A5082372151- Plant Disease Resistance and Genetics
- Chromosomal and Genetic Variations
- Plant Molecular Biology Research
- Plant-Microbe Interactions and Immunity
- Plant and Fungal Interactions Research
- Plant tissue culture and regeneration
- Wheat and Barley Genetics and Pathology
- Plant Micronutrient Interactions and Effects
- Plant Virus Research Studies
- DNA and Biological Computing
- Soil Carbon and Nitrogen Dynamics
- RNA Research and Splicing
- RNA modifications and cancer
- Research in Cotton Cultivation
- Mycorrhizal Fungi and Plant Interactions
- RNA and protein synthesis mechanisms
- Rice Cultivation and Yield Improvement
- Photosynthetic Processes and Mechanisms
- Microbial Community Ecology and Physiology
- Plant Reproductive Biology
- Transgenic Plants and Applications
- Genomics and Chromatin Dynamics
University of Washington
2023-2024
Seattle University
2024
Washington State University
2015-2023
Quality Research
2017
University of Idaho
2017
University of Tennessee at Knoxville
2017
Abstract Enhancers are cis-regulatory elements that shape gene expression in response to numerous developmental and environmental cues. In animals, several models have been proposed explain how enhancers integrate the activity of multiple transcription factors. However, it remains largely unclear plant factor activity. Here, we use Plant STARR-seq characterize 3 light-responsive enhancers—AB80, Cab-1, rbcS-E9—derived from genes associated with photosynthesis. Saturation mutagenesis revealed...
Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici, is a costly global disease that burdens farmers with yield loss and high fungicide expenses. This sophisticated biotrophic parasite infiltrates wheat leaves develops infection structures inside host cells, appropriating nutrients while suppressing the plant defense response. Development in most eukaryotes regulated small RNA molecules, success of host-induced gene silencing technology spp. implies existence functional RNAi...
Cultural practices, such as tillage, often have widespread impacts on phytobiomes. No-till has been increasingly adopted by wheat growers in the dryland cropping areas of inland Pacific Northwest United States to reduce soil erosion and decrease fuel labor inputs, yet there are limited data how conversion no-till plant-associated bacteria this highly productive system. To address knowledge gap, we evaluated bacterial communities bulk rhizosphere two locations (Idaho Washington) for 2 years,...
The genomes of flowering plants consist largely transposable elements (TEs), some which modulate gene regulation and function. However, the repetitive nature TEs difficulty mapping individual by short-read-sequencing have hindered our understanding their regulatory potential. We demonstrate that long-read chromatin fiber sequencing (Fiber-seq) comprehensively identifies accessible regions (ACRs) CpG methylation across maize genome. uncover stereotypical ACR patterns at young degenerate with...
Abstract The 3’ end of a gene, often called terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, massively parallel reporter assay, to measure the activity over 50,000 terminators from plants Arabidopsis thaliana Zea mays . We characterize thousands plant terminators, including many that outperform bacterial commonly used in plants. Terminator is species-specific, differing tobacco leaf maize protoplast assays. While...
MicroRNAs are small RNAs that regulate gene expression in eukaryotes. In this study, we analyzed the RNA profiles of two cultivars exhibit different reactions to stripe rust infection: one susceptible, other moderately resistant. Using libraries prepared from wheat infected with fungus (Puccinia striiformis), identified 182 previously-known miRNAs, 91 variants known and 163 candidate novel miRNAs. Known miRNA loci were usually copied all three sub-genomes, whereas often specific a single...
Abstract The 3’ end of a gene, often called terminator, modulates mRNA stability, localization, translation, and polyadenylation. Here, we adapted Plant STARR-seq, massively parallel reporter assay, to measure the activity over 50,000 terminators from plants Arabidopsis thaliana Zea mays . We characterize thousands plant terminators, including many that outperform bacterial commonly used in plants. Terminator is species-specific, differing tobacco leaf maize protoplast assays. While...
The wheat stripe rust fungus (Puccinia striiformis f.sp. tritici) threatens global production. Small RNAs (sRNAs) modulate plant defense induction, and RNA exchange between host microbe causes cross-kingdom gene silencing, but few examples are known in fungi. This study combined sRNA, parallel analysis of ends, expression data to discover sRNA-target pairs on each side the interaction. Specific 24 nt sRNAs were suppressed, while particular 35 fragments strongly induced upon infection. Wheat...
The transfection of maize mesophyll cells often involves digesting the plant cell walls to create protoplasts and then inserting DNA via electroporation or polyethylene glycol (PEG). Previous methods were developed produce tens thousands transfected at once. Here, we describe a straightforward method isolate transfect millions leaf in (Zea mays L.). This streamlined process removes certain common protoplasting steps, such as washing W5. Additionally, steps centrifugation, PEG-mediated...
Abstract Insulators are cis -regulatory elements that separate transcriptional units, whereas silencers repress transcription regardless of their position. In plants, these remain largely uncharacterized. Here, we use the massively parallel reporter assay Plant STARR-seq with short fragments eight large insulators to identify more than 100 block enhancer activity. The can be combined generate powerful abolish capacity strong viral 35S activate minimal promoter. Unexpectedly, when tested...
RNA sequencing of two organisms in a symbiotic interaction can yield insights that are not found samples from each organism alone. We present dataset focusing on the small fraction wheat plants (Triticum aestivum) infected with biotrophic pathogen stem rust fungus (Puccinia graminis f.sp. tritici). Simultaneous this agronomically important crop and its adversary lead to better understanding role noncoding RNAs both plant fungal biology. Small libraries were constructed mock-infected tissue...
Abstract The wheat stripe rust fungus ( Puccinia striiformis f.sp tritici ) poses a significant challenge to global production. Plant defense induction against pathogens is partly modulated by small RNA (sRNA) molecules that downregulate complementary protein-coding transcripts. Additionally, the two-way exchange between host and microbe involves cross-kingdom gene silencing impacts pathogen virulence, yet few examples are known among fungi. purpose of this study was discover RNA-target...
ABSTRACT Enhancers are cis -regulatory elements that shape gene expression in response to numerous developmental and environmental cues. In animals, several models have been proposed explain how enhancers integrate the activity of multiple transcription factors. However, it remains largely unknown plant factor activity. Here, we use Plant STARR-seq characterize three light-responsive enhancers— AB80 , Cab-1 rbcS-E9 —derived from genes active photosynthesis. Saturation mutagenesis reveals...