Integrating Biology and Code: Developing a Software Pipeline for Plastic Biodegradation

biology
analysis
code
bioinformatics
data wrangling
bash
By combining biology and coding, I developed a software pipeline to analyze RNA-seq data and uncover enzymatic pathways for plastic biodegradation. A step towards a greener future.
Published

May 17, 2022

I had the incredible opportunity to combine my passion for biology and coding in my undergraduate thesis project. Working alongside Dr. Rosa León-Zayas and Reed College, we aimed to identify enzymes involved in the biodegradation of plastic, specifically polyethylene terephthalate (PET). By sequencing the RNA of bacteria exposed to plastic, we analyzed gene expression and translated it into protein and enzymatic counterparts.

To ensure high-quality data, we developed an optimized software pipeline for cleaning and analyzing RNA-seq data. Despite a data loss in the control group, we successfully identified abnormal gene expression patterns and generated metabolic pathways for each bacterium in our consortium. Through extensive database searches, we discovered previously unknown enzymes that potentially contribute to PET degradation.

Flowchart of cleaning RNA-seq data and identifying enzymatic pathways

Fig. 1 - Flowchart of cleaning RNA-seq data and identifying enzymatic pathways. Created with Biorender.com.


I proposed a hypothetical enzymatic pathway for PET degradation, which marked a significant step towards combating global pollution. Our findings were presented at the Murdock College Science Research Conference and later published in the International Journal of Molecular Sciences. This research opens doors for the development of natural waste treatment facilities where bacteria biodegrade plastic waste, and potentially even genetically engineer bacteria to produce plastic polymers from waste materials.

Hypothetical enzymatic pathway for degradation of PET plastic

Fig. 2 - Hypothetical enzymatic pathway that I identified. A more thorough enzymatic pathway has been identified in the publication. Created with Biorender.com.


I am grateful for the collaboration with Dr. Rosa León-Zayas, Grace Sheehan, and our colleagues at Reed College, as well as the support from the NSF and the Murdock Trust. This project holds immense promise for a sustainable future, where biology and technology work hand in hand to address environmental challenges.