The Plasticity Project is a NSF-PGRP [(IOS-1238243; 1844803)] funded collaboration with the groups of Siobhan Brady and Neelima Sinha (UC Davis) and Roger Deal (Emory University) that continues with Mauricio Reynoso (Universidad Nacional de La Plata, Argentina). We developed and applied nuclear isolation (INTACT) and ribosome immunopurification (TRAP) technologies for isolation of chromatin, nuclear RNA and ribosome-associated mRNA in rice, tomato and Medicago to study responses to hypoxia, submergence, drought, phosphate starvation, and recovery from these stresses. We developed a collection of lines to access cell-specific nuclei and translatomes in roots and shoot meristems. Our methods are published and available as bench protocols. Plasticity Project 2.0 will continue with the development of inducible INTACT and TRAP and its application to evaluation of plant-mycorrhizal fungal interactions with new collaborator Uta Paszkowski (Cambridge University). Current researchers: Alex Borowsky, Garo Akmakjian.
The Multi-level Gene Regulation and mRNPome Projects
This project seeks to understand transcriptional and post-transcriptional gene regulation that is critical to plant responses. Following our initial demonstration genes upregulated by hypoxia are predisposed to efficient translation, we actively explore roles of chromatin, RNA binding proteins non-coding RNAs that that determine post-transcriptional gene regulation that is key to stress survival and developmental plasticity in plants. Using genetics and biochemistry we are capturing and characterizing the RNAs associated with a number of RNA binding proteins, including components of stress granules and processing bodies. Collaborators: Prof. Thomas Girke (UC Riverside); Prof. Leslie Sieburth and Dr. Reed Sorenson (University of Utah). Researchers: Dr Maureen Hummel, Dr Thanin (George) Chantarachot, Sonja Winte and many undergraduates. Past Researchers: Travis Lee, Jeremie Bazin, Reed Sorenson and Piyada Juntawong
The Systematic Evaluation of CellulaR ExporT (SECRET-ome) from plant cells is a new NSF-PGRP project (MCB-1546879) is developing additional TRAP lines for cell types of rice to explore secretory processes of rice that are involved in abiotic and biotic stress. This project is leveraging data from the Plasticity Project to follow targets relevant to meristem survival and plasticity in root traits relevant to submergence/waterlogging and flooding. The projects include development of methods for gene regulatory analysis and display of multi-cell translatome data. Collaborators: Thomas Girke (UC Riverside, co-PI); Wolf Frommer (Heinrich Heine Institute, Dusseldorf and Max Plank Institute, Köln, Germany, co-PI); Bing Yang (Iowa State University, PI); Dylan Kozma (University of Reno, Nevada). Current Researchers: Dr Matthew Prior, Jianhai Zhang, Alex Borowsky, undergraduate and high school students.
Translatomes and Ribosome Footprint Sequencing
Much gene regulation occurs at the cell specific and post-transcriptional levels. We developed methods for analysis of mRNA associated with ribosomes or specific RNA binding proteins in individual cell types.
Sub1 Rice and Beyond
Robust submergence tolerance and anaerobic germination tolerance can alleviate significant crop loss and lessen the manpower and herbicides required for establishment of rice plantations. Our USDA NIFA-funded collaboration with Endang Septiningsih (Texas A&M University; 2017-67013-26194) seeks to define a new QTL that further bolsters submergence tolerance. Key consultants: David Mackill (Mars Inc. and UC Davis), Abdel Ismail (IRRI), Takeshi Fukao (Virginia Tech), Julian Peña Castro. Researchers: Dr. Miguel Lopez, Alek Kettenberg, Dr. Matt Prior, Sonja Winte
Low Oxygen Sensing, Survival and Recovery Mechanisms
We work in this area with our key collaborators at Utrecht University Rens Voesenek and Rashmi Sasidaharan (Plant Ecophysiology Group, Utrecht University) and former group member Angelika Mustroph (Bayreuth University, Germany).
High Yield and Climate Resilient Crops
For the first time our group works on wheat in an International Wheat Yield Partnership (IWYP) project entitled “Three High-Value Genes for Higher Wheat Yield”, led by Stuart Roy (University of Adelaide, Australia). Our lab’s focus is on the impact of rice PSTOL in wheat on nutrient acquisition, biomass and seed production. We have developed robust methods for plant growth under controlled phosphate that enable rapid access to root systems for molecular analyses. Collaborators: Sigrid Heuer (Rothamstead), Roberto Gaxiola (Arizona State University). Researchers: Dr. Miguel Lopez and Alek Kettenberg
Waterlogging Tolerant Soybean
A new project with Professor Henry Nguyen and Heng Ye (U of Missouri, Columbia) funded by USDA NIFA (2019-67013-29313) is a gene-to-field characterization of the regulation and function of a SAUR gene associated with waterlogging tolerance and yield stability in soybean. Our role is to define the features of the gene and its regulation that confers waterlogging tolerance in the field. Researcher: Dr. Maureen Hummel.