FYRE Project Opportunties

2019 Edition

Project opportunities for the summer of 2019 are all described below on this page. The table below summarizes these opportunities.

Faculty Mentor


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 303B
Dr. Jeff Jeremiason Chemistry Trace metals and Pb isotopes in an African Crater Lake jjeremia@gustavus.edu; NHS 206C
Dr. Louis Yu Mathematics and Computer Science A study of the propagation of health related habits on Twitter lyu@gustavus.edu; Olin 306
 Dr. Amanda Nienow Chemistry Photochemistry of the herbicide dicamba anienow@gustavus.edu; NHS 106A
Dr. Jeff Ford Mathematics and Computer Science Mathematical modeling of the prevalence of suicide as a defense strategy against pathogens in E. Coli bacteria jford@gustavus.edu; Olin 307
Dr. Laura Burrack Biology Why are some centromeres better at accurately segregating chromosomes than others? lburrack@gustavus.edu; NHS 221A
Dr. Chuck Niederriter Physics The Development of inexpensive multispectral imagers chuck@gustavus.edu; Olin 211
Dr. Chuck Niederriter Physics Analyzing energy consumption of College buildings chuck@gustavus.edu; Olin 211
Dr. Dwight Stoll Chemistry Developing a predictive model for liquid chromatography separations dstoll@gustavus.edu; NHS 203
Dr. Tom Huber Physics Optical measurements of ultrasound waves huber@gustavus.edu; Olin 209
Dr. Brandy Russell Chemistry Protein structure, folding, and metal binding brussell@gustavus.edu; NHS 205A
Dr. Julie Bartley Geology Environmental monitoring in Seven Mile Creek Watershed jbartley@gustavus.edu; NHS 124A
Dr. Ian Hill Chemistry Design and synthesis of covalent organic framework monomers ihill@gustavus.edu; NHS 109
Dr. Jessie Petricka Physics Design and analysis of wireless power transfer models jpetrick@gustavus.edu; Olin 213
Dr. Amy Kochsiek Biology The effects of Bokashi compost tea on crop germination, growth, and resilience to drought conditions akochsie@gustavus.edu; NHS 329
Dr. Darsa Donelan Physics Atmospheric gravity waves in the atmosphere of Mars ddonelan@gustavus.edu; Olin 204
Dr. Jeff Dahlseid Biochemistry and Molecular Biology How are mRNA molecules recognized and degraded to regulate gene expression? dahlseid@gustavus.edu; NHS 221C


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 understanding 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. On this project, students can learn how to express, isolate, and purify proteins as well as work on synthetic routes to small molecules that bind to the protein.

Course Pre-requisites:CHE141


Project - Trace metals and Pb isotopes in an African Crater Lake

Faculty Mentor - Dr. Jeff Jeremiason

Project Description

A sediment core representing 250,000 years of sediment accumulation has been collected to reconstruct past climates. The core is an ideal sedimentary record as the sediments of Lake Challa accumulate with little mixing due to the morphometry and geological history of the lake. The dated core consists of almost 500 samples that Gustavus students will analyze for Pb isotopes, trace metals, and total Hg. Gustavus is also cooperating with other laboratories that are examining Hg isotopes in the sediment samples. This project is ideal for students interested in climate change and the use of geochemical techniques to reconstruct past climates. Students will process sediment samples and gain experience using an inductively couple plasma mass spectrometer (ICP-MS) and a mercury analyzer. Literature reviews, detailed geochemical calculations, and quantitative analysis will also be major parts of this FYRE project.

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


Project - A Study of the Propagation of Health Related Habits on Twitter

Faculty Mentor - Dr. Louis Yu

Project Description

Social media platforms has revolutionized the way people interact around the globe, and Twitter is one of the most popular among them. A micro blogging service, Twitter serves as both a social interaction platform and a news source. Several features on Twitter could be used to help depict the interests and behavior of a user. These include the user's biography, the social ties maintained, and the content of his/her tweets. The task of classifying tweets is problem in text classification. The classification of large text data sets is in-feasible manually. Accordingly, researchers had been using machine learning techniques to classify large sets of data. Our project consists of two tasks. First, we utilize the text classification capabilities of various machine-learning algorithms to find the most effective ways to classify tweets as pertaining to physical activities. Once we find a suitable machine learning technique, we want to look into an application. We apply our classified data to the task of quantifying individuals’ affection for exercising and test if there are any correlations between habits of friends in an online social network. We aim to investigate if individuals’ health related habits (such as those pertaining to diet and exercising) may effect their friends’ health related habits over time.

Yu Project

Course Pre-requisites: MCS-177 or enrollment in 178


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 and on surfaces of crops collected in 2017 and 2018, in the summer of 2019, 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 on plant surfaces.

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 greenhouse for use in the project, and the calibration and use of a new gas-phase reactor will be conducted.

Course Pre-requisites: CHE107 or CHE108


Project - Mathematical modeling of the prevalence of suicide as a defense strategy against pathogens in E. Coli bacteria

Faculty Mentor - Dr. Jeff Ford

Project Description

This project will involve building mathematical models of different processes by which we can study how diseases transmit through a colony of bacteria. Some E. Coli bacteria have evolved the ability to commit suicide when infected, which prevents pathogens from spreading to the rest of the colony. We are interested in determining how frequently the suicidal behavior must occur in order for it to be protective of the colony. For example, if a virus is introduced to a colony, but only one of the bacteria has the option to commit suicide after infection, the trait is generally not protective. We also know that not all E. Coli exhibit this behavior. The number of bacteria that are suicide-capable, such that the probability of the colony surviving infection is more than 50% is our main question. We will study this using differential equations and graph theory.

Course Pre-requisites: Pre-requisite knowledge of these fields is not necessary, but some background in calculus or discrete mathematics is necessary. Experience programming is also helpful, but not required.


Project - Why are some centromeres better at accurately segregating chromosomes than others?

Faculty Mentor - Dr. Laura Burrack

Project Description

During cell division, cells must accurately segregate replicated chromosomes into daughter cells in order to maintain the stability of their genomes. Many cancers have unstable genomes and exhibit aneuploidy, an abnormal number of chromosomes, due to errors in chromosome segregation processes. Chromosome segregation requires the attachment of a large complex of proteins called the kinetochore to a region of the chromosome called the centromere. The kinetochore connects the chromosomal DNA to the spindle microtubules that provide the forces needed for chromosome segregation during mitosis. Approximately 3% of cancer cells are estimated to have chromosomal alterations where the centromere location has changed. These new centromere locations are called neocentromeres. We have developed the yeast Candida albicans as a model organism to explore neocentromere formation and function. The FYRE project in the Burrack lab during the summer of 2019 would contribute to our work determining why some neocentromere positions exhibit higher chromosome loss rates than other locations. In particular, the project would focus on the role of transcription in centromere regions as a factor that affects chromosome segregation accuracy. Through this project, a student would learn a combination of molecular biology, microbiology, 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


Project - The Development of Inexpensive Multispectral Imagers

Faculty Mentor - Dr. Chuck Niederriter

Project Description

Multispectral imaging camera sensors on agricultural drones allow the farmer to manage crops, soil, fertilizing and irrigation more effectively. There are huge benefits both to the farmer and to the wider environment by minimizing the use of sprays, fertilizers, wastage of water and at the same time increasing the yield from crops. Multispectral camera remote sensing imaging technology use Green, Red, Red-Edge and Near Infrared wavebands to capture both visible and invisible images of crops and vegetation.

Commercially available multispectral cameras typically cost between $5,000 and $10,000 pricing them out of the range of many farmers. The goal of this project is to develop hardware and software that will produce similar or better data at much lower cost. We have done some work in the past involving inexpensive point and shoot still cameras with the infrared blocking filters removed. Similarly we have produced specialized imagers by removing the filters from integrated circuit video cameras, such as alpha particle detectors from Raspberry Pi cameras. 

We will test a variety of standalone cameras and cameras that interface to mini computers like Arduino and Raspberry Pi. Based on the spectral reflectivity of healthy and unhealthy crops and foliage, filters will be chosen to isolate important portions of the visible and near infrared portion of the spectrum. The images from a system of cameras will be combined in software to produce composite images and vegetation indices such as NDVI and NDRE which can be used to provide farmers terrific insights into the health of the soil and plants. Ultimately the best system of imagers will be packaged so that they can be flown on one of our drones and compared to commercial multispectral cameras.

Course Pre-requisites:


Project - Analyzing Energy Consumption of College Buildings

Faculty Mentor - Dr. Chuck Niederriter

Project Description

Each year Gustavus spends about 3 million dollars on energy, a figure that could climb as we renovate old building and construct new ones. But we may be able to keep energy costs under control while at the same time reducing the College’s carbon footprint simply by using less to accomplish the same tasks. Energy conservation is one of the four prongs of Gustavus’ energy plan, and in many peoples’ minds the first one that needs to be considered. We could install wind turbines, solar panels, and biomass generators to help produce the energy we use, but it makes a great deal of sense to control the consumption first so that we can size those items appropriately. 

Apart from Beck Hall, every building on campus was built at a time when there was very little concern for the amount of energy needed to run them. In order to obtain the LEED certification for that building, modern energy conservation techniques were employed in its construction. When Old Main was renovated, energy usage was a major consideration. But most other buildings on campus use substantially more than they need to or should. Determining how much more and devising ways to reduce energy consumption is the focus of this project.

For many years the College has monitored the amount of electricity used by every building on campus and made the data available on its web site. Because of this and several energy initiatives, like the energy wars competition, building occupants have made some changes resulting in decreases in consumption. But these gains have been modest while even a quick look at the data shows a lot more potential. For example, Olin Hall of Science consumes a nearly constant 80 kW of electricity 24 hours a day, seven days a week with only occasional short decreases to 40 kW and increases to 120 kW. Even in the middle of the night when most of the equipment used by students and faculty is off, the power requirement is the same. If we could make a dent in that “base” load, we could make a large difference in the annual electricity bill for Olin, as well as the size of its carbon footprint. In most cases, there is a direct link between the amount of electricity need to run a building and its heating and cooling needs, so reduction in electricity may lead to reduction in heating fueled by natural gas.

In order to study the details of how the electricity is used in building on campus, monitors will be installed on individual circuits inside the buildings allowing us to record their power requirements as a function of time. We should be able, for example, to determine how much power (and energy) is needed to run the elevator, or that which is associated to equipment plugged into outlets or hallway lighting. Recognizing where the energy is going will make it possible for us to design ways to reduce the consumption, save the College money, and help save the environment. 

The monitors will be installed by College electricians, but we will decide which circuits to monitor and for how long using building blueprints and other data. Data analysis will be done primarily in Excel and will involve straightforward mathematics. Initial modeling will also be done in Excel but may become more sophisticated as the project proceeds. Results will be in the form of recommendations to College officials on changes to each of the buildings studied. Since it is unlikely that all campus building will be studied during the summer, developing protocols for continuing studies in other buildings will also be an important outcome.

Other areas of energy consumption on campus will also be studied. Examples include possible energy savings from transitioning from a central heating facility to local natural gas furnaces and water heaters in campus building, savings from upgrading all lighting to LED, savings from turning off the Chapel lighting for part of the night, and potential savings from controlling the street lighting with light sensors instead of a timers. Some behavioral changes like more careful control of lighting and thermostats will also be studied with the goal of informing College administration of potential savings.

Course Pre-requisites


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


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. 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


Project - Protein structure, folding, and metal binding

Faculty Mentor - Dr. Brandy Russell

Project Description

In my research lab, we are studying a peculiar pair of proteins from the same organism: one binds Fe and functions to deliver O2 to muscle tissues, while the other binds Cd and seems to function to protect from Cd toxicity. The strange thing is that these proteins have very similar amino acid sequences (81% identical). We originally set out to identify structural differences between the proteins that could explain their different behaviors. However, every experiment we have done has only demonstrated an unexpected level of similarity in the two proteins’ metal binding properties. Student collaborators on this project will learn and use a variety of biochemistry and chemistry techniques such as protein purification, gel electrophoresis, protein folding experiments, spectroscopy, and oxygen-free sample preparation.

Course Pre-requisites: CHE107 or other college chemistry course with laboratory


Project - Environmental monitoring in Seven Mile Creek Watershed

Faculty Mentor - Dr. Julie Bartley

Project Description

I am seeking a first-year student to join our research team in conducting water quality monitoring in the Seven Mile Creek watershed near St. Peter. We are working with government agencies and locatl landowners to understand 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 polluted by nitrate, excess sediment, and other water quality parameters. Research has shown that pollution is related to the agriculture of our area, which is also the most important industry for our regional economy. Right now, more than a million dollars is being spent to install pollution control strategies for Seven Mile Creek. In effect, this is a large-scale experiment to probe the effects of voluntary implementation of technology and best-practices. Our project involves assessing these effects and communicating our results to governmental agencies and local landowners.

This summer, we will continue collecting and analyzing water and soil samples. As part of the research team, you will learn how to operate sampling equipment and begin collecting samples from streams. You will then learn laboratory techniques to measure water chemistry and pollutants. Through the project, you will learn about geology, hydrology, and environmental chemistry, and you may work with ecologists and aquatic biologists. Also, you may learn some of the 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 field, laboratory, and computer work; works well with people; and is curious about the interactions between our natural environment and human communities. Also, you 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, physics, or physical geography. Students who had advanced science courses in high school may also qualify.


Project - Design and synthesis of covalent organic framework monomers

Faculty Mentor - Dr. Ian Hill

Project Description

Porous materials play an important role in the catalytic synthesis and purification of commodity chemicals on an industrial scale. The size, shape, and chemical functionality of these pores in a material dictate its application, and the ability to control these properties could allow for the directed "on-demand" design of materials in tackling specified industrial challenges. Covalent organic frameworks (COFs) are crystalline, porous polymers that have near limitless tunability in pore size, shape, and functionality based on a variety of different monomer geometries and linking chemistries. One of the biggest challenges in the development of "on-demand" COFs actually relates to understanding and navigating the vast chemical space available and the expected results when choosing a synthetic system.

This project will focus on the synthesis of COF monomeric building blocks based on predictive computational results provided by collaborators at Lehigh University. Students will make the first steps in establishing a synthetic strategy for different linking chemistries and will carry out these strategies in lab. Synthesized monomers will be characterized using infrared spectroscopy, NMR spectroscopy, and mass spectrometry. Students on this project will be trained in the essentials of conducting a literature review; designing, executing, and characterizing organic syntheses; and building conclusions from analyzed data taken in aggregate. Students will also engage in interdisciplinary interactions with collaborators at Lehigh University.

Framework Structure

Course PrerequisitesEnrollment in CHE141


Project - Design and Analysis of Wireless Power Transfer Models

Faculty Mentor - Dr. Jessie Petricka

Project Description

The last major hurdle to an entirely wireless world is to be able to efficiently transfer reasonable amounts of power. One way this can be done is with strongly coupled magnetic resonance. In this project, the use of coupled, resonant circuits will be examined in both a computational and experimental way to determine their efficiency and effectiveness. Students will learn and use software programs to design and analyze models, and will construct those models to test their effectiveness. Successful applicants will have a solid mathematical background, and will have a strong interest in learning new computational tools.

Petricka Project

Course PrerequisitesPHY205 or MCS222


Project - The effects of Bokashi compost tea on crop germination, growth, and resilience to drought conditions

Faculty Mentor - Dr. Amy Kochsiek

Project Description

Farms that are certified as organic are required to use non-synthetic methods, such as compost, to enhance soil fertility and crop performance. “Bokashi” is a system that uses a suite of anaerobic micro-organisms to ferment organic matter and produce compost. We will extract the liquid portion of the compost (compost tea), use it as a nutrient amendment to soil, and measure its effects on crop germination, growth, and crop resilience during a period of water stress. Students will gain skills in quantifying plant growth, soil nutrient dynamics, managing data, and data analysis. We will be working closely with local organic producers to determine the crop types and to disseminate our findings.

Course Prerequisites: ENV/GEO 120 or BIO 101


Project - Atmospheric gravity waves in the atmosphere of Mars

Faculty Mentor - Dr. Darsa Donelan

Project Description

Atmospheric gravity waves are an important atmospheric phenomenon that transport energy and momentum from a source region to the location of wave dissipation. The absorption of the wave’s energy and momentum are understood to significantly affect the thermal and dynamical structures of the upper atmosphere. Atmospheric gravity waves have been studied extensively on Earth but due to observational limitations, the study of these waves in the atmospheres of other planets has been minimal. This project is an effort to study atmospheric gravity waves in the atmosphere of Mars.

Our current knowledge of the structure of gravity waves on Mars comes from radio occultations (e.g. Mars Global Surveyor), spacecraft observations (e.g. MAVEN), and in situ measurements from landers (e.g. Curiosity and Opportunity). This project will use wavelet analysis to investigate discrete wave structure in the atmosphere of Mars from Insight descent data. Atmospheric profiles at specific vertical wavelength will be reconstructed from this analysis. The amplitude and phase of these reconstructed waves will be compared to descent data from the Curiosity mission.

This summer, you will learn how to obtain data through the NASA Planetary Atmosphere Data Node. You will then learn how to interpolate the data to prep it for analysis. You will also learn how to take existing Python code and tailor it to our needs, in order to run a computational analysis. You will then learn how to interpret your analysis. Lastly, you will gain knowledge in the field of planetary science.

Course Prerequisites


Project - How are mRNA 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 a combination of biochemistry, genetics, microbiology and molecular biology as well as gain practice in experimental design and data analysis methods.

Course Prerequisites: BIO101 or CHE107 or CHE108