Cascade Project Descriptions

The projects available for Cascade Scholars are described below. Projects are organized alphabetically by the mentor's last name and by department. Remember: on the application form, you will be asked to rank your top three projects and to explain your interest in each.

Cascade scholars will engage with ongoing research in the lab investigating population-level variability in key physiological traits of Sphagnum magellanicum, an ecologically important species that inhabits a range of bog environments spanning from polar to equatorial regions around the world. Using a common garden approach, we will assess carbon, water and optical traits from populations collected across a broad latitudinal gradient spanning from northern Canada to Florida. The primary research stream revolves around measuring Sphagnum carbon exchange in response to climate drivers such as temperature. Here, students will measure photosynthetic carbon uptake and respiratory carbon losses using gas exchange techniques. A second research stream focuses on Sphagnum water relations. Here, students will use and develop psychrometric techniques and protocols for assessing tissue water potential under different environmental conditions, and relate these data to plant carbon uptake. Finally, a third research stream is focused on light relations of different Sphagnum populations. Here, students will use and develop optical techniques and protocols to assess light reflectance, transmittance and absorbance in Sphagnum capitula in order to better understand light capture and utilization among different S. magellanicum populations. Students will be encouraged to explore multiple research streams within the lab as part of their Cascade experience.

Many organisms synchronize their sexual maturity and/or reproduction with favorable climatic conditions, which increases the odds of producing successful progeny. Plants, in particular, make use of environmental cues, such as day-length and temperature, to gauge the optimal time to initiate the formation of the reproductive structures that produce gametes – a process termed reproductive development. While the genetic mechanisms that regulate reproductive development in response to seasonal cues are largely conserved among flowering plants (Angiosperms), it is not known how their distant relatives, the first plants to come on land, use environmental cues to signal the onset of reproduction. Mosses (Bryophytes), are among these early land plant lineages and can thus aid in answering this question. Specifically, the moss Physcomitrella patens is a genetically tractable model species with an increasingly sophisticated set of community resources, including a sequenced reference genome and well-established protocols for transformation and the creation of targeted gene knockouts. Importantly, phenotypic variation in seasonal responsiveness among P. patens accessions collected across Europe provides the means to identify candidate regulatory genes by comparing genomic sequence and gene expression between responsive and non-responsive groups. Based on such data, our group has identified several genes that may regulate seasonal reproduction in P. patens. The incoming student will work along with Summer Science Scholars to generate and characterize P. patens mutants in candidate regulators of seasonal reproduction. The student will gain experience with CRISPR-Cas9 targeted gene mutagenesis and plant transformation, along with techniques in statistics, evaluating gene expression, and plant development.

Earth is home to tens of millions of species, and almost all of them depend on plants, which use light and water to spin air into sugar. In doing so, plants power Earth's ecosystems and regulate its climate, but we still have much to learn about their evolutionary history and how they interact with their environments. Research in the Kerkhoff Lab is focused on the evolution of biodiversity and ecological function of plants, using both field research and computational data science approaches.

This summer, we have two Cascade projects available. The first is a field-based project in the Bishop's Backbone Forest on the BFEC. There we are studying how variation in the structure of the forest canopy influences carbon exchange. In particular, we are asking whether rates of soil respiration are correlated with the leaf area index, a measure of the total area available for photosynthesis. The second project, which is more computational in nature, utilizes data compiled by thousands of plant researchers to reconstruct evolutionary variation in leaf structure, with applications for both reconstructing paleoclimates and understanding how ecosystems will respond to future climate change. Cascade Scholars can gain experience with tree identification, field respirometry, hemispherical photography, image analysis, data management/analysis, and scientific communication. Because this kind of work frequently requires more than two pairs of hands or eyes, all lab members will, at times, help with both projects, which makes for a varied and fun work environment over the summer.

The metamorphosis of an aquatic tadpole to a terrestrial frog is a dramatic developmental transition that involves remodeling of multiple tissues. The thyroid hormone system is the master regulator of metamorphosis. An early response to thyroid hormone is the induced expression of Krüppel-like factor 9 (klf9), a transcription factor that governs the expression of other important genes with specific roles in tissue remodeling. Disruption of klf9 expression could have devastating effects on this process. My lab seeks to determine the basic mechanisms by which klf9 expression is regulated and how this can be altered by exposure to environmental contaminants. The Cascade project will involve a suite of assays to measure gene expression in both cultured frog cells and living tadpoles. The Cascade student will be expected to take substantial ownership of the project while working under my mentorship and that of a KSSS student with deep experience in the lab.

The Bacteria Lab has a special project for a Cascade scholar, analysis of the unique “red nose” bacteria Rhodoferax antarcticus. These bacteria were isolated from samples obtained by Dr. S. from field work on an ice-bound lake in Antarctica. At cold temperatures, the bacteria photosynthesize and grow, forming red “noses” of biofilm that creep along the lake sediment (or the interior of a test tube). In Antarctica, these red biofilms float up to the ice, migrate up through several years of freeze-thaw cycles, then blow off on the wind to be carried to a new lake. The growth properties of the blob-forming Rhodoferax will be studied as a function of temperature and salt concentration. Their genome sequence will be analyzed for antibiotic producer modules and cold-resistance genes. Antibiotic producer genes could be of interest because Antarctic antibiotics would never have encountered human-associated bacteria, so our microbiomes would lack resistance genes. Cold-resistance genes are of use for biotechnology, the development of industrial enzymes that are active at low temperatures. Rhodoferax antarcticus is one of several hundred unique Antarctic microbes predicted in our samples by phylogeny analysis. The Cascade Scholar will also have the opportunity to investigate other microbes from our samples that might be cultured.

Research in the Wright Lab focuses on the ecology and evolution of bird flight. This summer, we have two potential projects for a Cascade student. First, we are studying how baby bluebirds learn to fly. This experiment will test whether juvenile bluebirds develop flight ability faster when they can observe their parents flying than when raised in isolation from adult bluebirds. It will involve regularly testing measures of bluebird flight performance, including ability to generate lift sufficient to overcome gravity, take-off velocity and acceleration, ability to land on a perch, and in-flight maneuverability.

The second project will focus on sexual dimorphism of flight performance. In many bird species, males have larger flight muscles than females, but we don’t know why or how that affects their flight capabilities. Do larger flight muscles allow males to take-off faster? Are males more maneuverable? Do males fly more often than females? This project will involve filming wild bluebirds at their nest boxes around Gambier, as well as testing the flight performance of adult bluebirds housed in aviaries.

Both projects will involve mist-netting (a common method of capturing wild birds), handling wild birds, using high-speed video cameras, converting videos of birds flying into usable data, and analyzing results in R. Most of our work is easier when two or three people are working together rather than each trying to collect data and corral birds solo, so all students in the lab will assist with all projects. Because birds are most active shortly after dawn, some work days will begin at sunrise (e.g., when we’re trying to net wild birds). Most work, however, will take place during typical work hours. For more information, please contact Professor Wright (wright1@kenyon.edu).

If you look closely at a plant or animal you will see that life results from a variety of intertwined cyclical processes---heartbeats, neural signals, the sleep-wake cycle, etc. My research interests revolve around trying to understand the chemistry behind such phenomena using computational methods. (No prior knowledge of programming, etc. required, it is all on-the-job learning.)

We have two major projects in the lab. The first project involves understanding the chemical role of Ca2+ oscillations in astrocytes, a cell within the central nervous system. Asides from being an interesting chemical question, we believe this is important since neurodegenerative diseases, while being marked by deterioration of neurons, seem to be affected by the health of the neighboring astrocytes and microglia.

The second project involves gaining insight on the how cellular oscillators, like neurons and astrocytes, interact. Instead of using models of the cells, we are using more basic models (ex. FitzHugh-Nagumo) to understand how individual oscillators can influence one another to synchronize (ex. how neurons synchronize during epileptiform activity) or break an established order (ex. ventricular arrhythmia in the heart).

The Hofferberth lab focuses on the synthesis of organic molecules and the exploration of new reactions in organic chemistry. A CASCADE student joining the lab this summer would work with other research students in exploring a new chemical reaction we discovered, a vinylogous aldol reaction, that forms an important yet difficult to synthesize arrangement of carbon atoms termed an all carbon quaternary stereocenter. Such arrangements are found in organic molecules produced in nature and in many important pharmaceutical drugs and industrially important chemicals. The student would begin by learning laboratory techniques and operations required for organic synthesis and will progress to running their own reactions in support of the larger goals of the laboratory.

The focus of this project is to develop methods for conjugating bioactive compounds to carbohydrates in order to increase water solubility, bioavailability and their half-life in our body.

Project 1: (Developmental) We want to extend our recent work in establishing fluorescent lifetime measurement in the frequency domain. As applied to fluorescence microscopy, fluorophore lifetimes provide a quantitative probe of environment with the advantages of fast imaging and high contrast. The project advances our current apparatus by incorporating a homodyne detection method. A new researcher will gain experience with diode lasers, oscilloscopes, and a variety of photon detection systems. Additionally, he/she will become a master of signal analysis.

Project 2: (Research) Thermal lenses spectroscopy relies on a local temperature change in a sample upon laser irradiation. Because the technique is based on the direct measurement of absorbed optical energy, it is more sensitive than conventional absorption techniques. Until recently aqueous samples were considered poor candidates for a thermal lens; however, the aqueous micelles have been recently reported to enhance the thermal lenses of solubilized substrates. A new researcher will gain extensive experience with several laser systems and will explore the finer points of micelle formation.

The K. Rouhier research group is a plant biochemistry lab, focused on studying novel enzymes and pathways that affect plant growth and development. Research this summer will focus on finalizing the details of beta-alanine synthesis in plants. Beta-alanine is an important precursor in the formation of vitamin B5 and coenzyme A, a key component in lipid and amino acid metabolism. Previous evidence showed that uracil was likely the major precursor for beta-alanine, but recent work in our lab shows that branched-chain amino acids, particularly isoleucine, could also serve as key precursors. This summer we will be using a variety of techniques including GC-MS and NMR to trace the metabolic pathways between isoleucine and beta-alanine in the model plant organism, Arabidopsis thaliana, and more agriculturally relevant plants such as corn, lettuce, and tomato. The Cascade Scholar will assist in growing and maintaining our plant systems and preparing extracts for analysis, as well as learning proper use of GC-MS and NMR instruments.

My research group is interested in mosquito physiology as it pertains to spawning the next generation of pesticides. There are currently two potential projects for the summer of 2018. The first project entails the exposure of mosquito larvae (the aquatic life stage of the mosquito) to dyes that are only toxic in the presence of light. This project will teach a cascade scholar the life stages of the mosquito, the requirements for mosquito growth, the preparation of light-activated molecules, and the properties of visible light and reactive oxygen species. The second project involves the isolation of nucleic acids from various mosquito tissues to determine if a particular detoxification gene is being expressed. This process would involve learning the use of a dissecting microscope to harvest mosquito tissues, micropipettes while extracting RNA, and thermocyclers to quantify the amount of RNA present. Both projects will introduce the cascade scholar to the practice of electronic notebook keeping, provide opportunities for the scholar to discuss their research project with other scientists and non-scientists, and practice applying the scientific method to counteract mosquito-borne disease.

Error correcting codes are used everywhere data is transmitted from one place to another. Since their applications in early computers in the middle of the 20th century, deep space communication in 1960’s and 70’s, their use in compacts disks in 1980’s, and more recently in wireless communication, they have been an increasingly important part of modern life in information age. One of the main problems of coding theory is to construct codes that are as efficient as possible. Although much progress has been made in this problem since the beginning of the subject in 1948, there are still many instances where codes with best possible parameters are yet to be discovered. The design and implementation of codes rely on mathematical principals and tools. Searching for better codes is computationally challenging. Of the many different types of codes that have been designed, cyclic codes have a special place in coding theory. Providing a key link between coding theory and algebra, they are important for both theoretical and practical reasons. Cyclic codes and their various generalizations have been a good source of constructing best possible codes. In this project, we will explore cyclic codes and some of their generalizations from mathematical and computational perspectives. Building on the works of former Kenyon students who have done research in coding theory and contributed dozens of new codes to the database of best known codes (available at codetables.de), we will design algorithms to search for new linear codes with better parameters than the currently best known codes. A successful student for the project will have basic programming experience. Resources for necessary mathematical background for the research (relevant readings and guidance from the mentor) will be provided as needed.

The Kenyon Psychological Neuroscience Laboratory (KPNL) investigates the “social brain”; those brain areas that support perception of socially relevant stimuli such as emotional face expressions, gaze shifts, biological motion, and underlying social competencies such as the inference of another’s goals and intentions. To do so we use a combination of electroencephalography (EEG; aka “brainwaves”), event-related potentials (ERPs; a method for analyzing EEG data), and behavioral paradigms. Experiments in the lab are largely focused on face perception, which is a highly developed visual skill that is vital to typical social processing, and thus an ideal model system for advancing our understanding of the social brain. The extremely complex processes that support face perception are belied by the speed and ease with which we detect and identify faces, read facial expressions, interpret gaze direction, etc. The KPNL investigates the nature and timing of the neural processes that make such complex tasks feel so effortless. Specifically, research this summer will focus on two ongoing projects. The first uses EEG to investigate what visual information is necessary for the brain to “know” it is looking at a familiar face. The second uses EEG and behavioral measures to investigate the non-conscious processing of faces. In other words, does your brain detect the presence of a face even when you are not consciously aware of seeing it? Summer research students will contribute to these projects and gain experience in several aspects of cognitive neuroscience research, chief among them learning to acquire and analyze EEG/ERP data.

The Cosmology and Astroparticle lab at Kenyon studies the intersection of Astrophysics and Particle physics. We use numerical methods to model the dynamics of the Universe and its contents to probe what may have happened in the early, hot, dense environment of the early Universe. From this, we get information about how matter and energy interact in fundamental ways. Much of our work produces large datasets, these include information pertaining to the characteristics of the simulated universe. One major challenge we face is being able to take these datasets and reducing, analyzing and displaying the information therein. The Cascade scholar will be primarily responsible for data extraction, visualization and analysis. The scholar will learn how to use our software and work with other students in the lab to run simulations. The scholar will also be responsible for the development of our suite of visualization packages and statistical analysis tools.