumption that MTB orientation can be described by the statistical mechanics of atoms in a paramagnetic material. If these methods consistently measure magnetic moment values that are not equal to those determined by other methods (magnetosome dimensions, U-turn analysis, and rotational tendency), it can be concluded that the simple paramagnetic model is unable to completely describe MTB orientation. This would suggest the presence of non-thermal stochastic effects that randomize cellular orientation in addition to expected thermal fluctuations. Results of the present study support this scenario, but they do not conclusively implicate non-thermal stochastic effects in the orientation of MTB. Additional experiments will help determine definitively whether the paramagnetic model requires modification for application to MTB, possibly by incorporating a higher effective temperature, as observed in other biological systems. This research provides an example of a living system that cannot be explained entirely by the physics of its non-living counterpart.
Cody Koykka – Public goods games in finite populations
A prominent unanswered question in behavioural ecology is that of how cooperative behaviour can emerge and be maintained in groups of conspecific individuals. From the evolutionary perspective, defection is a more rational tactic and should therefore become prevalent in any population. However, observations have revealed contrary behaviour in most animal species. Several theories have been proposed to elucidate the prevalence of cooperative behaviour, yet these theories cannot explain the commonly observed phenomenon of cooperation between unrelated individuals when interactions are not repeated, nor do they provide sufficient insight into how cooperation evolved in animal species. This study seeks to enhance the understanding of the underlying biological mechanisms that initiate and maintain cooperative behaviour by combining evolutionary game theory and stochastic modelling. Assumptions made by previous mathematical models are rigorously tested through simulations. Certain mechanics of current models, such as the role of reputation, are altered so that they better predict the outcomes of interactions between conspecific individuals in highly social species. New mechanics, including the ability for individuals to punish defectors, are also introduced. These new mathematical models may better illustrate how various motivators of cooperation, including rewards, punishments, and reputation, can be used to efficiently maximize cooperative behaviour in a variety of situations.
Joshua Simmonds – Mathematical and computational aspects of fractals
Understanding fractals, their mathematical roots, and their geometric properties is an essential aspect for understanding the world around us. Fractals appear in abundance in nature, from growing plants to crystal structures, and are particularly useful in studies of chaotic dynamics. This research investigates the mathematical properties of certain fractals, especially the Mandelbrot set, and seeks to discover new types of fractals. The bulk of this research has been to design and program new computer software that, when given a generating function, draws the associated fractal and allows the user to interact with those fractals. The code has been written in Python, and allows the user to adjust the range and resolution of the display in order to enhance the fractal images and allow for in-depth analysis. The program selects an array of points in the complex plane, and uses a finite approximation for the infinitely iterated generating function at each of those points. The program has been used to produce a library of detailed and colorful images which are displayed and explained during the presentation. The more technical details of the workings of the computer program are instead included in the written thesis. Having tested and verified the software with generating functions of known fractals, the program has been extended to be able to render and explore unique new fractals. New generating functions were developed by manipulating the generating functions of known fractals, and the program was used to investigate whether or not these new functions exhibit fractal behaviour.
Fu An Tsao – Synthesis and coordination chemistry of a new ambiphilic ligand
Listeria monocytogenes is a gram-positive, food-borne pathogen that is responsible for serious illnesses upon infection. The pathogenicity of L. monocytogenes increases with the formation of biofilms, a large colony of cells surrounded by an extracellular matrix, as they become more resistant to antimicrobial techniques. In a recent screen, several ß-lactams were found to increase biofilm formation at concentrations below the minimum inhibitory concentration, whereas others did not. To determine the reason for this difference, the binding pattern of four cephalosporins (cefotaxime, cefmetazole, cefuroxime, and cefoxitin) and ampicillin to penicillin-binding proteins, their cellular target, was determined by using a fluorescent bocillin assay. There was noticeable differential binding of stimulatory and non-stimulatory ß-lactams to PBPD1. ß-lactams result in cell envelope stress by disrupting the regular production of the cell envelope, so to better understand the difference between stimulatory and non-stimulatory molecules, deletion mutants of both PBPD1 and CesK, the sensor kinase of a cell envelope stress response two-component system were made. Understanding of the processes involved in biofilm formation in L. monocytogenes will provide novel drug targets for Listeria monocytogenes.
Tia Harrison – Phylogeography of the African Clawed frog Xenopus laevis
Cytochrome P450 19A1 (aromatase) catalyzes the final, rate limiting step for the synthesis of estrogens in humans. It is a clinically validated target for the treatment of estrogen receptor (ER) positive breast cancer, which accounts for 75% of all breast cancer cases. Current inhibitors of aromatase suffer from a lack of specificity and can cause adverse drug-drug interactions due to their ability to inhibit other cytochrome p450 enzymes. Recent work by the McNulty group has discovered potent and specific inhibitors of aromatase. The inhibitors feature two aryl rings, a 1,2,3-triazole and a polar oxygen-containing moiety. The goal of this research was to create structurally similar compounds in order to explore the structure activity relationship (SAR) of the inhibitors. An aqueous Wittig methodology was developed to determine the necessity of the polar-oxygen containing group, and to substitute the triazole with other small aromatic heterocycles. An aldol-based methodology was used to explore the effect of halogen substitution in one of the aryl rings. All synthesized compounds were tested using a fluorescence assay based on the conversion of o-dibenzylfluorescein to fluorescein by aromatase. Preliminary results demonstrate that all synthesized compounds are sub-micromolar inhibitors of aromatase, but work must be done to ensure that the newly synthesized compounds maintain selectivity for aromatase.
Kriston Costa – PyZMM: An interface between ZMM and PyMOL for protein refinement and data analysis
Pollution of the Great Lakes has been a major environmental problem for several decades. The presence of pollutants in the Great Lakes region is not only perilous to the local environment, but also to the surrounding ecosystem. The most toxic pollutants are persistent organic pollutants (POPs). Numerous studies have been conducted to analyze the two most common and toxic POPs: polychlorinated biphenyl (PCBs) and mercury (Hg). Most studies have approached the problem of these pollutants by examining ecological trends including toxicology, and interactions between the lakes, sediments, and atmosphere. The purpose of this study is to mathematically model the flow of PCBs and mercury within the Great Lakes via Matlab so that the future trends of PCBs and mercury in each lake can be predicted. The ODE45 function in Matlab and Euler’s method were used to model the flow. Major assumptions of the model were uniformly distributed pollutants within the lakes and the disregard of inflow and outflow of small rivers connected to the Great Lakes. Future input amounts for both pollutants were predicted by comparing the experimental data and theoretical data from the model with experimental data from previous years. The model predicts that both pollutants will be present in all five lakes for at least five decades. To create a more accurate model, assumptions need to solved and more appropriate and precise data is required. The improved model can then be applied to pollution abatement and the preparation for containment of new contaminants within the lakes as they are introduced.
Rachel Young – Characterization of Non-Coding RNAs in Streptomyces
Atherosclerosis is a complex and chronic condition affecting arteries, characterized by stiffening and accumulation of lipid-rich deposits and immune cells along the artery wall. Though the condition progresses asymptomatically for much of adult life, it may eventually manifest itself clinically as coronary artery disease, myocardial infarction or peripheral artery disease. The objective of this research is to investigate an atherosclerotic mouse model, characterized by homozygous null mutations in both the high density lipoprotein receptor SR-B1, and the low density lipoprotein receptor (LDLR). In addition to mimicking human cardial features of atherosclerosis, this model has the added advantage of being diet-inducible, through a high-lipid diet, rather than developing the disease spontaneously. This study focuses on histological examination of early and late atherosclerotic markers in heart sections of SR-B1/LDLR double knockout (dKO) mice subjected to four different atherogenic diets: Paigen diet, Paigen diet without cholate, high cholesterol diet, and Western diet. Early markers include expression of the cell adhesion molecules, vascular cell adhesion molecule 1 (VCAM-1) and intercellular adhesion molecule 1 (ICAM-1), which facilitate recruitment and attachment of circulating immune cells to the blood vessel wall during nascent lesion formation. Analysis of late makers involves quantification of coronary artery occlusion as well as plaque accumulation in the heart sinus. Comparative analysis of the expression of these markers across all diets may contribute to characterization of the diet-inducible behavior of the SR-B1/LDLR dKO mouse strain, and reveal which diets or dietary components result in a phenotype closest to that which appears in the human form of the disease.