“Paving the Way for Regenerative Medicine: Curating Planarian Experiments in a Centralized Mathematical Database”
For more than a century, scientists have been captivated by the regenerative capabilities of the planarian flatworm, which can regenerate a full body from almost any type of amputation. To understand the mechanisms controlling this extraordinary ability, research approaches based on surgical, pharmacological, and genetic manipulations have been used extensively to produce a huge dataset of experimental results disseminated through the literature. The rise of sophisticated machine learning algorithms and computational power has brought upon a novel way of studying these fascinating creatures. The Lobo Lab has developed a mathematical ontology for encoding regenerative experiments, together with an artificial intelligence method to automatically infer mechanistic models of regeneration. In this project, we have curated hundreds of additional experiments into a formal database, called Planform, which stores, in a mathematical language, thousands of planarian experiments and results performed in the past decade. The data includes the details of the experimental interventions, such as drug additions, genetic interference, and surgical manipulations, and their effects on the resultant morphologies. This curated dataset not only deal with the growth and shape of the worm, but also show how the presence, or the lack, of key genes, results in different patterns and morphologies in the worm. Planform is a freely-available, centralized collection of information that helps the scientific community search efficiently for experiments and morphologies published in the literature. More importantly, this resource is essential for the application of artificial intelligence methods to automatically reverse-engineer models that explain the regulatory mechanisms controlling the regeneration in these worms. The new dataset is already published and freely available in the dedicated website (http://lobolab.umbc.edu/planform), helping human scientists and the automated computational approach to find better models of planarian regeneration. All these efforts will pave the way for the next-generation applications in human regenerative medicine.
How did you find the research opportunity?
I wanted to work in a lab that has implications in regenerative medicine because that is a field I am interested in researching. I gathered information about on campus labs and about what they research and saw that the lab of Dr. Daniel Lobo is most closely related to my research interests. I dropped by his office asking if there any available positions and luckily I was able to get an interview with him. I was fortunate enough to get the position and eventually started working in the lab.
Who is your mentor for your research project? How did you arrange to work with this person?
I met with Dr. Daniel Lobo from the Biology Sciences department to learn about his research and to see how I would be a good fit in the lab. Given my academic background and research interests, we decided that working with the Planform project would be most fitting to accommodate both my interests and the overall goals of the lab.
Do you get course credit for this work? Paid? How much time do you put into it?
Over the summer I got paid and currently I get credit. This semester I am putting in about 10-15 hours a week.
What academic background did you have before you started?
I joined the Lobo Lab at the end of my sophomore year and as a Biology major, I finished all my core courses and had solid STEM background as a result.
How did you learn what you needed to know to be successful in this project?
I was fortunate enough to have such helpful colleagues in the lab. Dr. Lobo especially played an integral role in my development as a researcher. He worked with me directly teaching me many of the skills I needed to acquire to be successful in this field of work.
What was the hardest part about your research?
The fact that I was working in a bioinformatics lab with on little background in programming was especially challenging. I had to learn a lot of things on my own before I could partake in some of the lab activities. Currently, I am in the process of learning the programming language, C++, so I could aid with a different lab project as well as my own.
What was the most unexpected thing?
I’m sure every member of the lab can agree that we’ve become more than a lab, we’ve become family. I never expected to develop such a close relationship with every member of the lab, especially Dr. Lobo. Most PI’s have a reputation of being very hands-off and uninvolved with the research. Dr. Lobo is different, however, as he plays an active role in the development of the lab and us as researchers. I get to work directly with him and honestly could not ask for a better mentor.
How does this research experience relate to your work in other classes?
My specific project in lab has significant connections to developmental biology and regenerative medicine, topics that consistently appear time and time again in all levels of Biological courses. Along with this, my project required me to read though a lot of academic literature, which has made me very proficient in that skill. Also it taught me a lot about academic writing, which has proven to be valuable in classes of all disciplines.
What is your advice to other students about getting involved in research?
Get started early!!! My biggest regret about research is that I didn’t get started as early as I should have. Working in a lab is a very rewarding experience that you learn a lot from. Getting involved early allows you to maximize what you gain and gives you enough time to pursue any long-term projects. Time is an invaluable resource and this is especially true with research.
What are your career goals?
After I earn my Bachelor’s I hope to attend medical school, become a doctor, and ultimately make a positive impact on the world.
What else are you involved in on campus?
- I am a Teaching Assistant for Biology 300L
- I am a Teaching Assistant for Biology 303
- I am a Learning Assistant for Chemistry 352
- I am a Writing Fellow for English 100
- I am a tutor at the Math Lab
- I am a tutor at the Writing Center
- I am the President, Vice President, and Treasurer for different UMBC clubs