SEAR Project Opportunties2024 Edition

SEAR Project opportunities for the summer of 2024 are all described below on this page. There will be at least 2 SEAR positions, with the potential of additional slots depending on grant funding. The table below summarizes these opportunities. You can find videos of the projects at this link. The information session held on Thursday February 8th, 2024 was recorded and the video can be found here. 

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Project - Identification of Stains on Fabrics Using AI

Project Description

Individuals who are blind or who are visually impaired struggle with visual identification tasks. A common concern of these individuals is that they are wearing appropriate, matching and aesthetically appropriate dress wear (Robinson & Lieberman, 2004). Several research projects have endeavored to assist with the task of identifying the colors or patterns of fabrics to help with fashionable and appropriate clothing choices (Rocha et al., 2023; Stangl et al., 2018; Yuan et al., 2011). One area that has not received as much attention in the accessibility space is that of identification of anomalies in clothing such as stains, faded areas or other visual imperfections. This project will create an application using computer vision techniques to identify and locate such anomalies in clothing, primarily the identification of stains. As an example, if a shirt has a stain on it from spilled sauce, the application will assist the user in locating the stain, identifying the source and suggesting ways of addressing the issue. Research has indicated potential success in identification of stains in images in a medical context (Xu et al., 2022). This project aims to apply similar strategies to identify stains on fabrics in a generic fashion distinguishing it from other markings, designs and so on. 
 

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Project - Exploring the Native Prairie Plant Rhizosphere Microbiome for Drought Resiliency

Faculty Mentor - Dr. Jim Parejko

Project Description

Over a billion microorganisms are present in a gram of soil. Of those billion microbes, many have essential roles in decomposition and nutrient cycling amongst other ecosystem services. When a plant seed germinates in soil, the young plant attracts certain soil microbes from the diverse soil microbial population to their roots by releasing organic molecules into their root zone, or rhizosphere. This select community of bacteria and fungi known as a ‘microbiome’ can be beneficial for the soil and plant but could also contain plant disease-causing pathogens. Each plant species has its own unique rhizosphere microbiome, and plants will change the type of molecules that they release based on the conditions they are growing under, thereby changing their microbiome. Native prairie plants of southern Minnesota are known to be resilient to changing conditions and particularly drought resistant. But little is known about the impact of climate change-driven drought on the rhizosphere microbiome of native southern Minnesota prairie plant species. By understanding the effect of drought on the rhizosphere microbiome of native prairie plants, we can better anticipate ecosystem-wide changes to microbial-driven ecosystem services like nutrient cycling. We might also leverage the unique prairie plant microbiome to engineer new bacterial or fungal inoculants to create more resilient conventional crops. By working on this project, a student will gain experience in sampling, growing plants in a growth chamber, experimental design, basic microbiology techniques, culturing bacteria and fungi, molecular biology, bioinformatics, and microbiome data analysis via the Python computer programming language.

Course Pre-requisites: None

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

Faculty Mentor - Dr. Jeff Dahlseid

Project Description

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: BIO101

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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

Course Pre-requisites: CHE107 or 106/108
 

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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: 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 the summer, you will work on an original research project to examine the ability of insects to tolerate environmental stresses, such as cold and dehydration. You will design and conduct experiments to investigate aspects of stress tolerance physiology insect. 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 - Morphology-environment relationships in stromatolites

Faculty Mentor - Dr. Julie Bartley

Project Description

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. This summer, we will investigate the relationship between stromatolite form and environment in a ~400-million-year-old geologic unit exposed in eastern Minnesota and Wisconsin. The project will involve a few days of fieldwork in addition to 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 - Toward understanding the epigenetic regulation of gene expression in P. falciparum

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, work on synthetic routes to small molecules and peptides that bind to the protein, and measure the how strongly the molecules interact with the protein.

Course Pre-requisites: CHE 141

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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. Our lab is currently focusing on the development of resistance to azoles, the most prescribed class of antifungals, in Candida albicans, the most common cause of invasive fungal infections. Experimental evolution experiments found recurring mutations associated with resistance and tolerance in a gene called ERG251 which has roles in the sterol biosynthesis pathway targeted by azoles. The FRYE project in the Burrack lab during the summer of 2023 will focus on determining the mechanism by which ERG251 mutations allow increased growth in the presence of antifungal drugs. 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 - 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 generate gene fusions and use 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: BIO101 or CHE107 or CHE108

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Project - Radio Wave Emissions for Exomoon Detection: A Study of Host Planet Magnetosphere
 

Faculty Mentor - Dr. Darsa Donelan

Project Description

Join us this summer in the search for exomoons, celestial bodies that orbit exoplanets beyond our Solar System. Despite numerous attempts, no exomoon has been confirmed to date and only a few have been identified as candidates. Our project will focus on utilizing the interactions between Jupiter and its moon Io, as well as those between the Sun and Jupiter, to study radio emissions and determine how they can be used to predict exomoon locations.

As part of NASA's Radio Jove Project, we will construct a permanent radio quad-dipole antenna and integrate dual-polarization spectrographs and wide-band antennas operating in the 15-30 MHz frequency range. Through scientific observations and collaboration with radio observatories, we aim to develop innovative analysis techniques, including deep learning, to enhance our search for exomoons.

This opportunity is open to all students and provides hands-on experience in radio astronomy, as well as exposure to cutting-edge research and technology. Join us in advancing our understanding of the universe and uncovering new discoveries in the exciting field of exoplanetary research.

Course Pre-requisites: None

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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 - Assessment of the Gustavus Adolphus Campus Forest

Dr. Amy Kochsiek

Trees are incredibly important in urban ecosystems. Not only do they decrease air pollution, store carbon, and diminish heat islands, but studies have also shown that interacting with green areas has positive effects on the human psyche. In 2000, a census of the Gustavus urban forest was completed. Now 24 years later, I would like to recensus the campus forest and using a US Forest Service software (ITree), analyze the campus forest census data for important ecosystem functions such as air pollution mitigation, carbon storage and sequestration, oxygen production, water runoff and other important metrics. The student involved in this project will gain skills in tree identification, data management and analysis, and scientific communication. 

Pre-requisites: None

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Project - Photodegradation of Herbicides 

Dr. Amanda Nienow

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.

Pre-requisites: CHE 107 or CHE 108

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