thesis.tex

\documentclass{ucbthesis}
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%\usepackage[acronym]{glossaries}
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%\newacronym{IID}{TFIID}{Transcription factor IID}
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\begin{document}

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\title{A dynamic conformational landscape underlies TFIID's ability to interact with core promoter DNA}
\author{Michael A. Cianfrocco}
\degreesemester{Fall}
\degreeyear{2012}
\degree{Doctor of Philosophy}
\chair{Professor Eva Nogales}
\othermembers{Professor James Berger \\
  Professor Robert Glaeser \\
  Professor Michael Levine}
\numberofmembers{4}
\prevdegrees{B.S. (Providence College) 2007}
\field{Biophysics}
\campus{Berkeley}

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\include{abstract}

\begin{frontmatter}

\begin{dedication}
\null\vfil
\begin{center}
For my dad.
\end{center}
\vfil\null
\end{dedication}

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\begin{acknowledgements}
The research presented in this thesis was originally initiated by my inspirational mentor, Eva Nogales. Throughout this work she has served as a constant collaborator, helping to troubleshoot at times of need while also challenging me to propose alternative models to explain our observations. Her efficiency, intensity, and creativity has served as a model for my growth as an independent scientist.\\
\indent As a complement to her leadership abilities, Eva has put together a fantastic laboratory environment that was essential for this research project. In particular, Patricia Grob taught me everything I needed to know about the electron microscope and data analysis, continuing to teach me new things through the entirety of my Ph.D. Jie Fang has been an amazing biochemist who purified all of the proteins discussed in this thesis, graciously working long hours to achieve extremely pure protein samples. Tom Houweling served as the computer specialist who developed and maintained a computer work environment that maximized the efficiency for everyone in the lab. Throughout automated data collection and acquisition, Gabriel Lander helped to teach me how to use Leginon and Appion while also providing critical feedback to my research. Teresa Tucker has been the life of the lab, keeping in touch with everyone and making sure everything runs smoothly. I have mentored two different undergraduate who helped to keep me focused on my research: Michael Lemus and Sumanjit Mann. Suman spear-headed the biochemical purification of Nanogold, helping me perform key experiments to define the organization of DNA bound to TFIID.\\
\indent Outside of the lab, I have had the fortunate experience of being a student within the Biophysics Graduate Group. By providing me with a stimulating environment of fellow students from a variety of disciplines, my research has been enhanced through the constant sharing of ideas. The flexibility of the graduate group helped me assemble a Thesis committee that was responsive to my questions while also providing creative feedback to the problems faced during my research. In particular, working with Robert Glaeser on phase-plate cryo-electron microscopy and image simulations has expanding my technical training in ways that I did not anticipate when I joined Eva's lab.\\
\indent There have been many people whose ideas and technical advice were essential for my research. Weili Liu and Robert Coleman (Albert Einstein College of Medicine) kindly spent many hours with me, discussing biochemical techniques and the implications of my work on TFIID. Robert Tjian also provided critical advice on my research and feedback on our manuscript. Andres Leschziner and Preethi Chandramouli were able to help me implement OTR successfully by providing me with the correct Euler angle conversion routine. The discussions and script sharing with Colin Ophus (NCEM) greatly enhanced my understanding of image formation within the electron microscope while also helping me with image simulations of gold clusters (work to published in the very-near future).  \\
\indent Despite all of these technical contributions from fellow scientists, perhaps the most important support that I received during my Ph.D has been from my family and friends. Their support has given me the confidence to tackle difficult scientific problems, knowing that I will always have a stable support base to which I can return: Rich, Matt, John, Genessa, Will, Greg, Andy, Hilary. It goes without saying that my dad has been a constant presence throughout this process, inspiring me to pursue science in a way that will ultimately benefit humanity. My mom and brother have been patient and supportive of my desire to discover more about myself, even though I've been living in California for the past 5 years.  Last but not least, my life partner Alice has served as bedrock for me over the last three and a half years, supporting me during the hard-times and celebrating with me during the good times. \\ 
\end{acknowledgements}

\end{frontmatter}

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\appendix
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\end{document}