SEAR Project Opportunties2025 Edition

SEAR Project opportunities for the summer of 2025 are all described below on this page. The table below summarizes these opportunities. You can find videos of the projects at this link. You can find the SEAR application here. The recording of the information session from January 22, 2025 can be found here

List of Projects and Faculty Advisors

Faculty Mentor

Department/Program

Project Title

Contact Information

Dr. Guarionex Salivia Mathematics, Computer Science, Statistics Creating a User Interface to Aid People with Visual Disabilities gsalivia@gustavus.edu; Olin 315
Dr. Dongji Feng Mathematics, Computer Science, Statistics Empowering Elementary Educators: AI-Driven Course Design with Large Language Models dfeng@gustavus.edu; Olin 303
Dr. Katie Leehy Biology Investgating novel mutations in telomere associated protein Ten1 kaleehy@gustavus.edu; NHS 3143
Dr. Dwight Stoll Chemistry Project 1: New tricks for an old dog – bringing big data to liquid chromatography dstoll@gustavus.edu; NHS 2324
Dr. Dwight Stoll Chemistry Project 2: Characterization of Green(er) Alternatives for Solvents used in Chemical Analysis dstoll@gustavus.edu NHS 2324
Dr. Julie Bartley Environment, Geology, and Earth Science Morphology-environment relationships in stromatolites jbartley@gustavus.edu; NHS 1103
Dr. Jeff Jeremiason Chemistry Project 1 - Conversion of an early hybrid car to a plug-in hybrid jjeremia@gustavus.edu; NHS 1141
Dr. Jeff Jeremiason Chemistry Project 2 - Ombrotrophic Bogs, Climate Change, and Metal Transport jjeremia@gustavus.edu; NHS 1141
Dr. Janie Frandsen Biology, Chemistry, Biochemistry & Molecular Biology How do bacteria use intricate regulatory networks to respond to environmental changes? jfrandsen@gustavus.edu; NHS 4533
Dr. Laura Burrack Biology How do fungal pathogens evolve resistance to antifungal drugs? lburrack@gustavus.edu; NHS 3144
Dr. Naomi Rushing Biology Investigating the Effects of Climate Change on Plant-Flowering Timing and Fitness rushingn@gustavus.edu; Nobel 2143
Dr. Amanda Nienow Chemistry Investigating the Photosensitization of the Degradation of Tembotrione and Mesotrione Herbicides with Natural Organic Matter anienow@gustavus.edu; Nobel 2326
Dr. Erik Gulbranson Environment, Geology, and Earth Science Environmental Impact of human conflict: the Thirty Year's War erikgulbranson@gustavus.edu; Nobel 1531

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Project - Creating a User Interface to Aid People with Visual Disabilities

Faculty Mentor - Dr. Guarionex Salivia

Project Description

Completing forms is often a challenging task for individuals with visual impairments (Feiz et al., 2019). Many forms, whether in paper format or as scanned electronic documents, lack the structural information necessary for assistive technologies to interpret and make them accessible. While prior research (Feiz et al., 2019; Billah et al., 2018) has developed solutions to help individuals locate specific fields on paper forms, these approaches are not helpful for users who are unable to write legibly on paper or interact with electronic forms.

This project aims to create a user interface (UI) designed specifically for individuals who are blind, have physical disabilities, or face other barriers to completing forms. The proposed UI will support multimodal interactions, incorporating features such as voice commands and tactile feedback to enable users to complete both paper and electronic forms. It will include prompts to guide users through the process and mechanisms for receiving their input, addressing the limitations of existing systems and ensuring accessibility for a wider range of users.

Referenes: Billah, S. M., Ashok, V., & Ramakrishnan, I. V. (2018). Write-it-yourself with the aid of smartwatches: A Wizard-of-Oz experiment with blind people. 23rd International Conference on Intelligent User Interfaces, 427–431. Tokyo, Japan. https://doi.org/10.1145/3172944.3173005; Feiz, S., Billah, S. M., Ashok, V., Shilkrot, R., & Ramakrishnan, I. V. (2019). Towards enabling blind people to independently write on printed forms. Proceedings of the 2019 CHI Conference on Human Factors in Computing Systems, 1–12. Glasgow, Scotland, UK. https://doi.org/10.1145/3290605.3300530 

Course Pre-requisites: MCS 177 and MCS 178; Strongly Suggested: MCS 189

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Project - Empowering Elementary Educators: AI-Driven Course Design with Large Language Models

Faculty Mentor - Dr. Dongji Feng

Project Description

We propose to leverage large language models (LLMs) and advanced prompt techniques to create an intuitive pipeline that supports elementary school teachers in designing their semester courses. By utilizing LLMs, we can generate personalized, curriculum-aligned course outlines, lesson plans, and activities based on subject areas, student needs, and educational standards. The prompt techniques will allow teachers to input specific requirements, such as student learning goals or class dynamics, ensuring that the generated materials are tailored to their unique teaching context. This AI-driven system can significantly reduce the time teachers spend on course planning, provide them with innovative ideas, and offer real-time feedback, ultimately enhancing the learning experience for students and empowering teachers to focus on creative and effective instruction.

Course Pre-requisites: MCS 177 and MCS 178; Strongly Suggested: MCS 189



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Project - Investgating novel mutations in telomere associated protein Ten1

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 projects in the Leehy lab during the summer of 2024 will utilize this ground-breaking technology to interrogate gene function through the identification and characterization of novel mutations in genes. Students will have the opportunity to work on two different projects in the model system Arabidopsis thaliana. Students will learn techniques in molecular biology, bioinformatics, cell biology, and microbiology.

Failure to precisely regulate telomeres can result in human diseases such as premature aging, chronic fatigue syndrome, and cancer. 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. This first research project focuses on understanding how the telomere protein, TEN1, performs protective and maintenance roles. To elucidate this role, the student will characterize a novel ten1 mutant recently created in the Leehy lab. The student will characterize telomeres in mutant plants 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 screen previously transformed plants to identify CRSPR/Cas9 gene edited plants. We will be utilizing high-throughput phenotyping to investigate the effects of stress on mutant plants identified in screens. Students will also get to create their own CRISPR/Cas9 targets to eliminate novel genes of interest to understand their function in relation to plant stress tolerance.

Students can pick which of the projects they would like to work on or elect to work on both. Interested students have the opportunity to learn basic programming with R and command line for development of the high throughput phenotyping data collection and analysis.

Course Pre-requisites: BIO 110/111

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Project - New tricks for an old dog – bringing big data to liquid chromatography

Faculty Mentor - Dr. Dwight Stoll

Project Description

Students participating in this project will join the wikiChrom team in the Stoll Laboratory. The primary aim of the “wikiChrom Project” (https://wikichrom.multidlc.org/) is to dramatically increase the rate of acquisition of retention data for the field of liquid chromatography, to ultimately deepen fundamental understanding about how liquid chromatography works, and accelerate method development in fields ranging from the life sciences to environmental science. Historically, a “large” dataset in the field of LC has been a hundred measurements. We are aiming to increase the size of these datasets by 100- to 1,000-fold, and are enthusiastic about the level of understanding and the pace of innovation that could be unlocked by this change. Students can contribute to this effort in many different ways, ranging from programming (i.e., coding) to improve our current data acquisition workflows and develop new ones, development of new instrumentation components and methodology to improve throughput and measurement precision, and data analysis exploration to build and apply new retention models in fields including pharmaceutical analysis and the chemical industry.

Course Pre-requisites: CHE 105/106 or CHE 110/111
 

Project - Characterization of Green(er) Alternatives for Solvents used in Chemical Analysis

Faculty Mentor - Dr. Dwight Stoll

Major shifts are underway in a several industries to improve upon the sustainability of industrial processes, with ultimate goals of net zero emissions by 2050, and a circular economy. Currently, many analytical methods used in the pharmaceutical and chemical industries are far from green, and involve highly toxic solvents with high environmental and energy costs (e.g. chlorinated solvents). Several research groups have begun working with alkyl carbonates (e.g., dimethyl carbonate, and propylene carbonate) as potential replacements for solvents such as acetonitrile. In this project we will characterize the performance of these carbonate solvents for use in applications including liquid chromatography, and as extraction solvents for studying the composition of polymers, for example. Students contributing to this work can expect to learn liquid chromatography and other analytical methods that will be used to characterize the performance of potential green(er) solvents.

Course Pre-requisites: CHE 105/106 or CHE 110/111


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Project - Morphology-environment relationships in stromatolites

Faculty Mentor - Dr. Julie Bartley

Project Description

This summer, students in my lab will be working on the following project: Stromatolites and Microbialites are fossil structures built by the interaction of microbes and mineral precipitation. The physical environment (e.g., water depth, water movement), chemical environment (e.g., salinity, oxygen levels), and the biologic processes (e.g., microbial
community) all influence the form of stromatolites and microbialites, though the relationships between processes and form are not well understood. Students working in my lab summer will continue work started last summer in investigating the relationship between stromatolite form and environment in a ~475-million-year-old geologic unit exposed in eastern Minnesota and Wisconsin. The project will involve a few days of fieldwork, followed by laboratory work that might include microscopy, electron microscopy, and geochemistry, depending on student interests.

Course Pre-requisites: Any introductory science course 

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Project - Conversion of an early hybrid car to a plug-in hybrid (Jeremiason #1)

Faculty Mentor - Dr. Jeff Jeremiason

Project Description

The Generation One Honda Insight was the first gas/electric hybrid vehicle sold in the United States. Battery technology has advanced dramatically since the first Insights were sold in 1999. It is now possible to replace the original nickel metal hydride batteries with more energy-dense lithium-ion batteries, allowing the car to operate on 100% electricity for over fifty miles. In this project, a student will explore the advancement of battery chemistries, install lithium-ion batteries and a battery control module (BCM) into an Insight, and program the BCM to run synchronously and independently from the gas engine. An independent throttle and battery regeneration joystick will also be installed to allow hand operation of the electric motor. This project is ideal for a student interested in electrical engineering, computer programming, and electrochemistry. An interest in cars and understanding their electrical components is also desirable.

Course Pre-requisites: None

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Project - Ombrotrophic Bogs, Climate Change, and Metal Transport (Jeremiason #2)

Ombrotrophic bogs are unique ecosystems that only receive nutrients from the atmosphere. They also store large amounts of carbon. Approximately 30% of soil carbon in the world is contained in peatlands, which include ombrotrophic bogs. Peatland ecosystems have been studied at the Marcell Experimental Forest (MEF), north of Grand Rapids, MN, since the 1960s. This project involves two ongoing projects at the MEF. The first one is a recent climate change experiment called SPRUCE (Spruce and Peatland Responses Under Changing Environments). In this experiment, large enclosures in a peatland at MEF were constructed where temperature and carbon dioxide levels are controlled. The primary objective is understanding if peatlands will begin giving up their large carbon stores and contribute to climate change. As part of this experiment, carbon flows within the peatland are being measured, and this project will measure Pb and other metals in the porewaters of the SPRUCE enclosures. The second project examines carbon flows from another peatland at the MEF. The Gustavus Environmental Chemistry laboratory has measured Pb and Hg flows from this peatland since 2009. One goal is to understand how carbon flows from the peatland are impacted by rising temperatures and relate these changes to the transport of metals from the peatland.

Course Pre-requisites: None

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Project - How do fungal pathogens evolve resistance to antifungal drugs?


Faculty Mentor - Dr. Laura Burrack

Project Description

Fungal infections are a serious global health concern with invasive fungal infections killing at least 1.5 million people per year worldwide. One of the contributing factors to high mortality rates for fungal infections is antifungal drug resistance. For example, many isolates of the newly characterized species Candida auris, are resistant to all commonly used antifungal drugs and have mortality rates >50%. 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. Genomic changes associated with drug resistance and tolerance can include point mutations, aneuploidy, an abnormal number of chromosomes, and/or recombination between chromosomes as well as duplication of the entire genome (ex. tetraploidy). The FRYE or SEAR project in the Burrack lab during the summer of 2025 will focus on determining how additional chromosomes (aneuploidy and tetraploidy) contribute to the evolution of drug resistance and tolerance in Candida albicans, the most common invasive fungal pathogen in the United States. Through this project, a student would learn a combination of microbiology, molecular biology, genetics, and bioinformatics techniques as well as gain practice in experimental design and data analysis methods.

Course Pre-requisites: BIO110/111 or CHE107/108 or CHE110/111


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Project - How do bacteria use intricate regulatory networks to respond to environmental changes?

Faculty Mentor - Dr. Janie Frandsen

Project Description

Bacteria must be able to respond to changes in their environment to survive stress and cause infections. To do this, they employ intricate networks to regulate gene expression, the process by which cells control if, when, and to what extent different cellular factors are produced. In bacteria, many of these regulatory networks utilize RNA in non- traditional ways. Small RNAs (sRNAs) are a class of regulatory RNAs that change gene expression by directly interacting with and acting upon messenger RNAs (mRNAs). Often, sRNAs target mRNAs for degradation or to prevent protein synthesis. sRNAs are widely used across bacterial species and are involved in maintaining homeostasis, virulence, and antibiotic resistance. We understand a lot about the processes sRNAs control but less about the molecular-level details of how sRNAs recognize and act on specific mRNAs. Increasing our understanding of 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 combat the monumental problem of
antibiotic resistance.

sRNAs are produced in response to a specific stimulus and regulate multiple different mRNA targets to mediate a major shift in gene expression. A regulatory hierarchy, a clear order in which the different targets are affected as the sRNA level increases, has been demonstrated for one sRNA and is expected to be true for other sRNAs. An open question in the field is how target prioritization is established; in other words, which features of the sRNA-mRNA interaction dictate which targets are bound first and which targets are only bound when sRNA levels peak? In this project, students will use either a pull-down asssy or a dual plasmid reporter assay to address the hypothesis that the accessibility of the sRNA binding site within the target mRNA plays a role in establishing a hierarchy of sRNA-target binding. Through this project, students will learn a combination of biochemistry, genetics, microbiology, and molecular biology techniques as well as gain practice in experimental design and data analysis.

Course Pre-requisites: BIO 110/111 or CHE 105/106 or CHE 110/111


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Project - Investigating the Photosensitization of the Degradation of Tembotrione and Mesotrione Herbicides with Natural Organic Matter
 

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 newish products seem to still be volatile enough to damage plants outside the application zone (leading to tense situations between farmers – google it!). This summer, we will explore how to examine the photochemistry and reactivity of dicamba in the gas-phase and may expand this work to examine the chemistry of other herbicides. 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: CHE 105/106 or CHE 110/111

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Project - Environmental Impact of human conflict: the Thirty Year's War

Dr. Erik Gulbranson

Human conflict has often been tied to climate change in seeking additional, outside, explanations for increases in the frequency or severity of conflicts. However, we have only recently begun to explore the effects of warfare on the environment and climate. What impact does warfare have on soil erosion, agricultural productivity and food security? What are the impacts on Earth’s climate when people are displaced or perish due to conflict? This project will address these questions by focusing on the Thirty Year’s War as a case study for the environmental effects of human conflict. This conflict was significant as it reflects a transition of Europe into the early modern period, covered a broad geographic area, and impact millions of people, mostly non-combatants. Your role as a first-year researcher or sophomore researcher on this project will be to conduct a stand-alone research project within this overarching theme, where the design of your project and strategy for executing the project will be mentored by Dr. Erik Gulbranson. Technical training in the various research methods used will also be conducted by Dr. Erik Gulbranson and/or collaborating colleagues, as applicable. You will also work alongside with a Gustavus senior as they are conducting their senior thesis work on this topic. Fieldwork for this project will be conducted in June in Germany; and laboratory work, syntheses of results and preparation for presentations will be carried out throughout the remaining summer.

Course Pre-requisites: ENV/GEO-120

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Project - Investigating the Effects of Climate Change on Plant-Flowering Timing and Fitness 

Dr. Naomi Rushing

We know that global temperatures are increasing as climate change progresses, but how does this influence plants during the growing season in places like Minnesota? Research has indicated that many plant species are flowering earlier than they have historically in response to warming temperatures. However, there has been limited research into the impacts of this change in flowering timing. How do changes in flowering timing influence interactions with key mutualists such as pollinators or rhizobia? What are the impacts on seed production and fitness? Prof. Rushing’s lab will use short lived annual plants to explore questions such as these. We will experimentally manipulate the timing of flowering in the growth chamber and then move our research plants outdoors, where we will record flowering timing, flower number, and seed production. We may also record pollinator visitation, pollinator effectiveness and/or root nodulation, as well as morphological or physiological characteristics of our plants. Students will learn how to analyze our data in R, be introduced to the use of aster modeling to assess fitness, and will have the opportunity to share their results with others via a poster session or presentation. 

Pre-requisites: BIO 110/111

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