2019 Projects: to be announced

David Altman, Physics

(1 Webber Scholar)

In the Altman lab, we study the motor protein myosin and how its functions are regulated in a cell.  The inside of a cell is crowded and highly organized. It is because of its ordered state that a cell is a dynamic and exciting environment. Molecular motors are the biomolecules that generate force and motion, and thus do the work that is necessary to maintain the cell’s organization.  Research in our lab seeks to understand how the molecular motor myosin functions in the cell by taking a two-fold approach. The first approach is to study myosins outside of the cell (in vitro). This allows us to reduce the complexity of the experimental system, but we must take the results from these experiments and extrapolate in order to understand how the motor actually functions inside the cell. The second approach we take is to study myosins inside a cell (in vivo). This means that the system is more complicated, with many other biomolecules complicating our experiment, but it also means that it is easier to understand the physiological relevance.

This summer, our work will focus on in vitro studies of two classes of myosin, myosin 2 motors from the nematode C. elegans and myosin 6 motors from humans.  We are interested in these motors because it has been hypothesized that their activities are regulated by forces that these motors experience in a cell.  Work will include expressing and purifying the proteins of interest, using fluorescence microscopy to observe the motion generated by these motors, and fitting the resulting data to kinetic models of the myosins' mechanical cycles.


Cooper Battle, Chemistry

(2 SCRP Students, 1 Webber Scholar)

Research in the Battle group focuses on studying non-covalent molecular assembly to better design fluorescent sensors that mimic the high sensitivity and responsiveness of cellular machinery. Our work falls into two main projects based on different types of biomolecules. The first project looks at developing a better understanding of higher-order nucleic acid folding to build “DNA nano-machines” that use conformational changes to detect RNA inside live cells. Long-term, this project aims to develop inexpensive and durable sensors for the early detection of cancer through sensing cancer-associated micro-RNA. The second project looks at synthesizing novel organic dyes and looking at changes in their behavior when they are encapsulated in supramolecular hosts as a way to better understand the function of fluorescent proteins. Long term, this project aims to develop broadly applicable sensors that can be used to help design drug delivery systems. I strongly encourage anyone interested in our research to take a look at the research section of my website where you can find both more detailed descriptions of the projects and a section containing overviews of the techniques we use in our work. 


Emma Coddington, Biology

(5-6 students)

We call our lab Newtworld because we study local rough-skinned newts, Taricha granulosa. Our lab could really be more accurately called Neurons in Action, because we actually study newts to discover new fundamental principles of behavior and decision-making shared by all vertebrate animals. Together, students and I co-create research projects to explore questions about how animals behave. Most past studies have centered on trying to understand the complexities of how stress and it’s counter-part love change behaviors and decision-making. It’s the ‘how’ of it that we are focused on – the mechanisms by which hormones and signaling molecules impact neurons in the hindbrain, and therefore fundamentally alter the decision-making process and ultimately behaviors. There will be two positions offered in my lab this summer to continue this work – one will hopefully involve whole-cell electrophysiology of neurons, and the other position will be invested in labeling hindbrain neurons and using the confocal microscope.  Together, we hope to build our understanding of what these neurons are doing!  Folks interested in growing lab skills in microsurgery, physiology, and imaging are encouraged to apply.

I am also growing a new line of research explicitly exploring the physiology and neurobiology of love. This work is a natural extension of the work on stress, as it is all centered on trying to understand how animals (including humans) do relationships and community. While I do have some past unpublished research on this topic in my lab, I anticipate that this summer would be spent exploring the scholarly and popular art & literature. The goal would be to paint a picture of what is known and unknown, including contextual understanding and practices. I anticipate leaning on work from a wide variety of sources including interpersonal neuroscience, neuroethology, psychology, sociology, anthropology, indigenous knowledge, queer and gender theory, race theory, creative non-fiction, fiction, film, theater and art. Folks interested in a broad scope project such as this, are encouraged to apply! 

Thirdly, a collaborator at Michigan State University and I have received additional NSF funding to explore the role of tetrodotoxin-producing microbes in newt evolution. Tetrodotoxin is a neurotoxin that is the primary method that rough-skinned newts, and a variety of other vertebrates (from Puffer Fish to salamanders) use to defend themselves against predators. It is a natural poison that kills by halting all electrically excitable cells in a vertebrate body (animals with a back bone!). The question is how are newts themselves not poisoned by it?  And how are they producing the toxic stuff? A call for applicants will go out at the same time that SCRP positions will be advertised. Two students will be selected and invited to work with me this semester learning the ins and outs of lab work, then head to Michigan State University to work with Dr. Heather Eisthen at a graduate research institution. If this experience interests you, keep an eye out, Dr. E and I will be sending out advertisements shortly.


Luke Ettinger, Exercise and Health Science

(1 SCRP Student) 

From the department of Exercise and Health Science, one SCRP position is available for the Summer of 2019.  Dr. Ettinger's laboratory is concerned with the accuracy and precision of human movement in the presence of neurological disease.  This summer research will be conducted both at Willamette University and at specialized treatment clinics in the Salem area.  Applicants must be familiar, comfortable and professional while working with clinical populations.  This research opportunity is ideal for students interested in the healthcare field or in clinical research.  


David Griffith, Chemistry

(1 SCRP Student)

In the Griffith research group, we are focused on understanding the chemical processes that control the fate of estrogens in aquatic environments. Estrogens are potent hormones that are excreted by vertebrates (e.g., humans and fish) and can enter natural waters through the discharge of treated and raw sewage. Estrogens disrupt the growth and proper development of aquatic organisms at extremely low (sub-ng L-1) concentrations. Yet, we know very little about the distribution and fate of estrogens in rivers, lakes, and oceans. To address this gap, my research group conducts fieldwork, laboratory, and modeling experiments to better understand environmental removal processes, characterize the primary mechanisms driving estrogen distributions, and develop methods to accurately measure estrogen concentrations in complex environments. We utilize a variety of analytical techniques, including high performance liquid chromatography, degradation kinetics experiments, tandem mass spectrometry, and high-resolution mass spectrometry. The results of our work will be used to mitigate the associated risk to aquatic organisms and human health. Projects this summer will focus on characterizing the fate of estrogens in local sewage-impacted river systems by measuring estrogen concentrations along river transects and developing predictive models using information about estrogen photodegradation, biodegradation, and flushing rates.   


Michaela Kleinert, Physics

(3 SCRP Students) 

This summer we will focus on the creation of hydrophobic surfaces with special emphasis on titanium, a metal that is commonly used in bone implants. Changing the hydrophobic properties of titanium implants can significantly affect how well a patient accepts the implant and how quickly they heal after surgery. In a related project, we will create metal and other nanoparticles through laser ablation. Nanoparticles are small and versatile and find applications in medicine, electronics, and engineering. While nanoparticles are commonly created through chemical reactions, creation through laser ablation leaves no chemical waste.


Rosa León-Zayas, Biology

(2 SCRP Students)

In the Leon-Zayas research lab, we are excited to understand the community composition and metabolic potential of microbial communities in various environments such as the deep ocean, the subsurface, and coral reefs. In order to answer questions about which microorganisms are present in these environments and what roles those organisms are playing in their ecosystems, we utilize computational biology tools to analyze DNA of the whole microbial community. Among the ongoing research themes in the lab are the discovery of genes involved in the production of novel bioactive compounds, for example antibiotics or anticancer. Also, we are looking to better understand microbial communities that live below the sediment surface in the ocean and hot springs, particularly searching for organisms called Lokiarchaea, that have been suggested to be the missing link between prokaryotes and eukaryotes.

This summer our research will focus on two different projects. The first project will involve the analysis of data from a Fijian coral reef to look for genes that are associated with secondary metabolite production. The second project will involve the analysis of sequence data from hot spring sediment samples and the potential culturing of organisms that are important parts of the microbial ecosystem in those environments. 


Melissa Marks, Biology

(2 SCRP Student, 1 Webber Scholar) 

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. 


Katja Meyer, Environmental Science

(2 SCRP Students, 1 Webber Scholar)

Today the global oceans are warming, becoming more acidic, and losing oxygen due to anthropogenic climate change. During Earth’s history, many intervals of rapid climate warming coincided with these same ocean chemistry changes as well as evidence for mass extinction. In the Meyer lab, we examine ancient climate change events to study the relationship between changes in the chemistry of the ocean and the response of marine animal ecosystems. Much of our work is focused on the end-Permian mass extinction, which resulted in the loss of over 95% of marine species and occurred ~252 million years ago. This summer students in the Meyer lab will work on two projects:

  1. Earth system modeling of ocean acidification: We will use the cGENIE Earth system model to examine the impacts of volcanic CO₂ emissions on ocean pH during the end-Permian and Early Triassic. Students will learn how to run model experiments and visualize model output.
  2. Geochemical proxy development: We will work to improve the tools geoscientists have for identifying the presence of euxinic (anoxic and sulfidic) conditions in ancient samples. Using both modern lake sediments and end-Permian rocks, we will examine the size distribution and isotopic composition of pyrite mineral grains found within these rocks as a proxy euxinic conditions. Students will use a variety of lab techniques to prepare samples and examine rock/sediment samples using scanning electron microscopy (SEM).

Scott Pike, Environmental Science

(1 SCRP Student)

The Colossus of the Naxians at Delos: Towards an understanding of the relationship between the kouros, its source, and the use of Naxian marble.

This geoarchaeological summer collaborative research project seeks to understand the meaning of the inscription on the base of the Colossus of the Naxians at the Sanctuary on Delos that reads “I am the same stone – both statue and base”. The exact meaning of this phrase has been interpreted to mean that either the stone used for both the base and statue are from the same quarry or, perhaps, that the statue and base came from one large block. In either case, the stone must have been imported from the marble-rich island of Naxos. But from which quarry or quarries did the estimated 32 ton figure come? 

A stable isotope study of the statue’s foot housed at the British Museum points towards a source in the southern portion of the island of Naxos in the same region that many of the Cycladic figurines from the Goulandris Museum of Cycladic Art in Athens are thought to have originated. Interestingly, there are no known ancient quarries in the southern part of Naxos. Where it was presumed that the Cycladic figurines were carved from rounded beach cobbles that washed up on shore, it is unlikely that Naxian sculptors would have found an unflawed 9 meter long block of marble lying on the beach. The data strongly suggest that there must be an as-yet undiscovered Archaic quarry in the south of Naxos.

This summer’s research will include an extensive field survey to locate, sample, map and characterize potential Archaic period quarries in southern Naxos. We will also improve the Mediterranean Marble Database by systematically collecting and analyzing white marbles found throughout the marble formation. Field samples will be shipped back to Willamette where they will undergo petrographic and stable isotope analyses. The data will then be compared to those obtained from the Naxian Colossus fragments to determine the source quarry for the status.

Field work will be from late May through early June followed by lab work back at Willamette.