Festival of Science 2017 - Student Abstracts
Festival of Science was held April 28th, 2017.
E. J. Curtis "The Effect of Structural Differences on Drug Interactions with DNA"
Chemistry Faculty Advisor: Samantha Glazier
In the field of allopathic medicine, when a certain medication is prescribed for an intended therapeutic effect, the efficacy of the drug, as well as the unintended side effects, can be highly varied between patients. A person’s genetic makeup is defined by the sequence of DNA that exists within his or her cells. Recent focuses in cancer biology have found not only that the DNA of cancer differs from the genome of otherwise healthy cells, but also that there exist genetic differences between cells of the same tumor.
Doxorubicin is a highly effective chemotherapy agent that has been used for the better part of a century. Though doxorubicin is well suited to kill many types of cancer, it has some serious side effects in much of the population. Doxorubicin produces harmful free radical oxygen species, that have the potential for both cardiotoxicity and higher order effects.
This study focused on characterizing the interactions of both doxorubicin and a doxorubicin analogue, doxorubicinone, with different types of DNA. Through a combination of spectroscopic techniques, we found that the interactions of the drugs were quite different from one another and the interactions varied greatly between different DNA sequences. These results may help researchers understand the reasons behind differences in drug efficacy between patients.
Vanessa Chilunda "Effects of Growth Stages and Sub-inhibitory Antibiotic Concentrations on Amyloid Protein Formation by Soil Bacteria"
Biochemistry Faculty Advisor: Nadia Marano
Functional amyloids are an important component of biofilms formed by bacterial communities. These amyloids are important due to their hydrophobic nature and other biochemical properties that help bacteria resist harsh conditions such as heat, pH, hosts’ immune systems and even some antibiotics. Studies have shown that subinhibitory antibiotic levels serve as signaling molecules that increase biofilm production and consequently bacterial resistance properties. Thus, I decided to study the effects of subinhibitory tetracycline concentrations on amyloid production in biofilms. Thioflavin T (ThT) spectroscopic assay was used to quantify the amyloid production. I found a statistically significant increase in amyloid production in one of the isolates when treated with 0.2 μg/ml and 0.5 μg/ml tetracycline concentrations. However, at higher tetracycline concentrations, amyloid production decreased. In order to elaborate on these results, I investigated the time taken by the bacteria isolates to produce maximum amounts of amyloid proteins in their biofilms. Bacteria concentration was estimated using absorbance at a wavelength of 600nm on spectrophotometer, and compared to bacteria count under a phase contrast microscope. I found that there was maximum amyloid production around day five when bacteria were cultured in liquid media. However, growing the isolates in liquid media for a longer period of time resulted to less cell-associated amyloid fibers compared to when cultured on agar plates. Currently, I am measuring amyloid production by bacteria isolates grown on agar plates instead of liquid media with different sub-inhibitory tetracycline concentration at different growth periods.
Isabel Bogacz "Analysis of Heterobimetallic Materials Through Raman Spectroscopy "
Physics Faculty Advisors: Catherine Jahncke and Adam Hill
Peak oil, global warming, and the modern energy crisis call for new solutions to harnessing and storing solar energy. Harnessing CO2 could provide an alternative fuel source through artificial photosynthesis. Photosynthesis stores energy from light as chemical fuels. In our work we study heterobimetallic materials. When these materials are hit with light, electrons on the outer edge of the molecules are excited to a less stable state. While in this excited state, the material will be able to split carbon dioxide into carbon monoxide and oxygen. Carbon monoxide is already heavily researched as an alternative fuel source. It is the act of obtaining carbon monoxide that eludes scientist. This project uses Raman spectroscopy to study these materials as they change carbon dioxide into carbon monoxide in order to better understand the mechanism involved in this reaction. We present the results of our initial studies where we add various amines or formic acid to our materials and observe the changes in the Raman spectra
Monica Bedford "Doping of Cobalt-Zirconium Heterobimetallic Material with Various Amine Ligands to Enhance Photochemical Carbon Dioxide Reduction "
Chemistry Faculty Advisors: Adam Hill, Catherine Jahncke
Hard-soft metal-metal complexes have been shown to reduce carbon dioxide (CO2). This reaction is one of the first steps in artificial photosynthesis, a way to combat rising levels of carbon dioxide. By inputting photons, an electron transfer (ET) occurs from the cobalt (II) center to the zirconium (IV) center. The excited electrons are then able to react with the carbon dioxide. However, a parallel process known as back-electron transfer (BET), wherein the electron relaxes back to the original energy level within the cobalt 3d orbitals, reduces the availability of excited electrons for further reaction. The energy levels of the cobalt 3d5 orbitals can be adjusted by substituting different amine ligands (triethylamine, diethylamine, diisopropylethylamine, azetidine, pyrrole, piperidine, and N-methylpiperidine) on the cobalt to make BET less energetically favorable. To judge the efficacy of the amine group in reducing BET, time-correlated single-photon counting fluorimetry measurements are considered in conjunction with the Raman spectra for carbon dioxide reduction with the same material.
Kelly Burke "Synthesis and photophysics of lanthanide/transition metal heterobimetallic complexes"
Chemistry Faculty Advisor: Adam Hill
Luminescent lanthanide ions have the potential for applications in the lighting industry, the creation of electroluminescent materials and medical imaging. However, their use is hindered by poor absorption cross sections. In order for luminescence to occur more easily, the lanthanide elements Eu, Tb and La have been paired with first-row transition metals, Co, Ni and Fe to create heterobimetallic compounds using air-free techniques. Hindered Lewis acid/base phosphinoamide ligands support direct electron donation from the transition metal to the lanthanide center, resulting in a significant increase in light absorption. The photophysical properties of the complexes were probed by time-correlated single photon counting phosphorescence spectroscopy, quantifying energy transfer through metal-metal bonds. The results provide an opportunity to explore the relationship between metal identity and excited state lifetime.
Wenyao Zhang "Probing the Reaction Mechanism of the Wagner-Jauregg Reaction: Hammett Study of 4-Substituted Styrenes "
Chemistry Faculty Advisor: Samuel Tartakoff
The mechanism of the Wagner-Jauregg reaction, long considered a double Diels–Alder reaction, was examined through the reaction of maleic anhydride and styrene derivatives. The Wagner-Jauregg reaction was expected to react in the same manner as the classic Diels–Alder reaction, giving a negative correlation in the Hammett plot. However, two other competing mechanisms were also possible. By taking advantage of proton NMR spectroscopy and observing relevant peaks, we could get the relative rate constants for four para-substituted styrenes (p-MeO, p-Me, p-H, p-Cl). The preliminary results suggest that, for the Wagner-Jauregg reaction of para-substituted styrene derivatives, the mechanism might be different for dienes with electron-rich groups (ERG) and with electron-withdrawing groups (EWG). Further experiments will be conducted on another styrene substrate with EWG to complete the Hammett plot and more accurate kinetic data will be collected by high-performance liquid chromatography (HPLC).
Jennifer Finan "Thermodynamic Characterization of a Novel Anthracycline/DNA Binding Mechanism "
Chemistry Faculty Advisor: Samantha Glazier
Anthracyclines are common antitumor antibiotics for cancer treatment characterized by a conjugated four ring system. These drugs bind to the DNA double helix preventing topoisomerase binding, thus halting cellular division. Three binding mechanisms for these drugs are intercalation, groove-binding, and less commonly, threading. A marketed anthracycline, doxorubicin, intercalates into DNA with a positive sugar moiety interacting with the negatively charged phosphate backbone, leading to a strong DNA/drug interaction. We synthesized doxorubicinone, which is an analogue without the sugar moiety, and discovered this change affected the DNA binding significantly. We have previously characterized the thermodynamics of the three binding modes in relation to changes in the DNA hydration layer. To measure these values, the fluorescence of both drugs is utilized in the osmotic stress method to determine the uptake or release of water molecules and the Van’t Hoff method to find the thermodynamic values. We found intercalators have a small disruption in the hydration layer and a small increase in disorder. Unexpectedly, doxorubicinone binding showed a large uptake of water molecules and a large decrease in disorder, meaning it is unique from the three described binding modes. The changes in DNA binding between these two drugs offers areas of study for both binding strength and specificity, which are the two main factors in drug effectiveness.
Kelsey Murphy "Elucidation of the Thermodynamic and Kinetic DNA Binding Mechanism of Anti-Tumor Drug By Fluorescence Spectroscopy"
Chemistry Faculty Advisor: Samantha Glazier
Proflavine is an antitumor antibiotic in the acridine drug family, which effectively works by interacting with DNA. We examine the role of water in the mechanism of binding and investigate the thermodynamic and kinetic profiles of this binding route with respect to the major and minor grooves of DNA. It has been previously thought that the drug enters directly through the minor groove to reach the final intercalated state. Intercalation refers to the insertion of a molecule between the planar purine and pyrimidine base pairs of DNA, perpendicular to the helical axis. Molecular dynamics calculations by Mukerjee et al. showed that the drug may start by pre-binding to the minor groove, but the lowest energy route to intercalation appears to be through the major groove. The major groove of DNA occurs where the backbones are far apart from one another with the nitrogen and oxygen atoms of the base pairs pointing inward toward the helical axis, while the minor groove occurs where they are close together with the oxygen and nitrogen atoms of the base pairs pointing outwards.
Intrigued by the possibility of entry through the major groove, we designed experiments to test thermodynamic and kinetic mechanisms. The thermodynamic binding profile of the drug in calf-thymus (CT) DNA was studied using fluorescence spectroscopy as the principle method of analysis. Water exchange values for the drug show a net uptake of 53.8 water molecules upon binding to CT DNA, and a Van’t Hoff analysis was performed in which the temperature of the titration was varied, resulting in a ΔH value of -44.64 kJ and a TΔS value of -73.91 kJ, suggesting an enthalpy driven process. The extremely unfavorable entropy is consistent with the large uptake of water molecules upon binding. Competitive binding studies were then performed in order to further classify the binding event with respect to how the drug interacts with the major and minor grooves. Hoechst 33258 was used to block the minor groove, resulting in a significantly lower binding constant for proflavine. Methyl green was used to block the major groove, which in turn resulted in a higher binding constant. This suggests the existence of a thermodynamic route and subsequent kinetic route of binding utilized by proflavine. We hypothesize that the blockage of the major groove induces a more stable thermodynamic route through the minor groove, and the blockage of the minor groove results in a less stable but more rapid kinetic route through the major groove. Subsequent kinetic analyses are currently in progress in an effort to further classify and elucidate the binding profile of proflavine in DNA.
Holland Gallup "A Standardization Method for SEM/EDS Determination of Copper, Lead and Mercury Concentrations in Human Teeth "
Chemistry Faculty Advisor: Ning Gao
Four main layers constitute the human tooth; the enamel layer, dentin layer, the pulp and the cementum. Due to the slow and complex formation of teeth, teeth may be subject to the uptake of different elements, including some toxic ones, which may become incorporated into the dentin layer over time. The retention of these elements can serve as a bioindicator to determine the degree of environmental exposure. In particular, heavy metals are of importance due to the large scale exposure from contaminated water sources, diet and potential leeching of mercury from amalgam fillings. Dental treatments or toothpaste may also lead to the incorporation of fluorine into the enamel layer. High levels of exposure to any toxic elements could lead to a wide variety of health complications. By analyzing the concentration levels of heavy metals and fluorine in human teeth, we can draw correlations between age, sex, geographical location and exposure to particularly harmful elements. Building upon the work of previous St. Lawrence University SYE students, we have synthesized dentine standards and created standard curves for different heavy metals (Hg, Sb, Cd, Zn, Pb, Cu) and fluorine using the Scanning Electron Microscope with an X-ray Energy Dispersive Spectrometer. In previous studies, in order to determine the concentration levels of heavy metals in teeth, the teeth were ground up and dissolved in a concentrated acid. However, our method allows us to analyze the elemental composition within different layers of the tooth. In particular, copper, lead and mercury standardized curves were focused upon this year.
Stephanie Johnnson "Factors Controlling the Wagner-Jauregg Reaction "
Chemistry Faculty Advisor: Samuel Tartakoff
While Lewis acids are widely used to accelerate Diels–Alder reactions, none have been investigated in relation to the Wagner–Jauregg reaction. The Wagner-Jauregg reaction is a double Diels Alder reaction which breaks the aromaticity of the reactants to form a bis-adduct with four new carbon-carbon bonds and two rings. The intermolecular Wagner-Jauregg reaction of maleic anhydride and trans-anethole generally proceeds over 3 hours at 80°C in the presence of dimethylaniline under solvent-free conditions, and produces a 60% yield of the
bis-adduct. Using Lewis acids, which coordinate to the dienophile to lower its LUMO energy, the reaction can be accelerated, allowing it to proceed at lower temperatures or in solution. A variety of Lewis acids were tested at different temperatures in an attempt to run the reaction at room temperature. Cerium (III) chloride catalyzed the reaction, with the best conversion produced in the presence of a Lewis base. The combination of CeCl3 and dimethylaniline allowed the reaction to proceed at room temperature and in 3 M solution.
George Misiewicz Using Chemical Oscillations to Determine the Antioxidant Strength of Wine: Development of an Undergraduate Laboratory"
Chemistry Faculty Advisor: Samantha Glazier
Oscillating reactions are a field in chemistry that encompass the foundations of numerical modeling, non-linear dynamics, and the theories behind organic interactions. Varying parameters such as the temperature, concentration, type of catalyst, and organic substrate, have profound physical effects on the reaction, such as changing the period of oscillation, the induction time, and colour of the reaction. Due to all of these variances, extensive research has gone into exactly how these reactions occur, and how they can help us learn more about our world. One such way is through close analysis of how certain compounds quench the reaction. Products containing phenols and chlorides are known to completely inhibit the oscillations through the prevention of the oxidative step that resets the entire reaction.
In this study we look at determining the antioxidant strength of different wines due to their phenolic content through the controlled quenching of a variant of the Belousov-Zhabotinskii reaction. The reported antioxidant strengths are relative to that of gallic acid, a known phenol present in all wines. It was found that red wines had a considerably larger antioxidant strength than that of white wines. It was also noted that the addition of wine significantly affected the reaction on a whole, such as a decrease in both oscillation period and amplitude. Additionally, we looked at how change in body temperature (hyperthermia, physiological, and high fever) alters the antioxidant effects of the wines through relative analyses and Arrhenius calculations. From this we are able to see that the higher the temperature, the greater the relative antioxidant value. This work was additionally designed as a possible undergraduate laboratory for physical chemistry students, focusing on kinetics, Arrhenius calculations, and phenol chemistry, and was successfully carried out with a class of seventeen students over a two-week period.
Kirsten Padalis "Optimizing a Thioflavin-T Assay using the Microplate Reader"
Biochemistry Faculty Advisor: Nadia Marano
Amyloids are proteins that are characterized by fibrils that have beta sheets which are perpendicular to the fiber axis. There are functional amyloid fibers that can be produced by bacteria as part of their biofilms. An assay optimized by Jordan Koloski using Thioflavin T, a
dye that fluoresces when bound to amyloid fibrils, was used to measure the growth of amyloids of different tetracycline resistant soil bacteria. This assay has been done by measuring the fluorescence using the Horiba FluoroMax Spectrofluorimeter. I created a new assay to be able to read and analyze the fluorescence on the Synergy HTX Multi-Mode Microplate reader. This plate reader can measure fluorescence on a 96 well plate so that more samples can be analyzed at once, which will help cut down time for gathering data allowing more trials to be performed. The assay was first optimized using aggregated insulin, which gives consistently high fluorescence then further studied with bacteria grown on plates. I concluded that the plate reader is not as sensitive at reading fluorescence as the fluorimeter. Therefore, the plate reader is a good way to check a lot of samples at once and to see which ones should be studied further using the fluorimeter.
Avery Peck "Exploring the Tandem Wagner-Jauregg/Diels–Alder Reactions "
Chemistry Faculty Advisor: Samuel Tartakoff
In this day and age, our ability to create begins at the molecular level. Chemical synthesis is a fundamental aspect of global industry ranging from materials science and manufacturing to pharmaceuticals. This makes the exploration of new methods and the development of old methodology a vibrant field as we look for new ways to create. In the early 20th century, a rapid and robust reaction was discovered that provides a way to build highly functionalized molecules with little waste. Many versions of this Diels–Alder reaction exist, with one in particular, the Wagner-Jauregg, being the focus of this study. My work is expanding on what is known about this reaction and its facility in chemical synthesis, which can be applied to numerous industrial applications. A number of reaction conditions have been manipulated to achieve the first intermolecular and subsequent intramolecular reaction. Modifications to the original diene and dienophile used in Wagner-Jauregg’s work, combined with various reaction temperatures, solvents and/or Lewis acid catalysis, has shown progress towards the formation of the desired adduct. Refining the ideal reaction conditions with the right substrates has revealed the sensitivity of the reaction with respect to each condition. This type of double Diels–Alder reaction further establishes the efficiency if this reaction in a wide range of applications.
Jamie Wilson "Analyzing the Levels of Mercury (Hg) in Rice and Rice Products Consumed by Residents and Students in St. Lawrence County, NY "
Chemistry Faculty Advisor: Ning Gao
It is common knowledge that a major source of mercury (Hg) in humans comes from the consumption of marine and freshwater fish. However, it is not widely known that Hg has also been found in terrestrial plants, and recent studies have proven that this may be another significant cause of Hg exposure for humans. This study pays particular attention to the levels of Hg found in rice and rice products consumed by students and residents of St. Lawrence County, NY. The AMA254 Mercury Analyzer, which uses direct combustion to analyze samples, determined the concentrations of Hg in a variety of raw rice grains, cooked grains, and rice-based products. Initial studies showed that the Hg levels diminished significantly in cooked rice products. In order to compare the raw rice to the cooked rice, the amount of mercury per grain was calculated. The average mercury content in the two types of raw rice grains was found to be 0.635 ng/grain and 0.786 ng/grain for the white rice and brown rice respectively. For the cooked rice, the average level came out to be 0.295 ng/grain and 0.046 ng/grain for white rice and brown rice respectively. Understanding that significant concentrations of heavy metals like Hg are found in commonly consumed plant materials, such as rice, will hopefully spark new studies on how the intake of these metals can be inhibited in plants.
Brenda Winn "Philatelic Table of the Elements as a Teaching Tool: Topics in Health and Medicine "
Chemistry Faculty Advisor: Larry G. French
A philatelic table of the elements has previously been assembled with each element portrayed by a postage stamp. 73 different stamp-issuing entities are represented. This table provides a platform to discuss the rich histories and applications of 114 elements. Four elements – nitrogen, silicon, arsenic, and chlorine – are represented by stamps celebrating their drug, human health, and medical fields. A French stamp celebrates the anniversary of the isolation of quinine (nitrogen), an anti-malarial medication, while a Cambodian stamp highlights the importance of malaria control via the use of DDT (chlorine). A Swazi stamp delves into the history of the Havelock Asbestos Mine (silicon) where lasting effects of lung cancer and mesothelioma present concern. A stamp issued by Germany celebrates the birthday of Ehrlich, who introduced the Salvarsan magic bullet (arsenic), the start of targeted chemotherapy. Narratives behind these four stamps will be developed to provide a new teaching tool for secondary or non-major science classes.