Julia Bailey-Serres studies the sensing, signaling and acclimation responses to abiotic stresses in plants. Much of the work of her group at UC Riverside’s Center for Plant Cell Biology focuses on low oxygen stress caused by flooding. Her team has characterized mechanisms of gene regulation and acclimation that enable survival of submergence and transient oxygen deprivation in rice and Arabidopsis. These mechanisms may be extended to other species. The research includes the characterization of mechanisms involving transcription and translation that are key to survival of and recovery from stress. Her research group applies multidisciplinary approaches that combine genetic, molecular, biochemical, and bioinformatics to address mechanisms from the sub-cellular to the whole plant level.

Research in the Brady lab focuses on understanding how a network of transcriptional interactions regulates tissue development and function and how these networks respond to the environment.

The Deal lab studies gene regulation in the context of plant development and in response to the environment. We are particularly interested in understanding the role of chromatin components in establishing cell type-specific transcription patterns, as well as how such patterns are altered by environmental changes.

Our technically-oriented role in the “Integrative Plasticity” project is to assist in the application of our cell type-specific transcriptome and epigenome profiling method (the INTACT method) to the crop species being studied. Scientifically, we are contributing to the project by studying the effects of drought and flood stress on gene expression in multiple root cell types of the model legume, Medicago truncatula.

Neelima’s research projects include understanding the process of plant parasitism, the genetic and molecular basis of compound leaf development in tomato, and the evolution of leaf complexity. Her lab is also using genomics approach to understand the genetic programs controlling fundamental developmental processes, and how genetic networks regulating both environmental responses and morphological form are integrated.

Transcriptional response of Alfalfa (Medicago truncatula) root cell types during drought stress and waterlogging

• Drought induced expression studies in alfalfa
• Waterlogged expression studies in alfalfa
• Stress memory inheritance in alfalfa

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Don is a 2nd year PhD student at UC Davis and researches the fundamental development in Arabidopsis and tomato roots.

Gene expression profiling in tomato (S. lycopersicum and S. pennellii) root cell types, including:

• generation of Gateway compatible INTACT and TRAP backbones
• cloning and characterizing cell-type specific promoters in tomato
• Agrobacterium rhizogenes-induced hairy root transient expression studies
• isolation of tagged nuclei and ribosomes from transgenic root material, grown also on drought and waterlogging stresses
• preparation and analysis of RNA-seq libraries

Preetveer first interned with the Sinha Lab as a senior in high school as part of the Outreach program. Captivated by the ability of plant cells to shift fate, Preetveer has been with the Sinha Group since the 2013-2014 school year. In her spare time she volunteers at clinics, plays the harmonium, and loves walking around with her camera.

Niba Nirmal is a second year undergraduate student studying Genetics and Genomics. Currently analyzing the morphological responses to flooding in root systems of the model crop species, Solanum lycopersicum, (domesticated tomato) cultivar M82, and the more drought tolerant wild tomato species, Solanum pennellii. Also characterizing whether Agrobacterium rhizogenes-induced hairy root cultures can develop aerenchyma in response to flooding. Phenotyping cell specific expression of TRAP and INTACT constructs.

Interest in development and plasticity in rice, focusing on drought and submergence stresses. Using a systems approach by developing INTACT and TRAP technologies in a cell and tissue type specific manner.

Gene regulation studies in specific cell types of rice (O. sativa) and M. truncatula:

• Optimization of tagged nuclei isolation by INTACT and ribosome profiling using TRAP in rice transgenic plants
• Preparation and analysis of RNA-seq and ChIP-seq libraries obtained from material purified by INTACT and TRAP under drought, submergence and waterlogging conditions

Transcriptional response of tomato (S. lycopersicum and S. pennellii) root cell types during drought stress and waterlogging

• Drought induced expression studies in tomato
• Waterlogged expression studies in tomato
• Bioinformatics analysis including RNA-seq and ChIP-seq analysis

Determining the function of T-DNA rol genes in Agrobacterium rhizogenes pathogenicity in infected M82 tomatoes through:

• identification of T-DNA and rol genes
• cloning cell-type specific promoters into tomatoes
• analysis of gene sufficiency using molecular cloning techniques
• analysis of gene necessity using CRISPR/Cas9 gene editing
• plant infection and propagation of tissue cultures

Donnelly is a genetics PhD candidate who enjoys “botanizing”, singing about science, and teaching. Her current research focuses on leaf development in domesticated tomato plants (Solanum lycopersicum) and their close desert wild relatives (Solanum pennellii) under water stresses. She’s also an avid knitter and cat wrangler.

Phenotypic and gene expression responses of cultivated tomato S. lycopersicum and wild tomatoes S. pennellii to water stresses

Project Manager and Outreach Coordinator for the UC-Davis group.