Winston Anthony

My experience interning at a small biotech company in St. Louis

When I began speaking with the CEO of Pluton Biosciences, the company that I would eventually intern with, we first began by defining the problems they try and solve. They develop revolutionary microbial products that aim to address some of the most relevant of society’s problems, such as lowering greenhouse gas build-up, increasing crop yield, and decreasing the spread of malaria-spreading insects. We decided to focus on a project designed to produce a novel method of carbon sequestration through use of specialized, bacteria enhancing soil amendments.

A “soil amendment” is any additive used to enhance the physical properties of soil; fertilizers are a common soil amendment used to replenish nitrogen lost to the previous seasons’ crops. Pluton aims to do more than just replenish spent nutrients, however. Pluton envisions a future where commercial growers can spray bacteria onto their fields at planting, and again at harvest, which will work throughout the year to store carbon and nitrogen. Carbon stored this way is removed from the atmosphere where it would collect as the greenhouse gas carbon dioxide, reducing the spread of global warming. On the other hand, stored nitrogen means less use of traditional fertilizers, a win-win for growers, the environment, and Pluton.

However, before this product can be brought to market, the efficacy of a bacterial soil amendment must first be tested. And thus questions of importance become: Can we detect the presence of this bacteria in fields after it has been added? Can we detect the genes which are most important to nitrogen fixation? Will this differ between fields in different states, in different areas of the United States? Preliminary data suggested that this bacterium could be found in some, but not all soil samples from both fields. I was tasked with building a computational pipeline that would look for bacterial DNA, and identify the genetic composition, specifically looking for genes which give the bacterium of interest the ability to take nitrogen out of the air and “fix” it into the soil. During the process of building this pipeline, I gained experience using cutting edge computational tools in the Amazon Web Services (AWS) cloud computing environment.

What became clear immediately during my internship experience, was how sheltered I was as a graduate student at WashU, with access to a private computer server run by IT professionals. Every piece of software I could ever need was already downloaded, installed, and loaded with a single command. Not so when using AWS! Instead, I was in charge of creating my own virtual machines, essentially specialized mini-computers which could then be loaded onto the cloud and run virtually. I was in charge of making sure that each machine was working correctly, could communicate with AWS service that stored the genetic data I was working with, and shut off correctly; this last part was especially important as every second of computing time is billed. I learned how a linux operating system works, how to set up a virtual private gateway on AWS, and a host of other extremely technical and specialized tasks. Most importantly however, I learned how to deal with the frustration of feeling as if you have been hitting your head on a wall for 6 hours trying to find a bug in your pipeline, but feel no closer towards fixing the problem. I learned data science best practices for storing data and writing code. I also gained valuable experience in working with a mentor in a small biotech company, where everyone wears many hats.

By the end of the internship, I had accomplished no actual computational biology; instead, I had gained experience working in an industry setting, and developed my own fully functioning computational pipeline. It was without a doubt one of the most useful experiences of my graduate career.