Measuring microbes : leveraging quantitative imaging to characterize heterogeneous systems across length scales
Abstract/Contents
- Abstract
- This dissertation addresses the question of spatial organization in living systems, a fundamental problem in understanding the physics of living systems. The structure and layout of the cell plays a key role in biophysical processes such as force transduction, diffusion, transport, and signaling. Using bacteria as a model system, I will present two examples of how cells generate, exploit, and interact with the spatial organization of their intracellular and extracellular environments. First, at the single-cell scale, I will discuss how L-forms (spheroplast-like, cell-wall deficient bacteria) of Escherichia coli can recover their normal rod-like shape without a pre-existing template. I will give a detailed, quantitative characterization of the recovery process at the morphological, biochemical, and molecular level. I will also discuss how our study of L-forms led us to investigate the mechanical properties of the bacterial outer membrane. Finally, I will propose that cell-wall synthesis is regulated by the local shape of the cell, giving rise to a biophysical model for rod morphogenesis. Second, at the community scale, I will discuss the vast, diverse, and poorly understood microbial ecosystem that resides in our digestive systems. I will present a quantitative image analysis platform for measuring host-microbe and microbe-microbe association in fixed sections of the intestinal tract, and show how diet shifts drive changes in the organization of the gut microbiome in gnotobiotic mice. In particular, I will demonstrate that polysaccharide starvation thins the host mucus layer, drives bacteria closer to host tissue, and alters clustering of several bacterial taxa.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2015 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Billings, Gabriel Humphrey |
|---|---|
| Associated with | Stanford University, Department of Physics. |
| Primary advisor | Doniach, S |
| Primary advisor | Huang, Kerwyn Casey, 1979- |
| Thesis advisor | Doniach, S |
| Thesis advisor | Huang, Kerwyn Casey, 1979- |
| Thesis advisor | Sonnenburg, Justin, 1973- |
| Advisor | Sonnenburg, Justin, 1973- |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Gabriel Humphrey Billings. |
|---|---|
| Note | Submitted to the Department of Physics. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2015. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2015 by Gabriel H. Billings
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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