Master’s Degree Research

I am fascinated by biology and the complexity of the human body. As I entered Stanford University as a graduate student, I seized the opportunity to spend some time away from the aerospace field and to immerse myself in the world of biology and microscale mechanical engineering. This page highlights work I did in the Pruitt Microsystems lab and at the Marine Biological Laboratory:

Bio-MEMS Research
MBL Physiology Course
Cell Mechanobiology Technical Reports

Through this work I gained skills in microscopy, MEMS fabrication and design, PIV, image processing, cell culture, cell physiology, surface chemistry, cell-cell junction biology, and interdisciplinary teamwork.

Mechanobiology of Cell-Cell Junctions

Upon joining Prof. Beth Pruitt’s lab, I quickly got up to speed on wet lab skills (cell culture, preparing labeled cells, working with proteins), microscopy, and MEMS fabrication and design.  With these tools, I started in the very exciting research space bridging mechanical engineering and cell biology. I focused on a research area called “mechanobiology” or studying the way proteins, cells, and tissues generate and respond to forces.

Strain Array Device from the Pruitt Lab

I initially worked with a device designed in the Pruitt lab called a “Strain Array.”  This device allowed us to stretch cells attached to an elastic membrane and study their remodeling and protein secretion response. Through this project I learned about PIV (Particle Image Velocimetry), MATLAB image processing, soft lithography, and cell physiology.

I became interested in the various proteins that biologists use in cell experiments to get cells to stick onto membranes and dishes.  I wanted to determine if different “adhesion proteins” would result in different cellular response to mechanical stimulation.  This involved learning about surface chemistry and cell-cell junctions.  I wrote two conference abstracts on this subject:
2011 Microtechnologies in Medicine and Biology Abstract
2011 MicroTAS Abstract

I was also interested in designing a cell culture system to look at cell-cell junctions in epithelial sheets and cell transmigration through endothelial sheets. With another graduate student, Armen Mekhdjian, I developed a project and preformed preliminary experiments for the design of a cell culture system to produce a suspended basement membrane for cell transmigration studies.

The idea was to design a micro-environment similar to the in vivo environment cells experience in epithelial and endothelial sheets.  We designed and manufactured an array of flexible microposts which we coated with adhesion protein to get cells to attach.  As the cells proliferated they grew into a sheet and deposited proteins that form a “basement membrane” on the underside of the cell.

The micropost array allows any movement by the cells to be tracked and translated into forces using simple beam bending theory.  The micropost array environment with a suspended basement membrane was designed to aid in the study of cellular forces during cell transmigration.

To read more details on this project, see my qualifying exam research proposal presentation:
Qualifying Exam Research Proposal PowerPoint Slides

Beyond the immense amount of experimental techniques I learned in the Pruitt lab, I gained experience in working on interdisciplinary teams. Working with our collaborators Prof. Alex Dunn in chemical engineering and Prof. James Nelson in bioengineering was an invaluable experience. I gained an appreciation for the complexity of biological systems.  The interdisciplinary teamwork and expertise is critical to really begin to understand mechanobiological systems in the body. I truly enjoyed my experience and have much gratitude towards my collaborators and teachers!

Marine Biological Laboratory Physiology Course

In the summer of 2011, I attended the MBL Cell Physiology Course in Woods Hole, Massachusetts. The course is designed to bring together PhD students, post-docs, and professors in biology and computational science to work on cutting edge problems in cell physiology. I worked on three different projects over the seven week course:

1. “Tyrosine phosphorylation and protein recruitment in focal adhesions” with Dr. Clare Waterman from the NIH.

We studied the dynamics of tyrosine phosphorylation and protein recruitment in the focal adhesions of U2OS cells. We were interested in how force cues cause focal adhesions to grow and strengthen through proteins opening in response to force and revealing binding sites. Experiments consisted of transfecting a special fluorescent probe and fluorescent adhesion proteins into U2OS cells and watching their dynamics during cell migration with spinning disc confocal microscopy. In addition, we seeded the cells on soft and stiff polyacrylamide gels to compare the affects of more or less tension in the focal adhesions.

2. “Focal adhesion protein stretching in vivo during motility and mechanotransduction” with Dr. Mike Sheetz from Columbia University.

GFP-talin concentrated on force post tips in an MEF cell

For this project, we used double-tagged Talin proteins to look at how focal adhesion proteins stretch during cell migration in mouse embryonic fibroblast (MEF) cells. We attempted to detect single molecules using super resolution microscopy.  In particular I worked on making the flexible force posts (0.5 μm in diameter, 1.5 μm tall, and 1 μm from center to center) that we used to monitor the cell movement.

3. “Quantifying transcription and pattern formation in developing fly embryos” with Dr. Rob Phillips from Caltech and Dr. Thomas Gregor from Princeton.

eve gene stripe development

This project focused on quantitatively understanding segmentation in drosophila embryos. We were interested in the first three hours of development before gastrulation.

During these three hours, the blueprint of the future adult organism is determined. One part of our project was to take live images of Giant and Eve dynamics. Giant is a gap gene and Eve in a pair rule gene. Eve had never been imaged live in vivo before this session! It was very exciting to experience something for the first time. The embryo pictured to the lift is a still image from our Eve movie.

Cell Mechanobiology Technical Reports

As part of the ME Course “Mechanics of the Cell”, I wrote a review paper on techniques to measure cell traction forces.
Cell Traction Force Review Paper

I worked with two other classmates in the ME course “Mechanics of Growth” to develop a finite element model of wound healing after sutures. During this project we got to speak with two plastic surgeons at the Stanford Hospital to learn about scaring as a result of sutures. We collaborated with them to determine some fundamental science questions about wound healing that we could try and illuminate using a computational model.   Wound Healing Modeling Project