Overview
Environmental pollutants continue to pose significant threats to human health, development, and ecosystems. Identifying the most harmful pollutants and understanding the mechanisms through which they exert their effects remains a key focus of developmental and environmental toxicology. As a computational scientist, my goal is to contribute to these efforts by developing mathematical and computational tools that elucidate toxicant-induced effects during embryonic development.
I collaborate closely with Dr. Karilyn Sant at the School of Public Health, San Diego State University (SDSU), who investigates the impacts of common water pollutants using the zebrafish model (Danio rerio). Together, with the support of Dr. Uduak George from SDSU’s Department of Mathematics and Statistics, we validate the tools I develop, combining experimental data with advanced mathematical modeling. This interdisciplinary collaboration has led to the successful exploration of various environmental contaminants and their impacts.
Research Highlights
danRerLib: A Python Package for Zebrafish Transcriptomics
Understanding differential gene expression pathways is crucial for identifying how organisms respond to environmental stressors. Zebrafish, with a transcriptome similar to humans, serve as a valuable model for studying development and disease. However, incomplete zebrafish pathway annotations can limit functional insights. danRerLib addresses this challenge by mapping zebrafish genes to human orthologs, allowing researchers to leverage more comprehensive human annotations. The package provides tools for functional enrichment analysis using up-to-date Gene Ontology (GO) and KEGG databases, offering a broader perspective on experimental results. Available on GitHub and PIP, with detailed documentation and tutorials. To learn more about this project, I recommend checking out the publication, associated documentation, and even a blog post I wrote about the topic with a mini-presentation on the work.
Complex Network Models for TCPMOH Induced Developmental Deformities
Tris(4cholophenyl)methanol (TCPMOH) is a recently discovered environmental water contaminant with an unknown origin. Although novel, it is highly persistent in the environment, bioaccumulates in marine species, and has been found in human breast milk. The increase in findings of TCPMOH in the environment and human samples poses itself as a possible threat to human development. My primary goal is to describe the effects of TCPMOH during development using the zebrafish model (Danio rerio) and mathematical modeling. Using microscopy, we have captured developmental timepoints to determine deformities in the zebrafish. A complex network model has been developed to analyze the association between deformities and mortality within and between experimental groups. With new environmental contaminants continually being discovered, the network model developed may be applied to determine the morphological damage any new toxicant may have.
Mathematical Models for Nutrient Absorption and Fish Growth
Optimal embryonic development plays a major role in the health of an individual beyond the developmental stage. Nutritional perturbation during development is associated with cardiovascular and metabolic disease later in life. With both nutritional uptake and overall growth being risk factors for eventual health, it is necessary to understand not only the behavior of the processes during development but also their interactions. I have developed ordinary and delay differential equation models to quantify the rate of yolk absorption and its effect on early development of a vertebrate model (Danio rerio). The model has been extended from a control space to a toxicant space to analyze the effects of perfluorooctanesulfonic acid (PFOS).