FYRE Project Opportunties

2022 Edition

Project opportunities for the summer of 2022 are all described below on this page. The table below summarizes these opportunities. You can find videos of the projects at this link

List of Projects and Faculty Advisors

Faculty Mentor

Department/Program

Project Title

Contact Information

Dr. Jon Grinnell Biology Conservation behavior of American bison grinnell@gustavus.edu; NHS 3101
Dr. Jeff Jeremiason Chemistry Lead (Pb) Cycling In Peat Bogs Impacted by Climate Change jjeremia@gustavus.edu; NHS 1141
Dr. Erik Gulbranson Geology Bosque, Bombs, and Bogs: Reconstructing paleoclimate and paleoecology of a Late Cretaceous volcanic landscape erikgulbranson@gustavus.edu; NHS 1531
 Dr. Jeff Dahlseid Biology, Chemistry, Biochemistry & Molecular Biology How are messenger RNA molecules recognized and degraded to regulate gene expression? dahlseid@gustavus.edu; NHS 4532
Dr. Rory McFadden Geology Partial melt microstructures within deformed high-grade metamorphic rocks from 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. Yuta Kawarasaki Biology Environmental Physiology of Stress Tolerance ykawaras@gustavus.edu; NHS 2341
Dr. Julie Bartley Geology Stromatolite layers as keys to environmental evolution jbartley@gustavus.edu; NHS 1103
Dr. Tom Huber Physics Noise Reduction in Ultrasound Measurements using Deep Learning huber@gustavus.edu; Olin 209
Dr. Melissa Lynn Mathematics, Computer Science, and Statistics Integrating Jupyter Notebooks with Runestone Interactive Using Doenet mklynn@gustavus.edu; Olin 303
Dr. Janie Frandsen Biochemistry and Molecular Biology Investigating the role of mRNA structure in bacterial gene regulation jfrandsen@gustavus.edu; NHS 4533
Dr. Darsa Donelan Physics Listening to the radio sounds of space as a method to detect extrasolar moons ddonelan@gustavus.edu; Olin 204

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Project - Conservation behavior of American bison

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 two to four 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 projects (e.g. waterfowl nesting & butterfly surveys) or management duties (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 will have interests in animals and conservation, have good observation skills, be in good physical condition, and be able to tolerate 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: None

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Project - Lead (Pb) Cycling In Peat Bogs Impacted by Climate Change

Faculty Mentor - Dr. Jeff Jeremiason

Project Description

Peat bogs in the northern hemisphere store immense amounts of carbon. As the climate warms, peat bogs may start to release some of the stored carbon leading to additional warming. The SPRUCE experiment at the Marcell Experimental Forest is an ongoing field study to address this issue. Multiple enclosures were built and carbon dioxide levels and temperature are being altered. Scientists are monitoring multiple environmental responses in the enclosures, including the production and transport of dissolved organic (DOC) in the enclosures. DOC is responsible for mobilizing Pb and other metals in peat environments. This project will examine Pb in porewaters over multiple years in the peat porewaters collected from multiple enclosures. The project will attempt to identify differences in Pb mobilization amongst the various enclosures. Students will gain experience operating chemical instrumentation and learn about the complexities of peat bogs, climate change and the fate and transport of Pb.

Course Pre-requisites: CHE107, CHE108, or ENV120



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Project - Bosque, Bombs, and Bogs: Reconstructing paleoclimate and paleoecology of a Late Cretaceous volcanic landscape

Faculty Mentor - Dr. Erik Gulbranson

Project Description

This project will introduce you to the field of paleoclimatology, through designing and conducting original paleoclimate research in both the field and laboratory settings. For this project, we will work towards understanding Late Cretaceous paleoclimate change in strata preserved in Big Bend National Park, Texas. The Late Cretaceous is notable in that this time period concluded with a mass extinction that caused the extinction of the non-avian dinosaurs. The dinosaur extinction was due to a massive 10km-wide extraterrestrial impactor that struck the Earth just off the coast of the Yucatán Peninsula. Our field location was one of the closest landmasses to this impact that would have survived obliteration by the impactor. Thus, our interest is in deciphering the affect of this impact on Late Cretaceous forested ecosystems in the broader context of the long-term paleoclimate changes that were occurring prior to the impact. The paleolandscapes of this region were diverse (hence Bogs), hosted productive forests (hence Bosque) that contained plants that normally lived near the equator, and were repeatedly affected by volcanism (hence Bombs). Thus, we have myriad opportunities to reconstruct paleoclimate through the analysis of fossil soils, fossil plants, and the science of dendrochronology. For this project you will focus on one of these methods, which will work in concert with ongoing student research in this area. This project will involve fieldwork in Big Bend National Park and laboratory work over the summer to study the paleoclimate history of this region and to collaborate with other student researchers working on this project.

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


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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 regulating genes is necessary for proper cell growth and development: mis-regulation is the basis for several 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 like degradation that alter mRNA levels 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 to determine their molecular features that are recognized by the proteins that carry out NMD and EMD. We have determined that both NMD and EMD affect the expression of CTF13, a gene that encodes an essential protein of the kinetochore complex at yeast centromeres. NMD accelerates the degradation of, and so has a direct effect upon, CTF13 mRNA, and we have identified the molecular features responsible. In contrast, EMD indirectly affects CTF13 expression, most probably through degradation of an mRNA, perhaps that of a transcription factor for CTF13. One project in the lab aims to determine the features responsible for recognition of another mRNA that we have identified and shown is degraded by NMD, which interestingly also encodes a kinetochore protein. A second project involves testing candidates for EMD that were previously isolated in a genetic screen to identify any that are degraded by EMD. A third project aims to identify those mRNAs from a set encoded by telomere-related genes that are degraded by NMD and to determine the corresponding features responsible for recognition.

Through these projects, students will learn content and use methods from biochemistry, genetics, microbiology and molecular biology as well as gain practice in experimental design and data analysis. 

Course Pre-requisites: BIO 101 or CHE 107 or CHE 108

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Project - Deformation conditions and paleostress estimates in fault zones

Faculty Mentor - Dr. Rory McFadden

Project Description

Partial melting of crystalline rocks plays a significant role in plate tectonics, mountain building, and the transfer of heat and mass in the earth’s crust. High-grade metamorphic rocks that experienced partial melting are called migmatites. Partial melting of migmatites is an important component of continental differentiation and it lowers crustal strength, which may enhance the localization of deformation in fault zones. Fault zones that deform migmatites are valuable regions to investigate the relationship between partial melting and deformation in the crust. When rocks undergo partial melting and deformation, microstructures and mineral assemblages reflect the processes and pressure-temperature (P-T) conditions they experienced.

In this project, we will collect and analyze data on deformed migmatites from two fault zones. Throughout the summer, we will use a polarizing light microscope and scanning electron microscope (SEM) to determine the mineralogy and characterize the partial melt microstructures of migmatites from a fault zone in the Fosdick Mountains, West Antarctica. Toward the end of summer (~3 weeks), we will conduct field-based geology research to map deformation features and zones of partial melting in the Mount Helen Fault Zone in the Wind River Mountains, Wyoming. Through this project, students will be introduced to lab techniques for studying crystalline rocks under microscopes and field-based geologic mapping approaches in high-grade metamorphic rocks. This project is ideal for students interested in geological processes, field-based research in remote locations, and/or electron beam instrumentation.

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


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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



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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 - Environmental Physiology of Stress Tolerance

Faculty Mentor - Dr. Yuta Kawarasaki

Project Description

During the course of their life time, organisms experience drastic fluctuations and changes in their environmental conditions. When such changes occur at extreme magnitudes, homoeostatic disturbance results in stresses and damages at the cellular level, and ultimately, causes organismal death. Survival of these organisms in such changing environments is promoted at least partly by their abilities to adjust physiological states - phenotypic plasticity. Rapid cold-hardening is a type of phenotypic plasticity that has been most extensively studied in insects. With its swift induction that occurs in a time frame of minutes (!) to hours, this response is recognized as one of the fastest acclimatory responses in nature.

Through FYRE, you will work on an original research project to examine effects of rapid cold-hardening in the fruit fly, Drosophila melanogaster, while further developing skills in scientific investigation and communication. You will design and conduct experiments to investigate aspects of rapid cold-hardening ranging from its underlying mechanism to ecological relevance. The model organism, Drosophila melanogaster is a particularly tractable system for this study because you will be able to compare this response among different strains with unique genetic backgrounds, as well as their effects on the reproductive fitness

Course Pre-requisites: BIO 101 and BIO 102

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Project - Stromatolite layers as keys to environmental evolution

Faculty Mentor - Dr. Julie Bartley

Project Description

Stromatolites are layered structures built by the interaction of microbial communities with their sedimentary environments. They represent some of the earliest records of life on Earth and occur throughout geologic history. We don't yet know, however, how a particular stromatolite acquires its large-scale morphology. In this project, we will investigate the growth histories of stromatolites by examining how their layers accumulate and change shape over time. Depending on student interests, the project might seek to connect growth histories with geochemical changes or with changes in the small-scale structure within individual layers. This project might interest a student with some experience in geology, chemistry, or biology.

Course Pre-requisites: None

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Project - Noise Reduction in Ultrasound Measurements using Deep Learning

Faculty Mentor - Dr. Tom Huber

Project Description

This project is focused on developing methods to apply machine learning/artificial intelligence to reduce noise in ultrasound measurements. By eliminating random noise in these measurements, it will improve acquisition time and accuracy of the results. The focus of this research is a method 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 this project, you will learn how to implement some of the leading-edge tools for deep learning including Python within Google Colab, and the Keras and Tensorflow libraries. You will gain experience performing measurements using a $300,000 Polytec laser Doppler scanning vibrometer along with conventional ultrasound transducers. 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: PHY 205

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Project - Integrating Jupyter Notebooks with Runestone Interactive Using Doenet


Faculty Mentor - Dr. Melissa Lynn

Project Description

The goal of this project is to create a framework for publishing interactive open educational materials on machine learning and data science, leveraging existing platforms.

Runestone Interactive is platform for online textbooks where students can test out code in the browser. Jupyter Notebooks are an interactive programming platform, commonly used for machine learning and data science. A project currently under development, Doenet aims to offer a platform for sharing and connecting open educational materials. In this project, we will use the Doenet API to integrate Runestone and Jupyter notebooks. The result would allowing data from a student’s work in a Jupyter notebook to be transferred back to Runestone, so that Runestone could track the student’s progress through these notebooks. 

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Project - Investigating the role of mRNA structure in bacterial gene regulation

Faculty Mentor - Dr. Janie Frandsen

Project Description

Bacteria employ many RNA-based mechanisms to regulate gene expression in response to environmental stress. Bacterial small RNAs (sRNAs) are RNAs that change gene expression by interacting with and acting upon messenger RNAs (mRNAs), the RNAs that carry the information necessary for protein synthesis. Often, sRNAs target mRNAs for degradation or prevent translation initiation by binding to the mRNA at the ribosome binding site, both of which result in a reduction in protein synthesis. sRNAs are widely used across bacterial phyla and are involved in maintaining homeostasis, virulence, and antibiotic resistance. Understanding how sRNAs work at the molecular level to control gene expression will aid in the development of novel antibiotics that target regulatory RNAs in bacteria, helping to combat the monumental problem of antibiotic resistance. Thanks to the mRNA COVID-19 vaccines, we are at a precipice of RNA dominating pharmaceutical development!

This FYRE project will focus on investigating the role mRNA structure plays in the regulation of bacterial gene expression by sRNAs. We will work to employ a systematic, genome-wide study of sRNA binding site accessibility for all sRNAs in Escherichia coli. This means we will assess the mRNA structure at EVERY known sRNA-mRNA interaction site in a single bacterium, and hopefully identify universal trends for sRNA binding site accessibility. That’s a lot of data to investigate! You will learn how to use computational tools and gain exposure to basic coding to analyze an existing data set that contains information about the structure of every mRNA in the cell. Based on the results from your genome-wide analysis, you will develop hypotheses about how the sRNAs regulate gene expression and we will work together to design and execute a laboratory experiment to address one hypothesis.

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Project - Listening to the radio sounds of space as a method to detect extrasolar moons

Faculty Mentor - Dr. Darsa Donelan

Project Description

This project will operate as part of NASA’s Radio Jove Project has been in operation for two decades as a way to introduce radio astronomy activities to students, teachers, and the general public. During this study, we will modify a radio telescope built by a Gustavus student, make scientific observations, and interact with radio observatories in real-time. To better study radio emission from Jupiter, we will add dual-polarization spectrographs and wide-band antennas in the frequency range of 15-30 MHz. We will use our study of the interactions between Jupiter and its closest moon Io, to investigate analysis techniques that can be used to search for extrasolar moons.

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