Plant Development Biologist

Mingyuan Zhu.

I was born and raised in Jiangsu Province, China, and earned my Bachelor’s degree at Tsinghua University in Beijing. I then joined Dr. Adrienne Roeder’s laboratory at Cornell University, where I studied developmental robustness. My PhD research, which integrated time-lapse confocal imaging with computational modeling, highlighted the crucial role of developmental timing in ensuring robust organ morphogenesis. Following this, I moved to Dr. Philip Benfey’s laboratory at Duke University, where my research focuses on the dynamic interactions between roots and their soil environment. My major project utilizes single-cell and spatial transcriptomic techniques to explore how rice roots respond to various soil conditions. As a plant developmental biologist, I am deeply interested in how organisms adjust their growth in response to environmental changes. I am particularly intrigued by circumnutation, the helical movement of root tips, which aids in root navigation through heterogeneous soil environments.

14.
Years
Plant Research
Experience

Great Experience

A deep and ongoing commitment to advancing the field of plant development

Many of life’s failures are people who did not realize how close they were to success when they gave up
PUBLICATIONS
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CONFERENCES
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MENTEES
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PAPER REVIEW SERVICES
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Molecule.

I am fascinated by the molecular mechanisms that drive plant development. The interplay of small molecules—such as DNA, RNA, proteins, and metabolites—can lead to the emergence of complex plant morphology.

Currently, I mainly use single-cell and spatial transcriptomics to unravel the molecular processes governing rice root development and its responses to soil stresses.

See Project

Cell.

My research explores the cellular principles underlying organ development, focusing on the dynamic behavior of rice roots.

By integrating 4D cellular growth tracking with cell-based computational modeling, I aim to uncover how interactions between cellular processes and environmental cues drive organ growth.

See Project

Organ.

Circumnutation plays a vital role in root penetration and navigation through obstacles (Taylor et al., 2021 PNAS). My research aims to uncover its broader biological significance at the organ level, particularly in how crop roots adapt their circumnutation frequency and amplitude to cope with various abiotic and biotic stresses.

See Project
2013-2020
Doctor of Philosophy
Ph.D. Plant Biology Cornell University
2009-2013
Bachelor

B.S. Life Sciences

Tsinghua University

Research Experience

2020 August - present
Postdoc associate
Dr. Philip BENFEY’s laboratory, Duke University, HHMI, Durham, NC USA https://sites.duke.edu/benfey/
2014 April – 2020 May
Research Assistant (PhD Candidate)
Dr. Adrienne ROEDER’s laboratory, Cornell University, Ithaca, NY USA https://roeder.wicmb.cornell.edu/the-roeder-lab/
February 2018 - April 2018
Research Assistant (Short-term visiting collaborator)
Dr. Arezki BOUDAOUD’s laboratory, ÉNS de Lyon, Lyon, Auvergne-Rhône-Alpes France
June 2012 - August 2012
Research Assistant (Summer Intern)
Dr. Laura OLSEN’s Laboratory, The University of Michigan, Ann Arbor, MI USA
November 2009 - May 2013
Research Assistant (Undergraduate)
Dr. Dong LIU’s Laboratory, Tsinghua University, Beijing, China

Conference talks

Quebec, Canada, August 2018
9th International Plant Biomechanics Conference
“A MYB domain protein controls organ size uniformity through affecting cell wall stiffness in Arabidopsis”
New York, USA, August 2019
Mechanisms of Plant Development, FASEB
“Timing of organ initiation by hormone signaling is critical for robust organ size”
Vermont USA, July 2022
Mechanisms of Plant Development, FASEB
“Integrating single-cell and spatial transcriptomics to understand rice root development”
North Carolina USA, November 2022
Duke DCMB seminar series
“Integrating single-cell and spatial transcriptomics to understand rice root development”
New York USA, November 2023
Cold Spring Harbor Laboratory Meeting - Plant Genomes, Systems Biology & Engineering
“Integrating single-cell and spatial transcriptomics to study rice root responses to soil compaction”
California USA, January 2024
Plant & Animal Genome Conference 2024 (Invited speaker)
“Exploring genetic adaptation and single-cell-level responses to soil compaction in wheat and rice”
California USA, July 2024
The 34th International Conference on Arabidopsis Research (ICAR 2024)
“Single cell and spatial transcriptomics reveal how rice root tissues adapt to soil stress”
Michigan USA, August 2024
3rd Plant Cell Atlas (PCA) Symposium (Invited speaker)
“Single cell and spatial transcriptomics reveal how rice root tissues adapt to soil compaction”
New York USA, August 2024
2024 Weill Institute Summer Retreat (Invited speaker)
“Single cell and spatial transcriptomics reveal how rice root tissues adapt to soil compaction”

Services

November 2023 – Present
Elected North American Early Career Scholar

North American Arabidopsis Steering Committee (NAASC) Serve as a member of the Diversity, Equity, Inclusion, and Belonging Award committee.
Organize the “Exploring Career Opportunities in Academia & Industry Panel” workshop at ICAR 2024.
Co-chair the “Sustainable Crops/Food/Bioproducts, Improving Photosynthesis” plenary session at ICAR 2024.

August 2023 - Present
Committee Member
Plant Cell Rubrics Committee - Plant Cell Atlas (PCA)
Organize and nominate speakers for an online webinar series “What are plant cell states?”.
July 2024 at ICAR 2024
Founding Leader
Founding Leader - Plant Method Exchange Platform (PMEX)
Officially launched: July 2024 at ICAR 2024
Official website: https://plant-methods.owlstown.net/
August 2023 - June 2024
Committee Member
Local Organizing Committee - New Phytologist, Next Generation Scientists Conference
Organize two breakout sessions: “Career transitions for PhD/Postdoc: Environment, PhysDev, and Biotech”. Co-chair the plenary session: “Session 6”.
June 2023 - Present
Member, Editorial Board
Plant Morphogenesis and Evolution Section, Frontiers in Plant Physiology
Topic Editor for the special issue: Advances in Computational Biology: Bridging Omics Studies and Development in Plants.
June 2018 – December 2020
Associate faculty member

F1000Prime (now H1Connect Faculty Opinions)
Write more than 15 recommendations for published manuscripts.
Recommendation example: https://doi.org/10.3410/f.737763007.793577589

April 2024
Outreach activity leader
FEMMES+ Capstone program.
Designed and organized a one-day outreach program introducing students from Durham (4th through 6th grade) to plant biology concepts and techniques
Engaged 19 local elementary school students (18 Females) in hands-on experience with dissecting microscopes and confocal microscopes.

Contact

FFSC Rm 4128
Duke University
124 Science Drive
Durham, NC 27708
We don’t see things as they are; we see them as we are.

Publications

Zhu, M.*, Hsu, C-W.*, Lucas, O. P., Taylor, I. W., Mijar, M., Nolan., T. M., Sadanandom, A., Bennett, M. J.^, Benfey, P. N. ^, Pandey, B. K.^. (2024). Single cell and spatial transcriptomics reveal how root tissues adapt to soil stress. Under revision by Nature.

Kong S. *, Zhu M.*, Scarpin M.R., Pan D., Jia L., Martinez R.E., Alamos S., Vadde B.V., Garcia H.G., Qian SB., Brunkard J.O. Roeder, A. H. ^. (2024). DRMY1 promotes robust morphogenesis by sustaining translation of a hormone signaling protein. Developmental Cell, In press.

Kong, S., Zhu, M., Pan, D., Lane, B., Smith, R. S., & Roeder, A. H.^. (2024). Tradeoff Between Speed and Robustness in Primordium Initiation Mediated by Auxin-CUC1 Interaction. Nature communication, 15(1), 5911.

https://doi.org/10.1038/s41467-024-50172-9
Kong, S., Zhu, M., and Roeder, A. H. ^. (2024). Self-organization underlies developmental robustness in plants. Cells & Development 203936. Invited review

https://doi.org/10.1016/j.cdev.2024.203936
Zhu, M., & Benfey, P. N^. (2023). Plant physiology: The to-and-fro of hormone signals to respond to drought. Current Biology, 33(3), R114-R117.

https://doi.org/10.1016/j.cub.2022.12.007
Zhu, M.*, Taylor, I. W.*, & Benfey, P. N^. (2022). Single-cell genomics revolutionizes plant development studies across scales. Development, 149(6), dev200179. Invited review

https://doi.org/10.1242/dev.200179
Rajanala, A., Zhu, M., Taylor, I., Pierce, C., Hales, M., Benfey, P. ^, & Goldman, D^. (2022). Modeling plant root circumnutation using cellular simulation. Bulletin of the American Physical Society, Y03. 013

https://ui.adsabs.harvard.edu/abs/2022APS..MARY03013R/abstract
Shao, Y., Lehner, K. R., Zhou, H., Taylor, I., Zhu, M., Mao, C. ^, & Benfey, P. N^. (2021). VAP-RELATED SUPPRESSORS OF TOO MANY MOUTHS (VST) family proteins are regulators of root system architecture. Plant Physiology, 185(2), 457-468.

https://doi.org/10.1093/plphys/kiaa036
Zhu, M., Chen, W., Mirabet, V., Hong, L., Bovio, S., Strauss, S., Schwarz, E., Tsugawa, S., Wang, Z., Smith, R.S., Li, C.-L., Hamant, O., Boudaoud, A.^, and Roeder, A.H.K.^ Robust organ size requires robust timing of initiation orchestrated by focused auxin and cytokinin signaling (2020) Nature Plants, 6(6), 686-698.

https://doi.org/10.1038/s41477-020-0666-7
Ripoll, J. J*., Zhu, M*., Brocke, S., Hon, C. T., Yanofsky, M. F., Boudaoud, A., & Roeder, A. H. (2019). Growth dynamics of the Arabidopsis fruit is mediated by cell expansion. Proceedings of the National Academy of Sciences, 116(50), 25333-25342.

https://doi.org/10.1073/pnas.1914096116
Zhu, M., & Roeder, A. H. (2020). Plants are better engineers: the complexity of plant organ morphogenesis. Current Opinion in Genetics & Development, 63, 16-23. Invited review

https://doi.org/10.1016/j.gde.2020.02.008
Hong, L., Dumond, M., Zhu, M., Tsugawa, S., Li, C.B., Boudaoud, A., Hamant, O. and Roeder, A.H., (2018). Heterogeneity and robustness in plant morphogenesis: from cells to organs. Annual Review of Plant Biology, 69, pp.469-495. Invited review

https://doi.org/10.1146/annurev-arplant-042817-040517
Hong, L.*, Dumond, M.*, Tsugawa, S.*, Sapala, A, Routier-Kierzkowska, A.-L., Zhou, Y., Chen C., Kiss, A., Zhu, M., Hamant, O., Smith, R.S., Komatsuzaki, T., Li, C.-L., Boudaoud, A^, and Roeder, A.H.K.^ (2016) Variable cell growth yields reproducible organ development through spatiotemporal averaging. Developmental Cell, 38(1), 15-32.

https://doi.org/10.1016/j.devcel.2016.06.016