Microfluidic-based Tools to Investigate Gene Expression and Regulation with Tissue-specificity during Aging in Caenorhabditis elegans

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Wan, Jason
Lu, Hang
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Aging is a complex, universal process that impacts us all differently. An increasingly important aspect of aging research is studying gene expression and regulation. Gene expression is age-, tissue-, and individual-dependent so it is important to capture all these pieces of information. While there are pooled-sample techniques that can measure the entire transcriptome (e.g., RNA-sequencing), they fail to capture this gene expression data on an individual level. There are single-animal techniques to measure spatial gene expression and individual-to-individual variability, but these lack throughput (both sample- and gene-throughput) and are thus difficult to scale for larger studies. In this thesis, I develop new microfluidic-based tools to address the limitations in single-animal assays to enable more robust gene expression studies in aging research. In Aim 1, I engineer a pipeline that allows for single-animal gene expression quantification with sub-cellular resolution by adapting single molecule fluorescence in situ hybridization (smFISH) in adult C. elegans using microfluidics. In Aim 2, I create two complimentary platforms to enable multiple cycles of smFISH, directly addressing the gene-throughput limitations. The first device is an electrokinetic/microfluidic hybrid device to enhance the reagent delivery of large, charged macromolecules. The second platform uses gentler reagents and allows for robust multicycle smFISH while retaining the tissue integrity of the samples. In Aim 3, I correlate age-related changes in neuronal functional responses and the underlying gene expressions in the context of mechanosensation. The completion of this thesis creates an array of new tools and frameworks that can improve the content of information we can gather on a single-animal level, enabling us to ask deeper questions in biology.
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