Research
Plant Development and Regeneration
What gives plants their remarkable capacity to regenerate whole organs? Plants grow indeterminately in adulthood through the activity of their meristems, which contain initials, or stem cells, that constantly replenish cells for continual organogenesis. We employ a regeneration system in which we completely excise most of the root meristem, including stem cells. The root then regenerates the entire meristem and resumes normal growth. We use this system to ask basic questions about the establishment of tissue organization long after embryogenesis is complete. We combine live imaging of regenerating roots with single-cell RNA-Seq analysis to coordinate the timing of events at the microscopic and molecular level, at the resolution of the single cell.
Algal Evolution Using Fluorescent Properties
Algal cultivation is a promising system for biofuels but, unlike agricultural cultivars, algae have not been adapted for human production systems. We use Fluorescence Activated Cell Sorting (FACS) to apply selective forces on algal populations to target very specific traits for biofuel improvement. We have adapted protocols that make use of fluorescent dyes or fluorescent properties of algae and can be used as readouts for specific traits. We select traits over multiple generations, similar to the domestication of crops in which repeated selection over many generations led to highly specialized agricultural crops. Here we optimize biofuel traits such as growth and oil accumulation using the algae/FACS system.
Evolution of Plant Roots
How did plant roots and the special cell types they contain evolve? The seedless vascular plant Selaginella is in a plant lineage whose ancestors appear to have branched off early in the evolution of land plants. This group of plants, the lycophytes, is the first to display a true root. It’s not clear that the Selaginella root is homologous to the roots of flowering plants. However, they share a remarkably similar structure, with a root cap, root hairs, endodermis, and auxin-triggered development. One striking difference is that most Selaginella roots in the mature organism arise from shoot structures, leading to a long-standing debate over whether the early outgrowth – called a rhizophore – is root- or shoot-like. We have employed transcriptional analysis of all Selaginella meristems in a global comparison of the similarity between the rhizophore transcriptome the embryonic root or the early shoot structure.
People
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Publications
A pan-grass transcriptome reveals patterns of cellular divergence in crops [PDF]
Nature (2023)
Plant glutamate receptors mediate a bet-hedging strategy between regeneration and defense
Developmental Cell (2022)
Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization
Science (2021)
Ground tissue circuitry regulates organ complexity in maize and Setaria
Science (2021)
Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud [PDF]
Frontiers in Plant Science (2020)
Just passing through: The auxin gradient of the root meristem [PDF]
Current Topics in Developmental Biology (2020)
Directions for research and training in plant omics: Big Questions and Big Data [PDF]
Plant Direct (2020)
Towards Building a Plant Cell Atlas [PDF]
Trends in Plant Science (2020)
The Selaginella rhizophore has a unique transcriptional identity compared with root and shoot meristems [PDF]
New Phytologist (2019)
Week-long imaging of cell divisions in the Arabidopsis root meristem [PDF]
Plant Methods (2019)
Power in Numbers: Single-Cell RNA-Seq Strategies to Dissect Complex Tissues [PDF]
Annual Review of Genetics (2018)
An Efficient Cell Sorting Protocol for Maize Protoplasts [PDF]
Current Protocols (2018)
Epigenetic memory and cell fate reprogramming in plants [PDF]
Regeneration (2017)
Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root [PDF]
Science Signaling (2016)
How many ways are there to make a root? [PDF]
Current Opinions in Plant Biology (2016)
A Case for Distributed Control of Local Stem Cell Behavior in Plants [PDF]
Developmental Cell (2016)
Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions [PDF]
Cell (2016)
The potential of single-cell profiling in plants [PDF]
Genome Biol (2016)
Plant Cell Shape: Trafficking Gets Edgy [PDF]
Dev Cell (2016)
Quantification of cell identity from single-cell
gene expression profiles. [PDF]
Genome Biol (2015)
Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis. [PDF]
Proc Natl Acad Sci USA (2014)
An undergraduate study of two transcription factors that promote lateral root formation. [PDF]
Biochem Mol Biol Educ (2014)
Plasticity regulators modulate specific root traits in discrete nitrogen environments. [PDF]
PLoS Genet (2013)
A map of cell type-specific auxin responses. [PDF]
Mol Syst Biol (2013)
Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture. [PDF]
Proc Natl Acad Sci USA (2013)
Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses. [PDF]
Dev Cell (2013)
TARGET: a transient transformation system for genome-wide transcription factor target discovery. [PDF]
Mol Plant (2013)
RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis. [PDF]
Plant Physiol (2013)
Fluorescence-activated cell sorting for analysis of cell type-specific responses to salinity stress in Arabidopsis and rice. [PDF]
Methods Mol Biol (2012)
High-throughput fluorescence-based isolation of live C. elegans larvae. [PDF]
Nat Protoc (2012)
Low-cost sequencing opens new insights into diverse plant genomes. [PDF]
Genome Biol (2012)
Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand. [PDF]
Proc Natl Acad Sci USA (2011)
Measuring cell identity in noisy biological systems. [PDF]
Nucleic Acids Res (2011)
Quantitation of cellular dynamics in growing Arabidopsis roots with light sheet microscopy. [PDF]
PLoS One (2011)
Predicting genome-wide redundancy using machine learning. [PDF]
BMC Evol Biol (2010)
The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo. [PDF]
Dev Cell (2010)
Built to rebuild: in search of organizing principles in plant regeneration. [PDF]
Curr Opin Genet Dev (2010)
Automated sorting of live C. elegans using laFACS. [PDF]
Nat Methods (2010)
Fluorescence activated cell sorting of plant protoplasts. [PDF]
J Vis Exp (2010)
Organ regeneration does not require a functional stem cell niche in plants. [PDF]
Nature (2009)
Positive fluorescent selection permits precise, rapid, and in-depth overexpression analysis in plant protoplasts. [PDF]
Plant Physiol (2009)
Slicing across kingdoms: regeneration in plants and animals. [PDF]
Cell (2008)
Cell-specific nitrogen responses mediate developmental plasticity. [PDF]
Proc Natl Acad Sci USA (2008)
News
Congratulations to Carlos Ortiz Ramirez!
Birnbaum lab postdoc will start his lab at Cinvestav, UGA-Langebio Mexico in January, 2020.
Keep an eye out for the Plant Cell Atlas meeting in March 28-30, 2020 at the Carnegie Institute for Science at Stanford. Ken is one of the organizers, contact him if you are interested in applying for attendance. See 2019 initiative paper in TIPS.
Birnbaum Lab Alum Wins Prestigious Intel ISEF 2016 Award for Plant Science
High school student Charlotte Keeley won First Award in the Plant Science category at the Intel ISEF 2016 competition, for her work on regeneration during her time in the Birnbaum lab. Charlotte's project, Plant Tissues that Fail to Regenerate Undergo Early Steps of Remodeling but Fail to Induce a Cytokinin Hormone Response was among 1,700 entries into the contest. Read the full press release and winner list here.
Lab Microscopy Footage Featured in the Imagine Science Film Festival
Excerpts from confocal timelapse movies of regeneration made in the lab were recently featured in the 7th Annual Imagine Science Film Festival, airing in NYC and in a satellite festival in Berlin.
Contact
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Center for Genomics and Systems Biology
12 Waverly Place
6th Floor
New York, NY 10003
Phone:
(212) 998-8257