Student Projects, 2003-2004
(Photo Gallery and Abstracts, courtesy of Dr. John R. Rupp)

Matthew Benard - Determining Critical Transcription Loci of the Promoter and Enhancer Regions of the 12-Liposygenase Gene.

Adviser: Michael Temkin

Research has suggested a relationship between high intake levels of dietary fats and the increased risks of many cancers including breast, prostate, and pancreatic. Of particular interest in the fat-enhanced tumorigenesis are the omega-6 polyunsaturated fatty acids - especially, the 20-carbon arachidonic acid (AA), whose metabolism generates biologically active molecules that may hold some involvement in the development of cancers. AA participates in the regulation of various organ and system functions such as the digestive, renal, and immune systems. However, the release of arachidonic acid from membrane phospholipids has been observed to have a critical role in the proliferation of tumor cells. The metabolites generated in the breakdown of AA have been found to prevent cellular apoptosis. Studies using HL-60 cells showed that cells grown in fatty acid deficient medium were 50% more resistant to apoptosis than cells grown in the presence of AA. The loss of apoptosis contributes to resulting tumorigenesis. As a result, AA metabolism has been studied as a target of intervention for treatments of cancers such as breast cancer, pancreatic cancer, and prostate cancer.

The intent of this project is to study the human form of the arachidonate 12-lipoxygenase enzyme - specifically the 5' upstream promoter and enhancer sequences of the 12-LOX gene (located on chromosome 17). These regions will be explored for areas of high importance in transcribing the 12-LOX gene. The amount of enzyme produced will be quantified after transcription has taken place with only a portion of the pre-selected enhancer/promoter region. This will allow for the identification of areas required for maximal transcription and will, therefore, afford possible sites for drug inhibition considerations.

John DeLorbe - Salvia Divinorum: A Home Grown Hallucinogen

Advisor: Dr. Larry French

Salvia Divinorum is a hallucinogenic plant used by the Mazatec people of Oaxaca, Mexico. The rare plant is a member of the mint family, and is indigenous to the Sierra Mazateca Mountains.(1) The primary active ingredient is Salvinorin A, a neoclerodane diterpene, and it is the most potent naturally occurring hallucinogen known. The molecular target of Salvinorin A is the kappa opioid receptor, and this receptor represents a molecular target for drugs that could possibly treat disorders such as, schizophrenia, Alzheimer's and bipolar disorder.(2)
The essential oil of a locally grown (Canton, NY) Salvia Divinorum cultivar will be extracted, and the diterpene Salvinorin A will be identified and purified using column chromatography and HPLC. Also, other previously identified compounds present, or any unidentified compounds will be identified using spectroscopic techniques including 1D and 2D NMR and GC-MS. This will provide a comparison to the compounds present in the wild plant to those of the locally grown plant. If a large amount of the pure Salvinorin A can be obtained, chemical modifications will be done to create analogs.

Robert Doran - Molecular Dynamic Simulations of Water-Quartz Interactions on Quartz Surfaces

Advisor: Dr. Jeffrey A. Greathouse

The objectives of this project are to explore the interactions involved in a quartz/water interface and the types of uranium surface complexes that form at this interface.
The formation of complexes on inorganic surfaces as thin layers has applications in the field of synthetic bone material growth on medical implants1. One kind of interaction is the adhesion of complexes onto inorganic surfaces. These interactions have similarities with the complexes formed by uranyl ions, UO22+. Nuclear waste management is currently being debated at the Yucca Mountain site. One issue concerns the interactions between the radioactive uranyl ions and the surrounding inorganic materials of the mountain.

Molecular Dynamic simulations are to be run to examine the possible interactions at the quartz/water surfaces. DL_POLY is the software that will be used to run each simulation. A flexible model for quartz2 and the flexible SPC model for water3 are to be used in the simulations. The quartz/water interactions will be examined on different Miller surfaces within the quartz.

One important reaction is that of hazardous uranyl ions in water on the surface of quartz. Uranyl ions will be placed in the quartz/water system to study the complexes that form on the quartz surfaces. All of the results will be determined within the constructs of MD simulations.
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1 - deLeeuw, Nora H.; Mkhonto, Donald. Computer Simulation Study of the Effect of Surface Pre-Relaxation on the Adhesion of Apatite Thin Films to the (0001) Surface of -Quartz. Chemistry of Materials. Vol 15, Number 8. April 22, 2003. pp 1567-1574.
2 - van Beest, B. W. H.; Kramer, G.J. Force Fields for Silicas and Aluminophosphates Based on Ab Initio Calculations. Physical Review Letters. Volume 64, Number 16. April 16, 1990. pp 1955-1958
3 - Mizan, Tahmind I.; Savage, Phillip E.; Ziff, Robert M. Molecular Dynamics of Supercritical Water Using a Flexible SPC Model. Journal of Physical Chemistry. 1994, 98, 13067-13076.

Alexis Kostun -Water Quality Study and Mass Modeling for the Little River Watershed

Advisor: Dr. Ning Gao

The concentration of various ions and dissolved oxygen in river water is of great interest to environmental quality assessment . These concentration data can be used to create a mass balance model, specifically in this study of the Little River Watershed.
Vernier probes will be used to monitor the concentrations of chloride, ammonium, calcium, and nitrate ions, dissolved oxygen, and pH of the water thereby yielding water quality data. The existing procedure will be refined to determine the necessary parameters to ensure reliable data. Another aspect of this project is to continue the development of a mass balance model for the Little River Watershed to evaluate its overall environmental quality. My aim is to complete the necessary components of an already existing, very simple mass balance model that had been constructed by a former student by using the STELLA computer software by generating my own field monitoring data and gathering additional data from other researchers on and off the St. Lawrence campus. The combined environmental and hydrological data sets will be compiled into the mass balance model to test its performance. The refined mass balance model will then be used to predict what the steady state conditions would be for the Little River Watershed when the inputs and outputs of the various chemical constituents are altered.

Josh Onyan - Ambient Air Quality Study at SLU

Advisor: Dr. Ning Gao

Continuing studies are being conducted to develop an interactive computerized mass balance model of the Little River watershed using the STELLA computer software. Water samples at varying locations along the Little River and ambient air samples at a location close to the watershed will be collected and analyzed. The resulting monitoring data will be incorporated into the mass balance model. This study will facilitate the evaluation of the environmental quality of the watershed.

To collect ambient air samples, an ambient air sampler needs to be created with existing technology. The apparatus consists of a cyclone, two denuders, and a filter pack. The cyclone device uses a set velocity of airflow to eliminate airborne particles larger than 2.5 m, which would not be of concern because they are too large to enter the respiratory system. The two denuders allow the collection of acidic or basic gaseous species present in ambient air. The filter pack contains multiple filters used to collect the particles entering through the cyclone and the two denuders.(2)

Using gravimetric analysis, scanning electron microscopy, and ion chromatography, the airborne particle mass concentration, gaseous acidic and basic inorganic species, ionic species and trace elements on airborne particles could be determined.(3) Thus an understanding on chemical composition and concentration levels of ambient air contaminants could be established.

Hannah Stella-Levinsohn - Computer Simulation of Uranyl Smectite Clays: Effect of Tetrahedral Charge on Interfacial Structure

Advisor: Dr. Jeffery A. Greathouse

Smectite clays are naturally occurring clay minerals. An understanding of the clay-water interface is important to many areas of geochemical interest. Montmorillonite and vermiculite are common clay minerals in the Nevada Yucca Mountain region, so a detailed picture of mineral-water interactions is important to understand the fate of radionuclides in groundwater. Negative charge sites in the tetrahedral layer of montmorillonite and vermiculite are due to substitution of Al3+ for Si4+. The cations in the aqueous reigon balance the negative charge in the system. By examining the effects of the tetrahedral Al charge on interlayer structure of sodium clays, we developed a more accurate model of clay-solution interactions. In our model, the charge on the tetrahedral Al is delocalized among surrounding oxygen atoms.

The Molecular dynamics program DL_POLY (1) will allow equilibrated Monte Carlo clay-water configurations to be simulated with a flexible molecule force field. The equilibrated system from the Monte Carlo simulations will be then converted into a file that can be read by DL_POLY. The flexible model force fields are important when investigating the surface relaxation at the tetrahedral charge site, and when looking at the movement clay OH group. The molecular dynamic simulations will be run to obtain adsorption energies and an understanding of the migratory tendencies of the uranyl ion.

1- Forester, T.R., and Smith, W., DL_POLY User Manual (CCLRC, Daresbury Laboratory, Warrington, UK, 1995.

Matthew Thompson - Computer Simulations of Smectite Clay Minerals

Advisor: Dr. Jeffery A. Greathouse

The study of clay-water interfaces has many applications, such as nuclear waste disposal, ground water contamination removal, and catalysis. Smectite clays are inorganic polymer sheets composed of an alumina octahedral layer between silica tetrahedral layers. These clays are characterized by a permanent negative charge residing in either the octahedral or tetrahedral layers. For this work there were two types of smectite clays used. We worked with vermiculite, and montmorillonite.
For our simulations there were two simulation methods employed. We first utilized a Monte Carlo technique in order to obtain a system that has been equilibrated. The next step in the process is then to use molecular dynamics to continue the simulation from the equilibrated systems. If the method proves to be viable it takes the project into a completely new direction because it will allow the simulations of clays to be conducted with flexible molecules, instead of rigid molecules.
For my senior year experience I hope to expand this work and introduce quaternary ammonium cations into the clay system. These simulations will hopefully lead us into new directions and bring more insight to our project. I will be taking smectite clay and placing these cations in the interlayer region and simulating the reactions with the clay layers. The method to complete this task is still unclear at this time and will be developed in the coming months. One thing is clear, a new set of potential parameters for these interactions will be introduced.

Prepared by John J. Rupp, October 2003