David Altman, Physics

application assignment

The inside of a cell is highly organized, and it is this order that allows a cell to function properly.
Important players in a cell’s ability to maintain an organized internal state are motor proteins, molecules that generate force and motion. These motors allow a cell to transport, compartmentalize, and order its components. Specifically, our lab is focused on myosin motors, which are involved in a variety of functions including muscle contraction, cell motility, cell division, and vesicle transport. Our lab seeks to understand how myosin activity is regulated within the crowded and dynamic environment of a cell. To draw a connection between our understanding of biological systems at the molecular and cellular levels, we explore these motors at a variety of size-scales and levels of complexity. 

Two projects will be the likely focus of our summer work: (1) Studies of individual myosin motors: We will study purified myosins one molecule at a time using an optical trap, a laser system that allows us to apply miniscule forces (1-trillionth of a Newton) to a motor. Our goal is to understand how forces experienced by a myosin alter and regulate its activity. (2) The role of myosin motors in cellular transport: We will study myosins’ roles in a human retinal cell line that is responsible for internalizing and disposing of waste, a process that is necessary for maintaining retinal health. In these experiments, we use the optical trap to apply known forces to motors as they are transporting this waste. Our goal is to relate force-sensitivities observed for individual motors to the force-dependent behavior of these motors inside a cell.

Cooper Battle, Chemistry

application assignment

Research in the Battle lab uses fundamental principles from biochemistry and organic chemistry to make a range of fluorescent sensors with structures and mechanisms inspired by biological systems. Our current focus is creating sensors made from DNA strands that function as nanoscale machines that fold and unfold in a controllable and predictable fashion. By using biological building blocks and mimicking natural functions, we can both create potentially useful sensors and at the same time gain a better understanding of how similar systems function in living cells as we try to replicate their functionality. 

Our current sensors are built from intramolecular guanine quadruplexes, which have gained increasing attention in the last 15 years as key structures in the regulation of gene expression, where their controlled folding and unfolding allows transcription factors to turn genes on or off. Instead of turning gene expression on and off, our sensors turn a fluorescent signal on or off to indicate the presence of a particular nucleic acid sequence. The sequences we’re interested in detecting are called microRNA and are central regulators of the translation of messenger RNA to proteins. In the last decade, microRNA have been found to be central players in a wide range of disease states, from cardiovascular disease and neurodegenerative diseases to diabetes and cancer. Work in the lab includes studies of basic quadruplex structure to better predict how and where they form, optimization of functional sensors, and we are starting to use fluorescence microscopy and breast cancer tissue culture to test our sensors in “real” conditions to detect cancer-associated micro-RNA.

Joe Bowersox, Environmental Science

application assignment

Fire and Ice 2024
Students in the Tree Lab will focus on examining ecological processes in the wake of two landscape scale disturbance events in Oregon in 2020 and 2021, using collected field data and dendroecological techniques engaging tree rings. There are two main prongs of the work: The first portion is to collect and analyze data from permanent plots established under a federal research permit within the Opal Creek Wilderness Area. This is a Doug Fir/Western Hemlock old growth ecosystem subjected to a major fire event, the 2020 Beachie Creek Fire. The Beachie Creek fire was initiated by a lightning strike, and ultimately burned over 78,000 hectares across wilderness and intensely managed forests, with mixed severity.  Many questions have been raised regarding fire behavior, fire impacts, and post-fire regeneration, and dendrochronological work in conjunction with additional field vegetation surveys can help us answer questions about past fire history, present fire behavior, and what is the likely path of succession. Data collection began during the summer of 2023; 2024 participants will put in at least four more plots. Field work will involve strenuous days in Opal Creek Wilderness, significant hiking, and data collection prior to returning to the lab for sample preparation and analysis.

The other portion of the project will be taking the existing oak samples from the 2021 Willamette Valley Ice Storm collected as part of the Oak Salvage Project and expand upon this data, focusing on collecting additional field samples from Oregon White Oaks throughout the valley in excess of 150 years of age --- seeking to close a noticeable gap in our data. The recent ice and snow storms of 2024 provide us with additional collection opportunities. Samples will then be processed and analyzed to, among other things, develop a regional and then a series of sub regional tree ring chronologies. These chronologies will then be used with task-specific statistical packages in R to not only look for marker years but also determine potential climate and drought signals and
other health impacts, such as pathogen and insect presence.  As we move to a broader spatial scale the question will be whether local ecological "noise" drops out and climate signals and other forest health signals manifest. 

Fire and Ice In the Tree Lab will involve a mix of field data collection, sample processing (including use of power tools), and then lab and computer analysis (including potentially extensive use of R).  Additional questions regarding individual factors of tree survival and decline may be pursued along the way.

Haiyan Cheng, Computer Science

application assignment

Optimizing software development process with Large Language Models (LLM)
Software development involves people, process and technology. Traditional software development uses a Waterfall model which requires written documents to be “checked off” sequentially between various development stages. Agile development model prioritizes adaptability and frequent product delivery, engaging stakeholders closely. With the accelerating power of Artificial  intelligence (AI), our research will explore and evaluate existing AI technology such as pre-trained Large Language Models (LLM) with a goal to integrate and test the capability of AI-assisted  software development processes. We plan to work on the following:  automating coding tasks, optimizing project management, and improving communication among multiple parties. By  understanding how AI affects software development, we hope to shed lights on developing competency-based students learning and justifying curriculum choices. Research activities involve literature surveys, case studies, tools evaluation and integration, and comprehensive assessments.

Lucas Cordova, Computer Science

application assignment

In the SCIS Software Research and Development (R&D) group, we collaborate with computing and cross-disciplinary students and faculty to propose, design, and build software apps using a human-centered design (HCD). HCD is an approach to creating software that prioritizes the needs, preferences, and behaviors of the end-users throughout the development process. We are currently investigating how the integration of learning theories such as inquiry-based learning (IBL), gamification (gaming theory), and artificial intelligence (AI) into pedagogical tools can enhance a learner’s ability to communicate to audiences having varying levels of domain  knowledge. These tools are designed to cater to a wide range of learning preferences and can provide a dynamic and engaging educational experience across disciplines. 

Two projects will likely be the focus of our summer work. (1) Investigate the integration of AI to help facilitate the learning process. In this research, we will abstract various levels of complexity from the end-user and measure the effect on the end-user in terms of having a seamless, intuitive, and personalized learning journey. (2) Investigate the integration of gamification elements into the learning process. We will explore how game-based approaches can enhance learner motivation.

Luke Ettinger, Exercise & Health Science

Program mission: Identify connection between diabetic neuropathy and movement disorders, specifically frozen shoulder disorder.  Previous work in our laboratory has established a connection between diabetic neuropathy and diminished proprioception (otherwise known as joint position sense).  Our present work aims to connect the proprioceptive discrepancy and movement disorders often found in this population.  

Current study: We hypothesize that peoples with Type 2 Diabetes Mellitus (T2DM) will demonstrate diminished ability to localize joint position sense (JPS) of the upper extremity compared to controls, but will experience similar limb localization to controls under ischemic conditions (Project from 2018).  Further, we hypothesize that peoples with T2DM and peripheral neuropathy will demonstrate scapular kinematic movements consistent with individuals with diseased shoulder (Shoulder impingement syndrome) SIS, which is often a precursor to frozen shoulder.  Our summer project will include traveling to Diabetic Support Services of Salem and recruiting participants during regular weekly meetings.  Recruitment of non-diabetic controls and data analysis will occur on non-traveling days. 

Kristen Gore, Data Science

application assignment

Survival analysis is the study of time until an event of interest. In engineering applications, it can mean time until a device breaks (reliability). In HR applications, these methods can be used to model time to promotion or job tenure. In health studies, it can be time until onset of a disease. Survival analysis methods are unique in that they are designed to handle cases in which the exact event time is unknown.

A major need exists to create an alternative to the current suite of R functions and packages. Many are not user-friendly, and few leverage the power of the Tidyverse to make analyses easier.  The primary objective of this project is to continue the development of the Survivalverse, a Tidyverse-centric R package for survival analysis and reliability methods. Student researchers would be responsible for contributing functions and sample datasets to the Survivalverse. They would also conduct a user experience pilot to gain feedback on the usability of their functions. This project has the potential to impact a wide variety of practitioners in academia and industry.

Heather Kitada Smalley, Statistics

application assignment

The Kitada-Smalley research group focuses on public opinion and survey statistics.  The  overarching goal of this group is to develop survey methodology to improve bias estimation, data quality, and the representation of historically undercounted populations.  This summer, students in this group will focus on one of the most important surveys conducted in the United States, the American Community Survey.  Students will be involved in all parts of the data science life cycle from data collection, cleaning, visualization, analysis, and reporting.  

Project Abstract: The American Community Survey (ACS) is conducted annually by the United States Census Bureau and is widely used by academicians and policy makers alike.  The ACS tracks several metrics of data quality, such as unit non-response rates and allocation rates, which can be considered a proxy for item non-response rates.  It has been shown that aggregated allocation rates vary across household language groups and lower levels of English speaking proficiency.  This can have detrimental effects to data quality in those communities resulting in biased estimates.  Given the applications and use of the data, it is imperative that they be  representative of the population for an equitable allocation of resources.  However, allocation rates are not the only point of concern, survey break-off may provide indications of significant respondent burden.  Thus, we implement survival analysis methods to analyze the interaction between survey break-off across household language and level of English proficiency.  The ACS employs multiple modes of data collection in sequence, which result in differential representation across modes, contributing an additional layer of complexity to the analysis.

Katja Meyer, Environmental Science

application assignment

Students in the Meyer lab will work to characterize summertime nitrogen cycling in the Mill Creek basin. This urban biogeochemistry research will give students experience in field sampling, geochemical analysis, and molecular techniques. I encourage students who are interested in biogeochemistry, urban pollution issues, and working in both the field and lab to apply.

Project description: Urban watersheds are characterized by changes in hydrology and increased pollutant and nutrient inputs from stormwater runoff. One result of urbanization is increased flooding risk because water from storm events moves more rapidly through streams, causing hydrologic “flashiness.” In response, municipalities frequently use structural storm control measures (SCM), such as rain gardens, stormwater wetlands, and detention basins, to encourage stormwater infiltration and slow the movement of storm water through streams. While the primary goal of SCM is to reduce flooding risk, they also improve water quality through plant uptake of metals and other pollutants. SCM have also been characterized as having enhanced nitrogen cycling and excess nitrogen removal through uptake or denitrification, which is of interest because of the importance of excess nitrogen removal on reducing downstream eutrophication of freshwater and coastal environments. Our understanding of nitrogen removal in SCM is incomplete, however, because of limited geographic coverage of relevant studies and because the controls on nitrogen cycling in urban watersheds remains poorly understood. This summer, students in the Meyer lab will continue to explore the idea that seasonal rainfall patterns influence nitrogen removal from SCM via denitrification. Studies such as this will help cities more effectively reduce nitrogen pollution in urban waterways and anticipate the impact of changing rainfall patterns on the biogeochemical function of storm control measures in a warming world.

Scott Pike, Environmental Science

application assignment

This project will support an undergraduate student with collecting, analyzing, synthesizing, and reporting on archaeological sediments collected from the final excavation season at the Ness of Brodgar in Orkney, Scotland. The final season of excavation promises to be a busy one with many hundreds of samples collected from the floors of multiple Neolithic monumental structures at the site. The student will employ hand-held portable X-ray fluorescent technology to identify chemical signatures to help not only differentiate between different cultural contexts, but also collaborate with staff archaeologists and other specialists to determine the activities that took place in these structures over 5,000 years ago. The SCRP fellow will collect, prepare, analyze, interrogate and prepare a report on their data within the time span of the project. This is a somewhat unique SCRP opportunity in that it is also an international study abroad experience. The fellow will be embedded with students from Willamette’s archaeology field school so they will also have a community outside of normal “work” hours.

Chris Smith & Rob Bills, Biology

application assignment

Coevolution, cooperation, and conflict
This project is a new collaboration between Rob Bills and Chris Smith that will combine desert
ecology, microbiology, and bioinformatics to understand how interactions between organisms
affect their evolution, ecology, and response to climate change.

Chris studies the pollination ecology of Joshua trees, the iconic species of the Mojave Desert. The interaction between the trees and the highly specialized yucca moths that pollinate them has been considered a model system for understanding the evolution of species interactions.Chris uses a combination of genetics and field ecology to understand how this species reproduces and how  best to conserve these remarkable plants. Rob studies the taxonomy, phylogeny, and ecology of fungi, with a special focus on mycorrhizal fungi - soil organisms that form associations with plant roots. This association can often be mutualistic; the fungi may provide nutrients to the plants in exchange for sugars and energy.

Recent work has revealed that Joshua trees form associations with mycorrhizae, and that these
soil organisms may enable the plants to better withstand heat and drought conditions. These
findings potentially upend years of work suggesting that the availability of pollinators is the primary factor determining Joshua tree reproduction. The Joshua tree is also a species of conservation concern due to climate change; recent legislation has granted them special protection in the state of California and they are candidates for listing as an endangered species under US law.

In a collaborative project, we will lead students in a field expedition of approximately 2 weeks in length to collect soil and roots, and to support ongoing conservation projects that protect and conserve Joshua trees. In the lab, we will develop pilot experiments and establish protocols to identify mycorrhizal fungi in Joshua tree roots, to image the fungi through microscopy, and to extract and sequence fungal DNA so that they can be identified using DNA taxonomy.

Chuck Williamson, Chemistry

application assignment

In the Williamson research group, we use lasers and other instrumentation to probe the chemical and physical properties of molecules. One major area of interest for us is the behavior of partially-miscible binary liquid mixtures. These are mixtures of two liquids, such as methanol and cyclohexane, which are completely miscible above a certain critical temperature, but separate into two layers for ranges of composition below that temperature. The separated layers, or phases, are also mixtures of the two liquids, but with differing compositions. We use elastic laser light scattering to make maps of this macroscopic behavior of binary liquid mixtures. These maps are called phase diagrams, and they show the temperature boundary between one-phase and two-phase behavior as a function of composition. Elastic light scattering also provides us with a measure of system critical opalescence as a function of temperature and composition, which let’s us determine several characteristic system critical amplitudes.

We explore microscopic behavior in binary liquid mixtures using Raman spectroscopy, a type of inelastic laser light scattering. Raman spectroscopy is similar to infrared spectroscopy in that we learn about molecular vibrational behavior from the spectra. This in turn lets us make connections to how the solvation shell structure in binary liquid mixtures is affected by composition and temperature.


Willamette University

Science Collaborative Research Program

900 State Street
Salem Oregon 97301 U.S.A.

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