Error correcting codes are used everywhere data is transmitted from one place to another. One of the main problems of coding theory is to construct codes that are as efficient as possible.
Although much progress has been made on this problem, there are still many instances where codes with best possible parameters are yet to be discovered. We have an ongoing research program addressing this challenge to which Kenyon students contribute substantially. Our main goal is to develop search algorithms to find new linear codes with better parameters than previously best known codes.
This is a challenging problem in coding theory with many open cases. Our research over a decade has been very successful. Many Kenyon students are record holders for dozens of best known linear codes. We produced many concrete results, publications, and presentations. Every year, research students in my group keep refining and improving the search methods. The insights, tips, and recommendations from their collective experiences are passed down to future students in the form of a document that we call “Guide” that is updated every year.
We have many more ideas to explore and expand the research in different directions. Our research is highly computational and the theoretical background is mostly from linear algebra. The Cascade scholar will work with other students to improve and generalize existing search algorithms developed by former Kenyon researchers. The work involves algorithm development, testing, and implementation as well as coming up with theoretical results (making conjectures and trying to prove them) based on computational results.
We will brainstorm and exchange ideas, share tips, and work on overcoming roadblocks together as a group. It will be a highly collaborative experience. The minimum background and qualifications for this position are a) significant experience in programming, b) basic knowledge of linear algebra.
Course requirements: Scientific Computing 118 and Math 224, or equivalent
What if durable material could, under the right conditions, suddenly break down into its individual components? What if a drug payload could be released from a polymer matrix only when specific physiological conditions are encountered? In 2017, a student in the Getzler lab serendipitously discovered a class of polymers whose degradation could be triggered by a Lewis acid catalyst and time or heat. Polymer degradation that might otherwise take months or longer occurred in a matter of days or hours. We have been building a library of monomers to explore the properties of these materials and the conditions under which they will degrade.
This summer, the team will tackle the last of three monomer synthesis steps, a Baeyer-Villiger oxidation. We know the process works and we are going to make sure that we have a process that generates the least waste, in the least time, with the highest yield and purity. You will work with two rising juniors and learn many fundamental skills of organic synthesis including experimental design, quantitative transfer, work-up, flash chromatography, TLC, NMR spectroscopy, and more.
Course requirements: two semesters of chemistry lab coursework
Consider the salt and water balance challenges faced by a mosquito during its short life cycle. Aquatic larvae live in freshwater and face osmotic water influx and diffusive salt loss. In contrast, terrestrial adults lose water by evaporation. Female mosquitoes confront a particular challenge after a blood meal — they must rapidly excrete a bolus of salt and water approximately equal to their pre-meal body mass. My research group studies the membrane transport proteins that allow mosquitoes and other insects to deal with these diverse challenges. These proteins also have roles in the nervous system because they influence the excitability of neurons.
We currently study a group of sodium dependent cation-chloride cotransporters (CCCs) from the yellow fever mosquito Aedes aegypti. These proteins carry salt across cell membranes, thus contributing to salt secretion or absorption. We have identified three genes that code for these proteins in mosquitoes. Two are only distantly related to the CCCs of vertebrate animals. We hypothesize that these proteins have evolved different roles to meet the diverse salt and water balance challenges in larval and adult insects.
Research students in my group use a variety of approaches, ranging from measurements of cation levels in insect blood and urine to molecular characterization of gene expression patterns. In addition to working with mosquitoes, we also use the fruit fly Drosophila melanogaster because it is a well-established model system. A Cascade Scholar who joins my research group will work collaboratively with other students on projects that combine physiological and molecular approaches. Example projects include 1) using antibodies to localize CCCs in larval and adult mosquito tissues and 2) evaluating function of fruit fly renal tubules after genetic knock down of CCC expression.
Course requirements: None
The annelid worm Lumbriculus variegatus can regenerate both head and tail regions lost to injury. Regeneration requires cell proliferation and thus DNA replication. During DNA replication, the ends of linear chromosomes (telomeres) erode, ultimately leading to cell senescence. The enzyme telomerase extends telomeres, so telomerase may be a key player in the regenerative process. We found an increase in telomerase reverse transcriptase (tert) mRNA during time points in regeneration when cell proliferation occurs. Intriguingly, we noted a decrease in tert mRNA at early (24 hour) time points. Literature points to reactive oxygen species (ROS) inhibiting telomerase, and unpublished data show an increase in ROS after Lumbriculus wounding.
Possible Cascade projects include:
• Inhibiting the ROS increase with antioxidants and examining if that impacts tert mRNA levels.
• Identifying factors that lead to tert upregulation later in regeneration. Various transcription factors may be in play; we can clone some of these and see if they are upregulated prior to the tert mRNA increase.
• Determining if telomerase protein activity matches tert mRNA levels, with an assay known as TRAP.
• Establishing the techniques of WISH (to examine spatial gene expression) and RNAi (to inhibit protein expression thus aiding functional determination) in Lumbriculus.
In addition to learning techniques, the Cascade student will maintain a lab notebook, unpack research articles, troubleshoot experiments and collaborate with other researchers.
Course requirements: None
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 of year 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 Physcomitrium patens is a model organism with a fully sequenced genome and well-established protocols that allow us to manipulate the genome to identify genes vital for reproductive regulation. Importantly, phenotypic variation in seasonal responsiveness among P. patens accessions collected across Europe has provided a 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 gene families that may regulate seasonal reproduction in P. patens and are using CRISPR-Cas9 targeted gene mutagenesis in order to analyze their function.
In a complementary approach, we are using a mutant screen to identify early reproducing mutant plants that lack proper seasonal regulation of reproduction, and then identifying candidate causal mutations using genomic approaches. An incoming student will work alongside a Summer Science Scholar to 1) validate and characterize CRISPR-Cas9 mutations in candidate regulators of seasonal reproduction, or 2) restore gene function in our early reproducing mutants using transgenic and CRISPR-Cas9 approaches to confirm the identification of causal mutations. In either project, students will gain experience with CRISPR-Cas9 targeted gene mutagenesis and plant transformation, along with techniques in statistics, phylogenetics, evaluation of gene expression, and plant development, all in a collaborative laboratory environment.
Course requirements: Biology 116 preferred but not required
Barn swallow eggs vary widely in the degree and distribution of speckles on the eggshell surface. Eggs (4-6) belonging to a single clutch laid by one female tend to look more similar to each other than eggs in other nests laid by other females. The signature hypothesis proposes that females pattern their eggs so they can recognize them, and therefore potentially spot an egg laid in the nest by another female (intraspecific brood parasitism).
This project aims to test the signature hypothesis by comparing the patterns on eggs in each of the females’ two clutches they lay over the entire breeding season. Evidence from other studies suggests that females produce similar looking eggs during both their clutches, but we have yet to confirm this in barn swallows.
A Cascade student will check nests frequently at multiple breeding sites, photograph every egg when the clutches are complete, and identify the female at each nest for both breeding attempts. They will use pattern recognition software to characterize the maculation (speckling) pattern on the eggs and quantify the repeatability of pattern between every female’s first and second clutch eggs.
Additionally, the Cascade student will also be an active participant in all aspects of Iris Levin’s research on social behavior in barn swallows. Students will net, band and monitor swallows during the breeding season and contribute to a variety of research projects, including a deployment of new proximity loggers to quantify social networks.
Beyond testing the new technology, the goal of the tag deployment is to understand multi-layer networks in barn swallows. We will ask how the spatial arrangement of the birds in the barn (where they nest) is related to the social network, and how both the spatial and social networks predict mating behavior.
Course requirements: Biology 115 and 116
Understanding photophysical processes in organic semiconductor thin films is key to developing materials for organic electronics applications. Yet in the solid state, spectroscopic characterization is complicated by heterogeneous molecular environments and intermolecular coupling. However, molecular morphology of film surfaces can be characterized in detail using infrared reflectance absorbance spectroscopy (IRRAS). In this project, students will prepare light-absorbing molecules to then spin-coat onto reflective substrates, to optimize the preparation of high quality samples for IRRAS characterization.
Course requirements: Coursework in physics and/or chemistry
Plants produce specialized metabolites for defense mechanisms, to attract pollinators, and to better resist other environmental stressors. In tomato (and tomato-related) plants, some of these specialized metabolites are produced by hair-like tissues on the surfaces of leaves called glandular trichomes. This summer we will be investigating a variety of primary and specialized metabolites produced by the glandular trichomes from tomato plants. The goal is to gain a better understanding of how the specialized metabolites are made and how their production affects the metabolism of primary metabolites such as fatty acids and amino acids. Scholars can expect to learn about primary and specialized metabolism in plants, use instruments such as gas chromatography-mass spectrometry, and work collaboratively with other members of the Rouhier research group.
Course requirements: None
My research group is interested in how mosquitoes remove unwanted or toxic molecules. This summer my research group is using molecular biology to determine if two particular transporters are involved in the transport of dye molecules. The project will introduce the scholar to microscopy (the harvesting of mosquito tissues), molecular biology (extracting RNA, amplifying DNA, and sequencing of that DNA), and microinjection (injecting RNA into cells for transporter assays). 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.
Additionally the scholar may be asked to assist with a project involving the treatment of water to prevent the development of mosquitos during their aquatic life stages.
Course requirements: None
Prenatal maternal stress during pregnancy has both immediate and long-term consequences for the health and wellness of pregnancy and the offspring, respectively. My lab is interested in how maternal prenatal stress alters fetal organ systems, predisposing offspring to immune dysfunction, specifically allergic asthma, later in life.
Previous work from my lab and others have shown that while the placenta actively serves as a buffer against maternal stress, protecting the fetus from direct exposure to elevated levels of maternal stress hormone (cortisol), it can also be altered by it. Interestingly, maternal stress-induced changes in placental gene expression and function can be transmitted to the fetus.
Cascade Scholars in my lab will work with more senior students to identify genes whose expression in the placenta is altered by exposure to stress hormone and unravel the molecular mechanisms that govern this change in expression. For this work, scholars will use human and mouse models.
Course requirements: Biology 116
Research in the Wright Lab focuses on the ecology and evolution of bird flight. This summer, we have multiple ongoing projects in which a Cascade scholar could participate. Most projects will focus on sexual dimorphism of flight performance. We will try to answer such questions as: do larger flight muscles allow males to takeoff faster? To do so, we will quantify maximum take-off ability in adult male and female bluebirds in controlled settings, examining the relative contributions of legs vs. wings in take-off as well as maximum take-off velocity and acceleration.
We will also try to answer questions like: Do males fly more often than females? In what contexts do males engage in showy flight behaviors? For these questions, we will film free-flying pairs of bluebirds as they go about their lives around their nest box.
All 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 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). When the weather is poor during the week, we may shift schedules to take advantage of nice weather for fieldwork on weekends. Most work, however, will take place during typical work hours.
For more information, please contact Professor Wright (firstname.lastname@example.org).
Course requirements: Biology 116
The universe can be unkind. The hot, dense, early stages of the universe should be — and may uniquely be — the only possible laboratory for extremely high-energy fundamental physics; it's secrets, however, are encoded in observations that must be focused through the lens of mathematical models. As it is an irreproducible system, and we must resort to inferring what the universe would be like, given a certain model and set of parameters, and then comparing those predictions to the quantities that we can observe. Measuring and constraining parameters of these mathematical models is an inversion problem that simultaneously requires us to evaluate, or re-evaluate, whether our mathematical models are relevant in the first place.
Broadly speaking, the great questions of cosmology and particle physics are perhaps less understood now than they have ever been: what mechanisms were relevant in the very early universe, what is the nature of dark matter and what physical mechanism drives the observed present day accelerated expansion of the universe. Concordance cosmology (Lambda-CDM) — the dark-energy dominated late universe with cold dark matter (CDM) and an early inflationary state — is but a set of mechanisms. At the same time that Lambda-CDM agrees very well with most cosmological observations, we find ourselves without unique mathematical models for these phenomena and no fundamental descriptions. The continued lack of direct detection of new physics at the LHC, direct detection of dark matter, or compelling descriptions of inflation or dark energy are more troubling now than ever and further presses us to wonder whether we are even asking the right questions. Perhaps that is why the seeming, 4ish-sigma$inconsistency between early- and late-universe measurements of Hubble's constant (the current-day expansion rate of the Universe) is so exciting.
The cascade scholar in our group will begin the summer by learning what all these words mean (!) and explore how we’ve used our numerical tools in the past. The scholar will then work with other students in the lab to extend an analysis of the early universe to incorporate new physics.
This is an opportunity for anyone who has interest in numerical work, the physics of the universe, particle physics, gravity (general relativity) or understanding more about how theoretical physics research is conducted.
Course requirements: PHYS 145