Characterizing bacterial physiology and diversity using microfluidic systems
Abstract/Contents
- Abstract
- Bacteria are ubiquitous and play essential roles across the biosphere from environmental nutrient cycling to human health. Despite their importance, most bacterial diversity remains unknown. Among known species, traditional techniques measure bulk properties of a bacterial culture and fail to account for single-cell variations. Microfluidic technology enables single-cell manipulation and alleviates technical limitations associated with traditional methodologies. In addition to enabling single-cell resolution, integrating microfluidic platforms in experimental approaches increases throughput, which benefits statistical analyses. This thesis discusses two applications for which high-throughput microfluidic systems enable data acquisition with single-cell resolution. The first application addresses growth dynamics of Synechocystis, a model photosynthetic bacterium. In this investigation, a custom microfluidic setup facilitates long term, single-cell tracking under various illumination conditions. Single-cell growth curves demonstrate rapid response to light-dark transitions and reveal an adder like mechanism for cell-size regulation. The second microfluidic-based experimental method investigates the diversity of uncultivable bacteria from environmental samples. The throughput of the microfluidic platform allows the generation of many sub-samples, enabling genome binning based on presence of genomic contigs across sub-samples. Multiple known and novel bacterial phylogenies are identified in hot spring samples from Yellowstone National Park. Finally, this thesis discusses prospects of continued scaling of microfluidic systems and associated technical challenges. Both on-chip and off-chip schemes are explored, including an on-chip microfluidic component for digital to analog pressure conversion and various off-chip pressure control interfaces. The increased functional integration of microfluidic platforms and their application in microbial investigations offer an exciting future for the scientific community.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2016 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Yu, Feiqiao Brian |
|---|---|
| Associated with | Stanford University, Department of Electrical Engineering. |
| Primary advisor | Quake, Stephen Ronald |
| Thesis advisor | Quake, Stephen Ronald |
| Thesis advisor | Horowitz, Mark |
| Thesis advisor | Huang, Kerwyn Casey, 1979- |
| Thesis advisor | Wang, Shan |
| Advisor | Horowitz, Mark |
| Advisor | Huang, Kerwyn Casey, 1979- |
| Advisor | Wang, Shan |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Feiqiao Brian Yu. |
|---|---|
| Note | Submitted to the Department of Electrical Engineering. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2016. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2016 by Feiqiao Yu
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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