Getting Started with Sequencing Analysis

It has been a few weeks and I thought that I would give some updates on my progress so far. I’m currently replicating methods from the paper Sex Speeds adaptation by altering the dynamics of molecular evolution (1). This paper provides a useful computational workflow for identifying mutations from sequence data. This past month I have come across a huge learning curve, using software that I have never come across before, specifically GATK (Gene Analysis Toolkit). My first research task is sequencing analysis, and given that I have very minimal experience using sequencing software, it has been quite a challenge. Nonetheless, I have enjoyed learning a lot from this experience. From deciphering and creating pipelines, troubleshooting errors and running 50+ hours commands (we have a huge dataset), I’m getting closer to having a working dataset that I will use for analysis.

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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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