2022 & 2023 Undergraduate Summer Research Program Participant

Home Department: Undeclared

2022 Research Project: “Integrating Differential Decay of Polycistronic mRNAs Into the E. coli Whole-Cell Model”

2022 Mentor: Markus Covert (Bioengineering)

The bacterium Escherichia coli whole-cell modeling project seeks to create a mechanistic, computational model of an E. coli cell. The project currently includes 43% of characterized genes and may prove a powerful tool for predicting complex behaviors. Predictions will help generate new experimental hypotheses, aid in bioengineering design, and integrate diverse datasets. Albert will mathematically and computationally model the widespread phenomenon of varying decay rates between mRNAs from the same gene cluster, which fine-tunes gene expression, and seek to integrate his model with Python into the whole-cell model. He will then experimentally validate his model with fluorescence-based or sequencing-based measurements of gene expression and RNA degradation. This work will help refine the Covert lab’s E. coli whole-cell model to better support their research of cellular functions.

2023 Research Project: “Using the E. coli Whole-Cell Model to Investigate Why E. coli Has Its Current Genomic Arrangement of tRNAs/rRNA Genes and Associated Growth-Rate Dependent Gene Dosage Effects ”

2023 Mentor: Markus Covert (Bioengineering)

E. coli is one of the most well-studied organisms in biology. The Covert Lab is trying to build a computational model of an E. coli that can simulate its growth on a computer by curating decades of data that have been experimentally measured from this organism. When completed, such a model would allow them to quickly test scientific hypotheses, design industrial strains, or even make novel discoveries by running a few lines of code, instead of conducting time-consuming and laborious experiments. Albert’s summer project will focus on expanding the predictive capabilities of this model by including a more detailed representation for the production of tRNAs, which are molecules in an E. coli cell that are responsible for carrying amino acids to proteins.