FYRE Project Opportunties

2018 Edition

Project opportunities for the summer of 2018 are all described below on this page. The table below summarizes these opportunities.

Faculty Mentor

Department/Program

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 303B
Dr. Joel Carlin Biology Diversity and environmental stress in marine fishes of the Gulf of Mexico jcarlin@gustavus.edu; NHS 336
Dr. Jon Grinnell Biology American bison behavior and conservation grinnell@gustavus.edu; NHS 328A
 Dr. Amanda Nienow Chemistry Photochemistry of the herbicide dicamba anienow@gustavus.edu; NHS 106A
Dr. Margaret Bloch Qazi Biology How good are old mothers? Investigating age-related changes in maternal protein investment in eggs mqazi@gustavus.edu; NHS 329
Dr. Laura Burrack Biology Functional consequences of increased kinetochore protein levels lburrack@gustavus.edu; NHS 221A
Dr. Dwight Stoll Chemistry Determination of musk fragrances in the environment dstoll@gustavus.edu; NHS 203
Dr. Dwight Stoll Chemistry Developing a predictive model for liquid chromatography separations dstoll@gustavus.edu; NHS 203
Dr. Dwight Stoll Chemistry Development of zirconia-based phases for separation of proteins by liquid chromatography dstoll@gustavus.edu; NHS 203
Dr. Brandy Russell Chemistry Protein structure, folding, and metal binding brussell@gustavus.edu; NHS 205A
Dr. Laura Triplett Geology Environmental monitoring in Seven Mile Creek Watershed ltriplet@gustavus.edu; NHS 124B
Dr. Ian Hill Chemistry Structure and composition dependence of rare-earth metal doping on luminescence in yttrium vanadate materials ihill@gustavus.edu; NHS 109
Dr. Darsa Donelan Physics Wavelet analysis of planetary atmospheres ddonelan@gustavus.edu; Olin 204

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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 understanding 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. On this project, students can learn how to express, isolate, and purify proteins as well as work on synthetic routes to small molecules that bind to the protein.

Course Pre-requisites:CHE141

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Project - American bison behavior and conservatio

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 three to five 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 management duties as well (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 willhave interests in animals and conservation, have good observation skills, be in good physical condition, and be able totolerate 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.

bison



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Project - Diversity and environmental stress in marine fishes of the Gulf of Mexico

Faculty Mentor - Dr. Joel Carlin

Project Description

The northern Gulf of Mexico holds a broad diversity of marine organisms never featured by nature documentaries or seafood menus. These animals are also challenged continuously by occasional oxygen deprivations, low-grade but chronic undersea drilling pollution, and acute devastation wreaked by oil spills. Be among the first scientists to research the identity, health, and population structure of an understudied and important marine community. Students can expect to gain skills with gross dissection, micro-dissection, sterile technique, DNA isolation, gene amplification, and genetic comparison. Participants are expected to submit a brief report that features quantitative analyses of results and a modest review of relevant scientific literature.

Course Pre-requisites: A minimum of one of the following courses: BIO101, BIO102, CHE107, ENV120


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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 aqueous solution and sorbed to the crop/plant surfaces to which they are applied (e.g., corn and soybeans). 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). Armed with a basic understanding of dicamba photochemistry in aqueous solution, in the summer of 2018, we will explore how to examine the photochemistry and reactivity of dicamba in the gas-phase while continuing to answer questions about the mechanism of reaction in solution.

Students in this lab are trained in methods used in experimental chemistry including experimental design, data acquisition, data analysis, and the presentation of results. Specifically, students learn how to use a high-pressure liquid chromatograph (HPLC), UV-Vis spectrophotometer, a fluorimeter, and a mass spectrometer, and how to analyze the data from each of these systems. Plants (corn and soybean) will be grown in the Gustavus greenhouse for use in the project.

Course Pre-requisites: CHE107

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Project - How good are old mothers? Investigating age-related changes in maternal protein investment in eggs

Faculty Mentor - Dr. Margaret Bloch Qazi

Project Description

A mother has tremendous influence on her offspring’s health. As females age, their offspring’s health declines. In my lab, we use the fruit fly as a model organism to investigate: 1) how offspring are affected by having old mothers, and 2) the mechanisms underlying these maternal age effects. Understanding how female age impacts offspring health has valuable implications for managing natural populations and understanding chronic health conditions in people.

There are two projects planned for the summer:

Project 1: Examine how maternal age affects her ability to provision eggs with protein. We are using a newly-developed method to measure protein content in eggs. By examining eggs from females of different ages, we will learn how age impacts a mother’s ability to develop healthy eggs.

Project 2: Explore how maternal nutrition affects offspring health through protein investment in eggs. We will alter the amount of protein in the female’s diet, then measure protein content in her eggs. From this, we hope to understand how maternal diet impacts her ability to pack protein into eggs.

In both projects, student collaborators will learn how to conduct protein assays and nutritional geometry assays; dissect under a microscope; organize and analyze data using SPSS; and create figures using Sigma Plot.

Course Pre-requisites: BIO101


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Project - Functional consequences of increased kinetochore protein levels

Faculty Mentor - Dr. Laura Burrack

Project Description

During cell division, cells must accurately segregate replicated chromosomes into daughter cells in order to maintain the stability of their genomes. Many cancers have unstable genomes and exhibit aneuploidy, an abnormal number of chromosomes, due to errors in chromosome segregation processes. Chromosome segregation requires the attachment of a large complex of proteins called the kinetochore to a region of the chromosome called the centromere. The kinetochore connects the chromosomal DNA to the spindle microtubules that provide the forces needed for chromosome segregation during mitosis. Cancer cells frequently have increased expression of kinetochore proteins. High levels of kinetochore proteins correlate with poor patient prognosis, but it is not clear whether the relationship is causative. We have developed the yeast Candida albicans as a model organism to explore the mechanistic consequences of overexpression of CENP-A, one of the kinetochore proteins, alone and in combination with other genetic changes and drug treatments. The FYRE project in the Burrack lab during the summer of 2018 would contribute to our work determining whether the higher levels of kinetochore proteins drive genome instability or whether the elevated levels are a side effect of other changes in the cell. Through this project, a student would learn a combination of molecular biology, microbiology, genetics, and cell biology techniques as well as gain practice in experimental design and data analysis methods.

Burrack Research

Course Pre-requisites: BIO101 or CHE107




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Project - Determination of musk fragrances in the environment

Faculty Mentor - Dr. Dwight Stoll

Project Description

Musks (e.g., tonalide) are a family of compounds used heavily by humans in a variety of personal care products. They are often used as fragrance compounds in products such as deodorant. Unfortunately it seems these compounds have some detrimental effects on aquatic life as the compounds are discharged from urban wastewater treatment facilities. In this project we aim to develop methods for determination of musk compound concentrations in the environment and study of their susceptibility to photodgradation. This work will involve development of sample preparation methods, as well as separation and detection methods based on gas and liquid chromatography and mass spectrometry. We anticipate collecting water samples from regional wastewater treatment facilities, as well as regional river sites. Students involved in this project will also interact with research collaborators working on this project at the University of St. Thomas and the University of Minnesota, Crookston.

Course Pre-requisites: CHE107


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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
 


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Project - Development of zirconia-based phases for separation of proteins by liquid chromatography

Faculty Mentor - Dr. Dwight Stoll

Project Description

Zirconia is a material that is uniquely suited to the analysis of biomolecules because of its extraordinary pH stability and mechanical strength. Unfortunately there are is only one commercial source for porous zirconia that is suitable for chromatographic purposes, and the offerings of this source are limited. In this project we will synthesize our own porous zirconia and modify it with the phosphate analog of ethylenediaminetetraacetic acid to impart a strong cation-exchange character to the particle that is known to be useful for the separation of antibody proteins. We will prepare chromatography columns using this material and compare the performance of the material to other commercially available options based on silica or polymer particles. 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. Ultimately we aim to explore the potential of these zirconia-based materials for use in two-dimensional liquid chromatography separations of proteins, which is currently a primary focus of the Stoll Laboratory.

Course Pre-requisites: CHE107


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Project - Protein structure, folding, and metal binding

Faculty Mentor - Dr. Brandy Russell

Project Description

In my research lab, we study protein folding with a particular focus on proteins that contain metal atoms and how they assemble the metal sites correctly during the folding process. Understanding how proteins fold is a key question in biology/biochemistry that could lead to improved predictions of protein structure, a better ability to engineer new proteins with novel functions, and a better understanding of many diseases that are caused or characterized by misfolded proteins. My research group uses simple metal-binding proteins and studies their folding and metal site assembly to shed light on how these processes work for more complex systems.

The system we are working on right now is a pair of proteins found in a certain marine worm called Nereis diversicolor. The first protein, called myohemerythrin, is an oxygen transport protein that contains two iron atoms; its function is analogous to that of myoglobin in mammals. The second, called metalloprotein II, binds one or more cadmium atoms, and is thought to protect N. diversicolor from the toxic effects of cadmium. Iron and cadmium have very different chemical properties, so it is surprising to see these two proteins with high amino acid sequence identity but different metal binding preferences. This summer, we will work on understanding why myohemerythrin binds iron and metalloprotein II binds cadmium, and how the different bound metals affect the folding process. We will use a number of basic chemical and biochemical lab skills including protein purification, UV-visible spectroscopy, working with air-sensitive samples, and more, depending on student interests within the project.

Russell Research

Course Pre-requisites: CHE107 or other college chemistry course with laboratory


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Project - Environmental monitoring in Seven Mile Creek Watershed

Faculty Mentor - Dr. Laura Triplett

Project Description

I am seeking a first-year student to join me in conducting water quality monitoring in the Seven Mile Creek watershed near St. Peter. We are working with government agencies and local landowners to study the connections between food production, land-use, water quality and habitat quality. The context of this work is that the Minnesota River, a major tributary of the upper Mississippi River, is impaired for (polluted by) nitrate, excess sediment and other water quality parameters. Research is showing that the pollution is related to the row-crop agriculture in our area, which is also the most important industry for our regional economy. Right now, over a million dollars is being spent to install pollution control strategies to improve Seven Mile Creek. In effect, this is a large-scale experiment to determine whether voluntary best practices and technologies can reduce sediment and nutrient pollution in a typical south-central Minnesota stream.

This summer, we will continue collecting and analyzing water and soil samples. Early on, you will learn how to operate sampling equipment and collect samples from streams. You will then learn laboratory techniques to measure water chemistry and pollutants. Throughout, you will learn geology, hydrology and environmental chemistry, and may work with ecologists and aquatic biologists. Also, you may learn some basics of GIS, and will certainly work closely with our partners at Nicollet County, the University of Minnesota, the Minnesota Pollution Control Agency and others. In short, this project is for someone who: enjoys learning new science; is excited about trying both field work and laboratory work; works well with people; and, is curious about Minnesota’s natural environment and human communities. Also, the student must have a valid driver’s license and be willing to obtain college vehicle certification.

Course PrerequisitesStudents must have had at least one course with a lab in geology, biology, chemistry and/or physical geography. Students who had advanced science courses in high school may also qualify.

Triplett Field WorkTriplett Lab Work

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Project - Structure and composition dependence of rare-earth metal doping on luminescence in yttrium vanadate materials

Faculty Mentor - Dr. Ian Hill

Project Description

Trace rare earth elements introduced into yttrium vanadate crystals produce luminescent materials that have applications as solid-state lasing media and have potential for use in electronic displays. While the development of this class of materials is ongoing, characterizing regions of structural and luminescent stability with increasing rare earth content remains a critical area to explore in predicting stable blends of doped yttrium vanadate.

Students on this project will learn about materials synthesis and characterization through making their own rare earth yttrium vanadate samples, determining product crystal structure using X-ray diffraction techniques, and characterizing their luminescence properties using a spectrofluorimeter. Students on this project will be trained in the essentials of conducting a literature review, designing experiments to collect evidence toward supporting academic assertions, and building conclusions from analyzed data taken in aggregate. Students will also engage in interdisciplinary interactions with collaborators at Minnesota State University, Mankato.

Course PrerequisitesCHE107

YVO4

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Project - Wavelet analysis of planetary atmospheres

Faculty Mentor - Dr. Darsa Donelan

Project Description

This project is an effort to study the atmospheres of planets and moons in our solar system. Our current knowledge of the structure of many of these planets and moons comes from radio occultations, ground-based stellar occultations, spacecraft observations, and in situ measurements. This project will investigate discrete wave structure as it travels through planetary atmospheres using a technique known as a wavelet analysis. The results of this simulation will then be compared with previous observations published in the literature to date.
This summer, you will learn how to obtain data through the NASA Planetary Atmosphere Data Node. You will then learn how to interpolate the data to prep it for analysis. You will also learn how to take existing Python code and tailor it to our needs, in order to run a computational analysis. You will then learn how to interpret your analysis. Lastly, you will gain knowledge in the field of planetary science.

Course PrerequisitesPHY195 or MCS177