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UNIVERSITY of CALIFORNIA Santa Barbara Delivery and Activity Of UNIVERSITY OF CALIFORNIA Santa Barbara Delivery and activity of toxic effector domains from contact-dependent growth inhibition systems in Escherichia coli A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Molecular, Cellular, and Developmental Biology by Julia Laura Elizabeth Willett Committee in charge: Professor Christopher S. Hayes, Chair Professor Anthony de Tomaso Professor David Low Professor Denise Montell June 2016 The dissertation of Julia Laura Elizabeth Willett is approved. _____________________________________________ Anthony de Tomaso _____________________________________________ David Low _____________________________________________ Denise Montell _____________________________________________ Christopher S. Hayes, Committee Chair February 2016 Delivery and activity of toxic effector domains from contact-dependent growth inhibition systems in Escherichia coli Copyright © 2016 by Julia Laura Elizabeth Willett iii To Jason iv ACKNOWLEDGEMENTS I would first and foremost like to thank Chris for being a great advisor and for allowing me to investigate a variety of engrossing research questions throughout my graduate work in his lab. I’m appreciative of all the opportunities that I have had to grow as a scientist and writer, present my research at conferences, and interact with incredible seminar speakers and colleagues. His enthusiasm for science and research is contagious. A number of collaborations made this work possible. I’m extremely grateful for our close (both literally and figuratively) collaboration with David Low and his research group, particularly former members Stephanie Aoki, Sanna Koskiniemi, Travis Smith, and Julia Webb. David is a tremendous scientist with whom scientific conversations are always inspiring. I am also grateful for our collaboration with Robert Morse and Celia Goulding at UC Irvine, as their crystallography expertise has provided invaluable insight into the structural world of CDI. Beatrice Ramm and Drew Endy at Stanford University provided an opportunity to work on a fun synthetic biology project well outside my microbiology comfort zone and created some really incredible videos of CDI, visualizing a process I’d been imagining for years. Additionally, I would like to thank all past and present members of the Hayes lab – I can truthfully say I’ve learned something from each and every person I’ve worked with throughout graduate school. It’s difficult to imagine these years without this camaraderie and our…shenanigans. Extra thanks goes to Fernando Garza-Sanchez for the insightful discussions, advice, and cookies. I’d also like to thank Alex Fields for making late nights spent working on the 3rd floor a little livelier. v My family and friends have been a great source of support throughout graduate school, and I’m thankful I was able to experience the eternal paradise that is Santa Barbara with such a wonderful group of people. I would especially like to thank my parents and brother for their never-ending love and encouragement and for turning everything into a teaching moment along the way. To Jason…any sentiments I could craft about reassurance, inspiration, and support would be inadequate and trite. I love you. Last but most certainly not least, a tremendous thank you to my forever first years. We didn’t come here to make friends, but I’d say we did a hell of a job at it. I look forward to your future coups d'état and the letters that are sure to follow. vi VITA OF JULIA LAURA ELIZABETH WILLETT February 2016 EDUCATION PhD Molecular, Cellular, and Developmental Biology Exp. 2016 University of California, Santa Barbara, Santa Barbara, CA BS Biochemistry 2010 University of Illinois at Urbana-Champaign, Urbana, IL Minor in Chemistry Distinction in the Major BS Food Science and Human Nutrition 2010 University of Illinois at Urbana-Champaign, Urbana, IL Honors in the Major RESEARCH EXPERIENCE Graduate Student Researcher 2010-2016 Department of Molecular, Cellular, and Developmental Biology University of California, Santa Barbara Advisor: Dr. Christopher S. Hayes ([email protected]) Used genetic approaches to identify translocation pathways utilized by toxins in contact-dependent growth inhibition (CDI) systems. Characterized activities of nuclease and pore-forming CDI toxins from Gram- negative bacteria. Analyzed phenotypic responses induced by delivery and activity of CDI toxins. Undergraduate Researcher 2008-2010 Department of Chemistry University of Illinois at Urbana-Champaign Advisor Dr. Yi Lu ([email protected]) Use aptamer-based approaches to build liquid-state DNA sensors for detection of metals in complex paint and water samples. Developed a chelation-based approach for reducing iron interference in lead paint sensor readings. Undergraduate Researcher 2007-2008 Department of Food Science & Human Nutrition University of Illinois at Urbana-Champaign Advisor Dr. Michael J. Miller ([email protected]) Bioinformatic analysis of carbohydrate transporters in 11 Lactobacillus genomes. vii TEACHING EXPERIENCE University of California, Santa Barbara Microbiology Laboratory Teaching Assistant 2015 Taught two sections of the senior-level microbiology lab course Developed two research-based modules to integrate laboratory research and classroom learning. Introductory Biology Laboratory Teaching Assistant 2011, 2012 Taught weekly laboratory sections and graded assignments. Covered general biology concepts including marine biology, ecology, phylogenetics, computational ecology, plant and human physiology, and evolution. Supervised student-led experimental design projects. University of Illinois at Urbana-Champaign General Chemistry II Teaching Assistant 2008-2009 Taught twice-weekly discussion sections for undergraduates in general chemistry. Topics included kinetics, electrochemistry, and introductory organic chemistry. Recognized on the “List of Teachers Recognized as Excellent” and ranked in the top 10% of chemistry teaching assistants during the Fall 2009 semester. INDUSTRIAL EXPERIENCE Research and Development Intern 2010 ANDalyze, Champaign, IL Adapted liquid-state DNA sensors for heavy metals to shelf-stable solid-state products for commercial applications. PUBLICATIONS 1. Morse RP, Willett JLE, Johnson PM, Zheng M, Credali A, Iniguez A, Nowick JS, Hayes CS, Goulding CW. Diversification of β-augmentation interactions between CDI toxin/immunity proteins. Journal of Molecular Biology. 2015 Nov 20;427(23):3766-84. http://dx.doi.org/10.1016/j.jmb.2015.09.020. 2. Willett JLE, Ruhe ZC, Goulding CW, Low DA, Hayes CS. Contact-Dependent Growth Inhibition (CDI) and CdiB/CdiA Two-Partner Secretion Proteins. Journal of Molecular Biology. 2015 Nov 20;427(23):3754-65. http://dx.doi.org/10.1016/j.jmb.2015.09.010. Review. 3. Willett JLE*, Gucinski GC*, Fatherree JP, Low DA, Hayes CS. Contact-dependent growth inhibition toxins exploit multiple independent cell-entry pathways. Proceedings of the National Academy of Sciences USA. 2015 Sep 8;112(36):11341-6. http://dx.doi.org/10.1073/pnas.1512124112. *indicates equal contribution Highlighted in Nature Reviews Microbiology (http://www.nature.com/nrmicro/journal/v13/n10/full/nrmicro3554.html) viii 4. Webb JS, Nikolakakis KC, Willett JLE, Aoki SK, Hayes CS, Low DA. Delivery of CdiA nuclease toxins into target cells during contact-dependent growth inhibition. PLoS One. 2013;8(2):e57609. http://dx.doi.org/10.1371/journal.pone.0057609. 5. Morse RP*, Nikolakakis KC*, Willett JLE, Gerrick E, Low DA, Hayes CS, Goulding CW. Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems. Proceedings of the National Academy of Sciences USA. 2012 Dec 26;109(52):21480-5. http://dx.doi.org/10.1073/pnas.1216238110. *indicates equal contribution HONORS AND AWARDS Graduate 2015 Doreen J. Putrah Cancer Research Foundation Conference Fellowship 2015 Best 5th year graduate student talk, MCDB Graduate Seminar Series 2015 1st place, MCDB Department Poster Competition 2014 Ellen Schamberg Burley Graduate Travel Scholarship 2013 Best 3rd year graduate student talk, MCDB Graduate Seminar Series 2012-2015 National Science Foundation Graduate Research Fellowship 2011 Charles A. Storke Award for excellence in graduate coursework Undergraduate 2010 William H. Jackson Merit Award for outstanding thesis in Biochemistry 2009 University of Illinois List of Teachers Recognized as Excellent 2009 Top 10% of Chemistry Teaching Assistants 2009 2nd place, LIGASE Biology Poster Competition 2007 Mansperger Scholar 2005-2008 James Scholar 2005-2008 Jonathan Baldwin Turner Agriculture Scholar 2005 Chancellor’s Scholar (top 5% of incoming class) ORAL PRESENTATIONS 1. Willett JLE, Jones AM, Gucinski GC, Garza-Sánchez F, Low DA, and Hayes CS. EF- Tu and EF-Ts are common cofactors utilized by contact-dependent inhibition (CDI) systems. Molecular Genetics of Bacteria and Phage Meeting. Madison, WI. August 2015. 2. Willett JLE, Morse RP, Goulding CW, and Hayes CS. Structural and functional analysis of contact-dependent inhibition nuclease toxins in the EC869 superfamily. MCDB Graduate Seminar Series. Santa Barbara, CA. January 2015. Awarded best 5th year graduate student talk by student vote 3. Willett JLE and Hayes CS. Rearrangement of insertion elements confers transient resistance to a contact-dependent inhibition toxin from Escherichia coli. MCDB ix Graduate Seminar Series. Santa Barbara, CA. March 2014. 4. Willett JLE, King O, and Hayes CS. Rearrangement of insertion
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