Kenneth Birnbaum

Developmental and evolutionary genomics of plants. The origin and genetic programming of cell types

The research in my lab focuses on two inter-related questions: How do multi-cellular organisms construct specialized cells and how do the genetic components of specialized cells change over evolutionary scales? The goal is to better understand how gene regulatory networks orchestrate cell maturation, a process that results in a set of highly specialized cell types. Thus, we focus on cellular differentiation, which is one of the key steps in organ formation and development in higher organisms. The approach of the lab combines genomics and molecular genetic tools. For example, we have pioneered a new technique to isolate cell types in plants using high-speed fluidics. From there, RNA from a specific cell type population is applied to microarrays to provide a profile of gene activity at the transcriptional level. Transcriptional profiles of cells can then be used to identify likely cell-specific regulators and infer properties of the genetic circuitry of cellular specification.

Two experimental approaches are being used to address this larger question. The first project is large-scale reverse genetics guided by a detailed map of gene expression in the root and other organs. As a case study in cellular development, we have started to analyze knockouts of genes that are highly enriched in xylem, which are the water-conducting cells of the plant's vascular system. We also use computational approaches to generate testable hypotheses on the targets of transcription factors that control xylem maturation. The second project is creating detailed maps of gene expression in the roots of other plant species, such as rice. This will help us to track changes in gene expression during evolution. We can then ask how genetic networks have changed over time to create new cellular attributes and, occasionally, new cell types.

Date of these PubMed search results: March 24 2020
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1. Directions for research and training in plant omics: Big Questions and Big Data.
   Plant Direct (2019 Apr) PMC6589541 free full-text archive
   Argueso CT, Assmann SM, Birnbaum KD, Chen S, Dinneny JR, Doherty CJ, Eveland AL, Friesner J, Greenlee VR, Law JA, Marshall‑Colon A, Mason GA, O'Lexy R, Peck SC, Schmitz RJ, Song L, Stern D, Varagona MJ, Walley JW, Williams CM
2. Week-long imaging of cell divisions in the Arabidopsis root meristem.
   Plant Methods (2019) PMC6446972 free full-text archive
   Rahni R, Birnbaum KD
3. An Efficient Cell Sorting Protocol for Maize Protoplasts.
   Curr Protoc Plant Biol (2018 Sep) PMC6135669 free full-text archive
   Ortiz‑Ramirez C, Arevalo ED, Xu X, Jackson DP, Birnbaum KD
4. Combinatorial interaction network of transcriptomic and phenotypic responses to nitrogen and hormones in the Arabidopsis thaliana root.
   Sci Signal (2016 Oct 25) PMID: 27811143
   Ristova D, Carre C, Pervent M, Medici A, Kim GJ, Scalia D, Ruffel S, Birnbaum KD, Lacombe B, Busch W, Coruzzi GM, Krouk G
5. How many ways are there to make a root?
   Curr Opin Plant Biol (2016 Dec) PMID: 27780106
   Birnbaum KD
6. A Case for Distributed Control of Local Stem Cell Behavior in Plants.
   Dev Cell (2016 Sep 26) PMC5076558 free full-text archive
   Rahni R, Efroni I, Birnbaum KD
7. Plant Cell Shape: Trafficking Gets Edgy.
   Dev Cell (2016 Feb 22) PMID: 26906728
   Rahni R, Birnbaum KD
8. Identification of a Stelar-Localized Transport Protein That Facilitates Root-to-Shoot Transfer of Chloride in Arabidopsis.
   Plant Physiol (2016 Feb) PMC4734554 free full-text archive
   Li B, Byrt C, Qiu J, Baumann U, Hrmova M, Evrard A, Johnson AA, Birnbaum KD, Mayo GM, Jha D, Henderson SW, Tester M, Gilliham M, Roy SJ
9. Transcriptome dynamics of the stomatal lineage: birth, amplification, and termination of a self-renewing population.
   Dev Cell (2015 Apr 6) PMC4390738 free full-text archive
   Adrian J, Chang J, Ballenger CE, Bargmann BO, Alassimone J, Davies KA, Lau OS, Matos JL, Hachez C, Lanctot A, Vaten A, Birnbaum KD, Bergmann DC
10. Quantification of cell identity from single-cell gene expression profiles.
    Genome Biol (2015 Jan 22) PMC4354993 free full-text archive
    Efroni I, Ip PL, Nawy T, Mello A, Birnbaum KD
11. Hit-and-run transcriptional control by bZIP1 mediates rapid nutrient signaling in Arabidopsis.
    Proc Natl Acad Sci U S A (2014 Jul 15) PMC4104873 free full-text archive
    Para A, Li Y, Marshall‑Colon A, Varala K, Francoeur NJ, Moran TM, Edwards MB, Hackley C, Bargmann BO, Birnbaum KD, McCombie WR, Krouk G, Coruzzi GM
12. An undergraduate study of two transcription factors that promote lateral root formation.
    Biochem Mol Biol Educ (2014 May-Jun) PMID: 24615800
    Bargmann BO, Birnbaum KD, Brenner ED
13. Plasticity regulators modulate specific root traits in discrete nitrogen environments.
    PLoS Genet (2013) PMC3764102 free full-text archive
    Gifford ML, Banta JA, Katari MS, Hulsmans J, Chen L, Ristova D, Tranchina D, Purugganan MD, Coruzzi GM, Birnbaum KD
14. A map of cell type-specific auxin responses.
    Mol Syst Biol (2013) PMC3792342 free full-text archive
    Bargmann BO, Vanneste S, Krouk G, Nawy T, Efroni I, Shani E, Choe G, Friml J, Bergmann DC, Estelle M, Birnbaum KD
15. Integration of responses within and across Arabidopsis natural accessions uncovers loci controlling root systems architecture.
    Proc Natl Acad Sci U S A (2013 Sep 10) PMC3773737 free full-text archive
    Rosas U, Cibrian‑Jaramillo A, Ristova D, Banta JA, Gifford ML, Fan AH, Zhou RW, Kim GJ, Krouk G, Birnbaum KD, Purugganan MD, Coruzzi GM
16. Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev Cell (2013 Feb 25) PMC3994294 free full-text archive
    Efroni I, Han SK, Kim HJ, Wu MF, Steiner E, Birnbaum KD, Hong JC, Eshed Y, Wagner D
17. RootScape: a landmark-based system for rapid screening of root architecture in Arabidopsis.
    Plant Physiol (2013 Mar) PMC3585581 free full-text archive
    Ristova D, Rosas U, Krouk G, Ruffel S, Birnbaum KD, Coruzzi GM
18. Fluorescence-activated cell sorting for analysis of cell type-specific responses to salinity stress in Arabidopsis and rice.
    Methods Mol Biol (2012) PMC4164160 free full-text archive
    Evrard A, Bargmann BO, Birnbaum KD, Tester M, Baumann U, Johnson AA
19. Nitrogen economics of root foraging: transitive closure of the nitrate-cytokinin relay and distinct systemic signaling for N supply vs. demand.
    Proc Natl Acad Sci U S A (2011 Nov 8) PMC3215050 free full-text archive
    Ruffel S, Krouk G, Ristova D, Shasha D, Birnbaum KD, Coruzzi GM
20. Measuring cell identity in noisy biological systems.
    Nucleic Acids Res (2011 Nov) PMC3241637 free full-text archive
    Birnbaum KD, Kussell E
21. Quantitation of cellular dynamics in growing Arabidopsis roots with light sheet microscopy.
    PLoS One (2011) PMC3120859 free full-text archive
    Sena G, Frentz Z, Birnbaum KD, Leibler S
22. Predicting genome-wide redundancy using machine learning.
    BMC Evol Biol (2010 Nov 18) PMC2998534 free full-text archive
    Chen HW, Bandyopadhyay S, Shasha DE, Birnbaum KD
23. The GATA factor HANABA TARANU is required to position the proembryo boundary in the early Arabidopsis embryo.
    Dev Cell (2010 Jul 20) PMID: 20643354
    Nawy T, Bayer M, Mravec J, Friml J, Birnbaum KD, Lukowitz W
24. Built to rebuild: in search of organizing principles in plant regeneration.
    Curr Opin Genet Dev (2010 Aug) PMC2931316 free full-text archive
    Sena G, Birnbaum KD
25. Fluorescence activated cell sorting of plant protoplasts.
    J Vis Exp (2010 Feb 18) PMC2896036 free full-text archive
    Bargmann BO, Birnbaum KD
26. Primer and interviews: Gene regulation in Arabidopsis thaliana. Interview by Julie C. Kiefer.
    Dev Dyn (2009 Sep) PMID: 19653311
    Benfey PN, Birnbaum KD
27. Organ regeneration does not require a functional stem cell niche in plants.
    Nature (2009 Feb 26) PMC2649681 free full-text archive
    Sena G, Wang X, Liu HY, Hofhuis H, Birnbaum KD
28. Positive fluorescent selection permits precise, rapid, and in-depth overexpression analysis in plant protoplasts.
    Plant Physiol (2009 Mar) PMC2649414 free full-text archive
    Bargmann BO, Birnbaum KD
29. Cell-specific nitrogen responses mediate developmental plasticity.
    Proc Natl Acad Sci U S A (2008 Jan 15) PMC2206617 free full-text archive
    Gifford ML, Dean A, Gutierrez RA, Coruzzi GM, Birnbaum KD
30. Global studies of cell type-specific gene expression in plants.
    Annu Rev Plant Biol (2006) PMID: 16669770
    Galbraith DW, Birnbaum K
31. Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines.
    Nat Methods (2005 Aug) PMID: 16170893
    Birnbaum K, Jung JW, Wang JY, Lambert GM, Hirst JA, Galbraith DW, Benfey PN
32. Transcriptional profile of the Arabidopsis root quiescent center.
    Plant Cell (2005 Jul) PMC1167541 free full-text archive
    Nawy T, Lee JY, Colinas J, Wang JY, Thongrod SC, Malamy JE, Birnbaum K, Benfey PN
33. Network building: transcriptional circuits in the root.
    Curr Opin Plant Biol (2004 Oct) PMID: 15337102
    Birnbaum K, Benfey PN
34. A gene expression map of the Arabidopsis root.
    Science (2003 Dec 12) PMID: 14671301
    Birnbaum K, Shasha DE, Wang JY, Jung JW, Lambert GM, Galbraith DW, Benfey PN
35. Using cauliflower to find conserved non-coding regions in Arabidopsis.
    Plant Physiol (2002 Jun) PMC1540231 free full-text archive
    Colinas J, Birnbaum K, Benfey PN