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Microfluidic Large Scale Integration and its Application to Systems Biology


Maerkl, Sebastian Josef (2008) Microfluidic Large Scale Integration and its Application to Systems Biology. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/5CMX-CV08.


The goal of biology is to understand how complex systems such as cells and entire organisms function. Systems Biology attempts to quantitatively characterize all components comprising these systems. A considerable task. Microfluidics provides a powerful tool for undertaking this endeavor. This thesis describes the development of Microfluidic Large Scale Integration (MLSI) using devices fabricated by Multilayer Soft Lithography (MSL). MLSI and fluidic components, such as multiplexers and free-standing membranes, serve as the infrastructure for performing large-scale biophysical measurements of biological systems. Transcription factor binding energy landscapes were determined using MLSI and MITOMI, a novel method for measuring molecular interactions. The biophysical characterization of transcription factors described herein were the first comprehensive measurements of its kind, and answered basic questions regarding how transcription factors recognize DNA. Furthermore, it was possible to predict the in vivo function of transcription factors using only the measured binding topographies and a genome sequence, indicating that biological processes can be predicted with high accuracy. More generally, the methods described in this thesis are generally applicable to understanding the properties of any biological system and should find broad usage in the field of Systems Biology.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:bHLH; microfluidics; MITOMI; protein interactions; Systems Biology; transcription factor
Degree Grantor:California Institute of Technology
Division:Engineering and Applied Science
Major Option:Biochemistry and Molecular Biophysics
Awards:Demetriades-Tsafka-Kokkalis Prize in Biotechnology or Related Fields, 2008.
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Quake, Stephen R.
Thesis Committee:
  • Arnold, Frances Hamilton (chair)
  • Fraser, Scott E. (co-chair)
  • Elowitz, Michael B.
  • Roukes, Michael Lee
  • Quake, Stephen R.
Defense Date:1 June 2007
Record Number:CaltechETD:etd-05222007-141119
Persistent URL:
Maerkl, Sebastian Josef0000-0003-1917-5268
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:5194
Deposited By: Imported from ETD-db
Deposited On:30 Nov 2007
Last Modified:29 Jan 2020 00:36

Thesis Files

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