David Altman, Physics
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. We seek 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 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 motor 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 allow a cell to internalize microscopic beads and use the optical trap to apply known forces to these beads as they are transported by myosin motors. Our goal is to relate force-sensitivities observed for individual motors to the force-dependent behavior of these motors inside a cell.
Students who are interested in multidisciplinary research in a biophysics lab are encouraged to apply. Depending on your specific project, you may have opportunities to develop skills related to biochemistry, cell biology, fluorescence microscopy, optics, and coding in Python.
Cooper Battle, Chemistry
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.
Daniel Borrero-Echeverry, Physics
Application Assignment coming soon
Joe Bowersox, Environmental Science
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. 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. 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.
9 weeks, May 23, 2023 to July 25, 2023
Calvin Deutschbein, Computer Science
While bugs in computer software are known and understood, they are only the tip of the iceburg. On January 3rd, 2018, the Spectre and Meltdown family of exploits were first reported. These new types of attacks target computer hardware and, having gone undetected for decades, demonstrated the degree to which existing hardware security for processors and other designs needed to meet new challenges. However, in order to design secure processors, designers must have some notion of what it means for a processor to be secure. Specification mining, a data mining technique to describe the behavior of software, offered a possible solution, but still comparatively novel to the hardware security research space. To describe a model of secure behavior hardened, researchers must first (1) generate large scale data sets describing computer hardware, (2) transpose these data sets into valid inputs to state-of-the-art data mining tools, and (3) construct data visualizations that capture tera-scale or greater datasets for human viewers.
Luke Ettinger, Exercise and Health Science
Application Assignment coming soon
Proprioception in Neuropathic Populations: This research involves investigating movement disorders and proprioception in special populations. Students interested in working in a biomechanics laboratory using advanced 3D motion capture and joint position sense testing are encouraged to apply!
Data collection will include electromagnetic sensors placed on the thorax, scapula and arm. Anatomic landmarks will be digitized using custom labview software. Students with a background in anatomy are strongly encouraged to apply. A headset display will be fit to each subject for a short period of time. Men will be asked to be shirtless during the procedure, women are asked to wear a sports bra or similar garments and therefore laboratory assistants will be needed to help ensure privacy for the participant. The project is minimally invasive, only adhesive tape will be applied to the skin. Each participant will take roughly one hour to collect proprioceptive and kinematic data. Data analysis will require familiarity with Microsoft Excel and simple quantification from array structured data. For those interested in working as a research assistant, this is a great opportunity to gain valuable insight into a biomechanical study with real world implications to clinical disease. The proprioception laboratory is set up in the back of Gatke Hall next to Lockard's blood laboratory.
Heather Kitada Smalley, Statistics
Data is a ubiquitous part of our lives and all disciplines, spanning both STEM and humanities. The Survey Quality Research Lab combines the hard skills of programming and statistical analysis with the soft skills of data visualization and communication to tackle wicked problems within a social context. In order, to make broad and unbiased conclusions it is essential to have high quality data that represents the population of interest. Work has been done to model various sources of survey error with the goal of building a counterfactual framework to remove biases from the data. These analytical methods account for complex sampling schemes and weighting structures. This work can be applied to diverse applications from the traditional, structured probability based establishment surveys to non-probability based unstructured data sources, the nexus of which is the focus on future research.
Students in the Survey Quality Research Lab use data science skills to work with large and complex datasets. Students who are interested in statistics, data science, computer science, and social sciences are encouraged to apply.
Katja Meyer, Environmental Science
Students in the Meyer lab will establish an urban biogeochemical research field site and begin to characterize 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 begin 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.
Chris Smith, Biology
The Smith Lab at Willamette University is seeking multiple summer research students to participate in a 9-week field and laboratory experience from May 15, 2023 - Jul 14, 2023. Research projects will focus on the ecology, evolution, and genetics of Yuccas and their yucca moth pollinators (Prodoxidae: Tegeticula). Students will have the opportunity to select and design their own research projects within the constraints of the study system and laboratory resources. Potential topic areas include questions in bioinformatics, climate change, phylogenetics, plant physiology, population ecology, and population genetics.
The program will begin with a 2-week field experience in the Mojave Desert, followed by six weeks in the lab at Willamette. Participants should have past coursework at the college-level in biology or an allied field. Participants should be prepared to work in a desert environment during late spring weather, walking up to ten miles per day over uneven terrain while carrying a backpack.