José receives HHMI-Simons Faculty Scholar Award

I was awarded a grant from the Howard Hughes Medical Institute and Simons Foundation to study the mysteries of how plants sense and response to water.  The grant will fund research in the lab over the next 5 years.  I am extremely thankful to the HHMI and Simons foundation for recognizing the fantastic work that my lab has pursued.  My special thanks to all the current and former post-docs and students who made this award possible!

GLO-Roots goes robotic!

Heike Lindner and Therese LaRue are starting to test a newly installed automated rhizotron-handling system for GLO-Roots.  The yet-to-be-named system was designed in collaboration with Modular Science, a Bay Area startup specializing in building robotic systems for biological research.  The system will enable automated delivery of plants to the GLO1 imaging system as well as automated determination of weight and addition of water, luciferin, saline solution, etc.  At max capacity, we will be able to image about 130 rhizotrons per day, which will enable us to conduct larger-scale experiments to understand the role of natural genetic variation in root system architecture and environmental responses.  Check out our teaser video of the system.

Quite Branches Blog highlights Sachs and GLO-Roots

Julius von Sachs is the father of modern plant physiology.  Blog by Ian Street highlights importance of Sachs and describes the intellectual connectivity between the work of our lab with this scientific tradition.  Sachs use of rhizotrons and the advances made through GLO-Roots are fueled by our understanding that plant biology makes sense only in an environmental context.

GLO-Roots paper published in eLife

Open Access paper available here.

Roots are mysterious organ systems that inhabit a world hidden by a veil of soil. Methods that lift this veil often sacrifice physiological relevance in exchange for visualization capability and experimental control. Such compromises may be incompatible with our desire to understand the adaptive mechanisms plants use to thrive despite environmental changes. We have devised a new method named GLO-Roots for Growth and Luminescence Observatory for Roots. GLO-Roots comprises an integrated solution for the growth, visualization and quantification of root systems in a diverse set of plant species including the eudicots Arabidopsis and tomato as well as grasses Brachypodium distachyon and Setaria viridis (unpublished). Our method enables the visualization of plant roots in thin sheets of soil using luminescence-based reporters. We codon-optimized a wide array of luciferase reporter genes and tested which isoforms worked best to reveal the root and, in dual color reporter assays, enabled structure and gene expression to be visualized simultaneously. Using the GLO-Roots system, we were able to simulate drought conditions and showed that Arabidopsis roots exhibit enhanced gravity responses that direct growth downwards towards deep-water resources. We also show that GLO-Roots is ideal for studying root-microbe interactions through the use of bacterial luminescence reporter systems. Working with Guillame Lobet at the University of Liege, we designed GLO-RIA, an image analysis package that automatically quantifies root systems imaged using GLO-Roots. Importantly, this software is able to relate root architectural features with gene expression and soil moisture to generate a true multi-dimensional understanding of root biology. This work is of particular significance as it provides a comprehensive method to study root growth and environmental response at late stages of the lifecycle and with physiological relevance unparalleled by other published systems. The GLO-Roots method is also the subject of a patent application filed in 2013.