Curriculum Vitae, David W. Taylor Page 1 of 7 Name

Curriculum Vitae, David W. Taylor
Name
David W. Taylor
Address
California Institute for Quantitative Biosciences
HHMI/University of California, Berkeley
742 Stanley Hall
Berkeley, CA 94720-3220
Lab Phone: (510) 666-3335
Fax: (510) 666-3336
Mobile Phone: (717) 856-9511
Email: [email protected]
Page 1 of 7
Education
2013
Yale University
Molecular Biophysics and Biochemistry
Advisor: Dr. Hong-Wei Wang
Ph.D., with distinction
2010
Yale University
Molecular Biophysics and Biochemistry
M.Phil.
2008
Syracuse University
Biochemistry
B.S., summa cum laude
Post-doctoral Training
2013–present University of California, Berkeley
California Institute for Quantitative Biosciences
Title: “Structure and Function of CRISPR RNA-guided surveillance complexes in
bacteria”
Advisors: Dr. Jennifer A. Doudna and Dr. Eva Nogales
Undergraduate and Graduate Research Experience
2009–2013
Yale University, Department of Molecular Biophysics and Biochemistry
Dissertation research
Title: “Structural basis for RNA processing by human Dicer”
Advisor: Dr. Hong-Wei Wang
2012
Visiting Student Researcher at California Institute for Quantitative Biosciences,
University of California, Berkeley
Title: “Automated macromolecular imaging of Dicer and Dicer-RNA complexes”
Advisors: Dr. Jennifer A. Doudna and Dr. Eva Nogales
Curriculum Vitae, David W. Taylor
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2011
NSF East Asia and Pacific Summer Institute Fellow at National Institute for
Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
Title: “Zernike phase-contrast cryo-EM of human Dicer and virus-like particles”
Advisors: Dr. Kuniaki Nagayama and Dr. Kazuyoshi Murata
2009
Yale University, Department of Genetics
Title: “Alternative miRNA biogenesis pathways in zebrafish”
Advisor: Dr. Antonio J. Giraldez
2008
Yale University, Department of Molecular Biophysics and Biochemistry
Title: “Structural basis for copper transport by eukaryotic chaperones”
Advisor: Dr. Vinzenz M. Unger
2005–2008
Syracuse University, Department of Chemistry and Department of Biochemistry
Title: “Development of nucleic acid sensors for pathogenic agents”
Advisors: Dr. Bruce S. Hudson and Dr. Phillip N. Borer
Summary of Thesis Research
Dicer plays a central role in RNA interference pathways by cleaving double-stranded
RNAs (dsRNAs) to produce small regulatory RNAs. Human Dicer can process long doublestranded and hairpin precursor RNAs to yield short interfering RNAs (siRNAs) or microRNAs
(miRNAs), respectively. In humans, Argonaute2 (AGO2) assembles with the guide RNAgenerating enzyme Dicer and either the RNA-binding protein TRBP or PACT to form a RISCloading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and
miRNAs from Dicer to AGO2. Here, I have used electron microscopy and single particle
analysis of human Dicer–RNA complexes and the RLC to gain insight into the structural basis
for human Dicer’s substrate preference and RISC-loading, respectively. My studies show that
Dicer traps pre-siRNAs in a non-productive conformation, while interactions of Dicer with premiRNAs and dsRNA binding proteins induce structural changes in the enzyme that enable
productive substrate recognition in the central catalytic channel. The RLC Dicer's N-terminal
DExH/D domain, located in a short base branch, interacts with TRBP, whereas its C-terminal
catalytic domains in the main body are proximal to AGO2. A model generated by docking the
available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction
suggests a mechanism for siRNA transfer from Dicer to AGO2.
Awards and Honors
2012
2011
2011
2010
AAAS/Science Program for Excellence in Science, Science
NSF East Asia and Pacific Summer Institute (EAPSI) Fellow, National Science
Foundation
Molecular Biophysics and Biochemistry Excellence in Teaching Award, Yale
University
Yale Scientific Teaching Fellow, Yale University
Curriculum Vitae, David W. Taylor
2010
2009
2008
2008
2007
2007
2004
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NSF Graduate Research Fellow, National Science Foundation
Associate Faculty Member, Faculty of 1000
Research Achievement and Academic Excellence Award, Syracuse University
Biology Department
Named Who’s Who Among American Colleges and Universities
Barry M. Goldwater Scholar, Barry M. Goldwater Foundation
Remembrance Scholar Finalist, Syracuse University
Syracuse University Academic Merit Scholar
Publications
1. M.L. Hochstrasser*, D.W. Taylor*, P. Bhat, C.K. Guegler, S.H. Sternberg, E. Nogales, J.A.
Doudna. (2014) CasA mediates Cas3-catalyzed target degradation during CRISPR RNAguided interference. Proc. Nat. Acad. Sci. Epub 18 Apr 2014.
2. M. Jinek*, F. Jiang*, D.W. Taylor*, S.H. Sternberg*, E. Kaya, S.H. Sternberg, E. Ma, C.
Anders, M. Hauer, K. Zhou, S. Lin, M. Kaplan, A.T. Iavarone, E. Charpentier, E. Nogales,
J.A. Doudna. (2014) Structures of Cas9 Endonucleases Reveal RNA-Mediated
Conformational Activation. Science 343, 1247997.
3. R.H.J. Staals*, Y. Agari*, S. Maki-Yonekura*, Y. Zhu, D.W. Taylor, E. van Duijn, A.
Barendregt, M. Vlot, J.J. Koehorst, K. Sakamoto, A. Masuda, N. Dohmae, P.J. Schaap, J.A.
Doudna, A.J.R. Heck, K. Yonekura, J. van der Oost, A. Shinkai. (2013) Structure and
activity of an RNA-targeting Type III-B CRISPR-Cas complex in Thermus thermophilus.
Mol. Cell 52, 135-145. [Previewed by N. Heidrich and J. Vogel. (2013) Same Same but
Different: New Structural Insight into CRISPR-Cas Complexes. Mol. Cell 52, 4-7.]
[Recommended by F1000.]
4. S.L. Wolin, C. Belair, X. Chen, S. Sim, D.W. Taylor, H.W. Wang. (2013) Noncoding Y
RNAs as Tethers and Gates: Insights from Bacteria. RNA Biol. 10, 1602-1608.
5. D.W. Taylor, E. Ma, H. Shigematsu, M.A. Cianfrocco, C.N. Noland, K. Nagayama, E.
Nogales, J.A. Doudna, H.W. Wang. (2013) Substrate-specific structural rearrangements of
human Dicer. Nat. Stuct. Mol. Biol. 20, 662-670. [Recommended by F1000.]
6. X. Chen, D.W. Taylor, C.C. Fowler, J.E. Galan, H.W. Wang, S.L. Wolin. (2013) An RNA
degradation machine sculpted by Ro autoantigen and noncoding RNA. Cell 153, 166-177.
[Previewed by B.J. Geiss and J. Wilusz. (2013) Ring around the Ro-sie: RNA-mediated
alterations of PNPase activity. Cell 153, 12-14.]
7. K.R. Bower-Phipps, D.W. Taylor, H.W. Wang, S.J. Baserga. (2012) The box C/D sRNP
dimeric architecture is conserved across domain Archaea. RNA 18, 1553-1562.
8. G.S. Hansman, D.W. Taylor, J.S. McLellan, T.J. Smith, I. Georgiev, J.R.H. Tame, S.Y. Park,
M. Yamazaki, F. Gondaira, M. Miki, K. Katayama, K. Murata, P.D. Kwong. (2012)
Curriculum Vitae, David W. Taylor
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Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody
that binds to a site occluded in the viral particle. J. Virol. 86, 3635-3646. [Cover of J. Virol.
86 December 2012] [Article of Significant Interest Selected from This Issue by the Editors.]
9. M.F. Roberts, D.W. Taylor, V.M. Unger. (2011) Two modes of interaction between the
membrane-embedded TARP stargazin’s C-terminal domain and the bilayer visualized
by electron crystallography. J. Struct. Biol. 174, 542-551.
10. D. Cifuentes, H. Xue, D.W. Taylor, H. Patnode, Y. Mishima, S. Cheloufi, E. Ma, S. Mane,
G.J. Hannon, N.D. Lawson, S.A. Wolfe, A.J. Giraldez. (2010) A novel miRNA processing
pathway independent of Dicer requires Argonaute2 catalytic activity. Science 328, 16941698. [Featured in Leading Edge: Molecular Biology Select. (2010) Ago2 Takes It from the
Top. Cell 141, 1093-1095.] [Rated as “Exceptional” by F1000.]
11. H.W. Wang, C. Noland*, B. Siridechadilok*, D.W. Taylor*, E. Ma, K. Felderer, J.A.
Doudna, E. Nogales. (2009) Structural insights into RNA processing by the human RISCloading complex. Nat. Stuct. Mol. Biol. 16, 1148-1153. [Featured in Leading Edge:
Molecular Biology Select. (2009) Bringing a Dicey Handoff into Focus. Cell 139, 639-641.]
*These authors contributed equally to this work.
Patents
“Structure-Guided Methods of Cas9-Mediated Genome Engineering,” BK-2014-078.
Talks, Workshops, and Posters
“RNA-induced structural activation of the RNA-guided endonuclease Cas9,” invited talk at
Beijing area cryo-EM meeting at Tsinghua University in Beijing, China, January 2014
“Molecular architecture of the RNA-guided endonuclease Cas9,” talk at Structure Supergroup at
California Institute for Quantitative Biosciences, December 2013.
“Structures of Type-II and Type-III surveillance complexes from bacterial immune systems,”
invited talk for Sackler Discussion Group at Yale University, September 2013
“Molecular architecture of the RNA-guided endonuclease Cas9,” poster presentation at Rewriting Genomes Symposium at University of California, Berkeley, August 2013
“Target recognition by RNA-guided surveillance complexes from a bacterial immune system,”
poster presentation at CRISPR conference in St. Andrews, UK, June 2013
“Perspectives on research and life in Japan,” invited talk for Japan Society for the Promotion of
Science (JSPS), San Francisco Office, April 2013
Curriculum Vitae, David W. Taylor
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“RNA structure confers substrate specific interaction and processing by human Dicer,” talk at
National Institute for Physiological Sciences in Japan, July 2011
“RNA structure confers substrate specific interaction and processing by human Dicer,” poster
presentation at Smith Family Awards Program For Biomedical Excellence in Boston, April 2011
“RNA structure confers substrate specific interaction and processing by human Dicer,” talk at
Yale University School of Medicine C-Wing Seminar Series, March 2011
“Structural basis for autoinhibition of human Dicer,” invited short highlight talk at Nucleic Acids
conference in Mexico, November 2010
“Big structural rearrangements in small RNA processing,” talk at Yale University School of
Medicine Structural Biology Seminar, April 2010
“Structural insights into RNA processing by the human RISC-loading complex,” poster
presentation at National Resource for Automated Molecular Microscopy (NRAMM) EM
Conference at Scripps Research Institute, November 2009
“Structural basis for RNA processing by the RISC-loading complex,” talk at Yale University
School of Medicine C-Wing Seminar Series, October 2009
“RNA processing by the RISC-loading complex,” poster presentation at the Sackler Institute
Inaugural Symposium at Yale University West Campus, August 2009
Teaching/Mentoring Experience and Career Development
2013–2014
Supervised Jack Kornfeld in the undergraduate research apprenticeship program
in the laboratory of Dr. Eva Nogales
2013
Guest lecturer on “RNAi mechanisms” in MB&B 743b at Yale University
Supervised and trained Vincent Yip (Dr. Susan J. Baserga’s graduate student) in
collecting cryo-EM images of disRNPs using LEGINON
2012
Guest lecturer on “RNAi mechanisms” in MB&B 743b at Yale University
2010–2011
Guest lecturer on “RNAi mechanisms” in MB&B 743b at Yale University
Teaching Assistant for graduate course Advanced Eukaryotic Molecular Biology
2009–2010
Theory and Practice of Scientific Teaching I and II (with Dr. Jo Handelsman)
Student-Faculty Academic Advising Committee for incoming Molecular
Biophysics and Biochemistry graduate students
Advanced Science Teaching Course
Teaching Assistant for graduate course Advanced Eukaryotic Molecular Biology
Supervised summer high school student in the laboratory of Dr. Hong-Wei Wang
Curriculum Vitae, David W. Taylor
2008–2009
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Fundamentals of Teaching Science Course
Student-Faculty Academic Advising Committee for incoming Molecular
Biophysics and Biochemistry graduate students
Supervised two first year graduate students during their rotation projects in the
laboratory of Dr. Hong-Wei Wang
Teaching Statement
I am a first generation college student. I have had the privilege of being part of a program
as an undergraduate at Syracuse University that taught underrepresented and underprivileged
high school students the basics of the undergraduate admissions procedure and application
process. This also included consideration of topics such as how to study for college courses and
adjust to living on their own. As an undergraduate, I presented a scientific poster on the
development of nucleic acid switches labeled with a luminescent probe for sensing the capsid
protein of HIV at the Syracuse University Mayfest. This event is for an audience of faculty,
undergraduates, and high school students from central New York. The day is primarily intended
to integrate education and research for non-science community members, especially the local
high school students. It was an exceptional opportunity to communicate the scientific
achievements in our lab in a general way to these younger students. I was able to effectively
disseminate a basic introduction to molecular biology and research, while exciting many of them
about discovery and the possibility of a career as a scientist. All of these experiences have placed
me in a unique position to reach students from underrepresented minorities in science education
and research training. I am highly motivated to do this because I am an underrepresented
population in education and science, can easily relate to them, and can employ the same
techniques that were effective in fostering my passion for science. Additionally, these programs
have taught me that the obligation to educate young minds and invoke curiosity for the life
sciences must be paralleled with a commitment to mentoring. I have had the opportunity to teach,
converse with, and mentor other scientists and students from all backgrounds through the various
stages of my educational career. My primary career goal is to be a professor of biochemistry and biophysics at a leading
research university, where I can take part in teaching students and training researchers at the
interface of chemistry, biology, and physics. I would like to be a professor for two major reasons.
The main incentive is the enjoyment I receive from asking questions about biological problems
and designing experiments to determine their answers. Secondly, I believe that teaching others is
a responsibility that should not be taken lightly. Passionate lecturing about science from a mentor
and professor as an undergraduate is a major reason I decided to undertake an education in basic
research. This professor would ask several word problems during class and ask us to hold up the
correct answer. He would march through the isles of the lecture hall shouting remarks such as
“good”, “excellent”, and “you’re on the right track” in response to our answers. I believe that I
have an obligation to perform this function for the next generation of thinkers. I plan to be an
inspiring teacher, scientist, and mentor by implementing scientific teaching into current
undergraduate courses aimed at educating the science majors and courses geared toward the
students fulfilling the basic science requirements. Scientific teaching involves bringing the same
rigor of science research into the classroom, teaching students to think like scientists, and using
active learning strategies that have been tried and tested.
Curriculum Vitae, David W. Taylor
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Any course that I lead would force students to focus on the details and reasoning behind
science in practice, moving beyond the memorization of disconnected facts. This is really how
the beauty of science becomes strikingly evident to young minds. The idea is simple: to prepare
future scientists and future scientifically literate community members; consequently, emphasis
will be placed on the logic, design, and analysis of experiments aimed at probing a specific
phenomenon. This will be achieved through case studies related to each topic. Therefore,
students who take my course will employ critical thinking skills to tackle challenging biological
problems, understand how to design and interpret experiments, read and intelligently discuss
primary research articles, ask insightful and relevant questions related to past and ongoing
research, and master the fundamentals and selected details of the topic. These learning objectives
will be evaluated based on a discussion section of primary literature articles, a term paper
incorporating the design of a proposal to further probe a phenomenon discussed in class, and
examinations that focus largely on applying the concepts of the course to a new question or in a
new context.
Science-major courses that I teach would emphasize the interconnections between the life
sciences and the physical sciences. This would involve the coverage of molecular and cellular
biology and the integration or presentation of all other associated concepts from other disciplines
including chemistry, physics, and mathematics as material from these disciplines are needed.
For example, a section devoted to the structure and function of membrane proteins would include
a discussion of the physics of ion transport and the chemical mechanism of lipid biosynthesis.
This avoids the situation of not understanding how material in one course relates to that in
another and really provides the basic knowledge hierarchy needed to become an advanced
student and independent scholar or expert. As for non-science major courses, I think it is
important to teach the everyday relevance of biology to these students. This may be the only
opportunity to reach these college students and the only exposure they receive to any topics in
the life sciences. Therefore, I think that teaching the practical uses of science in their lives is of
paramount importance. We need our citizens to be informed consumers, policy makers, and
problem solvers. Additionally, we may be able to recruit a more diverse group of scientists using
the scientific teaching paradigm outlined in this philosophy. For example, a section could be
devoted to how caffeine intake leads to stimulatory effects on the body. This should invoke a
great deal of curiosity because many of the students will probably be drinking coffee or energy
drinks at that moment, especially if it is an early morning lecture. For teaching and evaluating
this course, I would implement an active learning/assessment approach that involves the students
researching a topic pertinent to their lives and presenting this information to the rest of the class.

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