My name is Amy Rose, and I’m a post-bac in Anna’s lab this summer. I graduated last month with an Alt. Biology degree with an emphasis in Computer Science. Taking Anna’s classes in my first two years at Reed was the start of my interest in computational bio. I spent my junior year studying computer science at The University of Sussex, and after this summer I will be starting as a software engineer at Puppet here in Portland.
When it came time to find a thesis project, I thought it would be interesting to explore an area of biology that I hadn’t had time to study while at Reed. I was coadvised by Anna and Sam Fey, who is an ecologist. Sam’s research on thermal variation led me to my project, which focused on modeling the effect of thermal variation on freshwater phytoplankton using real world data.
Phytoplankton are ectothermic, which means that they are not able to regulate their own body temperature. Additionally, due to their small size it is difficult to empirically measure the variance in their body temperature due to movement through thermally variable environments. My thesis began to resolve the impact on movement on body temperature and fitness. In this context, fitness represents the overall change in population size of phytoplankton based on temperature-dependent birth and mortality rates.
Temperature data was collected from Sparkling Lake in Vilas County, Wisconsin at intervals from .5 to 3m throughout the lake with a frequency as high as every minute over a period of 26 years. We interpolated the collected data to fill in estimated temperatures over depths which were not collected, as seen in the figure below.
We created five algorithms representing different theoretical patterns of phytoplankton movement throughout the water column, which we plotted against the data. This gave us a framework to understand the limits of what body temperatures phytoplankton may be experiencing. The second stage of the project was to plot these simulated body temperatures against a function representing phytoplankton fitness.
This summer, we hope to extend my thesis research over space and time. For my thesis, we focused on a single season, but we’re currently looking at extending the movement algorithms over all 26 years of data. We’re also interested in exploring more datasets sourced from lakes in different geographical locations. Additionally, we’re analyzing the effects of changes to the fitness function.
Reed has finished for the year, but that doesn’t mean that students are done. Last week kicked off a slew of undergraduate researchers doing all kinds of research. In no particular order, here’s a taste of what people will be working on in the compbio lab. Stay tuned for occaisonal group updates.
Math-CS major Jiarong (Lee) Li ’21 and biology major Tunc Kose ’22 are going to develop algorithms to analyze a cell’s response to external signals (called signaling pathways). They will be working to extend ideas based on the original PathLinker paper and Ibrahim Youssef’s Localized-PathLinker paper.
Recent graduate Amy Rose Lazarte ’19 (alt. bio major with a CS emphasis) will continue to develop a resource and modeling framework for understanding the effect of thermal variation on freshwater phytoplankton. Co-advised by ecologist Sam Fey, she has developed a computational pipeline to analyze longitudinal lake temperature data using simulations of phytoplankton swimming strategies.
Biology major Tayla Isensee ’20 is working on identifying targets of retinoic acid signaling in zebrafish eye development. She has a hand in the wetlab work with developmental biologist Kara Cerveny, and she will be building a zebrafish protein-protein interaction network to find potential regulators to test. First, though, she’s going to hunt for retinoic acid response elements (RAREs) in the zebrafish genome to identify direct targets of retinoic acid.
Another recent graduate, neuroscience major Alex King ’19, will be wrapping up his thesis work to build a network that integrates gene, transcript, and protein relationships in order to identify dysregulated pathways in polygenic diseases based on genome-wide association study (GWAS) data.
Biology major Karl Young ’20 will be reading up on computational modeling in neuroscience, and figuring out the intersection of my world (algorithms for biological networks) and neurobiologist Erik Zornik’s world (neural circuits and how they affect behavior).
Last but not least, CS graduate Ananthan Nambiar ’19 will be getting his thesis ready to present as a poster at ISMB/ECCB in Basel later this summer. He modeled proteins as language with the help of his main advisor, natural language processing (NLP) expert Mark Hopkins in CS.