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Single-cell dissection of regenerating plant roots




Dr. Ken Birnbaum

April 17 at 12:20pm in the Fralin Auditorium, 102 Fralin Hall

Hosted by Dr. B. Bargmanmn


Plants can reform their growth centers known as meristems readily after injury or complete removal. We have tested many species for this property and this ability to re-organize the meristem from somatic cells is an apparent universal trait for all land plants with a true root. We are interested in root regeneration as a repair process but also to understand how this highly self-organizing structure assembles itself any developmental context. Much of our efforts have been focused on piecing together an “order of assembly,” where past work has pointed to embryonic ontogeny during regeneration. I will present recent work on using high coverage single-cell RNA-seq to essentially track regeneration cell-by-cell in a time series. This is allowing us to piece together the reformation of specific domains and signaling centers. One critical piece of missing information in these techniques is how early forming domains communicate to re-organize the meristem over a matter of days. I will present new techniques in which we block one major route of communication in plants, plasmodesmata, to analyze the effects on neighboring and distant cells. We are also developing proteomic techniques to identify cell-to-cell mobile transcription factors, a major signaling mode in plant development. 

Kenneth Birnbaum received a master’s in Environmental Science at the University of Wisconsin, Madison, and his PhD from New York University/American Museum of Natural history in 2000, studying conservation genetics of avocado landraces. Before that, he worked as a journalist, specializing in environmental issues including writing scripts for Earthwatch Radio during his masters work in Madison. In his postdoc with Philip Benfey, he developed new techniques to profile single-cell types in Arabidopsis, opening up new approaches in developmental genomics. He started his lab at New York University’s Center for Genomics and Systems Biology in 2004. The lab has focused on regeneration and root meristem organization, most recently using single-cell RNA-seq to dissect tissue organization and cellular transitions over time during regeneration. The lab combines live microscopy with global analysis and coordinates the two perspectives to examine re-assembly of the plant meristem during repair. The work has focused new attention on the mechanisms that enable regeneration of the plant’s growth centers.

There are no suggested readings for this seminar.


This seminar will be livestreamed and recorded on the Fralin YouTube channel.