FYRE Project Opportunties

2020 Edition

Project opportunities for the summer of 2020 are all described below on this page. The table below summarizes these opportunities.

Faculty Mentor

Department/Program

Project Title

Contact Information

Dr. Scott Bur Chemistry Designing small molecules that interrupt the regulation of gene expression in a malarial parasite sbur@gustavus.edu; NHS 4536
Dr. Jeff Jeremiason Chemistry Exploring new mercury analytical techniques jjeremia@gustavus.edu; NHS 1532
Dr. Erik Gulbranson Geology Paleoclimate and paleoecology of ancient polar forested ecosystems, Antarctica erikgulbranson@gustavus.edu; Mattson Hall 113
 Dr. Amanda Nienow Chemistry Photochemistry of the herbicide dicamba anienow@gustavus.edu; NHS 4534
Dr. Rory McFadden Geology Deformation conditions and paleostress estimates in deformed quartzites rmcfadde@gustavus.edu; Anderson Hall 225 
Dr. Laura Burrack Biology How does genome instability lead to drug resistance? lburrack@gustavus.edu; NHS 4530
Dr. Dwight Stoll Chemistry Developing a predictive model for liquid chromatography separations dstoll@gustavus.edu; NHS 3534
Dr. Tom Huber Physics Optical measurements of ultrasound waves huber@gustavus.edu; Olin 209
Dr. Jon Grinnell Biology American bison behavior and conservation grinnell@gustavus.edu; NHS 1533
Dr. Jeff Dahlseid Biochemistry and Molecular Biology How are messenger RNA molecules recognized and degraded to regulate gene expression? dahlseid@gustavus.edu; NHS 4532
Dr. Amy Kochsiek Biology Tracking evolution of a weedy plant species in response to nitrogen deposition akochsie@gustavus.edu; NHS 4401

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Project - Designing small molecules that interrupt the regulation of gene expression in a malarial parasite

Faculty Mentor - Dr. Scott Bur

Project Description

This research project uses the tools of chemistry (primarily analytical and synthetic organic) to understand the nature of protein-protein interactions (PPIs). PPIs are responsible for regulating gene expression and are central to understanding epigenetics. A version of the protein called GCN5 found in the malaria-causing parasite Plasmodium falciparum is important for gene expression in the organism, and a specific portion of the protein called a bromodomain is responsible for an important PPI. In order to understand how this protein regulates gene expression, we would like to disrupt this bromodomain’s PPIs 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. In addition, the other protein that interacts with our bromodomain is unknown. Making the specific protein fragments that could bind to the bromodomain will help us find the specific protein that interacts. On this project, students can learn how to express, isolate, and purify proteins as well as work on synthetic routes to small molecules and peptides that bind to our protein.

Course Pre-requisites:CHE141

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Project - Exploring new mercury analytical techniques

Faculty Mentor - Dr. Jeff Jeremiason

Project Description

In the organisms and the natural environment, mercury exists in organic and inorganic forms. The primary organic form, methylmercury (MeHg) is more toxic than inorganic Hg (iHg) and also bioaccumlates in aquatic and terrestrial foodchains. Standard analytical methods require two separate procedures to determine total mercury (THg = MeHg + iHg) and MeHg. More recent research suggests that liquid chromatography (LC) could be used to separate MeHg and iHg in some environmental samples . In this research we propose to separate iHg and MeHg and then directly analyze the Hg species on an inductively coupled plasma mass spectrometer (ICP-MS). Students interested in using advanced chemical instrumentation and who have mechanical aptitude are encouraged to apply.

Course Pre-requisites: CHE107, CHE108, ENV120, or GEO111



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Project - Paleoclimate and paleoecology of ancient polar forested ecosystems, Antarctica

Faculty Mentor - Dr. Erik Gulbranson

Project Description

Antarctica is currently a continent covered in ice, but for most of the history of this remote place it was home to a diverse and unique forested ecosystem. How did these ecosystems function under the extreme polar light conditions and climate seasonality? How does climate change affect the polar environments when they are not glaciated? Students can address these and other related questions for this project. 

Students who aspire to learn more about paleoclimate and/or working with fossil plant material from Antarctica to reconstruct fossil forests are encouraged to apply to this project. This research project can include one or more components of studying fossil plants and fossil soils from these ancient polar environments. You will gain hands on experience in the use of paleoclimate proxies, unique applications of chemistry to solve geologic problems, and how tree ring records can be measured in fossil wood samples as old as 250 million years! Literature readings, and discussions of the readings will also be a part of this project in order to have students become fully vested in this style of research. Involvement in public presentations and/or publication of project results will be greatly encouraged and assisted by your faculty mentor. Dr. Erik Gulbranson will be the lead faculty mentor overseeing these research projects.

Course Pre-requisites: ENV-120 or GEO-111


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Project - Photochemistry of the herbicide dicamba

Faculty Mentor - Dr. Amanda Nienow

Project Description

When pesticides (a broad category that includes 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. In our lab, we explore the photochemistry of pesticides in aqueous solution and sorbed to the crop/plant surfaces to which they are applied (e.g., corn and soybeans). In 2017, we started to examine the reactivity of dicamba, a chlorinated herbicide. The use of dicamba has been increasing in recent years due to reformulation of commercial products to reduce volatilization. However, these new products seem to still be volatile enough to damage plants outside the application zone (leading to tense situations between farmers). Armed with a basic understanding of dicamba photochemistry in aqueous solution, in the summer of 2020, we will explore how to examine the photochemistry and reactivity of dicamba in the gas-phase while continuing to answer questions about the mechanism of reaction in solution. 

Students in this lab are trained in methods used in experimental chemistry including experimental design, data acquisition, data analysis, and the presentation of results. Specifically, students learn how to use a high-pressure liquid chromatograph (HPLC), UV-Vis spectrophotometer, a fluorimeter, and a mass spectrometer, and how to analyze the data from each of these systems. Plants (corn and soybean) will be grown in the Gustavus or high school greenhouse for use in the project.

Course Pre-requisites: CHE107

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Project - Deformation conditions and paleostress estimates in deformed quartzites

Faculty Mentor - Dr. Rory McFadden

Project Description

Quantifying the deformation conditions that rocks experience within deep crustal (>15 km depth) fault zones (e.g. shear zones) can aid in our understanding of the strength of the Earth’s lithosphere, which has implications for plate tectonic and mountain building processes. When rocks experience deformation in the deep crust, they undergo metamorphism and dynamic recrystallization, which are controlled by temperature, strain rate, and differential stress. Minerals, such as quartz, that have undergone deformation and dynamic recrystallization can provide substantial information about the character and conditions of deformation. 

In this project, we will use a scanning electron microscope with electron backscattered diffraction (SEM-EBSD) and Matlab to determine quartz microstructure and recrystallized grain size in deformed quartzites. In conjunction with quartz flow laws, these results will be used to estimate paleostress and temperatures of deformation. Some quartzite samples preserve oblique structures called shear bands, which complicate the recrystallized grain size calculation. To assess the effect of shear bands on recrystallized grain size and paleostress estimates, we will analyze samples with shear bands. This project is ideal for students interested in geological processes, mineral physics, Matlab, or electron beam instrumentation.

Course Pre-requisites: Students must have had at least one course with a lab in geology, chemistry, or physics. 


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Project - How does genome instability lead to drug resistance?

Faculty Mentor - Dr. Laura Burrack

Project Description

Treatment with drugs provides a powerful evolutionary force that rapidly selects for changes in a cell’s genome allowing for better growth of that cell and all of its progeny in a stressful environment leading to the development of drug resistance. Drug resistance is a serious problem hindering effective treatment of a variety of infectious diseases as well as cancer treatment. For example, many isolates of the newly characterized species Candida auris, are resistant to all commonly used antifungal drugs. Genomic changes associated with drug resistance can include aneuploidy, an abnormal number of chromosomes, and/or recombination between chromosomes. Interestingly, many of these processes are shared in a wide range of eukaryotes from humans to plants to fungi, but others appear to be very specific for a particular species. The FRYE project in the Burrack lab during the summer of 2020 will focus on comparing and contrasting chromosome segregation and recombination mechanisms in two different fungal species (Candida albicans and Brettanomyces bruxellensis) to better understand how drug resistance develops and how similar or different the processes are among fungi. Through this project, a student would learn a combination of microbiology, molecular biology, genetics, and cell biology techniques as well as gain practice in experimental design and data analysis methods.

Course Pre-requisites: BIO101 or CHE107 or CHE108



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Project - Developing a predictive model for liquid chromatography separations

Faculty Mentor - Dr. Dwight Stoll

Project Description

Reversed-phase columns are the most widely used type of stationary phase used for High Performance Liquid Chromatography. In this project we will use the Hydrophobic Subtraction Model (HSM) of reversed-phase selectivity to characterize new chemistries recently introduced commercially and share the data with the global chromatography community using our website www.hplccolumns.org. This database is used by scientists around the world to facilitate their selection of one or a few column from hundreds of options in design of new chromatography methods. We will also explore the possibility of using HSM to predict separations of new mixtures of compounds. Students involved in this project will learn how to operate a liquid chromatograph, prepare buffers and solutions for the instrument, prepare samples for analysis, and use a variety of data analysis tools.

Course Pre-requisites: CHE107 or 106/108
 


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Project - Optical measurements of ultrasound waves

Faculty Mentor - Dr. Tom Huber

Project Description

This project is focused on developing methods to image ultrasound waves using optical measurements with a laser interferometer instead of conventional ultrasound measurement transducers. A unique capability of this technique is full-field measurement of traveling acoustic waves, similar to what can be seen in the video at https://youtu.be/igQhJHPADZk. A biomedical application of this technique is visualization of ultrasonic fields propagating through human heel bones, which is of relevance for determining osteoporosis. In addition to performing measurements using a $300,000 Polytec PSV-400 scanning laser Doppler vibrometer, we will be constructing and testing a low-cost laser system that would enable this measurement technique to be more widely utilized. 

In this project, you will gain experience performing measurements using the Polytec vibrometer along with conventional ultrasound transducers. You will also have the opportunity to set up and calibrate a laser interferometer system using a collection of electrical and optical measurement components. To minimize noise in measurements, you will be exploring application of sweep-frequency ultrasound similar to the technique that bats evolved for ultrasonic ranging, and you will also develop deep learning algorithms for machine learning. Additionally, you will learn how to program in the MATLAB language to automate acquisition processes and analyze data sets. Finally, you will help in preparing the results of this project for possible publications or presentations.

Course Pre-requisites: PHY195


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Project - American bison behavior and conservation

Faculty Mentor - Dr. Jon Grinnell

Project Description

Although once a keystone herbivore numbering in the millions on the Great Plains, most American bison now are kept and intensively managed on small reserves. Managers are often aware of the need to conserve genetic diversity, but less often are they aware of the value of maintaining behavioral diversity as well. This project will take place on one such reserve, the 8000 acre Ordway Prairie reserve of the Nature Conservancy in South Dakota, and seeks to characterize the value of bison behavior to genetic diversity. You will work as part of a team of three to five student researchers, contributing to the overall project goals as well as undertaking your own research project. The project runs from June to mid-August for 10 weeks, and includes 6-7 weeks of intense bison behavioral observation that will require learning to identify 15 or so individual bulls from natural markings, then recording their interaction, bellowing and mating behaviors over the course of the summer breeding season. In addition, you may be asked to help out with reserve management duties as well (e.g. fence repair, weed control,maintenance activities). You will be supervised by both myself and the reserve manager at Ordway. Ordway Prairie is in the rolling prairie pothole region of South Dakota, 10 miles west of Leola (popln 300) and 45 minutes NW of Aberdeen (the nearest city). Successful applicants willhave interests in animals and conservation, have good observation skills, be in good physical condition, and be able totolerate living in an isolated setting with few companions. Skills at taking good notes, using GPS receivers, experience with ATVs, and some mechanical aptitude are pluses. Housing provided on site.

Course Pre-requisites


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Project - How are messenger RNA molecules recognized and degraded to regulate gene expression?

Faculty Mentor - Dr. Jeff Dahlseid

Project Description

Fidelity in gene regulation is necessary for proper cell growth and development: mis-regulation is the basis for a number of human genetic diseases and cancers. One way cells regulate genes is 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. Deeping our understanding of the molecular mechanisms for mRNA degradation is important for evaluating the potential causes of clinical diseases and improving human health. We use bakers' yeast as a model system to 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 in order 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. Through these projects, students would learn content and use methods from biochemistry, genetics, microbiology and molecular biology as well as gain practice in experimental design and data analysis. 

Course Prerequisites: BIO 101 or CHE 107 or CHE 108

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Project - Tracking evolution of a weedy plant species in response to nitrogen deposition

Faculty Mentor - Dr. Amy Kochsiek

Project Description

Humans add approximately twice the amount of reactive nitrogen to ecosystems as is fixed by natural sources annually. This nitrogen fertilization can support enhanced growth of nitrogen-demanding species, which can alter plant community composition by decreasing species richness. It can also impact the ways in which plants allocate resources between vegetative and reproductive structures. In a previous study, seeds were harvested from female Silene latifolia within a long-term fertilization experiment with high nitrogen (50 g/m2/year), low nitrogen (16 g/m2/year), and unfertilized control plots. We are interested in assessing if there is differential growth in the offspring of females grown under these different fertilization regimes. Are parental plants able to confer a benefit to their offspring if they have grown in enhanced nitrogen environments? We will plant seeds harvested from females from the different fertilization plots in common gardens. We will then measure germination, growth, rates of photosynthesis, and allocation to vegetative and reproductive structures for both male and female offspring, to test if these variables differ between parents from different nitrogen environments. This experiment merges anthropogenic disturbance with evolutionary ecology in an attempt to “track evolution in action” and provide insight into how humans impact species persistence.

Course Prerequisites

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