FYRE Project Opportunties2021 Edition

Project opportunities for the summer of 2021 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 4536
Dr. Jeff Jeremiason Chemistry Mercury in the St. Louis River Estuary jjeremia@gustavus.edu; NHS 1141
Dr. Erik Gulbranson Geology Resurrection fern: assessing the structure and function of pre- and post-extinction terrestrial ecosystems during the Cretaceous-Paleogene mass extinction erikgulbranson@gustavus.edu; NHS 1103
 Dr. Amanda Nienow Chemistry Photochemistry of the herbicide dicamba anienow@gustavus.edu; NHS 2325
Dr. Rory McFadden Geology Deformation conditions and paleostress estimates in fault zones rmcfadde@gustavus.edu; NHS 1101 
Dr. Katie Leehy Biology Genome Engineering to Answer Big Biological Questions  kaleehy@gustavus.edu; NHS 3143
Dr. Dwight Stoll Chemistry Developing a predictive model for liquid chromatography separations dstoll@gustavus.edu; NHS 2324
Dr. Brooke Shields Biology A Model to Understand the Molecular and Cellular Causes of Neurodegeneration bshields@gustavus.edu; NHS 3535


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


Project - Mercury in the St. Louis River Estuary

Faculty Mentor - Dr. Jeff Jeremiason

Project Description

Mercury levels are elevated in game fish and other biota from the St Louis River Estuary (SLRE), a system characterized by mercury-contaminated sediments and high sulfate levels from upstream mining. Fish moving in and out of Lake Superior and seiche activity futher complicate understanding the mercury cycling and bioaccumlation up the food chain. The Gustavus Environmental Chemistry lab has been studying the St Louis River for almost a decade and continues to be involved in studies attempting to identify entry points of Hg into the food web and exploring potential remediation techniques. This project is both an environmental chemistry and analytical chemistry project. Students will be introduced to systems thinking, work in a trace-metal clean lab, and learn analytical and quantitative analysis techniques, and become familiar with instruments used to measure trace metals in the environment. Students will analyze sediment, water, larvae and soil samples. Field sampling is a possibility later in the summer.

Course Pre-requisites: CHE107, CHE108, or ENV120


Project - Resurrection fern: assessing the structure and function of pre- and post-extinction terrestrial ecosystems during the Cretaceous-Paleogene mass extinction

Faculty Mentor - Dr. Erik Gulbranson

Project Description

The end of the Cretaceous period marks one of the most high-profile and severe mass extinctions in Earth history, including the extinction of most of the non-avian dinosaurs. Following the extinction, it is hypothesized that ferns replaced many terrestrial plants that once occupied forested ecosystems, however the evidence for this hypothesis is indirect. However, other ecosystem restructuring, supported by multiple lines of evidence did occur, notably the proliferation of grasslands and the development of novel symbiosis of certain plants with N-fixing bacteria in the soil. How did terrestrial ecosystems respond to this mass extinction, in terms of their plant community structure and function? Did the mass extinction change the nature of mutualistic relationships of plants with soil bacteria and mycorrhizal fungi? Students can address these and other related questions for this project.

This project will include fieldwork in New Mexico, lands of the Navajo Nation and Pueblo peoples; and laboratory work in St. Peter, MN. The fieldwork component of this project is scheduled for approximately two weeks in the late spring/early summer (pending COVID-19 restrictions), followed by a return to Minnesota to conduct the various laboratory experiments. The field areas include areas near the Fra Cristobal Range in south-central New Mexico, and the Bisti/De-Na-Zin Wilderness in northwestern New Mexico. Students can expect to learn: 1) fundamental aspects of field methods in geology; 2) the identification and study of soils (in this case fossilized soils); 3) the identification and analysis of fossil trees; 4) the technique of dendrochronology; 5) and/or assist in the sampling for stable isotope analysis.

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


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 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 – Google it!). 

In summer of 2021, we will explore how to examine the photochemistry and reactivity of dicamba in the gas-phase. The beginning of the summer will focus on method development for the detection of dicamba in the gas-phase, including use of our new research grade GC-MS(!), and depending on the success with the method development, we will move into examining some basic photochemical reactions. This project is ideal for students wanting more experience with advanced chemical instrumentation as students will learn how to operate a gas chromatograph, solar simulator, and air sampling tools. Students will also use a variety of data analysis tools. 

Course Pre-requisites: CHE107


Project - Deformation conditions and paleostress estimates in fault zones

Faculty Mentor - Dr. Rory McFadden

Project Description

The strength of the Earth’s lithosphere 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 be used to quantify the deformation conditions rocks experience within deep crustal (>15 km depth) fault zones.

In this project, we will use data collected on a scanning electron microscope with electron backscattered diffraction (SEM-EBSD) and Matlab to determine quartz microstructure and recrystallized grain size on deformed quartzites. In conjunction with quartz flow laws, these results will be used to estimate paleostress and temperatures of deformation. Students interested in this project, will have the opportunity to either collect data on a SEM-EBSD or be a field assistant for two weeks on a research team conducting field-based geologic mapping of a fault zone in the Wind River Range (Wyoming). This project is ideal for students interested in geological processes, mineral physics, Matlab, or electron beam instrumentation.

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


Project - Genome Engineering to Answer Big Biological Questions 

Faculty Mentor - Dr. Katie Leehy

Project Description

CRISPR/Cas9 genome engineering has opened up a world of genome editing that scientists could only dream of just a decade ago. The FYRE project in the Leehy lab during the summer of 2021 will utilize this ground-breaking technology to interrogate gene function through generation of novel gene deletions. Students will have the opportunity to utilize CRISPR/Cas9 for two different projects in the model system Arabidopsis thaliana

Telomeres are repetitive DNA elements found at the ends of linear chromosomes that are protected by a suite of specific proteins. These proteins prevent telomere degradation, prevent illicit DNA repair at chromosome ends, and promote telomere elongation during cell division. Failure to accomplish any of these three tasks can result in human diseases such as premature aging, chronic fatigue syndrome, and cancer. The focus of this first research project is to understand how the telomere protein, TEN1, performs protective and maintenance roles. To elucidate this role the student will screen CRISPR/Cas9 transformed plants for a ten1 knock-out, as well as design their own CRISPR construct to target the Ten1 gene. After identification of a knock-out, the student will characterize telomeres to determine the role of TEN1 in telomere protection and maintenance. 

Climate change is already reshaping our world and having devastating effects on the production of crops all over the world. In order to feed the world’s growing population scientists and farmers need to work together to develop crops that can withstand increasingly extreme weather patterns. For the second project, students will be utilizing high throughput phenotyping to investigate the effects of stress on plants. Phenotyping will involve using Raspberry Pi miniature computers to automate imaging of plant growth over time in response to stress conditions. Images will be processed using state-of-the-art software in conjunction with the Julkowska/Nelson labs at the Boyce Thompson Institute to identify when and how plants change their growth patterns in response to stress. In addition to investigating the phenotypic effects on wild-type plants, students will use CRISPR/Cas9 to eliminate novel genes of interest to understand their function in relation to plant stress tolerance. Interested students will have the opportunity to learn basic programming in R, Python, and Linux command line. 

Course Pre-requisites: BIO101


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 - A Model to Understand the Molecular and Cellular Causes of Neurodegeneration

Faculty Mentor - Dr. Brooke Shields

Project Description

Several neurodegenerative diseases have similar molecular and cellular features. The first is the formation of protein aggregates. Additionally, the protein degradation pathways are unable to clear both the protein aggregates and perform their normal cellular functions. Further, damaged and dysfunctional mitochondria are present and the normal levels of biologically important metal ions (iron, copper, zinc, and magnesium) are imbalanced. However, it is unclear if these different features are causative or a result of neurodegeneration. For example, many of the proteins found in protein aggregates are known to bind metal ions. Yet, is the aggregation caused by the metal ion imbalance or is the metal ion imbalance a consequence of the protein aggregation? Do the protein aggregates inactivate the protein degradation pathways or is the inability to properly clear protein result in the protein aggregates. Additionally, several of these characteristics are connected with ubiquitin; the protein aggregates and dysfunctional mitochondria are coated with Ub and several metal ion transporters are mistargeted for degradation by ubiquitin. Ubiquitin (Ub) is a highly conserved, small protein that is covalently attached to target proteins. The attachment of Ub to proteins signals for their degradation. 

There are three ongoing areas of investigation in my lab: (1) the cross talk between the ubiquitin-dependent (proteasome and lysosome) and ubiquitin-independent (autophagy) protein degradation pathways, (2) the connection between protein folding stability and metal ion homeostasis, and (3) mechanisms that regulate the degradative enzymes (proteases and lipases) within lysosome.

Course Pre-requisites: BIO 101