Works (5)

Updated: July 5th, 2023 15:36

2021 journal article

Warm nights disrupt transcriptome rhythms in field-grown rice panicles

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 118(25).

By: J. Desai n, L. Lawas*, A. Valente, A. Leman, D. Grinevich n, S. Jagadish*, C. Doherty n

author keywords: climate change impact; nighttime temperature increase; global food security; diel transcriptional networks
MeSH headings : Agriculture; Biomass; Circadian Rhythm / genetics; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Oryza / genetics; Oryza / growth & development; RNA, Messenger / genetics; RNA, Messenger / metabolism; Reproducibility of Results; Temperature; Time Factors; Transcription Factors / metabolism; Transcription, Genetic; Transcriptome / genetics
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: June 22, 2021

2019 journal article

Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome

RNA, 25(6), 669–684.

author keywords: Oryza sativa; differential gene expression; splicing; reference genome; RNA-seq; transcriptome analysis
MeSH headings : Alternative Splicing; Base Sequence; Chromosome Mapping / methods; Gene Expression Profiling / standards; Genes, Essential; Genome, Plant; High-Throughput Nucleotide Sequencing; Oryza / classification; Oryza / genetics; Oryza / metabolism; Polymorphism, Single Nucleotide; RNA, Messenger / genetics; RNA, Messenger / metabolism; Reference Standards; Sequence Alignment; Transcriptome
TL;DR: It is concluded that even between two closely related genomes of similar quality, using the reference genome that is most closely related to the species being sampled significantly improves transcriptome analysis. (via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, ORCID
Added: June 4, 2019

2018 journal article

Neural Net Classification Combined With Movement Analysis to Evaluate Setaria viridis as a Model System for Time of Day of Anther Appearance

FRONTIERS IN PLANT SCIENCE, 9.

By: J. Desai n, E. Slabaugh n, D. Liebelt n, J. Fredenberg n, B. Gray*, S. Jagadish*, O. Wilkins*, C. Doherty n

author keywords: flower opening time; spikelet opening time; timing of anthesis; setaria; developmental stage; image analysis of plants; biological image classification
TL;DR: The suitability of Setaria viridis, the model for C4 photosynthesis, for such a role is examined, and an imaging system to monitor the temporal regulation of growth, flower opening time, and other physiological characteristics in Setaria is developed. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: November 12, 2018

2017 journal article

A VIGS screen identifies immunity in the Arabidopsis Pla-1 accession to viruses in two different genera of the Geminiviridae

PLANT JOURNAL, 92(5), 796–807.

By: M. Reyes n, M. Flores-Vergara n, O. Guerra-Peraza n, C. Rajabu*, J. Desai n, Y. Hiromoto-Ruiz n, J. Ndunguru*, L. Hanley-Bowdoin n ...

author keywords: Arabidopsis; BCTV; CaLCuV; geminivirus; gip-1; immunity; Pla-1; VIGS
MeSH headings : Arabidopsis / virology; Geminiviridae / immunology; Gene Silencing; Plant Diseases / immunology; Plant Diseases / virology; Plant Immunity; Quantitative Trait Loci / genetics
TL;DR: The recessive nature of resistance to CaLCuV and the lack of obvious candidate genes near the gip‐1 locus suggest that a novel resistance gene(s) confers immunity. (via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger (Web of Science)
13. Climate Action (Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018

2017 journal article

VapC toxins drive cellular dormancy under uranium stress for the extreme thermoacidophile Metallosphaera prunae

ENVIRONMENTAL MICROBIOLOGY, 19(7), 2831–2842.

By: A. Mukherjee n, G. Wheaton n, J. Counts n, B. Ijeomah n, J. Desai n & R. Kelly n

MeSH headings : Archaeal Proteins / genetics; Archaeal Proteins / metabolism; Bacterial Toxins / genetics; Bacterial Toxins / metabolism; Gene Expression Regulation, Bacterial / physiology; RNA Stability / physiology; Sulfolobaceae / genetics; Sulfolobaceae / growth & development; Sulfolobaceae / metabolism; Transcriptome; Uranium / metabolism
TL;DR: M. prunae utilizes VapC toxins for post-transcriptional regulation under uranium stress to enter a cellular dormant state, thereby providing an adaptive response to what would otherwise be a deleterious environmental perturbation. (via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018

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