Office: Biology 420
Phone: (970) 491-5773
Google Scholar: https://scholar.google.com/citations?hl=en&user=6NLH3KkAAAAJ
- Ph.D., Jawaharlal Nehru University
We are always looking for highly motivated and passionate researchers (Graduate Students and Postdocs) interested in plant biology. We are seeking candidates with expertise in genomics and bioinformatics tools to investigate plant processes at the molecular, cellular, and organismal levels. If you have expertise in these areas and are interested in joining our group, please send your CV to firstname.lastname@example.org. Members of our group will have opportunities to work with Professor Asa Ben-Hur’s group in the Department of Computer Science Department. His lab applies machine learning tools to all types of next-generation sequencing data to solve biological problems.
One of the fundamental questions in plant biology is how plants sense and respond to environmental (abiotic and biotic) and hormonal signals that regulate diverse cellular processes and various aspects of plant growth and development. Our group has been studying i) calcium-mediated signal transduction mechanisms with emphasis on calcium sensors and their target proteins, ii) mechanisms that regulate basic and alternative splicing of pre-messenger RNAs in response to stresses, iii) disease resistance, iv) cell wall degrading enzymes for biofuel production and iv) synthetic signal transduction circuits in plants. We use molecular, cell biological, genetic, biochemical, bioinformatics, and computational tools to accomplish our research goals. Arabidopsis, rice, maize, potato, and Miscanthus are used in our research. Studies on computational aspects of alternative splicing and protein-protein interactions are being done in collaboration with Professor Asa Ben-Hur in the Department of Computer Science at CSU.
In signaling research, our work is focused on calcium/calmodulin-mediated signal transduction mechanisms in plant growth and development, and plant responses to pathogens and abiotic stresses. Calcium is a key messenger in transducing diverse signals in plants. We have been particularly interested in calcium sensors and downstream targets of calcium sensors in understanding diverse cellular and physiological processes regulated by calcium. Using bioinformatics tools we have extensively characterized several gene families involved in calcium signaling. In a comprehensive screen for calmodulin interacting proteins, we identified over 100 calmodulin-binding proteins ranging from transcription factors to molecular motors. During the last twenty years we have been studying the function of several of these calmodulin-binding proteins in plant growth and development, and plant responses to various biotic and abiotic stresses. Our group has extensively characterized the function and regulation of a novel calcium/calmodulin-regulated microtubule motor protein involved in cell morphogenesis and cell division. We have identified several calmodulin target proteins that play a central role in plant disease resistance and abiotic stress responses and elucidated signaling pathways involving these proteins. Additionally, we demonstrated a critical role for a pollen-specific calmodulin-binding protein in pollen germination. We have generated and tested chimeric motors and receptors by combining modular domains from plant and animal proteins for potential applications in synthetic biology and nanobiotechnology.
In the gene regulation area, our focus is on precursor-mRNA splicing. Alternative splicing of pre-mRNAs is an important step in regulating transcriptome complexity and eventually proteome diversity. More recently, it has become evident that alternative splicing is coupled to nonsense-mediated decay to regulate the abundance of transcripts through a mechanism called regulated unproductive splicing and translation (RUST). Our group has been studying spliceosomal proteins, identified several putative splicing regulators, called serine/arginine-rich (SR) proteins, and analyzed their functions using a variety of genetic, biochemical, and cell biological approaches. By studying alternative splicing of Arabidopsis SR genes, we have demonstrated extensive alternative splicing (generation of over 90 splice variants from 15 genes) of this family of genes. Furthermore, our studies have demonstrated that stresses have a rapid and profound effect on alternative splicing, suggesting rapid reprogramming of gene expression at the splicing level. Recent studies suggest that plants can rapidly alter their transcriptome complexity in response to stresses by regulating alternative splicing of master splicing regulators.
Our current focus is on genome-scale analyses of targets of calmodulin-regulated transcription factors and stress-regulated alternative splicing in various mutants, using high-throughput next-generation Illumina, Pac-Bio, and Nanopore sequencing technologies to characterize plant transcriptomes, alternative splicing, and epitranscriptome. A comprehensive understanding of mechanisms by which plants respond to stresses will pave the way to engineer plants that are capable of growing well under adverse environmental conditions. Also, we engineer plants by introducing bacterial biochemical pathways into plants to produce novel chemicals in plants.
- Quantitative profiling of N6-methyladenosine at single-base resolution in stem-differentiating xylem of Populus trichocarpa using Nanopore direct RNA sequencing Genome Biol. 22:22, 2021
- Decoding co-/post-transcriptional complexities of plant transcriptomes and epitranscriptome using next-generation sequencing technologies. Biochem. Soc Trans 48: 2399-2414, 2020
- Phytophthora Effectors Modulate Genome-wide Alternative Splicing of Host mRNAs to Reprogram Plant Immunity. Mol. Plant. 13, 1470-1484: Featured as “Editor’s Highlight” Mol. Plant 123, 1348., 2020
- Wide-ranging transcriptome remodeling mediated by alternative polyadenylation in response to abiotic stresses in sorghum. Plant J. 102: 916-930., 2020
- The Arabidopsis splicing regulator SR45 confers salt tolerance in a splice isoform-dependent manner. Plant Mol. Biol. 100:379-390., 2019
- Analysis of transcriptome and epitranscriptome in plants using PacBio Iso-Seq and Nanopore-based direct RNA sequencing. Frontiers in Genetics 10: 253, pages 1-14., 2019
- Perspective on alternative splicing and proteome complexity in plants. Trends in Plant Science 20: 496-506., 2019
- Does co-transcriptional regulation of alternative splicing mediate plant stress responses? Nucleic Acids Res. 47: 2716-2726, 2019
- A survey of the sorghum transcriptome using single-molecule long reads.Nature Communications 7:11706 , 2016
- Ca2+/calmodulin Regulates Salicylic Acid-mediated Plant ImmunityNature 457: 1154-1158. Featured under “Leading Edge” section of Cell. , 2009