FYRE Project Opportunties2017 Edition
Project opportunities for the summer of 2017 are all described below on this page. The table below summarizes these opportunities.
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Project - Mitigating climate change: How effective are local landscapes in storing carbon?
Project Description
Within the last year, the global atmospheric CO2 concentration surpassed 400 ppm primarily due to human activities such as burning fossil fuels. One way to mitigate increased atmospheric CO2 concentrations is to store carbon in soils of terrestrial ecosystems. Previous work has shown that plants with more extensive root systems are more effective in enhancing soil carbon stocks. This suggests that restoring prairie ecosystems, where a diverse prairie plant community can have 10-fold more root biomass than a corn field, could increase carbon storage in soils. On the Gustavus campus as well as in the surrounding area there a many ways that landscapes are managed, ranging from high maintenance turf grass of lawns and conventional agriculture, to low maintenance natural areas such as prairies. This project will address the carbon storage potential of differently managed landscapes in and around the Gustavus campus with a particular focus on the restored prairie in the Arboretum.
To infer the carbon storage potential of a landscape, we will quantify plant diversity, above and belowground biomass, soil bulk density, and the carbon component of soil fractions that are related to long-term carbon storage. The student participant will become familiar with standard biomass and soil sampling techniques, as well as an introduction to the flora of tall-grass prairies. If time allows, we might also attempt to characterize mycorrhizal communities as they are important in soil structure and carbon dynamics. The student participant will become familiar with data organization and analysis in SAS or R, and graphing in Sigmaplot.
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Project - Resistance to heavy metal poisoning: studies of an essential iron-binding protein repurposed to mitigate cadmium toxicity
Faculty Mentor - Dr. Brandy Russell
Project Description
In my research lab, we study protein folding with a particular focus on proteins that contain metal atoms and how they assemble the metal sites correctly during the folding process. Understanding how proteins fold is a key question in biology/biochemistry that could lead to improved predictions of protein structure, a better ability to engineer new proteins with novel functions, and a better understanding of many diseases that are caused or characterized by misfolded proteins. My research group uses simple metal-binding proteins and studies their folding and metal site assembly to shed light on how these processes work for more complex systems.
The system we are working on right now is a pair of proteins found in a certain marine worm called Nereis diversicolor. The first protein, called myohemerythrin, is an oxygen transport protein that contains two iron atoms; its function is analogous to that of myoglobin in mammals. The second, called metalloprotein II, binds one or more cadmium atoms, and is thought to protect N. diversicolor from the toxic effects of cadmium. Iron and cadmium have very different chemical properties, so it is surprising to see these two proteins with high amino acid sequence identity but different metal binding preferences. This summer, we will work on understanding why myohemerythrin binds iron and metalloprotein II binds cadmium, and how the different bound metals affect the folding process. We will use a number of basic chemical and biochemical lab skills including protein purification, UV-visible spectroscopy, working with air-sensitive samples, and more, depending on student interests within the project.
Course prerequisites: CHE 107 or other college chemistry course with laboratory.
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Project - Mercury dynamics in the St Louis River Estuary
Faculty Mentor - Dr. Jeff Jeremiason
Project Description
The St. Louis River estuary is an important spawning ground for the Western arm of Lake Superior, and an important recreational resource in the region. Despite the largely remote regional setting, the St. Louis River estuary and its watershed have hosted significant industrial and resource extraction and harvesting activities for over 120 years. Along with other contaminants, mercury (Hg) concentrations in fish tissue are significantly elevated above those in Lake Superior and in upstream watershed. While the source of many contaminants has been linked to sediment contamination from industrial activities in the harbor, the origins of elevated Hg in fish tissue of the estuary is much less straightforward. In this project, a FYRE student will be assisting in collecting water and sediment samples, analyzing these sample for different forms of mercury, and interpreting results. The goal of the project is to further our understanding of how mercury cycles in the estuary to help determine why mercury levels in the fish are elevated. At a minimum, students applying for this position need to have taken two college chemistry classes and have a strong interest in studying natural systems and environmental geochemistry.
Course Prerequisites: CHE 107
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Project - American bison behavior and conservation
Faculty Mentor - Dr. Jon Grinnell
Project Description
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Project - Interrogating drug molecule binding using model systems
Faculty Mentor - Dr. Anna Volkert
Project Description
Hydrogen bonding has been accepted as a major cohesive force in biological systems such as DNA, RNA, enzymes, and proteins since the early 1900’s. Through molecular modeling, hydrogen bonding interactions have been shown to lead to significant changes in the infrared spectrum such as frequency shifts, band broadening, and peak intensity changes. Recently, the frequency shifts resulting from hydrogen bonding was used to calculate the bond strength and distance between the acceptor atom (typically oxygen) and donor hydrogen. Unfortunately, molecular models are limited to simplified systems and current experimental studies are limited to non-aqueous solutions which limits the applicability to complex biological systems. The narrow, unique, and aqueous compatible Raman vibrational features exhibit local environment dependent Raman vibrational energies and peak widths which is ideal for interrogating hydrogen bonding impacts in model biological binding sites. Additionally, molecular imprinted polymers (MIPs) can serve as model biological recognition elements as they contain a crosslinking monomer and a functional monomer that interacts non-covalently through multiple hydrogen bonds with target molecules forming selective recognition sites. The objective of this research is to investigate hydrogen bonding effects on Raman vibrational shifts of small molecules to develop methodology to predict how changing the nature of the hydrogen bonding impacts the binding environment for potential drug development applications such as serotonin-norepinephrine reuptake inhibitors (SNRIs).
This summer we will be synthesizing drug-imprinted polymers using photopolymerization and interrogating the selective binding environment using vibrational spectroscopy (Infrared and Raman). This work will include optimizing the imprinting experimental parameters in addition to comparing vibrational spectra of interesting drug molecules in solution vs. in the polymer matrix. This project is an exciting opportunity to gain research experience from the ground up and has applications to the fields of engineering, chemistry, and biology.
Course Prerequisites: CHE 141
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Project - Overwintering physiology and mechanisms of cold-tolerance in insects
Faculty Mentor - Dr. Yuta Kawarasaki
Project Description
My research program in environmental physiology focuses on the adaptations of insects for winter survival. In order to better understand the basis for these adaptations, my research employs a broad range of approaches from molecular techniques to whole-organism studies.
Ongoing research projects in my lab are:
- Characterization of overwintering energetics in the larvae of the goldenrod gall fly that inhabit within the stem galls of goldenrod plants. Samples had been collected through the winter of 2015-16 and 2016-17, and stored frozen. We will employ various biochemical assays to quantify energy reserve molecules, such as glycogen and lipids, in these samples. Considering that the winter this year (2016-17) had been uncharacteristically mild for Minnesota, we aim to examine its impacts on overwintering physiology of these larvae.
- Investigation of the underlying mechanisms of rapid-cold hardening (RCH) in flesh fly. The RCH response describes the ability of insects to swiftly adjust their physiological states to changing environmental conditions. We will employ various pharmaceutical drugs to inhibit certain cellular/molecular processes that had been speculated to be involved in this protective response in insects, and examine its effects on cellular survival. Alternatively, we may study the signaling pathway for the induction of RCH by using the Western blotting technique.
- Comparison of mitochondrial functions in cold- versus warm-acclimated insects. We will determine whether physiological changes that are elicited by the process of acclimation is manifested at the sub-cellular level – in isolated mitochondria.
Students interested in this project should visit here to make a reservation for meeting.
Course Prerequisites: BIO101 and BIO102
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Project - Studying a protein-protein binding domain of malarial PfGCN5
Faculty Mentor - Dr. Scott Bur
Project Description
Chemical biology is a multi-disciplinary field of study that uses the tools of chemistry (primarily analytical and synthetic) to understand biological systems. One area of intense interest is the nature of protein-protein interactions (PPIs). One of the clearest examples of the importance of PPIs involves the assembly of transcription factors during the transcription of DNA. One approach to understanding how these systems work is to selectively disrupt specific interactions and see what happens to the system. This requires the development of small, drug-like molecules that are used as molecular probes for the system. The Bur lab is using a Fragment-based ligand design (FBLD) strategy for to develop molecular probes for protein-binding domains, specifically in a binding region of a malarial protein. While some of this work has been started, there is opportunity to help develop the microbiology used to produce the protein of interest. There will also be opportunity to develop synthetic routes to small molecules that may bind to the protein.
Course Prerequisites:
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Project - Environmental monitoring in Seven Mile Creek Watershed
Faculty Mentor - Dr. Laura Triplett
Project Description
I am seeking a first-year student to join me in conducting water quality monitoring in the Seven Mile Creek watershed near St. Peter. We are working with government agencies and local landowners to study the connections between food production, land-use, water quality and habitat quality. The context of this work is that the Minnesota River, a major tributary of the upper Mississippi River, is impaired for (polluted by) nitrate, excess sediment and other water quality parameters. Research is showing that the pollution is related to the row-crop agriculture in our area, which is also the most important industry for our regional economy. Right now, over a million dollars is being spent to install pollution control strategies to improve Seven Mile Creek. In effect, this is a large-scale experiment to determine whether voluntary best practices and technologies can reduce sediment and nutrient pollution in a typical south-central Minnesota stream.
This summer, we will continue collecting and analyzing water and soil samples. Early on, you will learn how to operate sampling equipment and collect samples from streams. You will then learn laboratory techniques to measure water chemistry and pollutants. Throughout, you will learn geology, hydrology and environmental chemistry, and may work with ecologists and aquatic biologists. Also, you may learn some basics of GIS, and will certainly work closely with our partners at Nicollet County, the University of Minnesota, the Minnesota Pollution Control Agency and others. In short, this project is for someone who: enjoys learning new science; is excited about trying both field work and laboratory work; works well with people; and, is curious about Minnesota’s natural environment and human communities. Also, the student must have a valid driver’s license and be willing to obtain college vehicle certification.
Course Prerequisites: Students must have had at least one course with a lab in geology, biology, chemistry and/or physical geography. Students who had advanced science courses in high school may also qualify.
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Project - Molecular ion trapping and reaction rate measurements
Faculty Mentor - Dr. Jessie Petricka
Project Description
This project is an effort to measure the rate of ion collisions within a molecular ion trap. Research on molecular ions is important in many different fields. Some examples include: spectroscopy for comparing to astronomical data, chemical reaction rate measurements, precision studies of quantum mechanics, and tests of the time-variation of fundamental constants like the mass of the electron.
Previous work on this project has explored the production of ions with high power lasers and development of the trapping procedure. The current project will use the trap to measure the amount of ions in the trap as a function of time when the ions are present along side some other gas (for example, nitrogen). This measurement will allow for a calculation of the collision rate, which depends on interaction forces between the ion and the gas. Students working on this project will become familiar with laser, vacuum, control electronics and data acquisition systems. Students will also be exposed to computer design, control, and simulation programs.
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Project - Photochemistry of the herbicide dicamba
Faculty Mentor - Dr. Amanda Nienow
Project Description
When pesticides (a broad category of chemical compounds including herbicides, insecticides, and fungicides) are applied to fields, they can be dispersed into the environment in a variety of ways such as volatilization, run-off into water systems, or sorption by soil or plants. In addition, the compounds can be chemically transformed through chemical reactions or photodegradation. In our lab, we explore the photochemistry of pesticides in aqueous solution and sorbed to the crop/plant surfaces to which they are applied. We are starting a new series of experiments in the summer of 2017 examining the photochemistry of dicamba, a chlorinated herbicide. The use of dicamba in corn and soybean fields has been increasing in recent years due to reformulation of commercial products. We are interested in the chemical mechanism (i.e., how the compound reacts) of how this compound degrades when exposed to UV light; this will be explored from different aspects – What happens if we remove oxygen from the solution? What happens if we add natural organic matter (NOM) as a model of river water? What happens if we change the pH of the solution? What role do adjuvants from the commercial products play in the degradation? What products are formed under this various conditions?
Students in this lab are trained in methods used in experimental chemistry including experimental design, data acquisition, data analysis, and the presentation of the results. Specifically, students learn how to use a high pressure liquid chromatograph (HPLC), a UV-Vis spectrophotometer, a fluorimeter, and mass spectrometer, and how to analyze the data from each of these systems.
Course Prerequisites: CHE 107
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Project - Characterization of a new injection valve technology for two-dimensional liquid chromatography
Faculty Mentor - Dr. Dwight Stoll
Project Description
Liquid Chromatography is a separation technique with applications in areas ranging from drug discovery and environmental analysis, to neuroscience. Despite the fact that Liquid Chromatography was invented over 40 years ago in its modern form, it remains a very vibrant and exciting area of research. One particularly active area is the development of new technology to improve the performance of two-dimensional liquid chromatography (2D-LC). In the Stoll Laboratory we specialize in the development of 2D-LC, and are especially interested in and uniquely equipped to make advances in this area.
In this project we will characterize a prototype of a new valve design that aims to improve the ability to detect low concentration compounds in a variety of sample types ranging from urine to plant extracts and pharmaceutical drug products. We will look deeply into the details of how fluids move into and out of the valve to understand the impacts of these fluid dynamics on the performance of separations of real samples. Students interested in engineering concepts and understanding how chemical instrumentation works will find this work particularly appealing.
This project is a collaboration between the Stoll Group, a major instrument manufacturer, and the research group of Professor Sarah Rutan at Virginia Commonwealth University, who specializes in analysis of chromatographic data and modelling. Students interested in modelling, simulation, and computer programming will also find opportunities to build upon those interests in the context of this work.
Course Prerequisites: CHE 107
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Project - Centromere and telomere-related genes – their regulation in baker’s yeast
Faculty Mentor - Dr. Jeff Dahlseid
Project Description
In my laboratory, we are seeking to understand at a molecular level how genes are regulated through degradation of messenger ribonucleic acid (mRNA) molecules. mRNA molecules are copies of genetic information stored in the corresponding chromosomal DNA and are used by ribosomes to direct the synthesis of proteins. Changes in mRNA abundance usually alter the amount of the corresponding protein, so processes that alter mRNA levels such as degradation are important for regulating gene expression. Fidelity in gene regulation is necessary for proper cell growth and development: mis-regulation is the basis for a number of genetic diseases and cancers in humans. Deepening our understanding of the molecular mechanisms for mRNA degradation is important for evaluating the potential causes of clinical diseases and for improving human health.
Using bakers' yeast as a model system, we study two specialized mRNA degradation pathways, nonsense-mediated mRNA decay (NMD) and exosome-mediated mRNA decay (EMD). We are interested in identifying and studying mRNAs degraded by NMD and EMD to determine the molecular features that are responsible for their recognition. We have determined that both NMD and EMD affect the expression of CTF13, a gene that encodes an essential centromere protein. NMD accelerates the degradation of, and so has a direct effect upon, CTF13 mRNA. In contrast, EMD indirectly affects CTF13 expression, most probably through degradation of an unidentified mRNA, perhaps that of a transcription factor for CTF13. Projects currently available in my lab are all related to these lines of inquiry and may involve biochemical, genetic and molecular techniques.
Course Prerequisites: One semester college laboratory science course recommended.