FYRE Project Opportunties2023 Edition
Project opportunities for the summer of 2023 are all described below on this page. The table below summarizes these opportunities. You can find videos of the projects at this link.
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Project - Conservation behavior of American bison
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.
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Project - Investigating temperature tolerances in diploid and polyploid Solidago gigantea: implications for the invasive success of polyploids
Faculty Mentor - Dr. Angela Walczyk
Project Description
Upon introduction, invasive species are exposed to novel abiotic (i.e., non-living) and biotic (i.e., living) environmental factors (e.g., climatic differences, competition with native species) that can hinder invasion success if the invader does not possess traits to tolerate these unfamiliar factors. Polyploidy (the state of possessing more than two chromosome sets per cell) is highly prevalent within invasive plant species and could provide an additional source of genetic variation that allows invaders to tolerate and/or rapidly adapt to novel environments. For example, duplicate chromosome copies can lead to the sub- or neo-functionalization of genes (i.e., repetitive gene sequences accumulate mutations to evolve new or varied functions!). Such changes can enhance ecological tolerances and increase the potential range of phenotypic responses to environmental factors, thus allowing polyploids to potentially survive in a broader range of environments than closely related diploids (the state of possessing only two sets of chromosomes per cell).
Here, we will be testing the hypotheses that diploids and polyploids preform differently in different temperature environments using the non-model species Solidago gigantea (Giant Goldenrod). S. gigantea is an excellent species system to test this hypothesis because it has three polyploid variations native to North America (diploid – two chromosome sets; tetraploid – four chromosome sets; and hexaploid – six chromosome sets), and of these three ploidy variants only tetraploids have become noxious invaders in parts of Europe and Asia. I want to investigate why only the tetraploids became invasive! To do so, we will design and conduct an experiment where diploid, tetraploid (invasive and native), and hexaploid seedlings of Solidago gigantea (Giant Goldenrod) will be grown in low and high temperature conditions. Through this FYRE project, you will learn how to care for experimental plants, and you will learn how to collect and statistically analyzing germination, morphological (e.g., height, growth rate), and physiological (e.g., gas exchange metrics) trait data. Finally, you will help in preparing the results of this project for possible publications or presentations!
Course Pre-requisites: BIO 101 or BIO 102
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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.
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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 projects in the Leehy lab during the summer of 2023 will utilize this ground-breaking technology to interrogate gene function through the generation of novel gene deletions. Students will have the opportunity to utilize CRISPR/Cas9 for 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 screen CRISPR/Cas9 transformed plants for a ten1 knock-out and 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. 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.
Students can pick which of the projects they would like to work on or elect to work on both. Interested students will have the opportunity to learn basic programming with R and command line in addition to plant biology, cell biology, molecular biology, and biochemistry.
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
Julie Bartley (Environment, Geography, and Earth Sciences) has research projects that
investigate the relationship between early life and its environment. Julie mainly works on questions
regarding life on Earth, but has also explored the record of sedimentary processes on Mars.
Some of the projects that are ongoing in Dr. Bartley's lab are listed below. Dr. Bartley intends
FYRE student to select a project that matches their interests and prior experiences.
(1) 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.
(2) Interpreting the Surface of Mars is challenging, because we have only remotely-collected
data. Images and measurements collected by the rover missions to Mars have established
that Mars had liquid water at some point in the past. There are still many features, though,
that are perplexing. This project builds on work done by previous research students,
analyzing images collected by the Perseverance Rover to understand the processes that
influenced the surface of Jezero Crater.
(3) Understanding Ancient Fossils is sometimes tricky, because it is hard to match extinct forms
with microbes that are alive today. Furthermore, these organisms have experienced
decomposition, burial, mineralization, and sometimes heat and pressure during the
fossilization process. We don’t understand very well how these processes might obscure
our ability to interpret the original community structure. In this project, we will choose one
of the dimensions of alteration (e.g., decomposition or mineralization) and examine the
impact of this variable on the preservation of modern microbes as analogues to ancient
ecosystems.
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 - 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 - Isolation, Characterization and Biological Testing of Essential Oils and Natural Products Obtained from Native American Wild plum (Prunus americana) and the Common Sage (Salvia officinalis)
Faculty Mentor - Dr. Kennedy Nyongbela Dohjinga
Project Description
Natural products from plants have been a bedrock of drug discovery for many decades. They have provided more than half of all cancer medications. Paclitaxel (Taxol) which is one of the most used chemotherapy drugs against various cancer cells, was isolated from the bark of Taxus brevifolia. The anticancer vinca alkaloids notably vinblastine, vincristine and vincamine were isolated from the Madagascan periwinkle Catharanthus roseus. Native American flora harbors many medicinal herbs and spices that are used as food and medicines. This proposal seeks to isolate, characterize, and test essential oils and other natural products obtained from Prunus Americana, a Native America wild plum and the common Sage spice, Salvia officinalis, on various cancer and bacterial cell lines.
Expected Outcome of Project At the end of the project, it is hoped that the research student will: • Learn how to carry-out literature search • Learn the important role natural products and essential oils play in various applications such food, medicines, agriculture, and cosmetics. • Understand the important role plants and natural products, play in drug discovery and development efforts. • Learn the process of extracting and analyzing essential oils using various chromatographic and spectroscopic methods. • Learn the biological testing of the essential oils and other natural products on various bacterial and cancer cells. their use in various applications.
Course Pre-requisites: None
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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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