UNIVERSITY OF CALIFORNIA RIVERSIDE Metabolic Profiling of Primary and Secondary Biosynthetic Pathways in Angiosperms: Comparative Metabonomics and Applications of Hyphenated LC-NMR and LC-MS A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Chemistry by Kayla Anne Kaiser March 2012 Dissertation Committee: Dr. Cynthia K. Larive, Chairperson Dr. Dallas Rabenstein Dr. Julia Bailey-Serres Copyright by Kayla Anne Kaiser 2012 The Dissertation of Kayla Anne Kaiser is approved: ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ Committee Chairperson University of California, Riverside Acknowledgements I have not walked this road alone, many people supported me along the way, both in person and in memory. My time here at UCR has been absolutely magical. Thanks to the National Science Foundation, I was able to participate in an interdisciplinary graduate training experience (IGERT) which shaped the course of my graduate education from the day I arrived in Riverside. Receiving financial, professional, and moral support from two esteemed principal investigators, Cynthia Larive and Julia Bailey-Serres, is most certainly a once-in-a-lifetime experience and I feel immensely grateful for their effort. I was lucky enough to have mentors that remained actively engaged in my development as a researcher and as a person, who ultimately sent me across the country and around the world to participate in great science, enhancing my graduate training exponentially. Participating IGERT faculty in other departments including Natasha Raikhel, Kathy Borkovich, Linda Walling, Thomas Girke, Thomas Eulgem, Xumei Chen, Shou-wei Ding, Larry Li, Karine Le Roch, Stefano Lonardi, Dimitrios Morikis, Anandasankar Ray, Harley Smith, Patty Springer, Jason Stajich, Zhenbiao Yang, and Hailing Jin have been of more influence than they are aware. Young faculty such as Wenwan Zhong, Ryan Julian, Katherine Larsen, Greg Beran, Angelina Chang, and Richard Hooley have been encouraging and willing to share their expertise and experience with myself and other students in our department. They have shown me a path to joining them as tenure-track faculty, and I am humbled by their belief that I am capable of rising to such a rank. Chris Bardeen, Jason Cheng, Yinsheng iv Wang, Leonard Mueller, Pingyun Feng, Michael Pirrung, Chris Switzer, and Sean Cutler have each influenced my approach to doing science and living life. The balance and tone of our department is set by these dedicated faculty members, who do an excellent job of providing a workplace that is engaging and dynamic as well as world-class. Francisco Zaera, David Bocian, Robert Haddon, Chris Reed, Eric Chronister, and Tom Morton have played a role in my current success and have influenced my current idea of what it means to be a research professor. I would like to especially thank Mike Rettig and Dallas Rabenstein. Teaching for Mike brought me back to the enjoyment of university life and showed me that true commitment to excellence in teaching can appear effortless after many years of practice. Dallas has always offered me perspective beyond what my mind can even comprehend and I consider his contributions to my understanding of NMR and university education to be invaluable. My fellow IGERT trainees Colleen Knoth, Eddie Cao, Michelle Brown, Charles Jang, James Kim, Christiana Merrywell, Jolene Diedrich, Theresa Dinh, Augusta Jamin, Sean Boyle, Anna Charisi, Andrew Defries, Mindy (Rodriguez) Salus, Missy (Smith) Scranton, Ayesha Baig, Patrick Schacht, Moses Tataw, Shang Wu, Rae Yumul, Aaron Devries, Jessica Diaz, Robert Koble, and Yifan Lii have been an important component of the support web that caught me any time I started flying out of control. These people helped me survive the difficulty of forging complementation at the interface of chemistry, engineering, computational sciences and cell biology and have been the wind in my sails without even knowing it. IGERT support staff Carolina Stickley, Ronly Schlenk, and v Matt Collin helped me balance the additional workload with grace. Glenn Hicks has been a quiet yet steadfast mentor throughout my biological/professional development. My chemistry classmates Kim Worsley, Tony Ly, Bryce Davis, Matt Linman, James Wright, Robert Dillon, Julia Zhu, Kelly Theel, Sebastian Jezowski, Shinji Kaneko, Jessy Lemieux, Yingdi Liu, Christen Strollo, Olivia Alley, Candace Guerrero, Derek Chen, Ying Liu, Bruce Ford, Mark Hamza, Emily Spencer, Ben Moore, Ni Li, Samantha Schachermeyer, Jingjing Yao, Ana Gamboa, Angie Garcia, Aaron Moehlig, Sepideh Yaghmaei, Robert Carp, Aholibama Escobar, Thomas Owen, Tiffany Satoorian, have been immensely helpful. Together we weathered the storms and reaped the abundant harvest. My labmates in the Larive research group Bridget Becker and Albert Korir first introduced me to the beauty of NMR and efficient workflows. Kasie Fang and Christiana Merrywell laid the groundwork for my LC-MS and NMR metabolomic experiments, respectively. Stacie Eldridge was a role model and mentor such as I have never had, nor will ever have again. Jennifer Cruz opened my heart, body and mind, as well as my spirit, to new levels of enlightenment. John Limtiaco was my fellow soldier, marching through the Ph.D. process in step with me, making me feel as an equal and sharing the experience with him has been a great treasure. Chris Jones and Daryl Bulloch pushed me to go farther than I thought I was capable of going. In the words of the late John F. Kennedy, “a rising tide lifts all boats.” Without such dedicated and talented labmmates, I would not have achieved as much. Greg Barding is someone who I respect and admire greatly, it has been a real pleasure working with him. Derek Langslay might be an angel, vi not only did I enjoy his temperament and scientific contributions, but also he makes a strong pot of coffee almost every day. Consuelo Beecher is our current protégé and I predict she will have an abundant career. Our undergraduate researchers Thao Nguyen, Fernando Campos, Sarah Gutierrez, Layne Higgins, Archie Taylor, Arpana Vaniya, Nelly Membreno, Bailey Dickey, Erik Velez, John Nguyen, Patrick Salvenson, Amy Morris, Avi Ramkishun, Matt Manighalam, and last but not least, Vishwa Shah breathed life into our days and shared with us the experience of training and mentoring. I am so grateful to have worked with all of you. Visiting professor Szabolcs Béni and his wife Orsyla Molnár contributed their energy and expertise to our lab generously, and I am immensely grateful for their support. A few more words about Cindy: she has the biggest heart of anyone I know. She is absolutely unmatched in her dedication. Working with her has been like climbing Mt. Everest. Just as a mountain never leaves you feeling unsupported, she is rock-solid. By providing formidable challenges, she exhausted and humbled me. She showed me that by refusing to give up on the ascent, breathtaking heights can be reached. That’s how Cindy is. She can do the work of 10 grown men. No tall tales, she is actually that amazing. I also must acknowledge my stunning collaborators in the Center for Plant Cell Biology: Cristina Branco-Price, Angelika Mustroph, Julian M. Peña-Castro, Piyada Juntawong, Takeshi Fukao, Matthew Collin, Erin Brinton, Seung Cho Lee, Reed Sorenson, Rejbana Alam, Maureen Hummel, and Elaine Yeung. They showed me how to cultivate Arabidopsis and maintained good humor while I persistently presented data vii of a physicochemical rather than biological nature. Their suggestions and feedback throughout my time at UCR have been instrumental in developing my understanding of plant physiology, molecular biology, and genetics. The attention and encouragement provided by Julia Bailey-Serres was nourishment for my soul, allowing me to take greater risks in my learning process, knowing that she believed in my potential for success. Finally, a linchpin in my graduate education was my internship experience at the Max Planck Institute for Chemical Ecology in Jena, Thuringia (Germany). NMR and MS group leaders Bernd Schneider and Ales Svatos, respectively, were beyond hospitable and generous in the exchange of ideas and energy. Fellow NMR group members Christian Paetz, Kamel Shaker, Dirk Holscher, Jingjing Fang, Evalgelos Tatsis, Katia Gruner, and Claudia Cervellati must be acknowledged for their contribution to my grasp of natural product studies beyond model and crop systems (Arabidopsis, rice, corn). Phila Raharivelomanana, a visiting professor, freely shared her personal and professional experiences. My friends at the Institute, who welcomed me and integrated me into their program with open arms: Vojta Klusak, Daniel Giddings Vasso, Holger Danner, Andrea Liliana Clavio McCormick, Alexandra Schmidt, Filippo Scialo, Abu Farhan, Guanjun (Cookie) Li, Marko Petek, Filipe Yon, Variluska Fragoso, Hendrik Wunsche, Maja Miloradovic and Arjen van Doorn. Exchanges with these young researchers will undoubtedly form the basis of future collaborations, and I will never forget my 30 th birthday. A few influential artists and musicians who provided me with inspiration and momentum which helped me finish the experiments and writing summarized in this viii dissertation. I hereby acknowledge Beyoncé, Lady Gaga, Rhianna and Shakira for bringing girl power to my ears and helping me keep tempo while pipetting.