Lost in a Crowd: Observations of Single DNA Knots and Single Mammalian Cells

Abstract

This thesis is dedicated to my parents, to my mentors, Steve Quake and Mel Simon, to the other people in lab, especially the postdocs, who, really, taught me all the nuts and bolts of putting together an experiment and making it work, and to all the other friends along the way who made the journey so much fun. iv Acknowledgements I worked together with Heun Jin Lee on the knots project. He put all the instrumentation in place to perform the experiments, and throughout the experiment taught me to think and work systematically and effectively. I could have avoided many pitfalls and delays in that and subsequent experiments, had I followed his advice more diligently. Alex Groisman and Keith Matthews did some preliminary work on the knots project. In particular, Alex suggested the use of high-molecular weight PEG to increase viscosity without changing refraction index and also provided the initial oxygen scavenging recipe; the idea to use servo motors to control the optical elements was Keith’s. Theoretical predictions of knot sizes for the 71 knot, not published elsewhere, were kindly provided by Pietro Pieranski. He, Andrjez Stasiak, Doug Smith, Mei Wang, and Julius Su provided other helpful suggestions in the knots project. Members of the Quake group who taught me the art and craft of microfluidics included Emil Kartalov and Carl Hansen. The use of constrictions to control shear stress was suggested by Mike Diehl. All the biology for the signaling project was done in Mel Simon’s lab, and I’d like t