Summer 2020 Research Projects

Machine learning techniques in protein structure prediction - Dr. Renzhi Cao, Associate Professor of Computer Science

Machine learning technique in data science is widely used for big technology companies (e.g. Google, Intel, Facebook, Microsoft, etc.). It is a multi-disciplinary technique from advances of computer science, statistics, mathematics, physics and biology. One application is in bioinformatics field of protein structure prediction that researchers have been working on for more than two decades. The traditional methods for determining protein structure (X-ray and Nuclear Magnetic Resonance) are time consuming and expensive, we would like to tackle the research question how machine learning techniques (e.g., convolutional neural network, reinforcement learning) can be used for protein structure folding. Students are going to write computer programs to integrate the latest machine learning techniques on the platforms that big technology companies are working on, explore how to integrate machine learning techniques for protein tertiary structure prediction (e.g., given a predicted protein structure, students will predict a value to evaluate how accurate it is compared to the true structure of this protein), and analyze the data from previous Critical Assessment of protein Structure Prediction (CASP) experiment with our collaborators. In addition, if time allows, students may also work on analyzing data generated by Cryo-EM technique, which brings breakthrough recently for structural biology and would be useful for our external NSF grant application.

This research project will last 10 weeks.

Mapping a magmatic arc-accretionary complex near Cle Elum, WA - Dr. Peter Davis, Associate Professor of Geosciences

Metamorphic rocks exposed in the mountains around Cle Elum Washington state preserve minerals that are interpreted to record subduction related pressures and temperatures. These rocks have been correlated to others across and to the north in the Cascade range, however recent detailed work has shown that this correlation is incorrect (Davis and Lindmark, 2015; Davis and Stubbs, 2017), which has increased the importance of understanding, in detail, what the rocks near Cle Elum can show us about their tectonic history. Understanding this history is fundamental to understanding the larger structure of the crust that makes up Western Washington, which is intern critical for understanding current seismic hazards in this tectonically active region.

The type of analysis necessary for this project is done by characterizing the mineral species, 3D-spatial orientation of individuals and clusters, sub-grain alterations, and ultimately the regional variation of these features. This type of work is typical of geologists that study deep seated tectonic processes, and the basic tools and techniques that students will have learned in our classes and have access to in our department are sufficient in producing compelling results and new interpretations. Two students will focus on two known exposures south and north of Cle Elum. They will carry out a process of both field and laboratory exercises that will connect to previous work carried out by Dr. Peter Davis.

We expect to be able to show where and how subduction related Jurassic to Cretaceous aged rocks were juxtaposed with non-subduction related rocks of the same age. This work will go into a forthcoming journal article detailing the findings and solidifying Dr. Davis’s larger case for reinterpretation of the region, and will intern help other investigations such as seismic hazard analysis.

This research project will last 5 weeks. 

Using electrochemistry to detect biologically relevant molecules - Dr. Justin Lytle, Associate Professor of Chemistry

A variety of small organic molecules that are relevant to human biology are found within our central nervous system and as metabolites that are excreted by our bodies into the environment. Some of these molecules are responsible for relaying stimuli, such as the neurotransmitters dopamine and serotonin, and others are from medications that humans receive in the form of antibiotics and contraception. Our research group seeks to identify and quantify these molecules in control solutions and then extend our method to testing wastewater and environmental samples. These molecules exist in biological fluids and in wastewater at part-per-million and part-per-billion concentrations that we will detect using commercial carbon electrodes and porous, nanostructured carbon electrodes, which we will fabricate and test in our lab. We hypothesize that the large surface area of each porous carbon electrode will permit us to detect the relevant concentrations of these molecules in control solutions, create a calibration curve for each solution, and to one day extend this work to sampling environmental waters, such as Clover Creek and Puget Sound.

This research project will last 5 weeks. 

Building an embryo: Investigating how the cytoskeleton and adhesion molecules shape epithelial tissue architecture - Assistant Professor Lathiena Nervo

During embryonic development, tissue establishment is made possible by cell shape changes and migration. Epithelial cells are a polarized cell type that act as the building blocks for most tissues. These cells are organized into layered sheets with apical-basal polarity and are connected by intercellular adhesion complexes. The apically positioned adherens junction form of cell–cell adhesion structure observed in a variety of cell types, as well as in different animal species. A major function of adherens junctions is to maintain the physical association between cells, as disruption of them causes loosening of cell–cell contacts, leading to disorganization of tissue architecture. In order to direct proper tissue and organ formation epithelial cells must participate in coordinated cell shape changes and migration, which require cells to communicate with each other and remodel the cytoskeleton. This study focuses the process of tissue formation during embryogenesis in Drosophila. I use the fruit fly as a model system, taking advantage of its long history and deep database of knowledge about normal development, and its highly sophisticated genetic tools which allow me to manipulate cell biological machinery in powerful ways. My main objective is to discern which molecules in the adherens junction aid in the generation of contractile forces and how these forces contribute to the closing of the lateral epidermis during Drosophila embryogenesis. The actin-binding protein Canoe and its mammalian homolog Afadin mediate adherens junctions and actomyosin linkage. Among the binding partners of both mammalian and fly Afadin is ZO-1/Polychaetoid, an actin-binding protein that localizes to adherens junctions and in fruit flies. I am investigating the role of Canoe and its interaction with the ZO-1 homolog Polychaetoid to explore how the actomyosin cytoskeleton associates with adherens junctions during tissue elongation and collective cell migration during gastrulation. In my independent research program, I aim to help fill this gap in the field using a research strategy that proposes to identify novel Polychaetoid binding partners and determine their role in complex cell shape changes during tissue formation. This study will provide a deeper understanding how cells maintain tissue integrity while moving as an epithelial sheet, which could contribute insight into wound healing or human embryonic defect prevention.

This research project will last 10 weeks. 

Destroying the Solar System One Computer Simulation at a Time - Visiting Assistant Professor Sean O'Neill

Despite ample scientific evidence that our solar system has featured stable planetary orbits for billions of years and will continue to do so for the foreseeable future, astronomy students often ask what would happen to Earth’s orbit and the rest of the solar system if an interloping massive object, such as a rogue planet, star, white dwarf, neutron star, or black hole, were to pass nearby. Although the question is entirely academic in our case (for which we can all be thankful), higher rates of stellar interaction in dense star clusters potentially make this a very real issue for the stability of some extrasolar planet systems. We propose to disrupt our solar system in the safest way imaginable, namely through a series of numerical simulations that will explore the effects of massive astrophysical objects passing through our neighborhood. This project will also train students to operate PLU’s W. M. Keck Observatory for multiple scheduled summer outreach events.

This research project will last 10 weeks. 

Exploring the mechanism of adaptive mutagenesis in the yeast Saccharomyces cerevisiae - Associate Professor Tina Saxowsky

The Saxowsky laboratory has been exploring how cells gain adaptive mutations in response to a selective pressure (such as exposure to a drug) that causes growth arrest. In this context where cells aren’t dividing, the well-understood pathways that require DNA replication to generate mutations, particularly mutagenic replication past DNA damage, are not involved. Instead, we hypothesize that the effect of DNA damage on transcription, which must continue in order to provide the cell with the proteins it needs to function and survive, contributes to adaptive mutagenesis. Some types of DNA damage can be bypassed by RNA polymerase, directing the incorporation of a mutation in the growing RNA product. This results in a pool of mutant mRNAs, and potentially a population of mutant proteins that could alter the phenotype of the cell. If the mutant protein allows cells to resume DNA replication and convert this damage to a permanent mutation, the cell will have successfully acquired an adaptive mutation. Using the baker’s yeast Saccharomyces cerevisiae, we have gathered data in support of this hypothesis, including the observation that the mutations found in adaptive mutants most often correspond to DNA damage in the template strand of the target gene, where it is encountered by RNA polymerase during transcription. Unexpectedly, the replicational mutants that were sequenced as a control also show a bias for DNA damage on the same strand. However, the DNA sequence context around the mutation site (1-2 nucleotides upstream and downstream) seems to differ depending on whether the mutation is replicational or adaptive. This summer, we will undertake experiments to explore both the strand bias and the specific sequences within which these mutations arise in order to better elucidate the mechanism of adaptive mutagenesis.

This research project will last 5 weeks. 

Exploring the NatSci Fellows Program: What was the impact of our pilot year? - Assistant Professor Shannon Seidel

The NatSci Fellows program is an inclusive opportunity that all Natural Sciences majors (physics, computer science, mathematics, geoscience, engineering, chemistry, biology) can opt-into. The program encourages students to participate in 1) coursework support, 2) professional development, and 3) social and wellness related activities that will enhance their PLU experience and lead to increased sense of belonging and student success. The program is innovative in that it is the first in our division to use a “gamification approach” to incentivize student participation in activities that we believe will benefit them. We give students small rewards in the form of stickers in a booklet when they attend office hours or tutoring (coursework support), sit in on a departmental seminar or work with a career counselor (professional development), or attend a divisional social event or wellness opportunity on campus (social and wellness). If they meet the minimum requirements for each of the three categories listed above, they will achieve NatSci Fellows status where they will be eligible for an end of the year social, certificate of completion, and raffle prizes. This summer research project aims to assess the impact of the NatSci Fellows program in its first year to determine the extent to which it was successful in creating a sense of belonging among students in the Natural Sciences. Research students working on this project will have the opportunity to develop research questions, quantitatively and qualitatively analyze data, and present their results.

This research project will last 5 weeks. 

Characterizing the subglacial environment using glacier meltwater hydrochemistry - Associate Professor Claire Todd

This project will research subglacial environments on Mount Rainier in order to improve our understanding of the evolution of glaciers in a warming climate. To investigate the subglacial environment, we rely on meltwater sampled at the glacier terminus to measure the amount of water, sediment, and weathering products delivered from the subglacial environment. These samples document how glacier processes such as erosion and water storage respond to diurnal and seasonal changes in temperature and precipitation, and thus will provide insight into future, longer-term responses of Mount Rainier glaciers to climate change.

This research project will last 10 weeks. 

Tailored ROMP-based Solid Polymer Electrolytes and Single-Ion Conductors for Use in Ion Transport Applications - Professor Dean Waldow

This Research builds on past work developing new ion conducting solid polymer electrolytes. The objectives are to improve ion transport in using new solid polymer electrolyte materials for lithium ion battery applications as well as to improve ion transport and their use in organic mixed ionic and electronic conductor applications. The proposed new polymers are based on an oxanorbornene-dicarboximide monomer and will be synthesized using ring opening metathesis polymerization (ROMP). This base monomer allows a great deal of design flexibility where side chains will include flexible oligomeric ethylene oxides (high salt solubility), single-ion conducting units, and other groups which allow for a high glass transition temperature and modulus. ROMP also enables facile polymer design including homopolymers, random copolymers, and block copolymers. The properties of these new materials will be studied using dielectric spectroscopy, electrochemistry, atomic force microscopy, DSC, and other techniques. Any scattering data (X-rays or neutrons) that would be needed would be conducted with collaborators or at national laboratories.

This research project will last 10 weeks. 

Click-On and Unclick-Off Strategy for Customized Affinity Chromatography Media - Professor Neal Yakelis

Affinity chromatography is an important tool for the selective purification of biomolecules. We have developed a new reversible way to attach affinity ligand molecules to chromatography media by a nitroso Diels-Alder “click” reaction. The ligands could subsequently be removed by a retro-nitroso Diels-Alder “unclick” reaction. Monitoring of the attachment will be tracked using fluorescent dyes covalently linked to the chromatography substrate and ligand.

This research project will last 5 weeks.