Summer 2021 Research Projects

Machine learning techniques in protein structure prediction - Assistant Professor Renzhi Cao

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.

Emerging infectious diseases: threats to human and wildlife health - Assistant Professor Evan Eskew

Emerging infectious diseases are significant threats to both human and wildlife health. The devastating impacts of infectious disease across vertebrates are exemplified by the COVID-19 pandemic in humans, chytridiomycosis in amphibians, and white-nose syndrome in bats (the latter two wildlife diseases have driven severe population declines and even species extinctions). Nonetheless, major gaps in our understanding of infectious disease ecology remain. Therefore, for NSSURP 2021, I propose to mentor students in pursuit of two distinct research threads related to emerging infectious diseases. First, working with scientists at the Viral Emergence Research Initiative, students will collate and analyze existing data to understand how land use change might influence pathogen prevalence in wildlife. Because wildlife are major sources of pathogens that cause disease in humans, characterizing land use effects on pathogen dynamics represents a core element of future disease prevention efforts. Second, I will guide students in investigating a newly described wildlife disease of snakes, snake fungal disease (SFD). SFD is widely known from snake species in eastern North America but has only recently been detected in California and Idaho. Working with local museum institutions, we will seek to sample snake museum specimens for the causative pathogen of SFD, potentially documenting occurrence in Washington state as well as the historical distribution of the disease. This baseline information will be key to effective management of an emerging conservation threat to wildlife. In pursuing these research objectives, students will engage with the scientific literature, conduct novel data analyses, collaborate with scientists at other institutions, and gain experience with techniques in molecular ecology. Critically, I have chosen these specific research aims to be conducive to remote work, if necessary, and flexible enough to accommodate changes in research direction if the ongoing COVID-19 pandemic complicates existing plans.

This research project will last 10 weeks. 

Optimization, Synthesis and Conjugation-Based Characteristics of Benzofulvene Dimers - Visiting Assistant Professor Adam Glass

We aim to secure funding to further our work related to benzofulvenes (BF) and their derivatives. Funding for an undergraduate student researcher and reagents would greatly benefit and accelerate our research. We are confident that two years of funding would provide enough data to allow us to publish a highly reproducible synthetic approach with interesting optoelectronic applications related to the conjugation of BFs. Benzofulvenes are highly regarded fulvene derivatives. Which are arguably owed to their increasing presence in medicinal applications, molecular materials, use as synthetic precursors and overall intriguing physical and chemical properties. In particular, the properties associated with the conjugation of benzofulvenes have been shown to be quite interesting, as they relate to the possibility of tunable and perhaps non-linear optical properties. In prior work, we established a simple and direct microwave-based synthesis for the synthesis of functionalized benzofulvenes. To that end, we successfully modified and optimized a traditional route to the benzofulvene core ̶ utilizing substituted indanones to produce known and many novel functionalized benzofulvenes in three simple synthetic steps.

This research project will last 10 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. 

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 10 weeks. 

Glacial Geologic Research in Mount Rainier National Park - Professor Claire Todd

This research program focuses on glacial geologic research questions in Mount Rainier National Park. Students and Dr. Claire Todd will use glacial meltwater to determine the rate of glacial erosion, and to detect hydrothermal influence beneath glaciers. Another goal of our research this summer will be to determine the impact of rocky debris cover on glacier melt. Additional research questions may include exploring the causes behind debris flows originating from glaciers, or quantifying glacier retreat. Research tasks include collecting rock and/or water samples, analyzing water or rock samples in lab facilities at PLU, analyzing existing hydrologic datasets, analyzing satellite imagery, or studying time-lapse photography of a glacier terminus.

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.