Cellular Adaptation to Hypoxia: The Matrisome Connection

Low-oxygen environments are a significant stressor that cells must adapt to during development, aging, and disease states. This research explores how hypoxic conditions (0.5% O₂) influence the extracellular matrix (matrisome) of C. elegans through modulation of collagen gene expression.

Collagens serve as critical structural components that maintain tissue integrity, and their dysfunction is implicated in numerous human diseases. By uncovering how oxygen availability regulates collagen expression, we gain insight into fundamental adaptive mechanisms that may be conserved from nematodes to humans.

• C. elegans
• Hypoxia
• Matrisome
• Collagen Genes

Advancing Techniques for Live Organism Imaging

At the University of Washington (Dr. Alexander Mendenhall Laboratory, 2019-2020), I focused on developing innovative methodologies for visualizing biological processes in real-time. By implementing a complete photolithography workflow, I created specialized microfluidic devices that optimize the imaging of live C. elegans.

These advanced imaging platforms allow researchers to observe cellular and molecular processes with unprecedented clarity, providing crucial insights into biological mechanisms under various environmental conditions.

• Microfluidics
• Photolithography
• C. elegans
• Confocal Microscopy

The Biology of Aging and Lifespan Regulation

Working with Dr. Matthew Kaeberlein at the University of Washington (2018-2019), I contributed to research exploring the fundamental factors that influence lifespan. Using yeast as a model organism, I engaged in precise microdissection techniques and developed methods to quantify and analyze lifespan data.

This work provided valuable insights into the cellular and molecular mechanisms of aging, contributing to our understanding of how these processes might be conserved across species, including humans.

• Yeast
• Lifespan
• Microdissection
• MATLAB

Genomics and Bioinformatics: Bacteriophage Research

My early research experience at The Evergreen State College (2009-2010) involved the annotation of the Pseudomonas aeruginosa bacteriophage PEV2 genome. Working with raw DNA sequence data, I identified and characterized genes and their potential functions.

This work contributed to the broader understanding of bacteriophage biology and demonstrated the power of genomic analysis in understanding biological systems at the molecular level.

• Genomics
• Bacteriophage
• Annotation
• Bioinformatics

RNA Sequencing Experimental Analysis Workflow Using Caenorhabditis elegans

Authors: Robledo, J., Nahar, S. R., Ruiz, M. A., Hendricks, R. J., Burks, D. J., Ladage, M. L., ... & Padilla, P. A.

Published in: Transcriptome Data Analysis (2024), pp. 115-141. New York, NY: Springer US.

This methodological chapter establishes standardized protocols for RNA sequencing data analysis using C. elegans as a model system, providing researchers with a comprehensive guide for transcriptomic investigations.

Exploration and analysis of glucose-induced stress responses and cellular pathways in C. elegans

Authors: Hendricks, R. J., Ladage, M. L., Nahar, S. R., Robledo, J., Ruiz, M. A., & Padilla, P. A.

Presented at: 2024 C. elegans Conference: Aging, Metabolism, Stress, Pathogenesis, and Small RNAs in C. elegans, Madison, WI, United States (June 5–8, 2024).

This poster presentation detailed our findings on how excessive dietary glucose triggers specific cellular stress responses in C. elegans, offering insights into conserved metabolic pathways relevant to human health conditions.

Bridging Basic Science and Human Health

My research employs C. elegans as a powerful model system to uncover fundamental cellular mechanisms that are likely conserved across species. The insights gained from studying how these simple organisms respond to environmental stressors have far-reaching implications for understanding human health, particularly in the contexts of:

• Metabolic disorders and obesity
• Aging-related cellular dysfunction
• Hypoxia-related conditions (stroke, ischemia, cancer)
• Extracellular matrix disorders

Interdisciplinary Approach

My research integrates techniques and perspectives from multiple disciplines:

• Molecular Biology: Gene expression analysis, RNA sequencing
• Cell Biology: Live organism microscopy, fluorescent imaging
• Genetics: Mutant analysis, genetic screens
• Bioinformatics: Computational analysis of large datasets
• Engineering: Microfluidic device design and fabrication

This multifaceted approach allows for a comprehensive investigation of complex biological phenomena from the molecular level to whole-organism responses.