Science & Technology Expansion Program (STEP)
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STEP Faculty Research
The following faculty are participating in the NSF-STEP program for Summer 2014. Click on the Faculty Name to go to their main web page. You do NOT have to be a major in the specific department to participate in the research projects. For example, your major could be chemistry, but you could do research with a psychology faculty member. For your application, pick six potential research projects that seem interesting to you, regardless of your major. Don't worry if you don't understand the full research description; your faculty mentor will teach you what you need to know!
Dr. Jennifer Brofft (1 student )The focus of my summer research will be to continue efforts to understand what types of microbes impact the development of loggerhead sea turtle embryos. Last summer, we completed a survey of bacteria and fungi contaminating failed eggs collected from Jekyll Island, GA during the 2010 nesting season. Based on those efforts, we have identified several potential pathogens, including the bacteria Hahella chejuensis and the fungus Fusarium solani. We also obtained a sample set of failed eggs from Jekyll Island from the 2012 nesting season (67 total failed loggerhead eggs from 9 nests). The nests originated from different regions of the island (same general regions as sampled in 2010). Approximately half the nests contained eggs having pinkred pigmentation, which we observed in 2010. All eggs were aseptically opened, fluid and biofilms were collected/frozen for future analysis and the embryological stage of development was determined. For each nest, excavation sheets containing ancillary data were provided from the Jekyll Island Authority. This summer, we intend to utilize molecular approaches to determine the types of bacteria and fungi present in the 2012 eggs. This will allow us to have a robust dataset for publication (i.e. 2 non-consecutive sampling seasons for Jekyll Island). In addition to processing and analyzing last year’s dataset, we will be expanding our sampling efforts this summer to include failed eggs from other Georgia barrier islands. We will also be collecting samples to help determine the source of the organisms present in the eggs. This will involve sampling sand collected from the nests and attempting to sample the cloacae of nesting mothers on Wassaw Island, GA.
Dr. Matthew Draud: (1 student) NOT IN DROP DOWN MENU ON APPLICATION. PLease indicate Dr. Draud in the comment box if you are intersted in his project. Diamondback Terrapin Nesting Ecology: Diamondback terrapins (Malaclemys terrapin) are native to the South Atlantic Bight, inhabiting low to moderate salinity estuaries. They are important consumers in estuarine food webs and are an important keystone species in maintaining community stability and biodiversity. I initiated a study on Diamondback Terrapins in Long Island New York in 2000 which has continued for the past 12 summers. I am now bringing the project to Georgia and am planning to use Ossabaw island as my main study site. Previous Research Findings in NY: My goals were to estimate the population size, the sex ratio, and size frequencies in several large populations in the Long Island Sound. Although I caught many adults indicating populations numbering in the high hundreds, we caught very few juvenile terrapins and the adults we did catch were on average larger and older than those caught by earlier studies in the same estuary. The increased average size was caused by a lack of intermediate sized turtles in our samples. These data caused concern that the lack of smaller/younger year classes of terrapins is the result of poor recruitment and not simply a bias of sampling technique. Because turtles have long life spans, populations may exist for a long time, despite the complete loss of recruitment due to reproductive failure. In fact, it can take 10-15 years before obvious signs of a turtle population decline become evident, by which time it may be too late to intervene. Recruitment can be reduced due to skewed sex ratios, a paucity of sexually mature adults, the lack of suitable nesting habitat, and/or heavy predation of eggs, hatchlings, or juveniles. Preliminary data caused me to believe that the primary culprit in the Long Island Sound populations I have studied is the lack of suitable nesting habitat. I profiled the entire shoreline of the study area and found only sporadic suitable nesting habitat. Shoreline development, including the building of small sea walls, fences, and soft-sand beaches has eliminated much of the original nesting habitat. 2014 Research Objectives: My research objectives for the Summer of 2014 are to 1) identify and map the marsh habitat utilized by terrapins in and around Ossabaw island and 2) identify and map active nesting sites used by terrapins on Ossabaw island, 3) capture and tag terrapins utilizing habitats in and around Ossabaw island. I use passive, long-term, identification tags (PIT tags). PIT tags are encapsulated microchips, the size of a rice grain. Hand-held, battery operated, scanners send low energy radio signals that energize the microchip to transmit its unique number, which is subsequently displayed for the observer to record. Each chip sends a unique number, which can never be altered and which is permanent. Using binoculars, either on foot or in kayak, observers can locate terrapins and record GPS waypoints for various types of terrapin activities. For nesting, observers can watch nesting females from a distance without disturbing them. Once a female completes her nest, she is captured for measurement data and identification/PIT tagging, and the exact location of the nest will be identified by GPS and a map of the nesting area will be constructed. Eggs are excavated, counted, weighed, measured and returned. Nests are protected by hardware cloth cages constructed on site.
Dr. Sara Gremillion (1 student) The localization of COG proteins in fungal cells. Parasitic fungi are a major threat to the health of humans, animals and plants. Information about how fungi grow can lead to the development of new antifungal medicines and agricultural chemicals. This project aims to investigate the cellular proteins involved in proper fungal growth using the non-pathogenic fungus Aspergillus nidulans. An unknown protein has recently been identified as crucial for fungal development. This protein is similar to the COG2 protein found in other organisms. COG2 is part of the conserved oligomeric Golgi (COG) complex that helps maintain the structure and function of the Golgi apparatus. Through genetic manipulation, a green fluorescent protein (GFP) was attached to the COG2 protein in A. nidulans. Visualization of the GFP-COG2 in a live cell indicated that the protein localizes to the Golgi apparatus, proving that the hypothesized COG2 of A. nidulans likely has similar function to COG2 proteins of other organisms. The remaining COG proteins (COG1, COG3, COG4, COG6, and COG7) in A. nidulans will now be tagged with GFP to confirm their association with the Golgi apparatus.
Dr. Jay Hodgson (1 student) Records of historical climate and landscape evolution are readily available in many forms, including tree rings, ice cores, rock fossils, and sedimentary layers. My research utilizes the remains of diatoms, which are a major class of algae, stored in coastal marsh sediments. When they die, they settle to the bottom and form sequential sediment layers. Diatoms have cell walls made from silica and are very slow to compose, making it possible to extract and identify species of diatoms from thousands of years ago. Also, many species of diatoms are fastidious and require certain water conditions for living; many common indicator species are sensitive to pH, salinity, temperature, and sedimentary substrate. Therefore, diatoms are powerful tools in the reconstruction of changing paleo-environments. By extracting diatoms from sediment cores retrieved from barrier islands, I am currently investigating factors that were involved during the formation of the islands. I am particularly interested in understanding the historical climate of coastal Georgia, and the coastal southeastern United States in general, spanning from 6000 years ago up to today. Beginning around 5500 years ago, there was a hypothesized cooling trend and accompanying increased precipitation and flooding following the last deglaciation. Indicator diatoms should reveal past hydrogeologic conditions, particularly water depth changes, along the coast. Additionally, I plan to investigate historical hurricane frequency. When hurricanes hit the coast, their storm surge inundates inland water bodies, which increases the salt content of these waters. Changes in sedimentary diatoms should show frequencies of hurricanes by inferring changes in salt content of inland waters. The historical presence of marine diatom species in freshwater sediments also indicates storm surges.
Dr.Heather Joesting, Morphological and physiological adaptions to abiotic stress in coastal sand dune species. Decades of anthropogenic development have resulted in adverse modifications to the ecosystem processes that maintain coastal environments, as well as severe degradation of natural, highly productive habitats such as wetlands. Thus, future coastal management decisions need to focus on how to sustain anthropogenic development and coastal industry while maintaining natural coastal ecosystem processes. Natural stabilized sand dunes function as a barrier to storm wind and wave energy, providing protection to the productive habitats on the landward side of the island (Stallins and Parker 2003). Furthermore, artificially constructed sand dunes planted with native plant species has been shown to protect residential and commercial properties from storm waves and overwash (Feagin 2005). There is a tight coupling between the presence and cover of native sand dune vegetation and the formation, maintenance, and stabilization of sand dunes. Therefore, a thorough understanding of the growth and survival strategies of native sand dune vegetation will be critical in the implementation of artificial sand dunes as a part of coastal management strategies. Previous research on coastal sand dune vegetation has focused on the environmental variables that determine distinct vegetation patterns in coastal sand dunes (e.g., Boyce 1954; Ehrenfeld 1990), but few studies have investigated the morphological and physiological adaptions of native plant species that promote growth and reproduction in the sand dune habitat. This project proposes to investigate the relationship between leaf form (i.e., leaf size/shape, leaf inclination, leaf internal anatomy), leaf function (i.e., leaf temperature, leaf carbon gain), and the abiotic environment for several key sand dune species in northern coastal Georgia. Current research efforts with undergraduates is focused on determining the effect of leaf inclination on minimizing leaf temperature in large-leaf pennywort (Hydrocotle bonariensis) in the field and elucidating the structure and function of glandular leaf hairs in the sea elder (Iva imbricata) in the laboratory.
Dr. Melanie Link-Pérez (1 student) Molecular systematics and description of new species in the neotropical fern genus Adiantopsis More than 2000 new species of plants are discovered each year, many from specimens already preserved in the world’s herbaria. Dr. Link-Pérez recently described three new species of Adiantopsis based on specimens that had been in herbaria collections for periods between five and seventy years. The goal of this project is to complete the molecular and morphological characterization of ten new species identified by earlier research leading to formal description and publication of valid names for these taxa. Students involved in this research will gain experience with general molecular techniques, such as DNA isolation (from herbarium specimens on loan to the Armstrong Herbarium), polymerase chain reaction, and electrophoresis, as well as a foundation in phylogenetic analyses. The project also employs histological techniques to collect spore and stomata data for the species, along with quantitative morphological data using compound light microscopy and stereomicroscopy.
Dr. Traci Ness (1 student) Identification and characterization of immune receptors that recognize fungal infections in the mouth. The oral cavity is continually exposed to a variety of microbes and pattern recognition receptors (PRRs) are responsible for discriminating between microbes and initiating an appropriate immune response. Most PRR research has focused on immune cells; however, it is the epithelial cells that are present at the site of initial infection that must first recognize the invaders and alert and recruit immune cells to the site of infection. Dr. Ronald Garner (Mercer University) and I have begun a collaboration to investigate the recognition of the pathogenic yeast Candida albicans by PRRs in oral epithelial cells. The primary goal of this project is to identify the PRR repertoire of these cells and to characterize the changes that occur following stimulation with Candida. Ultimately, we will probe the PRR-Candida interactions that lead to the formation of signaling scaffolds on the surface of oral epithelial cells. These studies will provide us with a better understanding of oral immunity and may have applications in the treatment of oral diseases, including those caused by microbes and oral cancers. Students may be exposed to the following molecular biology techniques: DNA/RNA purification, Polymerase Chain Reaction (PCR), gel electrophoresis, mammalian cell culture, western blot, enzyme-linked immunosorbent assay (ELISA), flow cytometry, and fluorescence microscopy.
Dr. Aaron Schrey (1 student) Population Genetics, Molecular Ecology, and Ecological Epigenetics of Vertebrates Molecular markers can provide important information about ecological and evolutionary processes that shape an animal’s distribution. I use genetic and epigenetic markers to ask questions about how a species interacts with the environment and how the environment affects an individual’s phenotype. My research targets species conservation, natural resource management, invasive species biology, and basic questions about ecology and evolution. I have ongoing research projects with a range of focal species including; 1) how does increased water temperature affect bluegill sunfish, 2) why is the house sparrow such a good introduced species, 3) how does the eastern fence lizard adapt to fire ants, and 4) phylogeography and conservation genetics of several Florida scrub reptiles and amphibians (e.g. Florida scrub lizard, Six-lined racerunner, Peninsular crowned snake, southern toad, oak toad, greenhouse frog). The particular research project would focus on one research topic and would include multiple genetic techniques: DNA extraction, polymerase chain reaction (PCR), DNA sequencing, epigenetic analysis, and microsatellite genotyping.
Dr. Brent Feske, Dr. Scott Mateer (interdisciplinary project for 3-5 students) Biocatalysis: Making Drugs with Bugs - Biocatalysis is the use of microbes or their enzymes to do chemistry. A popular organism that has been used in biocatalysis is the Baker's yeast you can purchase at your local grocery store. Yeast is a single-celled organism that can live in a variety of environments because of its ability to utilize all kinds of molecules as food. This ability to "eat" all kinds of molecules is due to a diverse collection of enzymes that yeast uses to make or break chemical bonds. A family of enzymes in yeast, called reductases, are particularly important because they can produce alcohols. Recently workers at the University of Florida have placed 20 different yeast reductase genes into E. coli bacteria creating a library of bacterial clones, each over-expressing a single yeast reductase gene. We have utilized this library of clones to synthesize chiral pharmaceutical precursors such as the biologically active molecules found in drugs like Bestatin® , ProzacTM, StraterraTM, and Taxol® .
- BioOrganic Chemistry. This portion of the project will screen the previously described engineered E. coli (these E. coli are not harmful, but they kinda smell)for their ability to react with a variety of substrates. Once the screening process is complete, we will selectively choose specific reactions to scale up to verify the products structure. Upon completion of the scale up, some of these chiral compounds will be utilized to make a variety of pharmaceuticals or pharmaceutical intermediates. (Instrumentation used: Gas Chromatograph Mass Spectrometry (GCMS), Infrared Spectroscopy (IR), High Performance Liquid Chromatography (HPLC), Polarimetry, Nuclear Magnetic Resonance (NMR). Techniques Learned: Growth and storage of cell cultures, biotransformations, organic chemistry techniques, flash column chromatography, and other purification techniques.) Molecular Biology. We would like to gain insight into how the structure of the yeast reductase enzymes determine which mirror image of the alcohol (the left-handed or right-handed alcohol) is formed. Kayser, et.al., has found that the length of a region of the enzyme called Loop A (which stands for Substrate-Binding Loop A), plays an important role in determining whether the alcohol is left-handed or right-handed (we call this ability to form right-handed or left-handed molecules stereoselectivity). However, we have found that this isn't the entire story. Changing the amino acid sequence of Loop A in a reductase called YDL124w altered the enzyme's ability to form the different-handed alcohols. We plan to explore the role of amino acid composition in more detail by mutating each amino acid in Loop A one at a time, and then determine how these individual changes affect the stereoselectivity of the mutant enzymes. This systematic approach will enable us to determine the role each individual amino acid in Loop A plays in determining enzyme stereoselectivity. Students will be exposed to the following techniques: Mutagenesis, DNA cloning, DNA expression and purification, Polymerase Chain Reaction (i.e., PCR), Protein expression and purification, Restriction digests, Bacterial and eukaryotic cell culture, and Gel electrophoresis.
Sarah Burroughs, (1student) Design and Synthesis of Small Molecule Chalcone and Curcumin Analogs as Anti-Cancer and Anti-Bacterial Therapeutics New pharmaceuticals need to be developed in order to address the medical field’s growing needs in the areas of anti-cancer chemotherapies and drug-resistant bacterial treatments. Just as past scientists have successfully looked to nature for inspiration in the quest for new therapeutic agents, we plan to synthesize novel compounds, considered natural product analogs, which will function as anticancer and antibacterial agents. The two natural products we are interested in are chalcone and curcumin. Chalcones are a family of small molecules found in edible plants, many of which are used in traditional Chinese medicine and have been investigated by a variety of research groups for their wide range of biological activities, which include anticancer, antibacterial, and anti-inflammatory properties. Curcumin, the main ingredient of the Indian spice turmeric, is used in Ayurvedic (traditional Indian) medicine for its anti-inflammatory and anticancer properties. Curcumin and synthetic analogs of curcumin have been investigated by research groups worldwide as anti-cancer agents. As both curcumin and chalcone contain similar structural motifs, we plan to synthesize novel compounds, analogs of chalcone and curcumin, which will be evaluated for their potential as anticancer and antibacterial agents by our collaborators. Synthesis of these compounds will be accomplished in 1-5 steps, depending on the complexity of the target molecule. Once an initial library of compounds has been compiled, a structure-activity relationship model will be developed, which will identify key structural motifs and help to direct the project toward new, potentially more potent compounds.
Dr. Sarah Gray, Development and application of sensors to measure inorganic carbon in the coastal oceans. While we have a decent understanding of how carbon and other elements interact with the surface of open oceans, much is still unknown about these interactions in coastal and inland regions, due to the dynamic nature of these systems and the high costs associated with collecting samples in the field and sending them back to the laboratory for measurement. These regions, although small in area compared to the oceans and terrestrial biosphere, can contain very high levels of carbon dioxide (CO2). Since CO2 is a greenhouse gas, the emission and uptake of CO2 can have a large impact on global carbon budgets and future climate change. Increasing CO2 levels, and the associated drop in pH (acidification of waters), can be very detrimental to ecosystems and the organisms in them. This research examines inorganic carbon biogeochemistry at the intersection of inland and coastal waters. The objective of this project is to design and build inexpensive (hundreds of dollars) autonomous sensors that can precisely and accurately measure dissolved CO2 concentrations and fluxes into and out of riverine and coastal water bodies. Long-term, these new sensors will be used to determine CO2 fluxes in inland (marshes, streams, rivers) and coastal Atlantic Ocean waters. The coastal Atlantic is an interesting field site because it currently experiences frequent major storm events and declining fisheries that may be further impacted by future climate change. In addition to working on designing and building the new CO2 sensors, students will work with a laboratory UV-VIS as well as numerous field sensors that measure temperature, pressure, dissolved oxygen, and pH.
Gary Guillet, Trimetallic Complexes Incorporating Metallocenes to Facilitate Multielectron Reactions from First Row Transition Metals Metalloenzyme active sites commonly incorporate numerous 3d transition metal ions to facilitate substrate activation and modification. The metal ions in these active sites have, seemingly, tailored structural parameters that are necessary for proper function including the coordination geometries, donor strengths, and labile ligands in coordination sites among others. Many metalloenzymes are able to catalyze reactions under conditions that are currently impossible in the laboratory. To emulate the robust chemistry seen in metalloenzymes synthetic complexes that incorporate these design elements are needed. These could generate catalysts able to closely match the reactivity seen in metalloenzymes like reduction of dinitrogen to ammonia or methane to methanol to name a few. 1 This research project centers on synthesis of new ligand platforms able to accommodate multiple metal ions with the ion identity being highly modular to allow for extensive study of homo and heterometallic complexes. Cyclopentadienyl moieties are utilized in the ligand to form metallocene groups to harness their established reduction chemistry and to simplify analysis. A conceptual goal of the project is to facilitate multielectron reactions with substrates by extracting and depositing a single electron from multiple metal ions in concerted reaction steps.
Drs. Todd Hizer and Catherine MacGowan (2 students) Environmental Chemistry. Project 1: Investigating the Use of Hydrogels in the Removal of Metallic Ions from Polluted Water Sources. Heavy metal remediation from the environment must not only be effective but efficient. One possible approach involves the use of super absorbent materials such as polyacrylates hydrogels. Superabsorbent materials have the unique ability to absorb water by swelling to 300 times from their original mass and size; a characteristic that can be exploited. This project involves several areas of study: 1) Can the metal cation-hydrogel interaction be quantified? 2) Remediation effectiveness & efficiency: Does the metal ion’s valence state play a role in its interaction with the polymeric hydrogel to absorb water? 3) Is the interaction of the metal cation with the hydrogel reversible? 4) Do environmental factors such as pH effect the remediation process? Students will be introduced to the following instrumentation: Atomic absorption (AA), Ultra violet-Visible (UV-Vis) and X-ray fluorescent (XRF) and will learn a variety of analytical laboratory skills. The information gathered from the project’s data will be used to design a guided-inquiry chemistry laboratory module for general chemistry and eventually publication. Project 2: The goal of this project is to develop a kinetic laboratory experiment that monitors the hydrolysis of artificial sugar substitutes in food products using UV Spectrophotometry. A laboratory protocol will be designed as part of an inquiry-based chemistry laboratory module to be performed by general chemistry students to investigate the kinetics behind the metabolic hydrolysis of artificial sugars in food products.Analytical techniques and instrumentation such as the UV-Vis and/or fluorescent spectroscopy will also be used in this investigation in the research side of this project but also will play a role in the design and testing of the new laboratory modules.
Dr. Will Lynch (1 student) Nanoparticle Mediated Photochemistry in Relevant Environmental Samples. As a common source of environmental contamination, halogenated aromatic compounds have long been an area of intense study. Our studies have shown that ZnS nanoparticles (NP) are capable of catalyzing reactions under photo-reductive conditions. The ZnS particles on the order of 3.6 nm were shown to be effective agents for dehalogenating aromatic compounds. The project will examine the next phase of developing ZnS-NP into real world catalysts by studying matrix effects, catalytic efficiency and NP removal. It is important to address this issue of the impact of the environmental matrix on the catalytic behavior of these systems; i.e., will the common ions found in the environment enhance or inhibit the photochemistry? Doping of NP modifies the photochemical properties of ZnS, and hence we can use standard doping techniques to improve catalytic efficiency. Finally, the NP samples must be removed from the system, so the systems must be built such that they can easily be extracted. NP will be built with a magnetic core surrounded by the photoactive exterior or with magnetic dopants such that they may be removed mechanically with an external magnetic field.
Clifford Padgett, Oxygen-Iodine Halogen-Bonding Interactions via N-Oxyheterocycles and Organoiodine Compounds. This proposed research focuses on the use of halogen-bonding to generate crystal structures of various motifs. Halogen bonding, like hydrogen bonding, is of great importance in crystal engineering. These intermolecular bonds are strong enough to guide crystal growth and thus could be used to develop crystals containing various motifs. Halogen-bonds are a type of Lewis acid/base interaction that involves the donation of a lone-pair of electrons from a donor atom to the SIGMA* orbital of an acceptor atom (in this case a halogen atom). For effective halogen-bonding you need a highly polarizable atom and one that is not too strongly oxidizing; of the halogens, iodine and bromine are therefore the best candidates. The O-I system is a class of halogen-bonding complexes that have not been heavily explored. In order to investigate the usefulness of the O•••I halogen bond, the student would have to oxidize a nitrogen-containing heterocycle (eg. pyrazine, bipyridyl pyridine) to the N-Oxy form by using an acridine compound. Once the compounds have been synthesized, they will be complexed with iodine-containing compounds (e.g. I2, 1,4-diiodobenzene, 1,2,4,5-tetrafluoro3,4-diiodobenzene) and their crystal structures will be determined. These compounds were chosen to compare and contrast the nature of the O•••I halogen bond with that of the N•••I halogen bond, for which structures are already known. The chemistry involved in making the starting N-oxy heterocyclic compounds is sufficiently straightforward for undergraduates to do the reaction and purification. The formation of complexes should be as simple as mixing stoichiometric amounts of each material in an appropriate solvent and allowing slow evaporation to yield crystals.
Dr. Brandon Quillian (2 students) Development of Ruthenium (II) Homogenous Organometallic Catalysts for Non-Oxidative Coupling of Olefins and Arenes. Currently, my group is working on numerous projects ranging from organic synthesis to catalysis. A brief description of each project is shown below. This is a multidisciplinary study utilizing techniques and principles from organic, inorganic, organometallic chemistry and catalysis. To describe the overall project as succinctly as possible, we are making metals soluble in fairly non-polar, organic solvents to convert organic molecules into value added molecules and studying the mechanism of action. The organic scaffolding confers solubility to the metal in organic solvents, which allows characterization of the metal-organic ligand complex by common spectroscopic techniques. Because reactions occur through molecular collisions, soluble metal complexes should, in theory, react faster with organic substrates at lower temperatures; thus requiring less energy as compared to heterogeneous catalysis. In addition, the reaction of the metal-complex with organic substrates can be monitored by a number of spectroscopic techniques to determine the rate and mechanism of the reaction. Numerous analytical techniques are utilized in this study including nuclear magnetic spectroscopy, infrared spectroscopy, ultraviolent-visible spectroscopy, single X-ray crystallography, gas chromatography, mass spectrometry and cyclic voltammetry. Students who engage in his chemistry will be trained in handing air- and moisture sensitive compounds and will become familiar with a myriad different chemical disciplines. Project 1: Synthesis of Ru(II) organometallic olefin hydroarylation catalysts: From ethylbenzene styrene is produced and subsequently transformed into polystyrene, which is subsequently molded into insulating products. We are attempting to prepare ruthenium catalysts supported by organic molecules to convert benzene into alkyl benzenes by a less energy intensive and greener process. The main impetus of this project is to selectively prepare ethylbenzene at lower temperatures and good efficiency. Project 2. Screening Ru(II) organometallic alcohol dehydration catalysts: Although alcohols commonly dehydrate in the presence of strong acid, it is rare under basic conditions. A catalyst developed in my laboratory converts alcohols into their corresponding alkenes under basic conditions. These catalysts are currently being examined for applicability for other alcohols and its mechanism of action. Project 3. Coupling polymer-coated nanorods with a drug to prepare an anti-cancer therapeutic: In collaboration with Dr. Stone, my group is developing methods to selectively couple polymer-coated nanorods to an anticancer drug via a photo-labile linker. We are optimizing conditions to selectively connect the amine portion of the linker to the carboxylic acid moieties of the polymer and the alcoholportion of the linker with drug methotrexate. If this project is successful, we expect to produce a nanoroddrug conjugate system that spontaneous releases the drug under ultra violate radiation exposure. Project 4. Preparation of new organic ligands: Homogeneous catalyst design is heavily influenced by the organic support ligand. Small changes to the support ligand can equate to alternate reactivity. We are currently designing new organic ligands to support metals and examining these new ligand-metal support systems for new types of reactions and comparing reactivity of known reactions.
Dr. Mitch Weiland: (1 student) Identification of the Membrane Inserting Regions within Human Perforin. Innate immunity is a rapid and efficient surveillance system effectively detecting and eliminating intruding pathogens. In the event the innate immune system is excessively activated or dysregulated, the results can lead to attack of “self” cells. Recurrent bacterial infection, several autoimmune and neurodegenerative diseases, such as lupus or Alzheimer’s disease respectively, have been linked to such activity. Therefore, modulation of immune system components is considered a promising direction in drug discovery. However, before such drugs can be developed, the molecular details of how these innate immune proteins function needs to be elucidated. Recently the protein crystal structure of mouse perforin, a protein involved with innate immunity and a homolog of the human perforin, has been solved and was shown to contain two transmembrane helical bundles (TMH). TMHs in the bacterial protein perfringolysin-O (PFO), from Clostridium perfringens, have been well characterized and shown to insert into cell membranes, ultimately forming a pore-like structure capable of osmotic lysis. The goal of this research project is to use PFO as a scaffold protein to determine if the TMH regions within human perforin also function in membrane insertion. This will be accomplished by using recombinant DNA techniques to replace the existing PFO TMH regions with those in human perforin. Understanding the molecular details of perforin may allow pharmaceutical researchers to predict and create compounds that offer promising outcomes in the regulation of innate immunity. Students working on this project will be exposed to DNA purification, Polymerase Chain Reaction (PCR), gel electrophoresis, protein purification techniques, hemolytic assays, and western blotting
Computer Science and Information Technology
Dr. Ray Hashemi A Neural Network for Mimicking the Associative Memory Function of the Human Brain. A music note, a phrase, or a fragrant may vividly bring back a memory of special moment. Moving from a portion of data (a music note) to a past memory (memory of special moment) is known as associative memory and every one of us has experienced it. Human brain is an extraordinary vehicle for performing such a process. We propose to build an artificial neural network (ANN), based on the work of John Hopfield (Nobel Prize winner of Physics), that mimics the associative memory process of the human brain. The completion of the proposed ANN includes the following five steps: generating several simple “past memories,” designing a Hopfield neural network for absorbing the “past memories,” feeding a portion of a “past memory” to the ANN as input and observing the associative memory process, measuring the correctness of the associative memory process and identifying the smallest portion of a “past memory” that is necessary for bringing back the correct memory. The proposed project is fit for students who are interested in pursuing the field of engineering, computer science, physics, or mathematics.
Dr. Cameron Coates: (1 student) Dynamic Modulus Characterization of a Composite Internal Fixation System, Currently most long bone fractures are treated with internal plates and screws. The material properties of a healing bone are dynamic. Specifically the elastic modulus (measures of stiffness) increases as the bone heals and remains constant after complete healing. The elastic modulus of internal fixation systems remains constant during and after healing. The time dependency mismatch between bone modulus and fixation modulus, as well as the permanent compression introduced by the device, may result in osteopenia in the vicinity of the implant. Particularly if the implant is retained, this may lead to localized osteoporosis as the recipient ages. A novel composite fixation device is proposed that combines bioresorbable material and metal. In previous work incorporating Finite Element Analysis (FEA), we have estimated that the dynamic modulus of the device decreases at a rate that balances the rate of increase in the bone elastic modulus during healing. The device also relieves compression after healing, thereby eliminating any stress shielding effects during normal bone loading. This research project seeks to experimentally quantify the rate of reduction in elastic modulus, and characterize the material properties through mechanical testing. Computational models using Finite Element Analysis will also be developed in an attempt to simulate experimental methods. Testing is performed with a high capacity force transducer. Stress/strain profiles will be obtained and estimates of the elastic modulus made for various stages of bioresorption. Several samples will be soaked in solutions of varying acidity in order to mimic various resorption times prior to testing. Samples may also be tested or modeled (using FEA) to determine or predict, respectively, other material properties such as tensile strength, bending stiffness, yield strength, toughness, and resilience.
Dr. Tricia Brown (1 student) Chess problems or chess compositions have challenged game players and mathematicians for several hundred years. The n-queens problem in particular has been solved and generalized in many ways over the years and has inspired a multitude of questions. In a 2009 survey paper, Bell and Stevens ask,``given a queen already put on some square, when can n-1 other queens always be placed to give a solution, and if this is not possible, for what n is it possible?" Conjecture: For n>6 every square on an n x n chessboard gives rise to a solution of n independent queens.Historically, very few general solutions are known in the case n congruent to zero or two modulo six. We seek to find general n-queens solutions in these cases in order to prove the conjecture. This project is appropriate for a student in mathematics or computer science.
Dr. Jeffery Secrest (1 student) Particle Physics and The SNO+ Experiment. The SNO+ experiment is a 1 kilotonne scintillator detector located 2km underground in the INCO Crighton Mine outside Sudbury, Ontario, Canada. The detector contains about 9500 light sensitive detectors to pick up various signals due to different neutrino interactions. The SNO+ experiment's primary physics thrust is the search for neutrinoless double beta decay using an Nd-150 that has been dissolved in the scintillator. If this process is observed it would imply that neutrinos are their own anti-particle which would have deep ramifications in particle physics and for our understanding of how the world works. Other physics that would be probed will be the search for supernovas, solar neutrinos, geo-neutrinos, and neutrinos from local nuclear reactors. Currently my work is focused on the computer simulation/analysis package we are writing for the experiment. In particular, I am interested in the verification of different physics processes and optical properties of the code.