Rebecca Clements, Biology

Red Blood Cell Progenitors as Immune Sensors in Early Life

The Clements Lab studies how the immune system protects infants from viral infection. We’re particularly interested in an abundant yet surprisingly understudied cell type: the red blood cell. Red blood cells are traditionally viewed solely as oxygen carriers, not immune cells. However, emerging research suggests that immature red blood cell progenitors express components of innate immune pathways that detect and respond to foreign nucleic acids. Understanding whether and how these cells sense viral infection could reshape our understanding of antiviral defense in early life.

This summer, a Cascade Scholar will work alongside a Summer Science Scholar to investigate how human red blood cell progenitors detect and respond to foreign nucleic acids. Specifically, the student will:

  • Culture and differentiate human red blood cell progenitors under sterile conditions

  • Assess expression of innate immune signaling components in these cells

  • Use cell biology techniques to examine how and when nucleic acid sensing pathways are activated

  • Analyze and interpret experimental data in the context of primary scientific literature

Through this work, the Cascade Scholar will gain hands-on experience with mammalian cell culture, sterile technique, experimental design, fluorescence microscopy, and other molecular approaches commonly used in immunology and cell biology. Students will also maintain a detailed lab notebook, participate in lab meetings, read and discuss primary research articles, and develop their scientific communication skills.

By contributing to this project, the Cascade Scholar will help advance our understanding of antiviral immune defenses in newborns while gaining foundational research skills in a collaborative laboratory environment.

Highly recommended: Scholars should have completed BIOL 115/116 and BIOL 109/110

Karen Hicks, Biology

Using genetics to study seasonal responses in the moss P. patens

Many organisms use seasonal cues, such as day length and temperature, to synchronize their reproduction with favorable conditions. For example, our study organism, the moss P. patens, reproduces in the fall, but not in the summer, in response to daylength and temperature cues. Although many different flowering plants use the same genetic mechanisms for regulation of seasonal reproduction, our previous research suggests that the moss P. patens uses a distinct and novel downstream pathway to regulate reproductive development in response to seasonal cues. Our current research program seeks to discover how this novel downstream pathway works — what are the genes and proteins involved, how are they regulated, and how do they connect to one another? We welcome Cascade Scholars to work alongside a Summer Science Scholar to 1) use quantitative genetic mapping to discover novel genes that drive natural variation in seasonal responses; 2) create knockout mutations in candidate genes to test their requirement for proper seasonal reproduction. Through this work, Cascade Scholars will gain experience with DNA isolation, genetic cloning, CRISPR-Cas9 targeted mutagenesis, and plant transformation, as well as gain expertise in plant development and seasonal responses and build skills in reading primary literature, all in a collaborative laboratory environment. Recommended coursework: BIOL115-116 and preferably also BIOL109-110.

Ethan Hillman, Biology

Exploring the Indole Lactic Acid Biosynthesis Pathways in Bifidobacteria

Gut microbes produce a wide array of bioactive metabolites that influence human health, yet the enzymes responsible for many of these transformations remain uncharacterized. Bifidobacterium species, common members of the gut microbiome, have been implicated in the production of Indole-3-lactic acid (ILA), a derivative of tryptophan metabolism with potential immunomodulatory and neuroactive effects. However, the specific genes encoding aromatic lactate dehydrogenases (ALDHs) responsible for this transformation remain to be validated.

This project will use E. coli to express and purify candidate ALDH genes from Bifidobacterium species to assess their role in ILA biosynthesis. Students will clone target genes into expression vectors, induce protein production in E. coli, and purify the recombinant enzymes. Enzyme function will be confirmed through biochemical assays measuring ILA production. This work builds on previous efforts in our lab to functionally characterize microbial enzymes involved in biosynthesis of host-interacting metabolites, expanding our understanding of gut microbial contributions to host health.

Cascade scholars will gain hands-on experience with molecular cloning, recombinant protein expression and purification, and enzymatic assays. Students interested in microbiology, genetics, and microbial metabolism will gain valuable research skills while contributing to the broader understanding of beneficial microbial metabolites. Students will also learn how to engage with scientific literature and craft both oral and written presentations. 

Expected Project Start Date: Week of May 27
Students should have completed BIOL 115/116 and BIOL 109/110

Peter Kropp, Biology

Analysis of Iron-Induced Germ Cell Death

Mitochondria are the powerhouse of the cell, but when that powerhouse malfunctions it can lead to many different types of cellular dysfunction. In the Kropp Lab, we study mitochondrial diseases - situations where mutations to one gene cause mitochondrial dysfunction and, consequently, diseases in humans. To understand these diseases, we use a microscopic round worm called Caenorhabditis elegans which allows us to understand the molecular and cellular biology of these diseases in a system that is easy to work with.

One of the diseases we study is called MEPAN Syndrome, and our worm model has multiple problems with its germ cells (the precursors of sperm and eggs). We have preliminary evidence that there is increased cell death in the germ cells, and we want to try to figure out why. Our working hypothesis is that iron is dysregulated causing a specific type of cell death called ferroptosis. The Cascade scholar working on this project will help to test whether or not this hypothesis is correct and, if it is correct, can we rescue the cell death by reducing iron stress.

The student working on this project will learn skills in: 1) C. elegans maintenance and manipulation, 2) Fluorescent imaging and analysis, 3) western blotting, and other techniques as needed.

Kamesh Regmi, Biology

Plants, as photoautotrophic organisms, manufacture sugars in their leaves (i.e. source) and distribute them through a specialized vascular network called the phloem to heterotrophic sinks — energy-hungry organs like roots and seeds that cannot produce their own food. A plant’s total productivity is intrinsically tied to how efficiently the photosynthates are transported, and simply maximizing photosynthesis will instead lead to feedback inhibition. To bypass this bottleneck and maximize productivity, we hypothesize that empowering the transport of sugars from source to sinks, such that either (i) more sugars are pushed out of the source, or (ii) more sugars are
pulled into the sinks, would be viable biotechnological strategies to improve plant productivity [1,2].

Figure 1: The consensus model for phloem loading in Arabidopsis thaliana based on
References 3 – 10.

INTELLECTUAL MERIT
In the Regmi Lab, we use model plant Arabidopsis thaliana to test the aforementioned hypothesis. Within this larger framework, we are currently working towards energizing the transport of photosynthesized sugars out of the source leaves. From several studies in model dicot Arabidopsis, we now not only know the proteins involved in the active movement of sugar into the phloem cells, but also the putative order in which they function during sugar delivery [Figure 1; 3 – 10]. The photosynthesized sugar first passively moves via plasmodesmata from photosynthetically active mesophyll cells into phloem parenchyma (PP) cells where they are effluxed into the cell wall space by Sugars Will Eventually Be Exported Transporter (SWEET) facilitator proteins [6]. This cell wall space separates the PP cells from the adjoining companion cells (CCs), and the sugar needs to be actively loaded into CCs by sucrose/proton symporters (SUTs) [9]. This secondary active transport is powered by plasma membrane-localized P-type ATPases in the CCs [5, 10]. The CCs are where the sugars get concentrated before being transported to the sinks via neighboring sister cells called sieve elements (SEs). To maintain a supply of ATP to power the ATPases, some of the imported sugars in CCs are metabolized by the Sucrose Synthase (SUS) enzyme [3, 4, 8]. As such, we hypothesize that the phloem-specific and constitutive overexpression of a constitutively active P-type H+-ATPase (AHA3) in Arabidopsis will enhance the flux of sugars out of photosynthetically active leaves [2]. Felicia Liu ‘26 and I collaborated last summer as part of KSSS to construct chimeric plasmids that would allow us to overexpress a constitutively active P-type H+-ATPase in a constitutive (p35S::tAHA3) or a phloem-specific (pCOYMV::tAHA3) manner [2].

EXPERIMENTAL STRATEGY
In the summer, the Cascade scholar will assist the Kenyon Summer Scholar in selecting homozygous, single T-DNA insertion lines. Once the seeds from the T0 plants are dry, it will be time to select for transformants. It will be very important to select multiple T1 plants from each transformation event, and as such, we will isolate a minimum of five independent transformants from each vector (Figure 2)2. We have no control over how many insertions occurred. Having too many insertions can cause artifacts from over-expression, and such a construct will likely be silenced in subsequent generations. We will know if we obtained a transformant with a single insertion because it will segregate 3:1 in the T2 generation. We also have no control over where the T-DNA will be inserted. If our insertion occurs in a coding region, it may cause unexpected phenotypes. For most downstream phenotypic analysis, it is appropriate to begin working in the T2 generation. The selection process itself can affect the growth of resistant plants, so we will also want to know the effect of the insertion in the absence of selection [11]. In the process, the Cascade scholar will learn the following skills:

  1. working under sterile conditions in a laminar
    flow hood,
  2. making selective media to grow and select transgenic Arabidopsis,
  3. setting up and running PCR to genotype transgenic Arabidopsis,
  4. growing and tending to Arabidopsis plants to collect seeds,
  5. apply concepts learned in BIOL115/116 (e.g. Mendelian genetics) for
    selection of homozygous transgenic Arabidopsis line.

REFERENCES

  1. Yadav, U. P., Ayre, B. G., & Bush, D. R. (2015). Transgenic approaches to altering carbon
    and nitrogen partitioning in whole plants: Assessing the potential to improve crop yields and nutritional quality. Frontiers in Plant Science, 6, 275.
  2. Liu, Xinyi, Tiffany Yang, and Kamesh Regmi. "Vector construction for the Constitutive and Phloem-specific Overexpression of a truncated P-type H+-ATPase, AHA3, in Arabidopsis thaliana." (2025).
  3. Nolte, Kurt D., and Karen E. Koch. "Companion-cell specific localization of sucrose synthase in zones of phloem loading and unloading." Plant Physiology 101.3 (1993): 899-905.
  4. Martin, Thomas, et al. "Expression of an Arabidopsis sucrose synthase gene indicates a role in metabolization of sucrose both during phloem loading and in sink organs." The Plant Journal 4.2 (1993): 367-377.
  5. Lerchl, Jens, et al. "Impaired photoassimilate partitioning caused by phloem-specific removal of pyrophosphate can be complemented by a phloem-specific cytosolic yeast-derived invertase in transgenic plants." The Plant Cell7.3 (1995): 259-270.
  6. DeWitt, Natalie D., and Michael R. Sussman. "Immunocytological localization of an epitope-tagged plasma membrane proton pump (H+-ATPase) in phloem companion cells." The Plant Cell 7.12 (1995): 2053-2067.
  7. Chen, Li-Qing, et al. "Sucrose efflux mediated by SWEET proteins as a key step for phloem transport." Science 335.6065 (2012): 207-211.
  8. Pizzio, Gaston A., et al. "Arabidopsis type I proton-pumping pyrophosphatase expresses strongly in phloem, where it is required for pyrophosphate metabolism and photosynthate partitioning." Plant physiology 167.4 (2015): 1541-1553.
  9. Truernit, Elisabeth, and Norbert Sauer. "The promoter of the Arabidopsis thaliana SUC2 sucrose-H+ symporter gene directs expression of β-glucuronidase to the phloem: evidence for phloem loading and unloading by SUC2." Planta 196.3 (1995): 564-570.
  10. DeWitt, Natalie D., Jeffrey F. Harper, and Michael R. Sussman. "Evidence for a plasma membrane proton pump in phloem cells of higher plants." The Plant Journal 1.1 (1991): 121-128.
  11. He et al. Selecting Homozygous Transformed Plants. (2013) Michigan State University.

Natalie Wright, Biology

Why do male and female birds (sometimes) differ in their flight anatomy?

My lab is studying why in some species of birds, males have larger flight muscles than females, but in other species, the pattern is reversed, and in still others, the sexes exhibit no difference in flight muscle size. We take two approaches to these questions: First, we are compiling a dataset of skeletal measurements of a thousand species of birds (measurements of bones are excellent proxies for the sizes of the muscles that attach to those bones). Second, we test the functional effects of sexual dimorphism in flight muscle size by studying flight biomechanics. This summer, we will have active projects using both approaches. The Cascade Scholar may choose which project they wish to focus on, but there will be opportunities to help with all projects in the lab and therefore learn many skills.

For the first project, we will travel to a museum research collection to take digital photographs of bird skeletons. Back in the lab, we will measure bones from the digital photographs we took in the museums. We will also compile data on life history and ecological traits to test which of these traits predicts sexual dimorphism in flight muscle size. We will spend most of the summer in Gambier, but will make a one-week trip to natural history museums to collect data (TBD; e.g., the Smithsonian National Museum of Natural History in Washington, D.C., or the Field Museum in Chicago). All travel expenses will be paid for by Wright’s grant, including hotel and food while away from Gambier.

For the second project, we will examine whether male and female house sparrows, which differ in their flight muscle size, have different takeoff flight biomechanics. We will capture house sparrows around Gambier and use high-speed video cameras to film standardized takeoff flights in the lab. We will be continuing an experiment from last summer assessing flight maneuverability through an obstacle course. We then digitize these videos to calculate velocity, acceleration, wingbeat frequency, and other measures of flight performance. After experimentation, we will euthanize the birds (they are an invasive species), dissect them to measure flight muscle and heart sizes, and test whether these or other morphological characters (e.g., wing size, shape) predict flight performance within this species.

A third project will involve studying 3D flight of wild tree swallows and Eastern bluebirds in the field. We will hike to nest boxes at the BFEC and around Gambier and set up three GoPro cameras to capture 3D, high-speed videos of birds flying to and from their nest boxes. We aim to understand how these two different aerial insectivores differ from each other in their flight biomechanics, as well as how males and females within each species differ from one another in their wild, natural flight.

The Cascade Scholar will learn basic bird biology and ecology, physics and aerodynamics of flight, how to identify bird bones, how use ImageJ to take measurements from photographs, how to safely handle wild birds, how to collect data from videos, museum-quality dissection techniques, and data analysis and visualization in R. No previous knowledge is necessary, but some prior experience using R is helpful (e.g., having taken BIOL 109/110, STAT 106, STAT 206, or STAT 226).

Please note that summer research in the Wright Lab will take place either May 11-July 11, or May 18-July 18 (depending on the Cascade Scholar’s preference). We must start early in the summer in time with the birds’ breeding season.  

Yutan Getzler, Chemistry

Bespoke Polymer Degradation

If you love working with both your hands and your mind, and will have completed two semesters of chemistry lab by this summer, this may be the project for you.

We seek to build polymeric materials whose functional lifetimes can be rationally tailored. Polymers, sometimes called plastics, are large molecules synthesized by the repeated linking together of many small molecules (monomers). The properties of a polymeric material stem from its size, shape, and repeat unit. Properties we value at one point in a compound’s life, such as durability, may become harmful. Controlling how material properties change over time may mitigate these harms.

Cascade Scholars who join the group this summer will help complete the synthesis of a small library of monomers for use in this project. Most of these monomers have not previously been reported in the scientific literature, so you may bring a new molecule into being. The monomer synthesis is three steps long, two of which have been completed by your predecessors. To honor the value of their work and these materials, you will start the summer learning to perform the relevant synthetic transformation on a closely related, commercially available, starting material. When you feel ready, you will tackle the new work.

You will master the standard techniques and tools of organic synthesis, including aqueous workups, thin layer chromatography, rotary evaporation, flash column chromatography, recrystallization and NMR spectroscopy.

Nathanael Hunter, Chemistry

The Hunter lab uses synthetic inorganic chemistry to study the behavior of the group 14 elements, especially germanium and silicon, in molecular compounds. Students work across many different areas of chemistry, ranging from studying the spectroscopic properties of these synthesized compounds using instrumental techniques, to testing their competency to catalyze reactions common to organic chemistry. Observations made in the laboratory are investigated further using computational chemistry techniques with the goal of correlating the molecular geometry and orbital population to the spectroscopic or chemical behavior shown. The Cascade scholar will work collaboratively with other Hunter Lab student researchers and will be trained in synthetic and spectroscopic techniques typically used in inorganic chemistry. 

Preferred coursework: At least CHEM 121 (or 122). 

Kerry Rouhier, Chemistry

Stress, Survival, and Synthesis: Unlocking Plant Metabolic Pathways

Our research group is interested in the enzymes, intermediates, and pathways that help organisms grow and respond to stress. For example, when plants are stressed by outside factors they break down branched-chain amino acids, such as valine, as alternative sources of energy. They may also use these molecules to make specialized metabolites, such as acylsugars, to help protect the plant from infection or pests. This summer we will be focusing on two projects that aim to characterize important metabolic enzymes - one involved in valine degradation and another in acylsugar synthesis. The Cascade scholar will learn many common molecular biology and biochemistry lab techniques such as cloning and protein expression, purification, and enzyme functional characterization to better understand the role of these enzymes in plant growth and defense processes. Additionally, the scholar will learn how to read and analyze primary literature and improve their written and oral scientific communication skills. No previous knowledge or experience is necessary, but having taken courses such as CHEM 123/126 or BIOL 109/110 is preferred. Research for this project will be conducted from June 1 - July 31, 2026.

Matthew Rouhier, Chemistry

How Do Mosquito Kidneys Sort Friend From Foe: Understanding Xenobiotic Transport In Aedes aegypti Renal Tubules

My research group is interested in mosquito kidney function, particularly how mosquitoes remove unwanted or toxic molecules like dyes. This summer my research group is using microinjection to determine if two particular classes of transporters are involved in the removal of dye molecules. The project will introduce the scholar to microscopy (preparing and injecting mosquitoes with dyes) and molecular biology (extracting RNA, amplifying DNA and sequencing of DNA). In addition, the scholar will practice electronic notebook keeping, discuss their research project with other scientists and non-scientists, and practice applying the scientific method within the context of fighting mosquito-borne disease.

Noah Aydin, Mathematics & Statistics

Coding Theory: Search for Good Classical and Quantum Codes

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 the 1960's and 70’s, their use in compact disks in 1980’s, and more recently in wireless communication, they have been an increasingly important part of modern life in the information age. Quantum error correction  is a critical  component of building large scale quantum computers. It is  possible to obtain quantum codes from classical codes with certain properties.

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 the 1940s, there are still many instances where codes with best possible parameters are yet to be discovered. Various mathematical ideas and tools have been developed to search for and construct good codes. 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 a certain generalization of cyclic codes  known as polycyclic codes, 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, as well as quantum codes with good parameters. Students interested in this project should have taken Linear Algebra and should have programming experience.

Frank Peiris, Physics

Optical Properties of 2D-semiconductor Thin Films

Light-matter interactions in materials from IR to UV regions of the electromagnetic spectrum are governed mainly by their property called the dielectric function, which couples via Maxwell’s Equations to alter the propagation of electromagnetic waves in a material. Microscopically, these alterations occur because the waves interact with electrons and phonons (i.e., quanta of lattice vibrations) of the material. Consequently, by measuring the dielectric function of a material, the "sociology" of electrons and phonons inhabiting the material can be recovered. 

Students working in the lab use spectroscopic techniques to determine the dielectric function of a variety of materials including semiconductors and other novel materials. Besides learning the experimental techniques, Cascade Scholars who join the group this summer will learn how to model the experimental spectra in order to recover the dielectric function of a material. Working collaboratively with other student researchers, the Cascade Scholars will pursue a research project on a series of 2D-semiconductor thin films, investigating their optical properties in a wide spectral range spanning from far-IR to UV.

Dates: May 11 - July 18
Preferred coursework: PHYS 140 and PHYS 145

Tom Giblin, Physics

Cosmic Preheating in the Lab

Recently, analog gravity experiments have opened up a new avenue through which to study cosmological processes by proxy.  Working in concert with the analog gravity group at the University of Nottingham, this project will examine how numerical simulations of preheating can help validate these experiments and explore how these experiments can extend our understanding of preheating.

Coursework:  PHYS 140/145 (and lab).

Sarah Murnen, Psychology

LGBTQ+ TV and Social Media's Role in Queer Youth's Identity Status and Well-Being

The purpose of this study is to extend and replicate a study in which the authors found a positive association between LGBTQ+ TV exposure and identity affirmation and resilience among queer youth (Dajches & Barbati, 2024). Our study will extend the media measurement to include exposure to a broader range of LGBTQ media, including social media representations. We will examine how LGBTQ media exposure more broadly defined relates to both a sense of queer identity and indicators of well-being among a group of queer young adults sampled from Prolific. The first part of the summer project will involve collecting and revising measures from previously published research and creating an online survey. The survey will be administered and data analyzed in the second part of the project. A declared major in anthropology, psychology, sociology, or GSS is preferred along with an interest in learning more about quantitative research methods. 

References

Dajches, L., & Barbati, J. L. (2024). Queer on TV: Using the minority stress model to explore the role of LGBTQ+ television exposure in LGBTQ+ audiences’ psychological well-being and identity status. Psychology of Popular Media, 13(4), 721-728. doi.org/10.1037/ppm0000548