Creating the Processing Pipeline

The early stages of my research have been comprised of creating a pipeline of computer scripts that can process the large amounts of genomic data I have. Because the files I’m dealing with are incredibly large (10gb text files) none of the data cleaning and processing can feasibly be done by hand. I’ve tried several strategies to do this, and after weeks worth of failed attempts, I was able to get the major file processed and broken down into much more reasonably sized files that I now have to work on further to fully process to the point where I can use them to create a phylogeny.

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Seven days, Population eight, and Nine Ball

In the lab this week, I continued to transfer beads for my first cycle of evolution this summer. I was really impressed with myself because I managed to go the entire week without dropping a bead. It can be so difficult at times to get the beads out of the glass tubes, to wash them, and then put in the microcentrifuge tubes without dropping one or messing up at a single step. I am typically holding my breath the entire time because I am so anxious about it. This is such a huge accomplish for me and am glad that I have the opportunity to document this eternally. Other than my project, this week I helped out Dr. Murphy with some of her ongoing projects. I learned how to streak and made YPD glycerol plates.

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Defrosting, Detours, and a Debrief on Evolution

Last week was my first week of summer research. I was actually very excited to come back to campus. Relaxing at home is wonderful and much needed after finals, but with all the time in the world on my hands I started to get a little antsy. At the end of the semester, I paused my experiment by storing my yeast populations in glycerol and freezing them. Freezing the yeast puts them in a dormant state. When I returned for the summer, I knew I would be able to start exactly where I left off. For the first couple of days, all I did was prepare myself to start evolving again by getting all my equipment ready. I grow the yeast in glass tubes filled with evolution medium, basically sugar water. I spent a good portion of Monday autoclaving (sterilizing) and washing old tubes, making evolution medium and filling up clean tubes with it. At the beginning of last week, all but one of the autoclaves in the ISC was broken, so it was quite an adventure having to go back and forth to the third floor to get all my work done.

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Identifying the Genetic Underpinnings that Drive the Transition of Commensal Yeast Microbes to Opportunistic Pathogens

The unique relationship between humans and commensal microbes is a critical component of human health. Recent studies have shown that this relationship can be altered by the microbial evolution of social behaviors. Biofilms are complex microbial communities that can be found in a variety of environments. The formation of biofilms plays a vital role in driving the virulence of many microbial pathogens that are capable of infecting humans, and has allowed these organisms to survive in hostile environments. In fact, many commensal microbes have evolved into virulent, opportunistic pathogens through this mechanism. Currently, there exist a number of studies on the genetic basis underlying this transition among bacterial species in clinical settings. However, research on the evolution of virulence in medically relevant fungal species is lacking. For my research project, I intend to investigate the genetic underpinnings that result in the transition of a commensal microbe to an opportunistic pathogen by tracking the genomic changes in particular phenotypes that play a role in virulence. Specifically, I will determine whether the genetic variants uncovered in  S. cerevisiae yeast strains isolated in a clinical environment are the same genetic variants that are selected for when virulence evolves de novo in the lab.

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Abstract: Uncovering the Role of MK-STYX in Neuronal Development

In recent years, neurological diseases like Alzheimer’s, ALS, Parkinson’s, and dementia have become much more prevalent. Yet, the mechanism and development of such diseases largely remain enigmatic, and treatment is generally limited to supportive care. Neurodegenerative diseases generally involve a disruption in communication between neurons, whether by cell death or by fewer connections with other neurons (Gao and Hong 2008). My research centers on MK-STYX (mitogen-activated protein kinase phosphoserine/threonine/tyrosine-binding protein), a protein implicated in neuronal development. MK-STYX belongs to a group of proteins called pseudophosphatases, which lack catalytic activity but have homology to enzymes that dephosphorylate proteins, phosphatases (Hinton et al 2010). Though MK-STYX is catalytically inactive, it still plays a role in many cell signaling pathways, including cellular stress response, apoptosis, and neuronal development (Flowers et al 2014, Hinton et al 2010, Niemi et al 2011).

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