2022 Projects (subject to change)

  

David Craig, Biology

Application Assignment

  1. Carr Thesis Slides
  2. Carr and Craig: Oregon Birds
  3. Bisbee Grant: Wineries as oak and nuthatch refugia

The Craig team is piloting a new project focused on a unique bird named the slender-billed white-breasted nuthatch (Sitta carolinenses aculeata). This nuthatch is considered to be rare across most of the Willamette Valley, but can be locally common in stands of Oregon white oak (Quercus garryanna) like those found on our main campus, in Bush Park, and at the Zena campus. Many aspects of the nuthatch’s natural history are unknown, but because they are declining quickly, they have been designated as an Oregon species of concern. Recent genetic discoveries suggest the subspecies will be elevated to a full species, which means in the near future, we may have an officially listed threatened species breeding on campus. Factors causing the decline of nuthatch populations are reported to be loss of large‐diameter oaks. Students need to be ready to spend the majority of their time outdoors and enjoy early morning hikes in all types of weather. If you are curious about birds and trees and are concerned about climate change, no experience is necessary. As a pilot project, there is excellent potential for motivated students to be creative and influence the long-term trajectory of the Craig lab. 


Alison Fisher, Chemistry

Application Assignment

Research in the Fisher lab centers on the discovery and characterization of novel enzymes involved in the production of volatile organic compounds (VOCs) by plants. Plant emissions of VOCs introduce over 500x109 kg of carbon into Earth’s atmosphere each year, significantly impacting air quality, stratospheric ozone depletion, and climate change. While most plant VOCs are secondary metabolites involved in plant defense, many of the functional roles of plant VOCs are unknown. Recently our group has focused on characterizing enzymes involved in VOC production in mosses to better understand the function and evolution of VOC emissions from plants, as mosses represent some of the closest living relatives of the first plants to colonize land.

 Currently, we are working to characterize the first moss S-adenosyl-L-methionine (SAM)-dependent halide methyltransferase from the moss Physcomitrella patens. SAM-dependent halide methyltransferases catalyze the transfer of a methyl group from the SAM coenzyme to a halide ion to produce volatile methyl halides (Figure 1). In many plants, this reaction gives rise to methyl chloride and methyl bromide; these VOCs transport chloride and bromide radicals to the stratosphere, where they function in the catalytic breakdown of the ozone layer. However, the function of this enzyme in plants remains a mystery. By characterizing the first moss SAM-dependent halide methyltransferase, we hope to better understand the functional role this enzyme plays in plants and why this enzyme evolved in land plants. 


Karen Holman, Chemistry

Application Assignment

Research students in Professor Holman’s lab use the moniker “Ru Crew” based on their interest in ruthenium. For the past twenty years, members of the Ru Crew have been working to unveil details of the fundamental chemistry of ruthenium-based anti-cancer drugs. Students working on these exciting projects make significant contributions to this particular subfield of inorganic chemistry that appear in three (soon to be four) published research articles. Because ruthenium-based drugs have the potential to revolutionize chemotherapy for metastatic cancers, our primary focus is to investigate the fundamental chemistry of Ru-based drugs in order to understand details of the chemical reactions that are most relevant in the bloodstream and in cells, and well as in aqueous phase before intravenous injection.

Summer researchers in the Ru Crew must have completed two semesters of Organic Chemistry (including lab) which will be useful in their first task to synthesize a ruthenium-based anti-cancer drug.  Each student will then choose a specific chemical system to study where they investigate the reaction between the drug and DNA, a protein, or another biologically relevant molecule. Along with synthetic and purification methods, the primary techniques utilized fall within the realm of spectroscopy: UV-Vis, fluorescence, and/or NMR. 


Melissa Marks, Biology

Application Assignment

In the Marks lab, we study Caulobacter crescentus, a Gram negative bacteria that lives in freshwater lakes and streams.  We use a variety of genetic, molecular, biochemical, and cell biological tools to investigate how they survive and thrive in their natural environments. In particular, this summer, we will be working to better understand how differences in the ability of cells to acquire and use nutrients may contribute to their survival in stressful conditions. Many projects in the lab are technically quite simple (I've taught 4th and 5th graders to use them) and there are no specific course prerequisites for participation in my research program. You will learn all of the techniques and scientific background as we go.  Successful students in my research program are curious, hard-working, willing to ask questions, observant, self-directed, and willing to work in teams of 2-3. 


Scott Meyer, Chemistry

Application Assignment

Ion channels play an essential role in many biological functions and have been implicated in multiple diseases. As such, there is a need for new potent, bioactive small molecules that can act as ion channel blockers and as probes for biomedical research. Tetracaine is a known small molecule ion channel blocker that binds to diverse molecular targets. The objective of the research in my lab is to develop tetracaine derivatives as reversible ion channel antagonists with high affinity, longer lifetimes, and high selectivity for cyclic nucleotide-gated (CNG) ion channels. The long- term goal is developing an understanding of the structure-activity relationships of tetracaine to design new therapeutics for blinding retinal diseases, such as retinitis pigmentosa (RP). CNG channel blockers have shown great promise for treatment of RP, but there is a critical need for the development of a new generation of blockers with greater selectivity for rod CNG channels and ease of delivery. The project will test the central hypothesis that modifying the three main regions of tetracaine will improve ion channel block by enhancing the affinity, selectivity, and lifetime of the molecule in biological systems.

The research will be focused in two areas: (1) Tetracaine derivatives with enhanced potency for blocking CNG channels will be synthesized. The tail region will be altered to elucidate the role of the aniline proton as well as to optimize binding. The aromatic core will be modified with electron-withdrawing substituents, both exocyclic and endocyclic, to enhance affinity, selectivity, and water solubility. The effect of modifying the lipophilicity of the tail and the position of substitution on channel binding affinity and selectivity will also be measured. All derivatives will be tested for potency as blockers of human rod and cone CNG channels using patch-clamp electrophysiology following expression in the Xenopus oocyte system. (2) Tetracaine derivatives will be created with increased lifetimes and enhanced hydrolytic stability. To reduce the rate of tetracaine metabolism due to hydrolysis of the ester linkage, tetracaine derivatives with a modified head-linkage group, including an inverted ester and amide head linkage, will be generated to take advantage of enzyme specificity. In an attempt to better understand the role of the carbonyl group, it will be replaced with ether and amine functionalities. The hydrolysis rates will be measured via a butyrylcholinesterase assay.


Scott Pike, Environmental Science

Application Assignment

This summer’s geaoarchaeological researcher will work at an on-site field science laboratory in
Orkney, Scotland to undertake geochemical analysis of archaeological samples recovered from
the Late Neolithic (roughly 5,500 years ago) Ness of Brodgar archaeological site. The sediments are from floor deposits collected from various monumental-scaled enigmatic structures within the site. The geochemical data is an integral part of a multi-method, multi-year approach to identify and interpret different use areas within the large structures. The on-site laboratory is equipped with a handheld x-ray fluorescent spectrometer (pXRF) that will be used to extract geochemical data from recently excavated samples recovered during the current and past excavation seasons. Lodging and travel costs to Orkney are covered by the SCRP program.

The SCRP participant will be conducting research alongside archaeologists and archaeological
scientists in a dedicated-space located at the site excavation house. The researcher will prepare samples, conduct pXRF analysis following established protocols, process the data, and interpret results. The research will incorporate the previous years’ data to look for geochemical patterns within the floor sediment samples. 

The researcher will be embedded within Willamette’s archaeology field school at the Ness of Brodgar. They will live with the field school students at Brown’s Hostel in Stromness, ride in the same van to and from site, attend the field school’s weekly lectures and participate in the various field trips. The SCRP participant is also expected to adhere to the same rules and regulations of the field school students and contribute to the proper upkeep of the hostel. Note that the inclusive dates for this project are from July 9 -August 19. 


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 carbon disulfide, 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. Currently our research efforts are focused on how a binary liquid system is affected by the addition of a third component. With a third component, the coexistence curve becomes a coexistence surface, and the critical point becomes a critical line. We are exploring whether this critical line is actually independent of the identity of the third component, much like a colligative property. 


Rosa León Zayas, Biology

Application Assignment

This summer we will be working on advancing the research of our most recently NSF funded work on PET Plastic degrading bacteria. By studying the metabolic capacity of microorganisms that degrade PET Plastic, we can better understand their mechanisms for degrading one of the largest sources of pollutants, single use plastics, with the ultimate goal of building upon that potential to generate a more efficient degradation process in order to eventually assist with the reduction of this manmade environmental pollutant. During the summer we will be particularly looking at the genes that are actively being used by the bacteria (RNAseq), so we can understand how these organisms are actively degrading the PET plastic. We will be learning how to use computational tools to answer biological questions by interrogating RNA sequences from the organisms. Previous knowledge on computational language is not required.

Willamette University

Science Collaborative Research Program

Address
900 State Street
Salem Oregon 97301 U.S.A.
Phone
503-370-6013

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