Skip to main content
eScholarship
Open Access Publications from the University of California

Scholarly Works (42 results)

  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2013)
The diverse effects of the plant hormone ethylene on development and growth are shaped by the actions of a master regulator of transcription, EIN3.
    Cover page: When the time is ripeCreative Commons 'BY' version 4.0 license
    • Thesis
    • Peer Reviewed
    UC Davis Electronic Theses and Dissertations (2023)

    ABSTRACTThe plant vascular system is comprised of specialized tissues known as xylem and phloem. The interconnected network of xylem vessel elements, with their elongated structures and reinforced secondary cell walls, form a hydraulic system that enables efficient and uninterrupted water transport throughout the organism, contributing to plant growth and fitness. In the first chapter, genetic and genomic methodologies are employed to illustrate the conservation and repurposing of transcriptional regulation within the xylem network in Solanum lycopersicum. Key transcriptional regulators of xylem cell differentiation are identified in the tomato root, uncovering a partial conservation of the xylem developmental master regulators (VND6 and VND7) between Arabidopsis and tomato. Furthermore, through functional validation of putative orthologs of known xylem patterning and differentiation genes, examples of conservation (HD-ZIPIII TFs) as well as a novel regulator (SlKNAT1) are revealed in the tomato xylem regulatory network. The focus of the second chapter is directed towards the function of VND6 and VND7 in the Arabidopsis inflorescence stem. An integrated approach combining glycome profiling, an in vitro immunoanalytical platform, and in situ immunolocalization was employed to identify, for the first time, the differential abundance of specific cell wall biopolymers at cellular resolution in vnd6 and vnd7 mutants. Further gene expression profiling reveals perturbed expression of multiple cell-wall associated genes in the mutant backgrounds that could partially contribute to the observed cell wall phenotypes in the mutants. The third chapter delves deeper into functional conservation within the VND transcription factor family in the tomato root. It is demonstrated that various tomato VND TFs have iii expression in the vascular tissue in the root and are sufficient to induce ectopic xylem differentiation. The results here emphasize both the evolutionary conservation and distinct variations within the VND TF family concerning xylem development between two evolutionarily distant plant species. Lastly, utilizing an inducible VND7 system, an investigation is conducted on the hysteretic or memory feature associated with a bistable switch system linked to xylem cell fate determination. The findings obtained from this study indicate the necessity of an alternative inducible system, one that possesses both the "on" and "off" features. Such a system is crucial for the effective exploration of VND7-dependent hysteresis in the xylem cell differentiation. The research presented here has broad implications for understanding the molecular mechanisms underlying the plant vascular system, which is crucial for efficient water transport and plant growth. This understanding can have applications in areas such as agriculture and forestry, where efficient water use and plant growth are essential. Additionally, the insights gained from this research can inform the development of new strategies for improving plant growth and crop yields in the face of climate change and other environmental challenges. Overall, this research has significant potential for advancing our knowledge of plant biology and contributing to the development of sustainable agriculture practices. This study expands our knowledge of the molecular mechanisms governing xylem cell differentiation. It highlights both similarities and differences in the gene regulatory network of xylem across different plant species. Additionally, this research sheds light on the

    functions of VND6 and VND7 in regulating secondary cell wall composition, challengingthe earlier notions regarding functional redundancy within the VND gene family.

      Cover page: Transcriptional Regulation of Xylem Development and Secondary Cell Wall Composition
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2024)
      Plant roots navigate the soil ecosystem with each cell type uniquely responding to environmental stimuli. Below ground, the plants response to its surroundings is orchestrated at the cellular level, including morphological and molecular adaptations that shape root system architecture as well as tissue and organ functionality. Our understanding of the transcriptional responses at cell type resolution has been profoundly enhanced by studies of the model plant Arabidopsis thaliana. However, both a comprehensive view of the transcriptional basis of these cellular responses to single and combinatorial environmental cues in diverse plant species remains elusive. In this review, we highlight the ability of root cell types to undergo specific anatomical or morphological changes in response to abiotic and biotic stresses or cues and how they collectively contribute to the plants overall physiology. We further explore interconnections between stress and the temporal nature of developmental pathways and discuss examples of how this transcriptional reprogramming influences cell type identity and function. Finally, we highlight the power of single-cell and spatial transcriptomic approaches to refine our understanding of how environmental factors fine tune root spatiotemporal development. These complex root system responses underscore the importance of spatiotemporal transcriptional mapping, with significant implications for enhanced agricultural resilience.
        Cover page: The transcriptional integration of environmental cues with root cell type development.
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2018)
        Plant organs consist of multiple cell types that do not operate in isolation, but communicate with each other to maintain proper functions. Here, we extract models specific to three developmental stages of eight root cell types or tissue layers in Arabidopsis thaliana based on a state-of-the-art constraint-based modeling approach with all publicly available transcriptomics and metabolomics data from this system to date. We integrate these models into a multi-cell root model which we investigate with respect to network structure, distribution of fluxes, and concordance to transcriptomics and proteomics data. From a methodological point, we show that the coupling of tissue-specific models in a multi-tissue model yields a higher specificity of the interconnected models with respect to network structure and flux distributions. We use the extracted models to predict and investigate the flux of the growth hormone indole-3-actetate and its antagonist, trans-Zeatin, through the root. While some of predictions are in line with experimental evidence, constraints other than those coming from the metabolic level may be necessary to replicate the flow of indole-3-actetate from other simulation studies. Therefore, our work provides the means for data-driven multi-tissue metabolic model extraction of other Arabidopsis organs in the constraint-based modeling framework.
          Cover page: Integration of large-scale data for extraction of integrated Arabidopsis root cell-type specific modelsCreative Commons 'BY' version 4.0 license
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2023)
          This article comments on: Mutinda S, Mobegi FM, Hale B, Dayou O, Ateka E, Wijeratne A, Wicke S, Bellis ES, Runo S. 2023. Resolving intergenotypic Striga resistance in sorghum. Journal of Experimental Botany 74, 5294–5306.
            Cover page: The genetic basis of plants battle against witchweeds: linking immune responses to distinct resistance mechanisms.Creative Commons 'BY' version 4.0 license
            • Article
            • Peer Reviewed
            UC Davis Previously Published Works (2014)
            Here, we present the draft genome of Rhizobium rhizogenes strain ATCC 15834. The genome contains 7,070,307 bp in 43 scaffolds. R. rhizogenes, also known as Agrobacterium rhizogenes, is a plant pathogen that causes hairy root disease. This hairy root induction has been used in biotechnology for the generation of transgenic root cultures.
              Cover page: Draft Genome Sequence of Rhizobium rhizogenes Strain ATCC 15834Creative Commons 'BY' version 4.0 license
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2010)
              Abstract Background Biological processes occur on a vast range of time scales, and many of them occur concurrently. As a result, system-wide measurements of gene expression have the potential to capture many of these processes simultaneously. The challenge however, is to separate these processes and time scales in the data. In many cases the number of processes and their time scales is unknown. This issue is particularly relevant to developmental biologists, who are interested in processes such as growth, segmentation and differentiation, which can all take place simultaneously, but on different time scales. Results We introduce a flexible and statistically rigorous method for detecting different time scales in time-series gene expression data, by identifying expression patterns that are temporally shifted between replicate datasets. We apply our approach to a Saccharomyces cerevisiae cell-cycle dataset and an Arabidopsis thaliana root developmental dataset. In both datasets our method successfully detects processes operating on several different time scales. Furthermore we show that many of these time scales can be associated with particular biological functions. Conclusions The spatiotemporal modules identified by our method suggest the presence of multiple biological processes, acting at distinct time scales in both the Arabidopsis root and yeast. Using similar large-scale expression datasets, the identification of biological processes acting at multiple time scales in many organisms is now possible.
                Cover page: Detecting separate time scales in genetic expression data
                • Article
                • Peer Reviewed
                UC Davis Previously Published Works (2021)
                Plant synthetic biology requires precise characterization of genetic elements to construct complex genetic circuits that can improve plant traits or confer them with new characteristics. Transcriptional reporter assays are essential to quantify the effect of gene expression regulator elements. Additionally, transcriptional reporter systems are a key tool in understanding control of gene expression in biology. In this work, we construct and characterize a dual color luciferase ratiometric reporter system that possesses several advantages over currently used reporters. It is ratiometric, thus reducing variability and increasing consistency between experiments; it is fast, as both reporters can be measured at the same time in a single reaction, and it is less expensive to perform than current dual luciferase reporter assays. We have validated our system quantifying the transcriptional capability of a panel of promoters and terminators commonly used in synthetic biology with a broad range of expression magnitudes, and in a biologically relevant system, nitrate response.
                  Cover page: A Ratiometric Dual Color Luciferase Reporter for Fast Characterization of Transcriptional Regulatory Elements in Plants.
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2019)
                  Abscisic acid (ABA) is a drought stress signaling molecule, and simple methods for detecting its levels could benefit agriculture. Here, we present proof-of-concept detection for ABA in aqueous solutions by the use of a mixture of Cyanine 5.5 (Cy5.5) fluorophore- and BHQ3 quencher-conjugated endogenous ABA receptor pyrabactin resistance 1 like proteins (PYL3). These dye-conjugated PYL3 protein form dimers in solutions without ABA and monomerize upon ABA binding. When they are in dimers, fluorescence of Cy5.5 is either nearly completely quenched by the BHQ3 or 20% quenched by another Cy5.5. Consequently, mixtures of equal amounts of the two protein conjugates were used to detect ABA in aqueous solution. As the ABA concentration increased from <1 μM to 1 mM, the intensity of fluorescence detected at around 680 nm from the mixture was more than doubled as a result of ABA-induced monomerization, which leads to halt of quenching and recovery of fluorescence of Cy5.5 in monomers. Kinetic modeling was used to simulate the fluorescence response from the mixture and the results generally agree with the experimentally observed trend. This work demonstrates that fluorescence measurements of a single dissociation reaction in one spectral region are adequate to assess the ABA concentration of a solution.
                    Cover page: Toward Development of Fluorescence-Quenching-Based Biosensors for Drought Stress in Plants
                    • Article
                    • Peer Reviewed
                    UC Davis Previously Published Works (2023)
                    In the summer of 2021, we held a community workshop at the International Congress of Arabidopsis Research (ICAR) aimed at early career researchers and focused on values-based lab leadership. Here, we elaborate on ideas emerging from the workshop that we hope will allow current and future group leaders to reflect on and adjust to the rapidly evolving nature of the academic scientific enterprise.
                      Cover page: Running a research group in the next generation: combining sustainable and reproducible research with values-driven leadershipCreative Commons 'BY' version 4.0 license
                      Top