A5081855361- Bioinformatics and Genomic Networks
- Gene Regulatory Network Analysis
- Gene expression and cancer classification
- Photosynthetic Processes and Mechanisms
- Plant Molecular Biology Research
- Single-cell and spatial transcriptomics
- Genetics, Bioinformatics, and Biomedical Research
- Plant Stress Responses and Tolerance
- Lipid metabolism and biosynthesis
- Antioxidant Activity and Oxidative Stress
- Plant tissue culture and regeneration
- Plant nutrient uptake and metabolism
- Iron Metabolism and Disorders
- Plant Gene Expression Analysis
- Plant Micronutrient Interactions and Effects
- Algal biology and biofuel production
- Phytase and its Applications
- Bayesian Modeling and Causal Inference
- Mitochondrial Function and Pathology
- Machine Learning in Bioinformatics
- Electrowetting and Microfluidic Technologies
- Neuroinflammation and Neurodegeneration Mechanisms
- Greenhouse Technology and Climate Control
- Ion Channels and Receptors
- Genetic Neurodegenerative Diseases
Georgia Institute of Technology
2014-2025
Iowa State University
2004-2017
AID Atlanta
2014
Indian Institute of Technology Bombay
2012
New Mexico State University
1999-2003
Brassinosteroids (BRs) are important regulators for plant growth and development. BRs signal to control the activities of BES1 BZR1 family transcription factors. The transcriptional network through which BZR regulate large number target genes is mostly unknown. By combining chromatin immunoprecipitation coupled with Arabidopsis tiling arrays (ChIP-chip) gene expression studies, we have identified 1609 putative genes, 404 regulated by and/or in gain-of-function bes1-D mutant. targets...
Abstract Brassinosteroids (BRs) regulate plant growth and stress responses via the BES1/BZR1 family of transcription factors, which expression thousands downstream genes. BRs are involved in response to drought, however mechanistic understanding interactions between BR signalling drought remains be established. Here we show that factor RD26 mediates crosstalk signalling. When overexpressed, BES1 target gene can inhibit BR-regulated growth. Global studies suggest act antagonistically a subset...
Vitamin A deficiency (VAD) affects over 250 million people worldwide and is one of the most prevalent nutritional deficiencies in developing countries, resulting significant socio-economic losses. Provitamin carotenoids such as β-carotene, are derived from plant foods a major source vitamin for majority world's population. Several years intense research has resulted production 'Golden Rice 2' which contains sufficiently high levels provitamin to combat VAD. In this report, focus on...
Abstract The immutans (im) variegation mutant of Arabidopsis has green and white leaf sectors due to the action a nuclear recessive gene, IMMUTANS (IM). This gene encodes IM protein, which is chloroplast homolog mitochondrial alternative oxidase. Because ofim accumulate noncolored carotenoid, phytoene, likely serves as redox component in phytoene desaturation. In this paper, we show that global impact on plant growth development required for differentiation multiple plastid types, including...
A vertical microfluidic plant chip technology is developed to establish a powerful experimental framework for high-throughput and precise phenotyping.
The biosynthesis of capsaicinoids in the placenta chilli fruit is modelled to require components fatty acid synthase (FAS) complex. Three candidate genes for subunits this complex, Kas, Acl, and Fat, isolated based on differential expression, were characterized. Transcription these three was placental‐specific RNA abundance positively correlated with degree pungency. Kas Acl mapped linkage group 1 Fat 6. None linked pungency locus, C, 2. KAS accumulation Western blots placental extracts...
Abstract Arabidopsis (Arabidopsis thaliana) immutans (im) has green and white sectoring due to the action of a nuclear recessive gene, IMMUTANS. The sectors contain normal-appearing chloroplasts, whereas abnormal chloroplasts that lack colored carotenoids defect in phytoene desaturase activity. Previous biochemical molecular characterizations leaf revealed alterations suggestive source-sink relationship between im. In this study, we use an Affymetrix ATH1 oligoarray further explore nature...
Variegation mutants offer excellent opportunities to study interactions between the nucleus-cytoplasm, chloroplast, and mitochondrion. in immutans (im) mutant of Arabidopsis is induced by a nuclear recessive gene extent variegation can be modulated light temperature. Whereas green sectors have morphologically normal chloroplasts, white are devoid pigments accumulate colourless carotenoid, phytoene. The hypothesized arise from cells that avoided irreversible photooxidative damage whereas...
High phytate content in staple food crops is a major barrier to successful iron biofortification. We have exploited the low phytic acid 1-1 (lpa1-1) mutant of maize generate transgenic plants with up-to 70 μg/g seed through endosperm-specific overexpression soybean ferritin, resulting more than 2-fold improvement bioavailability. The levels bioavailable achieved this study greatly exceed any thus far and closely approach values estimated nutritional impact on target populations. Gene...
Reverse engineering the whole-genome networks of complex multicellular organisms continues to remain a challenge. While simpler models easily scale large number genes and gene expression datasets, more accurate are compute intensive limiting their applicability. To enable fast reconstruction networks, we developed Tool for Inferring Network Genes (TINGe), parallel mutual information (MI)-based program. The novel features our approach include: (i) B-spline-based formulation linear-time...
Constructing genome-wide gene regulatory networks from large-scale expression data is an important problem in systems biology. While several techniques have been developed, none of them parallel, and they do not scale to the whole genome level or incorporate largest sets, particularly with rigorous statistical techniques. In this paper, we present a parallel method integrating mutual information, processing inequality, testing detect significant dependencies between genes, efficiently...
Integrative analysis of large-scale single cell data collected from diverse populations promises an improved understanding complex biological systems. While several algorithms have been developed for RNA-sequencing integration, many lack scalability to handle large numbers datasets and/or millions cells due their memory and run time requirements. The few tools which can do so by reducing the computational burden through strategies such as subsampling or selecting a reference dataset, improve...
Chloroplasts are crucial for the process of photosynthesis, as well developmental and environmental sensing. One important mechanisms sensing is retrograde (plastid-to-nucleus) signaling, whereby state chloroplast signaled to nucleus, resulting in alterations gene expression proteins, usually at transcriptional level. Retrograde signaling was early studied carotenoid-deficient plants that contain, upon exposure high light, photooxidized plastids arise because an inability quench ROS produced...
Ferritin−iron has been shown to be as bioavailable ferrous sulfate in humans. Thus, biofortification breed crops with high ferritin content is a promising strategy alleviate the global iron deficiency problem. Although present all food crops, its concentration varies between species and varieties. Therefore, successful requires method rapidly measure concentrations crops. The objective of this study was develop simple reliable ELISA using an anti-ferritin polyclonal antibody detect various...
The plastid terminal oxidase (PTOX) is distantly related to the mitochondrial alternative (AOX). Both are members of diiron carboxylate quinol (DOX) class proteins. PTOX and AOX contain 20 highly conserved amino acids, six which Fe-binding ligands. We have previously used in vitro planta activity assays examine functional importance sites. In this report, we conduct alanine-scanning mutagenesis on 14 other sites using our assay procedures. found that fall into three classes: (i) Ala-139,...
Abstract By analyzing two large atlases of almost 4 million cells, we show that immune‐senescence involves a gradual loss cellular identity, reflecting increased heterogeneity, for effector, and cytotoxic immune cells. The effects are largely similar in both males females were robustly reproduced atlases, one assembled from 35 diverse studies including 678 adults, the other OneK1K study 982 adults. Since mean transcriptional differences among cell‐types remain constant across age deciles,...
Learning Bayesian networks is NP-hard. Even with recent progress in heuristic and parallel algorithms, modeling capabilities still fall short of the scale problems encountered. In this paper, we present a massively method for network structure learning, demonstrate its capability by constructing genome-scale gene model plant Arabidopsis thaliana from over 168.5 million expression values. We report strong scaling efficiency 75% to 1.57 cores Tianhe-2 supercomputer. Our results constitute...
Pre-processing of microarray data is a well-studied problem. Furthermore, all popular platforms come with their own recommended best practices for differential analysis genes. However, genome-scale network inference using collected from large public repositories, these methods filter out considerable number This primarily due to the effects aggregating diverse array experiments different technical and biological scenarios. Here we introduce pre-processing pipeline suitable inferring gene...
Reconstruction of genome-scale networks from gene expression data is an actively studied problem. A wide range methods that differ between the types interactions they uncover with varying trade-offs sensitivity and specificity have been proposed. To leverage benefits multiple such methods, ensemble network combine predictions resulting developed, promising results better than or as good individual networks. Perhaps owing to difficulty in obtaining accurate training examples, these hitherto...
This paper reports a simple and effective approach to control statistical pore size distributions within electrospun nanofibrous membranes (ENMs), by choosing appropriate spinning times of electro-spinning deposition. Mean diameter ENMs decreases exponentially with increasing time. pore-size method is demonstrated regulate amount heat energy reaching microfluidic seed growth chips (SGC) thus temperature seeds on the chips, without using sophisticated semiconductor manufacturing techniques or...