Recent Internship Highlights
Contributed by Aiden Aceves (2018): During the summer of 2018 I spent three and a half months working as a data scientist in the structural biology group at The Genomics Institute of the Novartis Research Foundation (GNF). While GNF employs a team of data scientists as part of their informatics group, I was the first data scientist in the structural biology group. This granted me to opportunity to work closely with the Director of Structural Biology, a talented leader, structural biologist and programmer. My main task was the development and subsequent application of a framework for conducting machine learning on structural data. This was an exciting mandate, as I possessed excellent resources and mentoring, and was given the freedom to implement and test creative ideas. In addition to expanding my knowledge of machine learning, I learned about packaging, project structuring and documentation. Prior to this experience, most of the code that I had written was only for me. If someone else wanted to use, or even read it: good luck! Because the tools I wrote had to be usable on a variety of machines and by scientists with varying levels of computational experience it was critical that I developed better habits. Throughout the summer I met with the structural biology group regularly to train them to use the tools I developed. This process provided me with valuable feedback about software features and documentation to add, potential applications for the software, and how to communicate effectively. The work that I did was tremendously rewarding, and has spawned ongoing planning of a long-term collaboration. I am grateful that I was able to experience working at a medium-sized site like GNF, and among such driven and bright colleagues.
Contributed by Heidi Klumpe (2018): This summer, I interned in the Biology department at Amyris (Emeryville, CA). This 10-year-old, 400-person company engineers yeast to produce useful molecules. High rates of homologous recombination in yeast, coupled with an army of robots and custom software, make metabolic engineering at Amyris exceptionally rational and high-throughput. So far, this pipeline has generated yeast strains that produce farnesene (a precursor to many other useful molecules) and squalane oil (which forms the basis for their direct-to-consumer skincare) at the kilogram scale.
For my project, I explored how a relatively simple but ad hoc step in the engineering pipeline could be automated with Amyris’s existing technology. Working on something very different from my thesis, I discovered (and partially filled) gaps in my knowledge of yeast and chemistry, but also took stock of my core set of skills that apply to any scientific problem: problem definition, experimental design, and data analysis. What I most enjoyed was mapping certain quantitative features of the biology onto clear boundaries for success for different automated solutions.
Overall, the most meaningful part of this experience was meeting PhD-level scientists who said working at Amyris satisfied all their scientific goals. It made me consider how a scientist selects their career goals, which I discovered are surprisingly similar between an academic PI and industrial project manager. Each sets a scientific trajectory toward a hard goal require cutting-edge technology and knowledge we don’t have yet, maneuvers the confines of available money and resources, manages teams of scientists to carry out this work as various team members see fit, and knows the majority of their success comes down to careful written and oral communication of their work to their scientific community. The key differences are how you pick the scientific trajectory (though each are subject to certain unglamorous boundaries in their planning) and the values and composition of that scientific community. Ultimately, I enjoyed Amyris for many of the reasons I enjoy Caltech: inspiring scientific problems and generous, creative coworkers.
Contributed by Anu Lakshmanan (2018): During the summer of 2018, I had the unique opportunity of doing a research internship at Synlogic, Inc. in Cambridge, Massachusetts. Compared to conventional drugs based on synthetic chemicals, Synlogic is pioneering the development of a novel class of ‘living medicines’ or ‘Synthetic Biotics’ by using synthetic biology principles to genetically re-program beneficial probiotic bacteria. While at Synlogic, I closely worked with the Microbial Engineering and Discovery Sciences (MEDS) team to design and build new probiotic strains, as well as test newly built strains for desirable functionalities that would expand and optimize future versions of Synlogic’s clinical candidates. I was fortunate to be involved in multiple projects at different stages of development: from genetically engineering probiotic therapeutics for new disease targets to downstream characterization of clinical drug candidates. This enabled me to collaborate and work with scientists from many other groups such as Bioanalytics, In Vivo Pharmacology, Process Development and Manufacturing Sciences. The experience gave me valuable insight into the processes involved in translating an innovative scientific idea into a therapeutic product that could benefit patients.
This was my first foray into research outside academia and while I was excited to see how R&D was carried out in the corporate biotech space, I had some reservations about how I would fit into the industry culture and whether I would have the scientific freedom to explore and implement new ideas as an intern. However, my fears were put to rest during the very first week of my internship when my manager at Synlogic encouraged me to discuss and implement new, relevant project ideas during my time there. Besides contributing to several ongoing high-impact projects, I was also able to work on an independent pilot project to generate useful data for the company. While putting my previous research skills and experience to good use, I also got valuable exposure to cutting-edge tools and techniques currently used in synthetic biology and drug development. At the end of my internship, I presented my research findings and conclusions to a large team of senior researchers and team leaders including the CSO, which was very well-received.
I consider my internship at Synlogic to be a valuable and enriching learning experience that opened my eyes to exciting research opportunities outside the academic setting. It was especially satisfying to see the direct application of my research to create and/or improve a therapeutic with the potential to alleviate patient suffering. I am extremely grateful to the Biotechnology Leadership Program at Caltech and Synlogic for giving me this opportunity to do an industrial internship, and even wish that I had done this earlier in my PhD program. Based on my experience, I would highly recommend all students to consider doing an industrial internship during graduate school to gain exposure to different R&D pipelines outside academia. Last but not the least, I strongly believe that the industrial experience will help me make a more informed decision about my next step after graduate school and allow me to actively explore new ways in which I can contribute to improving human lives through biomedical research.
Contributed by Pradeep Ramesh (2018): This summer, I had the pleasure of interning at EvoRx Technologies Inc, a small start-up in Pasadena, CA, which focuses on evolving cyclic-peptides that can either activate or inactivate specific biochemical pathways within the cell. Given my broader interest in starting a company down the road, I felt that working at a small startup would offer insight into the funding and management challenges of an early stage venture. In addition, I chose this company in order to learn about a topic that I am interested in pursuing during my post-doctoral studies. Although my background in physics and bioengineering was quite different from those of the scientists currently employed by the company, I was nonetheless able to contribute in a unique way.
My main project consisted of developing new biochemical assays to interrogate the efficacy of evolved cyclic peptides – in practice, this meant (a) applying my knowledge of molecular biology to build and purify protein constructs which would then serve as test platforms and (b) learning solid-phase peptide synthesis in order to synthesize new variants of successful compounds. While learning about the company’s design-build-test pipeline, I observed that one of the rate limiting steps in the process was whether or not the evolved compound could successfully cross the cell membrane. I realized that this problem could perhaps be tackled using Machine Learning, since the rules for cell-uptake are reasonably well understood. Consequently, using data on cell-potency for compound variants, I set out to build an ML algorithm that could learn from the data and thereby predict the cell-permeability of new variants. While I was not able to complete this work within the timeframe of the internship, I was happy to introduce a new concept to the company, which may prove to be useful in the near future.
Contributed by Ruijie (Kelly) Zhang (2018):
This summer I was an intern with the Biology Department at Amryis, in Emeryville, CA. Amyris is a synthetic biology company whose platform is to use designer yeast to transform sugar into value added products. The Biology Department, the research arm of Amyris, is responsible for creating strains of engineered yeast which produce the desired molecules. Automation plays a huge role at Amyris, which relieves the scientists of many mundane tasks so they have more time for design. With strong internal collaborations across departments, this talented team of scientists and their army of robots can accomplish metabolic engineering goals incredibly quickly.
During my time as an intern, I worked with a team of scientists to create a strain of yeast with improved efficiency for the production of a target molecule. Working on something very different than my PhD project allowed me to appreciate an entirely new field of science. As an experimentalist, I learned to translate what I learned about designing experiments for my PhD project to a different system. This experience in industry has taught me many lessons about project management. Working together with a team to achieve a common goal requires team members to break down a problem into discreet sections and deliver the results of these sections on the agreed timeline— useful lessons that I will apply my future work!
Amyris is an exceptional company to intern for. The scientists who work there are extremely passionate about science and work hard to foster a positive environment. I met many scientists there whom I greatly respect and I believe this company will lead the way in using microorganisms for the green production of chemicals.