STEP Faculty Research
The following faculty are participating in the NSF-STEP program for Summer 2012. 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. Robert Gregerson (1 student): Genetics of Spanish Moss Spanish moss (Tilandsia usneoides) is a common epiphytic plant on the Southeastern coast. It is often found attached to trees and shrubs, but because it derives none of its nutrients from its partner plant, it can even grow on power lines, fences and other non-living entities. Without a root system, Spanish moss must derive all its nutrient from the aerial water that it contacts. I have two related projects that will explore nutrient uptake in this fascinating plant. One component builds upon prior student work that isolated and identified several genes that code for proteins responsible for assimilating inorganic nutrients from aerial water. Expression patterns for these genes will be determined to assess how the plant regulates the timing of gene activation. The second project will examine photosynthetic carbon utilization. The chloroplast genome of Spanish moss will be isolated, fragments cloned, and the DNA sequence of the organelle genome determined.
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) Using diatoms to reconstruct historical climate records in coastal Georgia Records of historical climate change are readily available in many forms, including tree rings, ice cores, rock fossils, and sedimentary layers. I study the remains of diatoms, which are a major class of algae, stored in lake and marsh sediments. These organisms live in water, and when they die, they settle to the bottom of the water body and form sequential sediment layers. Diatoms have cell walls made from silica and are very slow to compose. It is possible to extract and identify species of diatoms from thousands of years ago. Also, many species of diatoms are fastidious (i.e., “picky”) and require certain water conditions for living. The most common variables affecting diatom growth include water temperature, pH, and salt content. As the climate changes, the water conditions of the lakes and marshes also change. Along with these water condition changes, certain species may have increased growth whereas other species may have decreased growth. Therefore, it is possible to retrieve core samples of diatoms from the bottoms of lakes and marshes, identify the proportions of species, reference their environmental preferences, and make conclusions about climate patterns through time. I am particularly interested in understanding the historical climate of coastal Georgia, and the 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. If coastal Georgia experienced this climate, then changes in diatoms in lakes and marshes will show this. Additionally, I plan to collaborate with researchers at the Skidaway Institute of Oceanography 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.
Dr. Melanie Link-Pérez (1 student) Phylogenetic placement and characterization of Adiantopsis alata Prantl, a neotropical fern with a murky taxonomic history The fern species Adiantopsis alata was named and described by Karl Anton Eugen Prantl in 1883. He based his definition of the species on two plant specimens, one collected by Bernhard Luschnath in Brazil and one collected by Sir Robert Hermann Schomburgk in Guyana. Previous research in the Link-Pérez lab has confirmed that the Luschnath and Schomburgk specimens actually represent two different species, which means that the name Adiantopsis alata needs to be clarified by assigning a definitive “type” specimen to it, a process known as lectotypification. Currently, the Link-Pérez lab is describing several new species of Adiantopsis from the Guyana Shield, one of which includes the Schomburgk specimen. Therefore, our research group will be selecting the Luschnath specimen as the lectotype for A. alata.The research for the summer session will be focused on collecting molecular and morphological data to support the lectotypification of Adiantopsis alata and to discover its evolutionary relationships (phylogenetic placement) with other members of the genus. Our lab has ten specimens that we’ve identified as A. alata, which will provide ample material for our studies; since many of the collections were made in recent years, the probability is high that we will isolate quality DNA that will amplify readily. Our plans are to isolate DNA from our specimens, amplify two chloroplast genes, and sequence them. We will then incorporate A. alata into our existing phylogenetic tree and explore how the species fits into the biogeographic history and character evolution demonstrated in the genus. Other plans include employing histological techniques to collect spore and stomata data for the species, along with other morphological data obtained using stereomicroscopy. If time permits, we will extend our efforts to include the three new species that we are describing from the Guyana Shield, since we recently obtained additional material to include in our molecular and morphological studies on those taxa.
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.
Biocatalysis, Molecular Biology and Computational Chemistry
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.
Drs. Todd Hizer and Catherine MacGowan (1 student) This project has three areas of investigation 1) the interaction of superabsorbent polymeric materials with multi-valent metal cations; 2) the efficiency of metals remediation by superabsorbent materials and, 3) absorption kinetics. Analytical techniques and instrumentation such as the atomic absorption, UV-Vis, fluorescent spectroscopy and others will be used in these investigations. With the information and data gathered from this research project new guided-inquiry laboratory modules and curriculum materials will be designed. The STEP student(s) will not participate
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.
Dr. Delana Nivens (1 student) Role of DOM on the Photochemistry of Salt-Water Pollutants. We are purifying humic, fulvic and tannic acid compounds from the marshes near Savannah and examining their binding to both metals and organic compounds. In addition, we are examining the roles of these compounds in the photochemistry of pollutants in the complex saltwater marsh environment. Humic substances (HSs) are the most abundant natural nonliving organic material in aquatic environments. HSs are complex dissolved organic molecules (DOM) produced when organic matter such as proteins, fats, roots, dead organisms and excrement decompose oxidatively. DOM have been implicated as precursors to drinking water disinfection byproducts. The HSs also bind, sequester and regulate metal ions in the environment. We are studying this binding via spectroscopic techniques such as fluorescence, IR, NMR, and AA spectroscopy. Humic and fulvic acid purification is performed via a standard literature method accepted by the International Humic Substances Society. Tannic acid purification is via an acetone/water extraction procedure. We have begun examining the binding of both metal ions and organic pollutants such as the herbicides 2,4-D (2,4-Dicholorophenoxyacetic acid) and 2-Methoxy-3,6-dichlorobenzoic acid (Dicamba), the insecticide permethrin, the pollutant hexachlorobenzene and the anti-bacterial agent Triclosan with HSs and TAs. We are designing multi-component environmental models to help us examine the degradation products of the pollutants. The models systematically change the composition of a multi-component mixture to determine which, if any, of the environmental compounds have an effect on the photochemistry of the pollutant. Students will examine the photo-bleaching of purchased standards or humic, fulvic and tannic acids in the presence of a complicated chemical matrix containing, for example, metal ions typically found in saltwater.
Dr. Brandon Quillian (2 student) 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 (no student for summer 2012) 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) Cameron Coates Recommendations for Hardware Removal in Forearm Long Bone Fracture: A Numerical Approach There is not a general consensus regarding if and when hardware should be removed in many cases of fracture fixation. The orthopedic surgeon must consider the potential risk for re-fracture or neural injury, carcinogenesis, metal sensitivity, pain caused by implants and economic implications. Additionally, the type and magnitude of physical activity performed by the patient after implant removal, patient age, gender and general health also influence the decision. In many cases, the experience of the surgeon and the culture of the healthcare environment in which the surgeon was trained or currently practices seem to influence their prognosis for or against hardware removal after fracture healing. The factors involved are substantial; however the impacts of the majority of these factors are measurable. Therefore the decision does lend itself to a numerical approach.This work describes and applies an inexpensive decision analysis model specifically for the removal of hardware where the internal fixation was applied to long bone fracture in the forearm. The model is easily integrated with existing commercial hardware and is designed such that orthopedic surgeons need not be technologically exceptional in order to use it. An online survey (http://www.surveymonkey.com) will be created that addresses the influence of the aforementioned factors on their decision to recommend hardware removal or retention. Data from the survey as well as clinical data from the literature will be combined and used in a predictive algorithm with cross validation. The fully parametric proportional hazards model will be used, in which the baseline hazard function, is parameterized according to a Weibull distribution of the implant failure times.
Failure in this case encompasses physical as well as physiological complications that might necessitate medical action. Model predictions are compared to results for specific case studies in which data from a few influential factors are outside normally expected values. Additional programming and numerical modifications are made in order to process these extreme cases.
Dr. Bill Baird (1 student) Sensor Design and Construction - I plan to continue working on instrumentation to detect natural phenomena. I expect to have three seismometers with GPS systems installed at different campus locations by the end of the Spring semester, and t I will add lightning detection capabilities to each station. When complete, the stations should be able to localize sources of seismic activity (although significant seismic events are rare in Georgia, the devices are supposed to be able to detect a magnitude 7.0 quake occurring anywhere in the world. Since the three stations have access to very precise time information through the GPS, coincidence techniques will allow us to identify genuine large-scale events and to reject local disturbances (doors slamming, etc.). It is to be expected that the largest source of disturbances registered by all three seismometers will be thunderstorm activity. The lightning detection and ranging systems will be combined with a multi-microphone system I have already developed for use in locating the direction to a sound source. By leveraging the relatively long distance between stations and the precise timing, I expect to be able to illustrate concepts such as travel times for sound waves in both air and ground.
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.