Festival of Science 2018 was held Friday, April 27, 2018.
Jack Mechler - Biochemistry, Faculty Advisors: Nadia Marano and Lorraine Olendzenski
Isolating and Characterizing Functional Amyloid Fibers from Microbacterium sp.
Functional bacterial amyloids make up an important structural component of biofilms, and little is known about their variance in structure throughout nature. This research aimed to adjust isolation procedures developed by Heather Raimer (2017) for an archaeon, to obtain amyloid fibers from Microbacterium sp. that was isolated from the soil of a pig farm by Abby Korn (2014), and shown to test positive for amyloids using the Thioflavin T (ThT) assay by Hunter Berrus (2015) and Jordan Koloski (2016). ThT assays during different bacterial growth conditions showed that the Microbacterium produce more amyloids closely associated with the cells when grown on agar plates, as opposed to liquid media. Early protein isolation trials showed that amyloids more closely associated with the cells were better candidates for isolation. Therefore, plate-grown amyloids were separated from the cells using sonication, and purified from other components using differential centrifugation and polyacrylamide gel electrophoresis. To further purify this amyloidogenic material, and to characterize the monomers that it is composed of, it was depolymerized in formic acid, further purified with differential centrifugation, dried in a speedvac, and resuspended in both water and formic acid with 1M urea. The sample in formic acid and urea was run on an SDS-page gel to determine the size of its monomers and the extent of the purification, and the sample in water examined under a scanning electron microscope, according to previously derived methods. Isolating and imaging these novel functional amyloids will be another step in our understanding of bacterial amyloids.
Funding: University Fellowship
Alexis Haley - Chemistry, Faculty Advisor: Adam Hill
Luminescence of Lanthanide/Transition Metal Heterobimetallic Phosphinoamide Complexes
Due to their combination of long luminescence lifetimes and higher absorption cross-sections, heterobimetallic complexes containing lanthanides and transition metals are becoming increasingly suitable for applications in photocatalytic processes and bioimaging techniques, as well as offering the opportunity to study energy transfers between d and f orbitals. Non-radiative quenching of the excited state competes with luminescence. The competition may be optimally studied in a family of three-fold symmetric complexes with phosphinoamide ligands, which provide stability for the transition metal-lanthanide center’s dative interaction and aid in its metal-to-metal charge transfer (MMCT). The first-row transition metals Fe, Co, and Ni are paired with lanthanides La, Eu, and Tb to investigate their metal-metal interactions via their luminescent lifetimes and quantum yields. The results are compared with monometallic complexes and free metal ions in solution.
Funding: Chemistry Department
Alissa Stone - Chemistry, Faculty Advisor: Adam Hill
Synthesis of Cobalt-Zirconium Heterobimetallic Sites on a Silica Nanoparticle Substrate
Co-Zr-SiO2 nanoparticle heterobimetallics are useful for performing artificial photosynthesis due to d-d electron transfers between metals. The metal-to-metal charge-transfer (MMCT) transition should exist between Co(II) and Zr(IV) based on previous studies. Zr-SiO2 nanoparticles and Co-Zr-SiO2 nanoparticles were made using air-free techniques. The monometallic and heterobimetallic products were analyzed using FT-IR, UV-vis, and fluorescence. The heterobimetallic sites are useful in determining and understanding the MMCT transition.
Natasha Turyasingura - Chemistry, Faculty Advisor: Emily Dixon
A Study of Gene Regulation in Yeast under Stress: The Mechanism of Binding of Rpd3 to the Promoter Region of NDP genes in Saccharomyces cerevisiae
When Saccharomyces cerevisiae yeast cells are subjected to stressful conditions, the cells respond by altering certain cellular processes to adapt and survive. One such stressful condition is nutrient deprivation. The TOR pathway has been found to be a central regulator of both cell size and proliferation. Rapamycin is a small molecule that binds to and inhibits the TOR protein eliciting a transcriptional response that is reminiscent of nutrient deprivation. This transcriptional response results in the activation and repression of specific groups of genes. The repression of select genes has been studied to occur by the action of the histone deacetylase Rpd3. Rpd3 binds to the promoters of rapamycin-repressible genes via the transcriptional repressors Dot6/Tod6 to the GATGAG sequence in the promoter region. Here, we investigate whether Rpd3 binds to the promoters of NDP genes to activate them in the same way that it binds to the promoters of genes repressed by Rpd3. To do this, we approach the question in two ways: we delete the GATGAG sequence in the promoter of the GAP1 gene to determine if Rpd3 still binds to the GAP1 promoter; and we tag Rpd3 in a Dot6/Tod6 mutant to determine whether the presence of Dot6/Tod6 is necessary for the binding of Rpd3 to the promoter of GAP1 (and other NDP genes).
Funding: Biology Department
Philip Park, Chemistry, Faculty Advisor: Matthew Skeels
Determination of Lead and Other Heavy Metal Contamination of Maple Syrup - Produced in St. Lawrence and Chittenden Counties
This study investigates the magnitude of heavy metal contamination in maple syrup. The ingestion of lead (Pb) by humans can be toxic, potentially leading to health-related issues, such as memory loss, heart disease, and reduced fertility. While the United States banned the use of leaded paints for household uses in 1978, lead contamination remains a concern from existing sources of leaded paint and water pipes, solder, and smelting. In the maple syrup industry, many pieces of equipment, including the metal taps and tin collecting buckets used in the sugaring process, have been known to contain leaded materials. To determine the extent of lead contamination in maple syrups we evaluated syrup samples with a Perkin Elmer Flame/Graphite Furnace Atomic Absorption Spectrometer. The syrup will be collected from a variety of sugar farms in St. Lawrence County (NY) and Chittenden County (VT). In addition to lPb, the concentration of other metals, including Copper (Cu), Zinc (Zn), Mercury (Hg), and Iron (Fe) will also be determined. By analyzing the concentration of lead and other metals in maple syrup, it could show the extent to which different pieces of equipment in the sugaring process are able to contaminate maple syrup.
Rachel Pineda - Chemistry, Faculty Advisor: Matthew Skeels
Comparative Assessment of Heavy Metal Concentrations in Various Vegetables via GFAAS/FAAS
Dietary exposure to heavy metals, namely lead (Pb), copper (Cu), and zinc (Zn), has been identified as a risk to human health through the consumption of vegetable crops. This study investigates the magnitude of heavy metal contamination in vegetable samples at 2 sites: Philadelphia, PA (urban) and Canton, NY (rural). The foodstuffs investigated in this study include pumpkins, potatoes, tomatoes, peas, carrots, turnips, peppers, etc. These produces were dried in a convection oven for an average of 19 days, ground into fine particles using a Wiley mill, subjected to acid digestion using nitric acid, and analyzed in independent replicates of 2 using Graphite Furnace Atomic Absorption Spectrophotometry (GFAAS) and in replicates of 3 using Flame Atomic Absorption Spectrophotometry (FAAS). High concentrations of heavy metals in vegetables might be related to their growth in or near industrial settings. The effect of industrialization on the production of vegetables from small scale gardens will be assessed. .
Tyler Guido - Chemistry and Biology, Faculty Advisors: Ning Gao and Jill Pflugheber
Human Teeth as a Bioindicator for Environmental Exposures
The human tooth is comprised of four primary layers; enamel, dentin, pulp and cementumToxic elements such as heavy metals and fluorine can accumulate in these four layers of the tooth over time. When looking at heavy metal accumulation, these four tooth layers may serve a greater purpose as bioindicators for environmental hazards that individuals have been exposed to over time. By analyzing the concentration levels of heavy metals and fluorine in human teeth, we might be able to draw correlations between gender, age, and possibly geographic location to infer both the extent and sources of exposure for particularly harmful elements. Building upon the work of previous St. Lawrence University SYE students, improving an analytical protocol when using a Scanning Electron Microscope (SEM) with an X-ray Energy Dispersive Spectrometer (EDS) will create standard curves with significantly improved accuracy and precision. This will allow for the quantification of concentrations of toxic elements in teeth. Calibration curves with improved accuracy and precision have been created using previously made standards for elements Pb, F, Cd, and Zn. New Hg standards have also been made, using EDTA as a ligand to keep Hg stable under high vacuum when analyzing via EDS. Using these standard curves with improved accuracy and precision, quantification of heavy metals and fluoride in the dentin, enamel, and root layers of the tooth is being done using human teeth. The teeth analyzed will be classified by age, gender, and by the absence or presence of amalgam fillings.
Amanda Kennedy - Chemistry, Faculty Advisor: Ning Gao
An Analysis of Denitrification Effectiveness Using UV/Vis Spectrometry
Nitrate in groundwater systems, typically sourced from fertilizer runoff, has detrimental environmental effects as it causes eutrophication at river mouths, and can potentially cause methemoglobinemia, or “blue baby disease” when found in drinking water at high concentrations. Previous research done at Ryerson Polytechnic University has shown that chemical denitrification of groundwater is possible using powdered aluminum. This reaction was tested under laboratory conditions, in which the percent decrease in nitrate was observed using UV/Vis spectrometry with solutions held under basic conditions. Based on the lack of effectiveness in this process when attempting to get comparative results to the literature, a photocatalytic method using blue LED light was attempted to boost the percent reduction by exciting the molecules during the reaction so the reaction would proceed more effectively. PH dependency for this reaction was also explored, as there is a notable difference in absorption of UV light between initial solutions and the same solution under basic conditions, even before reacting with aluminum. Results for this experiment may have been skewed by partial reduction of nitrate ions into nitrite, as both species absorb in the same ultraviolet range, and are difficult to determine separately.
Timothy O’Brien - Chemistry, Faculty Advisor: Ning Gao
An Independent Study in Food Chemistry: A Healthy Menu
A sample menu of nutritionally balanced soups, salads, appetizers, main courses, desserts was developed to offer healthy options for a balanced, multiple-course meal or series of dishes that could be eaten over the course of a day. For each dish, the tastes, flavors, and textures are listed. To better describe flavors and the process by which foods are sensed by the body, a background in flavor science, retronasal olfaction, and neurogastronomy is provided. For each food item, carbohydrate, protein, and lipid daily values were discussed and evaluated. Macronutrient composition was analyzed as well. Sources of both soluble and insoluble fiber are mentioned and their importance in the body is discussed. Vitamins and minerals and the processes in which they are taken up by the body are considered as well as their importance in bodily functions.
Danielle Couture - Chemistry, Faculty Advisor: Samantha Glazier
Characterizing the Binding Mode of the Doxorubicin Derivative doxy to DNA
Doxorubicin is a DNA intercalator that binds with its planar carbon rings stacked between DNA base pairs and its sugar group locked into the minor groove. A doxorubicin derivative, doxy, has been synthesized by Haley Anchukaitis and Dr. Tartakoff. Doxy’s major difference is the removal of the sugar moiety from one of the carbon rings. This difference is significant because as doxorubicin binds to DNA, the first step in the intercalation mechanism is electrostatic interaction between the positively charged sugar and the negatively charged backbone of the DNA. Once bound, the sugar moiety stabilizes the drug-DNA interaction. The new derivative is expected to either intercalate like the parent compound or bind in the minor groove of DNA. Since the derivative compound is neutral, it is only somewhat soluble in aqueous solution, and standard methods for determining the binding mode are unfeasible. In this project, a DNA melting protocol was developed to determine the binding mode of the compound. DNA intercalators stabilize DNA and raise its melting temperature, while groove binders do not influence the stability of DNA and leave the melting temperature unchanged. The preliminary results obtained from melting curves using an absorbance based method indicated that the binding mode of doxy is most similar to groove binding. The data obtained by this protocol yielded indistinct sigmoidal curves, which led to the development of a fluorescence based method. This method, which uses 1000-fold less material, can be used to determine the binding mode of novel drug compounds like doxy.
Funding: Chemistry Department
David Bain - Chemistry, Faculty Advisor: Samantha Glazier
Examining the Intercalation of Nogalamycin with DNA
There exists a class of small, flat molecules with the ability to insert (intercalate) themselves between DNA base pairs to disrupt replication and transcription. This makes them ideal candidates for cancer and tumor treatment, conditions which rely on the DNA replication process for abnormal cell growth. This project seeks to better understand the kinetics and thermodynamics behind the intercalation of one such drug, nogalamycin, with DNA, particularly, by which groove (major or minor) it intercalates. By utilizing nogalamycin’s fluorescent properties, and alternately blocking each groove with known major and minor groove binders, methyl green and Hoechst 33258 respectively, the pathway can be established via stopped-flow fluorimetry; these methods are novel and results can be compared to computational studies. Thus far, we have shown that nogalamycin undergoes small amounts of photodecay, but the fluorescence of nogalamycin is not affected by the presence of the groove binders. A binding time of nogalamycin with DNA has also been established.
Kelsey Murphy and Avery Peck - Chemistry
Faculty Advisors: Dr. Samantha Glazier and Dr. Samuel Tartakoff
Synthesis and DNA Intercalation Mechanism Characterization of Novel Chemotherapy Drug Analogs
Proflavine is a synthetic acridine drug that in recent years has been studied as a DNA intercalator in cancer treatments to kill tumor cells. The biological activity of the drug is associated with its ability to bind to DNA, however cardiotoxicity is a major issue associated with such drugs. This necessitates an increased understanding of the binding mechanisms of these drugs to optimize drug structure-activity relationships in order to minimize toxicity and increase specificity and efficacy. Although not fully understood, it was assumed that proflavine enters directly through the minor groove of DNA to reach the final intercalated state, but recent molecular dynamics calculations proposed an unusual binding mechanism involving the major groove. The major groove was previously thought to be uninvolved in the binding event, prompting the investigation of major and minor groove involvement in intercalative pathways of small drug molecules. This study seeks to functionalize proflavine, a small intercalator, at its amino groups so as to vary molecular electronics, polarity, and size to determine how molecular functionality may change DNA binding mechanisms with respect to the major and minor grooves of DNA. Our investigation utilizes fluorescence spectroscopy competitive binding studies with Hoechst 33258 and methyl green, minor and major groove binding dyes, to examine how the binding constants of small intercalating molecules respond when access to each groove is inhibited. Proflavine is subjected to a variety of synthetic manipulations in order to sample the structure-activity profile of drug intercalative mechanisms.
Abigail Enders - Chemistry, Faculty Advisor: Samuel Tartakoff
Determining the Mechanism of the Wagner-Jauregg Reaction by Analysis of Reaction Rates: A Kinetics Study
Synthetic organic chemistry focuses on converting simple starting materials into complex molecules, which are then used to make plastics, pharmaceuticals, synthetic fibers, and other valuable commercial products. The Wagner-Jauregg reaction (a reaction that forms complex, polycyclic molecules) has long been viewed as a double Diels–Alder reaction but research on the mechanism has not been conducted. A correct understanding of the mechanism should allow us to determine if there is a reactive intermediate, which could be intercepted to form new, interesting products. Our research examined competing mechanisms for the Wagner-Jauregg reaction by comparing relative reaction rates using Nuclear Magnetic Resonance spectroscopy (NMR), then conducting a Hammett analysis. Various substituted styrenyl substrates with electron withdrawing groups (EWG) and electron donating groups (EDG) were reacted with maleic anhydride and analyzed. The preliminary results show that the reaction pathway is likely analogous to the well-understood Diels–Alder reaction for many, but not all, substrates.
Funding: Ronald E. McNair Post-Baccalaureate Achievement Program
Anne Buck - Chemistry, Faculty Advisors: Samuel Tartakoff
Progress Towards Efficient Synthesis of Morphine Analogues Using the Wagner-Jauregg Reaction
A Diels-Alder cycloaddition allows for the creation of two new sigma bonds along with a new six membered ring. This reaction occurs as a result of the pi bonds found in the diene and dienophile being higher in energy and therefore less stable, interacting to produce more stable sigma bonds. The Diels Alder reaction allows for different conformations to be produced depending on how the diene interact with the dienophile resulting in new steriocenters. The Wagner-Jauregg reaction, is a specialized Diels Alder reaction in which the diene is an aromatic ring. Aromatic compounds are exceptionally sable and unreactive due to an extended conjugated network. It normally requires very harsh conditions to cause an aromatic ring to react, which is the main challenge of the Wagner-Jauregg. This method can be used in the production of opioid- like compounds. Opioid molecules are composed of 5 rings, with the proper one ring starting material, through a Wagner-Jauregg reaction it is possible to create a three-ring structure in one step. Two starting compounds were produced through Wittig reactions followed by purification via column chromatography and characterization via proton nuclear magnetic resonance. These compounds then underwent a series of variable reaction conditions, such as high temperatures, to try and promote a Wagner-Jauregg intermolecular cycloaddition with maleic anhydride. Up to the present date, we have produced a compound with highly electron withdrawing functional groups, which we are trying to currently characterize.
Funding: University Fellowship, Stradling Scholarship Fund
Haley Anchukaitis - Chemistry
Faculty Advisors: Samuel Tartakoff and Samantha Glazier
Synthesis of Doxorubicin Analogs for DNA Binding Studies
Anthracyclines are used in the medical field for their antitumor activities. One of the most common drugs of this class, doxorubicin (DOX), has been used to treat cancers in the breasts, ovaries, and lungs. The mode of action for DOX is intercalation between the base pairs of DNA, which disrupts translation and replication. The planar structure of DOX allows the rings to slide in between the base pairs, while the sugar moiety interacts with the minor groove. The sugar connects to the minor groove via hydrogen bonding between the amine of the sugar and the sugar-phosphate backbone of DNA. To determine how the absence of those hydrogen bonding interactions affect the binding mode, multiple DOX analogs were synthesized. The DOX analog 7,10-dihydro-6,11-dihydroxy-naphthacenedione required a four-step synthesis and was recovered in fairly low purity. The main difficulty with this synthesis was optimizing the double Claisen rearrangement reaction conditions. Further attempts have also been made to introduce an amine group onto this tetracyclic structure to mimic the DOX amino-sugar, making interaction with the minor grove of the DNA backbone possible. DOX-aglycone was synthesized by hydrolyzing the sugar off of the fourth ring. The analogs are currently undergoing kinetic studies to test how well and with what mechanism they bind to DNA.
Funding: University Fellowship: Robert L. Stiles P’71, University Fellows Endowment and the Daniel F. ‘65 and Ann H. Sullivan Endowment for Student/Faculty Research