2012 Projects in Natural Sciences and Mathematics

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Projects in the Natural Sciences and Mathematics (NSM)

Choose a disciplinary area for a quick link to the associated projects.

Biology  Chemistry  Physics  Computer Science  Neuroscience  REU (Environmental Science)

(or view projects in the Fine Arts, Humanities, Social Sciences, and Interdisciplinary Studies-AHSSI)


 CHEMISTRY

Jennifer Klein – Muscle Protein and Molecular Dynamics – 3 students

Experimental Biochemistry and Molecular Biophysics
We cannot survive more than minutes without oxygen — nor have we escaped vulnerability to oxidative stress. Disease and biological aging are familiar contexts in which the role of oxidative ‘damage’ to DNA, lipids, and proteins has been recognized, even popularized by the promotion of antioxidants for longevity and disease resistance. Under normal conditions, too, cells sensitively detect and respond to cellular redox state to maintain balance. Our goal is to understand how molecules sense, respond, and are eventually damaged by oxidative stress. We will examine how post-translational protein modifications associated with oxidative stress trigger functional and structural changes in the proteins involved in muscle contraction. We will also test the role of antioxidant systems in recovering protein function after oxidative modification.

Undergraduate projects will focus on the impact of oxidative stress on protein structure and function using a variety of techniques that include molecular biology to create proteins for site-directed spectroscopy, Dictyostelium cell culture and protein expression, carrying out biochemical assays, mass spectrometry and biophysical spectroscopy. Qualifications include pursuit of a degree in biology, chemistry or physics.

Computational Biochemistry
Undergraduate projects include carrying out molecular dynamics simulations of muscle regulatory and contractile proteins. The project will involve in silico modeling of post-translational modifications, molecular dynamics simulations, and the option to carry out related experiments in the laboratory. The oxidative modifications we will study are related to the progression of biological aging, skeletal muscle disease and heart disease. Qualifications include pursuit of a degree in biology, chemistry, physics or mathematics/computer science, with a strong interest in computational biology.

Greg Muth (3 projects):

Selection and characterization of algal communities toward the development of stable cultures for the production of renewable fuels – 1 student

The dwindling of natural energy resources, combined with growing concerns over the effects of CO2 emissions on climate, is contributing to an increasing worldwide interest in the development of renewable energy resources derived from biological sources. Microalgae have been suggested as a potential source of bioenergy due, in part, to their high productivity and low land use requirements [1]. The increased interest in microalgal biofuels represents an opportunity to pursue basic science research in biology and chemistry that can, in turn, inform the search for and development of alternative fuels. A key component in the success of microalgae as a source of biofuels is optimizing lipid production in mass culture. Our research focuses on (1) lipid accumulation in native algal species as a function of nutrient availability, CO2 concentration, light, etc. (2) the evolution of stable algal communities from mixtures of native species via selection under laboratory growth conditions, and (3) the characterization of the biochemical and genetic changes in algae as they adapt to various environments.  Students interested in environmental studies having a strong background in chemistry are encouraged to apply.  Preference will be given to individuals willing to continue the project during the academic year.

Chemical analysis of probiotic cultures used in organic farming – 1 student

This collaborative project is to support research being conducted in collaboration with Costa Rican farmers who are interested in understanding how cultures of Mountain Microorganisms (MM) can increase crop yields in a sustainable manner.  Mountain microorganisms are native bacteria and fungi found in the leaf litter of forests or in grassy areas that are reported to have a wide variety of beneficial properties when applied to agricultural crops or mixed with soil or compost.  We know that while there are some commonalities, there is no standard use or preparation of MM and the effectiveness of the applications are also widely varied.  The goal of this project is to develop analytical methodology to study the chemical and biological properties of MM cultures under a variety of conditions.  Students interested in microbiology and chemistry are encouraged to apply.  Preference will be given to applicants willing to continue the work during the academic year.

Science Education and Outreach: A Revolution in the Classroom – 1 student

This non-traditional summer research project continues our community outreach effort to get elementary students excited about science and gives Oles the opportunity to inspire our next generation of researchers. The goal of the summer portion of the project is to research and develop hands-on classroom activities for elementary school students centered on the principles of renewable energy. The project continues during the academic year with training of volunteers and dissemination of the materials and curriculum throughout the community in a science-outreach program. This project is ideal for a student interested in science education. A vital component for the success of this project is coordination and implementation during the academic year.  Preference will be given to those individuals able to do so. (Project will go forward pending receipt of external funding.)

Douglas Beussman (3 projects):

Human Scent Differentiation – 1 student

This project will involve using GC/MS techniques to characterize human scent profiles. Slight differences in normal human scent patterns are used by canines to differentiate humans. We are interested in developing a laboratory-based technique that can be used to investigate these scent differences. The volatile organic compounds found in normal human scent are at extremely low concentrations, often ppb or ppt levels and thus require a very sensitive technique to profile these compounds. Possible applications of this GC/MS scent profiling method include forensic case work and disease state detection.

Isotope Ratio Fiber Analysis – 1 student

This forensic-based project will use the isotope ratio mass spectrometer at St. Olaf. This project will look at small differences in isotope ratios of fibers, such as cotton or wool fibers. By determining the isotope ratios, the geographical or manufacturing origin of the samples can often be determined, thus providing valuable information about the source of the material and potentially supply a link between a suspect and forensic evidence found at a crime scene.

Tetrahymena Proteomics – 2 students

This NSF-funded project includes collaborating with Dr. Cole in the Biology Department, as well as research groups at Drake University in Iowa, Claremeont Colleges in California and Missouri State University, on the identification of proteins isolated from Tetrahymena thermophila, using proteomic methods. Isolated proteins will be digested and analyzed using mass spectrometry techniques with the MALDI-TOF/TOF instrument and screened against a database of proteins predicted to exist based on the genome. Peptides from potentially identified proteins will be fragmented in the mass spectrometer in order to sequence the peptides for confirmation of protein identification. (Project will go forward pending receipt of external funding.)

Robert Hanson – Molecular Visualization – 1 student

Current projects are in the area of molecular visualization, spanning the fields of chemistry, biology, physics, computer science, and mathematics. I am looking for students with broad interests that span two or more of these fields. There are actually four possible projects, depending upon student interest. All are highly collaborative, requiring good interpersonal skills and an interest in expanding one’s knowledge in a variety of areas. None require experience in computer programming, although some such experience could be useful. (A) Development of new methods of visualization of biomolecular contacts. This project will focus on the development of accessible methods for visualizing enzyme active site and receptor binding of small molecules. This work will be done in collaboration with a research group at South University, a school of pharmacy in Charlotte, NC. Preliminary work on this project was carried out in our group by Erik Wyatt ’14 during summer 2011. We are now in the process of publishing that work and looking for developing concrete applications, especially in the area of pharmacy education. (B) Development of new methods for visualization of energy states in crystals and polymeric systems. This project will be carried out in collaboration with theoretical chemistry and solid-state physics groups in England and Italy. To date there are very limited tools available for the depiction of energy states (phonon vibrational states as well as electronic states) in solids. We will be working with research groups to create novel visualizations in this area. (C) Development of new methods for the visualization of orientational differences and changes in biomolecules involved in protein folding, active site binding, and other dynamic systems. This project, an extension of work done in our group by Dan Kohler ’10, Sean Johnston ’10, and Steven Braun ’11, would be carried out in collaboration with research groups at the University of Minnesota and the University of Washington. (D) Development of authoring tools for the depiction of organic and bioorganic reaction mechanisms. This project, in collaboration with the University of Massachusetts, Amherst, and Leeds University (England), is the most organic-chemistry-related project. It aims to develop easily accessible methods of building the sorts of visualizations we recently added to the Molecular Playground. This project is an extension of work done by Hai Nguyen (Carleton, ’13) in our group this past fall.

Dipannita Kalyani – Development of Novel Transition Metal Catalyzed C-C and C-CF3 Bond Forming Reactions – 2 students

My research interests center around the development of transition metal catalyzed organometallic transformations. There are two projects I am excited to have students work on this summer:

I. Transition Metal Catalyzed Decarboxylative Allylic Trifluormethylation
The introduction of a trifluoromethyl (CF3) group can bring about remarkable changes in the physical, chemical and biological properties of organic compounds. Hence, the development of efficient, cost-effective, and environmentally benign methods for the synthesis of trifluoromethylated compounds has been an intense area of research in recent years. In particular a major thrust in this field is the use of inexpensive reagents such as trifluoroacetate as the source of [CF3]. One of the projects in my research group will explore the development of a novel transition metal (Pd or Ni) catalyzed strategy for the synthesis of allylic and aromatic trifluoromethylated compounds using trifluoroacetates as the trifluoromethyl (CF3) source.

II. Nickel-Catalyzed C-H Arylation Using Phenolic Electrophiles
The ubiquity of hydrocarbons (including arenes and alkanes) in petrochemical sources has resulted in a continuously growing demand for selective functionalization of C-H bonds. In particular, the development of atom economical, cost-effective, and environmentally friendly methods for the construction of C-C bonds using hydrocarbons is very desirable. This is because C-C bonds are structural motifs found in a variety of compounds including fuels, pharmaceuticals, agrochemicals, conjugated materials, and commodity chemicals. The overall goal of the proposed research is the development of mild, and efficient construction of C-C bonds by nickel-catalyzed cross-coupling of phenolic electrophiles with hetereoarenes, arenes, and alkanes. The inexpensive nature of nickel in conjunction with the naturally abundant and/or readily accessible phenol electrophiles are expected to make this methodology a significant advancement over the currently known C–C bond forming reactions.

Students working on these projects will gain experience both in the synthesis and purification of organic compounds as well as the optimization of catalytic reactions. They will learn and develop expertise in laboratory methods including 1) the use of the glove box and air-free Schlenk techniques, and 2) use of NMR spectroscopy and GC. Students will also engage in regular group meetings where they will present the results of their projects and brainstorm ideas with me and their peers on ways to further their research. In all, these projects will enable students to apply both new concepts as well as classroom topics to address unmet challenges in chemistry.

Laura Listenberger – Mechanisms of cellular lipid storage – 2 students

Excess lipid is stored inside cells in structures known as lipid droplets. Despite their importance in obesity-related disorders, little is known about how lipid droplets are formed or broken down inside cells. One candidate for regulating these processes is a protein known as perilipin 2. The Listenberger lab is exploring the function of perilipin 2 and the way in which it recognizes and binds to the surface of lipid droplets. Students use a variety of biochemical techniques to address these questions including mammalian cell culture, subcellular fractionation, polyacrylamide gel electrophoresis, and western blotting. This work will be conducted from June 11-August 17th. (Also listed under Biology.)

Elodie Marlier – Development of low-valent first-row transition metal complexes – 1 student

Metal centers with low oxidation states or low-valent metal complexes have been of great interest for bond activation considering these species are highly reducing. Specifically, my research interest has been in carbon-halogen (C-X) bond activation due the large contamination of volatile organic compounds in our groundwater supply. My goal is to synthesize low-valent metal complexes that show reactivity towards C-X bonds. The first step in this project will require the use of organic chemistry to synthesize monoanionic tetradentate ligands. Once prepared, a ligand will be metallated with a first-row transition metal and reduced to a more reactive oxidation state under inert atmosphere. Students can expect to gain experience in both inorganic and organic synthesis including air-sensitive techniques such as the use of a Schlenk line and a glovebox. The characterization of these compounds will also require the use of a variety of techniques such as NMR, mass spec, UV-vis and IR. Additionally, metal complexes that can be crystallized will be submitted to the University of Minnesota X-ray crystallography lab for crystal structure determination.

Jeff Schwinefus – Cosolute Interactions with Nucleic Acids – 3 students

Do you have an interest in biochemistry, physical chemistry, or computational biology? If so, then I just may have a project you will be interested in. This research project is appropriate for biology, chemistry, or physics students that have completed the Chem 121/123/126, Chem 125/126, or CH/BI 125/126/127 introductory course sequences.

Cosolute Interactions with Nucleic Acids
For several years my research group has explored the stability of folded nucleic acids, from simple, short DNA duplexes to complex RNA structures. Much of our effort has focused on the effect of neutral organic molecules like urea or amino acids (which we generically call cosolutes) on the stability of folded nucleic acid structures. We use a mix of uv-absorbance, differential scanning calorimetry, vapor pressure osmometry, solubility measurements, and molecular dynamics simulations to determine the excess (or deficiency) of these cosolutes near the newly exposed surface area of an unfolded nucleic acid structure. If the interactions between cosolutes and the specific functional groups on the newly exposed nucleic acid surface area are thermodynamically favorable, the stability of the folded nucleic acid will be lower in aqueous cosolute solutions relative to water alone.

In lab this summer, we plan to explore biologically relevant nucleic acid structures such as bulged domains in RNA duplexes, and triplex and G-quartet structures in DNA. Each of these nucleic acid structures expose different surface areas upon unfolding (different in both area and chemical functional group composition) and provide new opportunities to test and refine predictions from biopolymer folding theory.

COMPUTER SCIENCE

Richard Allen  A Research Tool for Digital Humanities – 1 student

Digital Humanities (DH) is fast becoming both a subfield of computer science as well as a field of study and research within the humanities.  Computer science developed as an interdisciplinary field with applications across a wide spectrum of fields.  Recently, those applications include tools for creating and extending research in the humanities.  The goal for this summer’s work will be to create a tool for computing, retrieving, and comparing signatures of documents.  With this tool one will study document authorship, compare a given document to an overall average of a collection of documents, detect the importance of subject matter in documents, create variants of a given document and compare them.  An important component of the project will be the creation of a robust graphical interface.

Richard Brown (2 projects):

CSinParallel: Parallel computing for all CS students – 1 student

Recent changes in computer architecture mean that all CS students now need competency in parallel computing in order to be prepared for their careers. Student researchers in the CSinParallel project have a unique opportunity to contribute to this international movement in CS education, by helping to research, develop, produce, and improve modules for teaching parallelism being made available to colleges and universities across the country at csinparallel.org. This summer’s projects include researching and creating modules that focus on parallel design patterns and “exemplar” applications to other disciplines and concerns, such as DNA comparison and traffic flow analysis; improving portability and performance of WebMapReduce; researching, documenting, and deploying CSinParallel modules on new parallel computing platforms; and preparing materials for publication. Special equipment includes St. Olaf’s Beowulf clusters, 32-core computers, LittleFE portable cluster, and high-performance graphics cards for accelerated computations, as well as external resources provided by Intel and Amazon.  Preparation: Minimum of CS 251; CS 300 or equivalent knowledge of parallel computing is an asset. (Project will go forward pending receipt of external funding.)

HiPerCiC: Making power computing available in all disciplines – 1 student

High-performance parallel computing has much to offer nearly any discipline on campus, since such resources makes it practical to consider research questions that were impractical before now.  Some current St. Olaf examples: automatically and expediently searching millions of pages of text for word usage patterns;  simulating hundreds of thousands of different plants to assess the way the respond to nitrogen-rich environments over time;  and analyzing political blog postings over time to explore how their emotional content relates to current events.  In this project, a student researcher will design and program a customizable user-interface framework to make parallel computing applications accessible and convenient for students and faculty in non-CS disciplines.  The resulting framework will form the foundation for a forthcoming experimental interdisciplinary course that will focus on the creation and deployment of new and ongoing applications of high-performance computing in all disciplines.  Preparation:  Good programming skills and interest in user interfaces and/or applications of CS; CS 284 is an asset.

BIOLOGY

Anne Walter – Physiological Exploration – 1 student

I have several physiology-related projects in mind for the summer and will complete them depending on student interest and available funding. 1) We have on-going work on the enzyme lactate dehydrogenase with projects in fish, fiddler crabs and even E. coli to discover kinetic parameters and isozymes. The research is both new basic science and focused on developing a new Animal Physiology lab (piloted Fall 2011) as an example of physiological adaptations to the environment. 2) We have a project related to membrane properties and how these are dependent on membrane composition. There are enzymes to study, lipid assemblies to prepare and characterize using fluorescence and other tools. 3) A bio-math project to take my current Animal Physiology lab manual and add mathematically rich modules to each exercise. This requires assembling resources and figuring out some interesting problems that students can do numerically or with algebra and calculus.

Michael Swift – Zooplankton Ecology in Northern Minnesota Lakes – 2 students

Zooplankton are the herbivore trophic level in lakes and form the important link between algae and fishes. Zooplankton have incredibly interesting behavior. Several vertically migrate in the water column – they swim from deep in the lake where it is dark to the surface each evening to feed and swim back down to avoid visually-feeding fishes at dawn. Some, like Chaoborus andLeptodora are predators that feed on other zooplankton species. Some, like Polyphemus, swim around and around together in large “swarms” near the shore. Students will have the opportunity to study these or other aspects of zooplankton ecology in Low Lake and nearby beaver ponds in northern Minnesota. Research projects will be conducted in a semi-wilderness setting at the Coe College Wilderness Field Station (WFS) near Ely, MN. Students must be willing to study aquatic biology by canoe, live and work in an atmosphere of intensive teaching and research, and work independently and cooperatively. Students will begin their research on campus (1+ weeks), complete their field sampling at the WFS where I’ll be teaching aquatic ecology (5+ weeks) and complete their project on campus (2+ weeks). Potential research projects include: the effects of prey size and swimming ability onChaoborus predation; patterns of diel vertical migration by Chaoborus larvae or Daphnia; characteristics of swarming behavior ofPolyphemus; zooplankton biodiversity – distribution of zooplankton taxa in the Low Lake area. (See additional position under Environmental Science REU below.)

Laura Listenberger – Mechanisms of cellular lipid storage – 2 students

Excess lipid is stored inside cells in structures known as lipid droplets. Despite their importance in obesity-related disorders, little is known about how lipid droplets are formed or broken down inside cells. One candidate for regulating these processes is a protein known as perilipin 2. The Listenberger lab is exploring the function of perilipin 2 and the way in which it recognizes and binds to the surface of lipid droplets. Students use a variety of biochemical techniques to address these questions including mammalian cell culture, subcellular fractionation, polyacrylamide gel electrophoresis, and western blotting. This work will be conducted from June 11-August 17th. (Also listed under Chemistry.)

Kim Kandl – RNA1 in the worm C. elegans – 2 students

RNAi, or RNA interference, is a post-transcriptional gene silencing mechanism found in plants, animals and fungi. RNAi is thought to have evolved in these organisms as a viral defense mechanism, but scientists have found that this normal cellular process can be used in the lab to knockdown genes of interest and the resulting phenotype of the organism can then be studied. Researchers can then infer the function of the gene that was knocked down. The purpose of this project is to use RNAi to knockdown genes we are interested in studying in the nematode worm C. elegans. Students will be able to design their projects from start to finish. Along the way, students will learn molecular genetics techniques including PCR, cloning, restriction digest analysis, reverse transcription and gel electrophoresis, and they will become familiar with the care and maintenance of worm cultures and use of worm databases. The broader goal of this project is to develop the RNAi technique for use in the Intermediate Genetics or Molecular Biology laboratories.

Jay Demas and David Van Wylen – Non-visual photoreceptors: irradiance detection in high contrast environments and sensitivity to hypoxia – 1 student

The light sensitive portion of the eye, the retina, signals the brain about the pattern, intensity, and wavelength of light striking the retina. However, this information is used for more than just seeing. A special class of retinal neurons called melanopsin retinal ganglion cells (mRGCs) mediate behaviors that depend on light, but not on vision. These behaviors include constriction of our pupils and photoentrainment, the synchronization of our brain’s internal clock (i.e. circadian pacemaker) with the external environment. Melanopsin, for which these cells are named, is a light sensing protein that makes mRGCs intrinsically photosensitive. In other words, mRGCs can respond to light without the help of the rod and cone photoreceptors responsible for vision. Given mRGCs’ ability to see without additional input from other retinal neurons, it is surprising that mRGCs are, in fact, extensively connected to the rest of the retina. They receive a constant barrage of information derived from rods and cones about the light striking the retina.

We will address two important questions this summer. First, we will investigate whether and how this input from other neurons in the retina helps mRGCs accurately report light levels. Specifically, we will determine the contribution of rod and cone derived input on the estimate of mean light levels in visual environments with varying amounts of contrast. Second, we will investigate the relative sensitivity to oxygen levels of the intrinsic and rod/cone derived mRGC light responses. We will tackle these questions using mice as a model system to take advantage of available genetic mutants. Students will use multielectrode arrays and pupil constriction, a behavior mediated by mRGCs, to record and compare light responses from mouse mRGCs with and without input from other retinal neurons. (See also related project under Environmental Science REU below.)

Steve Freedberg  Population Genetics and Behavioral Ecology of the Smooth Softshell Turtle – 1 student

We will be studying the population genetics and behavioral ecology of the smooth softshell turtle (Apalone mutica) in the Minnesota and Mississippi Rivers in Minnesota. Using a combination of radio tracking and molecular analysis, we will identify
key aspects of their within-population movement and population genetic structure that will inform evolutionary models as well as conservation policies. By comparing measures of genetic variability with other turtle species possessing differing sex determining systems, we hope to also gain insight into how sex determination pattern impacts mutation accumulation over time. Work will include field trapping of turtles throughout southeastern Minnesota, DNA extraction and optimization of molecular markers, and population genetic analysis. (See also related project under Environmental Science REU below.)

Kathleen Shea  Ecology of the St. Olaf Natural Lands – 2 students

Students working with me will focus on applied research on the St. Olaf Natural Lands studying biodiversity, growth patterns, and soil characteristics in forest and prairie ecosystems restored after agricultural use. We will also work on maintenance of restored forest and prairie areas, and examine the effects of different agricultural practices on soil quality and agricultural yields. We documented an increase in prairie biomass production after the large prairie burn in fall 2010. We will examine biomass production in 2012 and determine if it is linked to burn pattern, plant species diversity, soil nutrient levels or soil respiration. We will also measure carbon and nitrogen content in plants and soils to track changes in carbon stocks and nutrient use. Pollinators are critical to the success of many species in the prairie and we plan to collect baseline data on pollinator diversity.

As part of the long-term maintenance of the Natural Lands we will work on several projects. Invasive species are a constant problem in managing natural areas and we will focus on removal of buckthorn, reed canary grass and garlic mustard. As the size of the natural lands has increased more wildlife is using the area. We will monitor deer exclosures with the long-term goal of determining the effects of deer herbivory on tree seedling growth. Students will learn to identify the possible bird species using a series of nest boxes set up as a bluebird trail and will monitor nesting success of bluebirds and other species using the nest boxes. We will also set up a series of 20 x 20 m plots for long-term study of tree growth. Once the plots are set up tree diameter will be measured and future measurements will document tree growth and carbon storage.

The agricultural studies involve working with local farmers to document soil characteristics, nutrient run-off from fields and optimum levels of fertilizer needed to both make a profit and reduce nutrient run-off from fields. Research on soil properties, plant nutrients, farming methods, and economic returns provide “on-farm” research to help farmers make appropriate decisions about nitrogen management. Results will be compared among farms with different farming methods from conventional tillage, to no-till and sustainable farming such as the rotational production system developed by the Rural Enterprise Center.

Students will have the opportunity to explore their own research questions related to the projects described and will work with other St. Olaf or REU students. In addition to an interest in fieldwork and a biology background, experience with GIS and/or statistics would be helpful. Students working during the summer will be encouraged to use some of this research as the basis for an independent research project during the academic year. (See additional positions under Environmental Science REU below.)

PHYSICS

Brian Borovsky – The Molecular Origins of Friction – 2 students

In my research group, we investigate the physics of friction on small length scales. We are interested in testing the limits of the classical laws of friction, those simple relations involving friction coefficients that may be familiar from introductory physics textbooks. Do these laws apply to systems that are very small, with characteristic lengths on the order of micrometers or nanometers? What molecular-level mechanisms are responsible for generating frictional forces and heat?

By pressing a high-resolution force probe onto the vibrating surface of a quartz crystal, we create a microscopic high-speed contact subject to friction. The speeds and contact sizes involved are the same as those encountered in cutting-edge technologies such as microelectromechanical systems (MEMS) and computer hard drives. There are excellent opportunities to engage in both the theoretical and experimental aspects of this work. One area of emphasis is to develop the probe-quartz resonator technique itself as a fundamental tool for measuring frictional interactions. The full potential of this novel method has yet to be realized, in terms of making quantitative force measurements on an absolute scale.

In addition, we are engaged in collaborative work with investigators from Luther College and Auburn University to study a class of monolayers called alkanephosphonates that may be effective coatings for micromachines assembled from metal oxides rather than silicon. We are studying lubricant films consisting  of a single layer of chain-like hydrocarbon molecules. Our goal is to determine how the length of the lubricant molecules and the choice of substrate affect the levels of friction. Current models point to the importance of mutual interactions among the molecules in establishing a well-ordered layer with a minimum number of pathways for energy dissipation.

Jason Engbrecht – Field Research Robotics – 2 students

For a number of years we have been developing a robotics program at St. Olaf and now have many capabilities with sophistical sensor and control system. We now want to turn our attention to the invention of field research robotics at St. Olaf. Specifically, we will be working on the development of robots for research in grassy and underwater environments. Students well suited to this project will have a strong background in physical principles (i.e., physics courses) as well significant program experience. They should also be interested in constructing mechanical systems with metal and wood working techniques and have at least cursory understanding of electronics.

Angela Reisetter  SuperCDMS: Search for Dark Matter  1 student

I work in a collaboration called SuperCDMS, which is one of the leading dark matter searches in the world. We’re hoping to discover what most of the matter making up the universe is. Dark matter is thought to be some kind of heavy particle that interacts weakly with normal matter, and we have a detector underground in the Soudan Underground Laboratory in northern Minnesota which will be able to identify it if we run into it. The background rate at the mine is about 1 Hz, and we have a few years of data, with new data coming in from new detectors, so there is quite a bit of work to sort out the backgrounds from any potential signal (the dark matter). Most of the summer will be spent at St. Olaf doing analysis tasks we are interested in (there are many to choose from, since we have a lot of data to work with), and/or simulation studies, and/or a neutron counter project to study the backgrounds in the mine. Coding can be done in Matlab, a very simple language, or in more advanced languages (C++, perl)  if the student desires.

Bob Jacobel and Knut Christianson  Ice and Climate Geophysics Group (CEGSIC) – 2 students

The world’s glaciers and ice sheets are a critical element in the global climate system now undergoing major change. Our group uses geophysical techniques: ice-penetrating radar and satellite imagery, to examine the surface, interior and base of ice sheets and glaciers. The characteristics of ice internal ice layers and the basal conditions that we measure with our radar, give us information about the evolution of the ice and enable us to study relationships between ice flow and climate change.

Currently we are in the second year of an Antarctic multidisciplinary research project, a collaboration of biologists and geoscientists studying a series of connected lakes beneath the ice in Antarctica. We completed the first year of field work in 2010-11 and are now in the process of acquiring data from a second site during the current Antarctic summer. Our work in the summer of 2012 will focus on the analysis of data from these first two field seasons in preparation for drilling into one of the lakes.

Members in our group work extensively with computers and software to analyze ice-penetrating radar data and satellite imagery as well as learning to write new code in Matlab. We also utilize geopositioning satellite (GPS) data and satellite remote sensing imagery, together with geographic information software (GIS), to establish the spatial context for our radar results. Part of our summer research involves using radar and GPS in a local field setting so that all in the group have the opportunity to acquire new data and work through the analysis process from start to finish. We will read papers and proposals from our colleagues and present our own results to the community. Our research is supported by grants from the Office of Polar Programs, National Science Foundation.

NEUROSCIENCE

Gary Muir  The Neural Basis of Navigation – 1 student

My research program is guided primarily by questions about the neural mechanisms of spatial cognition and navigation. The firing activity of “head direction” cells is thought to represent the animal’s perceived “sense of direction,” or orientation, but how is this signal generated and maintained? How does this neural activity relate to the animal’s navigational decision-making behavior? I am also particularly interested in the role these cells play in enabling us to re-orient following a period of mis-orientation. To answer these questions, students will have the opportunity to observe a “behaving” brain in action by recording the activity of single neurons while freely-moving rats perform spatial tasks. Students will be involved in small animal handling, surgery, and behavioral training; single-unit electrophysiological data collection and analysis; and public psresentation of results. Students interested in continuing the research project into the academic year are especially encouraged to apply.

REU (Environmental Science)

Steven Freedberg  Ecological barriers to interspecific gene flow in freshwater turtles

In the absence of barriers to gene flow, interspecific hybridization is predicted to result in the loss of genetic distinctness between the hybridizing species and the ultimate extinction of one parent species. Recently, my lab has identified a complex of freshwater turtle species (Graptemys sp.) that are capable of hybridization and gene introgression in parts of their range. This gene exchange is noteworthy in light of the fact that the species diverged several million years ago and show extensive morphological and behavioral divergence. These turtles are characterized by distinct ecological niche differentiation, with dietary specialization ranging from molluscivory to herbivory to insectivory.

We are interested in examining the consequences of recent secondary contact and hybridization in these turtles in a large area of sympatry in Weaver Dunes, Minnesota, where phenotypic observations indicate that hybridization is ongoing. Specifically, if hybrids are trapped in an “adaptive valley” between dietary specializations, they may not be optimally suited to exploit either resource, presenting an obstacle to gene flow between species. The proposed project will utilize genetic markers for the mitochondrial control region and a nuclear intron to quantify the extent of hybridization in this region. (See also related project listed above.)

Paul Jackson  Ecosystem assessment of an impaired coldwater brook trout stream

Brook trout are native to Minnesota, but have been lost or displaced from many of their native habitats due to pollution, habitat destruction and competition with non-native species. Several streams in southeastern Minnesota, however, are currently under threat of pollution, nutrients, sedimentation, and E. coli, mostly from surrounding agriculture. A local brook trout stream is no exception; Rice Creek (also known as SpringBrook), is currently listed as impaired for nitrate, turbidity, and E. coli, largely due to its agricultural watershed. The student involved in this project will complete a monitoring program for temperature, a longitudinal temperature profile, turbidity (i.e. sedimentation), and nutrients in the brook trout stream to help us better understand current conditions and identify potential “problem areas” in the stream. Building on the results from the previous year we will also investigate some aspects of trout ecology – including determining essential habitat/spawning areas and food sources. The information gained from this study will provide valuable insight and background that will help guide future restoration and conservation efforts in this stream. The student will be advised by Dr. Jackson, working closely with local government units, non-profit watershed partnerships, Trout Unlimited and the Minnesota Department of Natural Resources.

Kathleen Shea  Ecology of the St. Olaf Natural Lands

Students working with me will focus on applied research on the St. Olaf Natural Lands studying biodiversity, growth patterns, and soil characteristics in forest and prairie ecosystems restored after agricultural use. We will also work on maintenance of restored forest and prairie areas, and examine the effects of different agricultural practices on soil quality and agricultural yields. We documented an increase in prairie biomass production after the large prairie burn in fall 2010. We will examine biomass production in 2012 and determine if it is linked to burn pattern, plant species diversity, soil nutrient levels or soil respiration. We will also measure carbon and nitrogen content in plants and soils to track changes in carbon stocks and nutrient use. Pollinators are critical to the success of many species in the prairie and we plan to collect baseline data on pollinator diversity.

As part of the long-term maintenance of the Natural Lands we will work on several projects. Invasive species are a constant problem in managing natural areas and we will focus on removal of buckthorn, reed canary grass and garlic mustard. As the size of the natural lands has increased more wildlife is using the area. We will monitor deer exclosures with the long-term goal of determining the effects of deer herbivory on tree seedling growth. Students will learn to identify the possible bird species using a series of nest boxes set up as a bluebird trail and will monitor nesting success of bluebirds and other species using the nest boxes. We will also set up a series of 20 x 20 m plots for long-term study of tree growth. Once the plots are set up tree diameter will be measured and future measurements will document tree growth and carbon storage.

The agricultural studies involve working with local farmers to document soil characteristics, nutrient run-off from fields and optimum levels of fertilizer needed to both make a profit and reduce nutrient run-off from fields. Research on soil properties, plant nutrients, farming methods, and economic returns provide “on-farm” research to help farmers make appropriate decisions about nitrogen management. Results will be compared among farms with different farming methods from conventional tillage, to no-till and sustainable farming such as the rotational production system developed by the Rural Enterprise Center.

Students will have the opportunity to explore their own research questions related to the projects described and will work with other St. Olaf or REU students. In addition to an interest in fieldwork and a biology background, experience with GIS and/or statistics would be helpful. Students working during the summer will be encouraged to use some of this research as the basis for an independent research project during the academic year. (See additional positions under project listing above.)

Diane Angell  Prairies and Small Mammals

This summer we will continue projects trapping small mammals in remnant and restored prairies in and around Northfield. Prairies are one of our most endangered biomes and small mammals play crucial roles as predators, prey, seed dispersers and grazers.

We will have several goals this summer. We will trap at multiple locations to look at the species composition of remnant and restored prairies. We will explore the food resources that different species of small prairie mammals rely on by using stable isotope analysis of fur clippings. Finally we will continue to focus on the prairie vole (Microtus ochrogaster), a species categorized by the state of Minnesota as a species of special concern. The prairie vole has disappeared from much of southern Minnesota as prairie has been converted to cultivated land. Remaining populations are essentially isolated on small patches of prairie remnants. Research students need to be independent and motivated! Evenings setting traps and early morning trap checks are required.

Diane Angell – Biodiversity and Sustainable Agriculture

This project will be the start of a large collaborative group working on longer term research related to sustainable agriculture in and around Northfield. Understanding and quantifying the effects of different agricultural practices on biodiversity continues to be important as farmers and government entities consider the costs and benefits of these practices. We will collaborate with other St. Olaf faculty to compare the pollinator, bird and small mammal diversity on different farms. Pollinator surveys will focus on bumblebees (Bombus spp.) and will follow up on surveys conducted during the summer and fall of 2011. Birds will be surveyed visually and small mammals will be live trapped. A knowledge of area birds and a willingness to learn the different Minnesota bumblebees will be important. Research students also need to be flexible and comfortable working with a variety of people with different backgrounds as they interact with local farmers.

Jean Porterfield and John Schade  Linking Genetics and Environmental Science

Wetland ecosystems are an important landscape feature, performing myriad ecosystem services, including purifying water and supporting biodiversity. Wetlands are also a source of trace gases such as methane (CH4) and nitrous oxide (N2O), both of which are powerful greenhouse gases. On the St. Olaf College campus, 15 wetlands have been restored since 1992 to preserve biodiversity and to mitigate runoff of nutrients and other pollutants to downstream ecosystems. These wetlands range in size from small, ephemeral prairie potholes to large permanent ponds, and fluctuate substantially in depth of surface water throughout the year. Although the benefits of wetland construction are generally thought to outweigh the costs of greenhouse gas emissions, this is still controversial, particularly given the possibility that global warming may stimulate higher rates of trace gas production as wetlands get warmer.

A complex set of microbial processes contributes to net production of CH4 and N2O in wetland soils. Our objective in this work is to investigate CH4 and N2O dynamics in wetland soils on the St. Olaf College campus using laboratory and field experiments to estimate rates, and molecular analyses to identify the organisms involved and to link process rates to microbial diversity and the presence of specific functional genes. We also plan to explore the possible use of 13C and 15N natural abundance and isotopic tracer experiments to measure process rates, and to identify when and where these processes are significantly influencing trace gas emissions.

Jay Demas – Ecological Light Pollution and Circadian Photoreception

Most organisms organize their behavior on a daily schedule. For example, nocturnal species, such as mice, are relatively active at night (foraging for food, mating, etc.) and are relatively quiescent during the day. An internal clock in the brain, the suprachiasmatic nucleus (SCN) regulates the timing of these daily behaviors. The roughly 24 hour periodicity of the clock is intrinsic. However, to be useful this clock must be synchronized with the outside world. A small group of neurons in the retina, called mRGCs, are wired directly to the SCN and report light levels indicating whether it is currently daytime or nighttime, a process termed photoentrainment. These neurons express melanopsin, a light sensing protein that makes them intrinsically photosensitive.

This evolutionarily ancient system for sensing daily rhythms in environmental lighting evolved in a world free from the pollution of artificial lighting. Light pollution is growing faster than the human population and recent changes in lighting technology (e.g. LEDs) have led to changes in both the amount and spectral content (i.e. color) of this pollution. The ecological impact of disrupting circadian rhythms is poorly understood, but is likely to chronically stress some species, modify the relative timing of daily behavior between species, and alter the onset of seasonal behaviors such as migration. (See also related project listed above.)

Michael Swift – Zooplankton Ecology in Northern Lakes

Zooplankton are the herbivore trophic level in lakes and form the important link between algae and fishes. Zooplankton have incredibly interesting behavior. Several vertically migrate in the water column – they swim from deep in the lake where it is dark to the surface each evening to feed and swim back down to avoid visually-feeding fishes at dawn. Some, like Chaoborus andLeptodora are predators that feed on other zooplankton species. Some, like Polyphemus, swim around and around together in large “swarms” near the shore. Students will have the opportunity to study these or other aspects of zooplankton ecology in Low Lake and nearby beaver ponds in northern Minnesota. Research projects will be conducted in a semi-wilderness setting at the Coe College Wilderness Field Station (WFS) near Ely, MN. Students must be willing to study aquatic biology by canoe, live and work in an atmosphere of intensive teaching and research, and work independently and cooperatively. Students will begin their research on campus (1+ weeks), complete their field sampling at the WFS where I’ll be teaching aquatic ecology (5+ weeks) and complete their project on campus (2+ weeks). Potential research projects include: the effects of prey size and swimming ability onChaoborus predation; patterns of diel vertical migration by Chaoborus larvae or Daphnia; characteristics of swarming behavior ofPolyphemus; zooplankton biodiversity – distribution of zooplankton taxa in the Low Lake area. (See additional position under project listing above.)