Works (45)
Updated: April 3rd, 2024 19:34
2024 article
A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses
Laosuntisuk, K., Vennapusa, A., Somayanda, I. M., Leman, A. R., Jagadish, S. V. K., & Doherty, C. J. (2024, January 30). PLANT JOURNAL, Vol. 1.
author keywords: gene expression; RNA-Seq; normalization methods; Sorghum bicolor; abiotic stress responses; diel transcriptional changes
onlinelibrary.wiley.com (publisher PDF)
Sources: ORCID, Web Of Science
Added: February 1, 2024
2024 journal article
Conserved plant transcriptional responses to microgravity from two consecutive spaceflight experiments
FRONTIERS IN PLANT SCIENCE, 14.
author keywords: transcriptional profiling; adaptation to spaceflight; Arabidopsis; microgravity (mu g); plants
TL;DR:
Two separate spaceflight experiments conducted on the International Space Station uncovered microgravity unique transcriptional changes and highlight the validity and importance of an onboard 1 g control.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: February 1, 2024
2024 article
Flexible Self-Powered Organic Photodetector with High Detectivity for Continuous On-Plant Sensing
Schrickx, H. M., Gyurek, S., Moore, C., Hernandez-Pagan, E., Doherty, C. J., Kudenov, M. W., & Brendan T. O'Connor. (2024, February 8). ADVANCED OPTICAL MATERIALS, Vol. 2.
author keywords: flexible photodetector; on-plant sensing; organic photodetector; plant health monitoring; self-powered photodetector; soil remediation
Sources: Web Of Science, ORCID
Added: February 19, 2024
2024 journal article
Mitigating Illumination-, Leaf-, and View-Angle Dependencies in Hyperspectral Imaging Using Polarimetry
Plant Phenomics.
Source: ORCID
Added: April 1, 2024
2023 article
A normalization method that controls for total RNA abundance affects the identification of differentially expressed genes, revealing bias toward morning-expressed responses
Laosuntisuk, K., Vennapusa, A., Somayanda, I. M., Leman, A. R., Jagadish, S. V. K., & Doherty, C. J. (2023, October 29).
TL;DR:
It is demonstrated that adding external RNA spike-ins as a normalization control produces differences in RNA-Seq analysis compared to traditional normalization methods, even between two times of day in untreated plants.
(via Semantic Scholar)
Source: ORCID
Added: February 1, 2024
2023 review
Auxin-cytokinin interplay shapes root functionality under low-temperature stress
[Review of ]. TRENDS IN PLANT SCIENCE, 28(4), 447–459.
MeSH headings : Cytokinins / physiology; Indoleacetic Acids; Temperature; Meristem / genetics; Plant Roots / physiology; Arabidopsis Proteins / metabolism; Arabidopsis / genetics; Gene Expression Regulation, Plant / genetics
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID
Added: April 17, 2023
2023 journal article
Comparative transcriptome analysis reveals candidate genes for cold stress response and early flowering in pineapple
SCIENTIFIC REPORTS, 13(1).
Sources: Web Of Science, ORCID
Added: February 26, 2024
2023 journal article
Hybrid spatial-temporal Mueller matrix imaging spectropolarimeter for high throughput plant phenotyping
APPLIED OPTICS, 62(8), 2078–2091.
MeSH headings : Multimodal Imaging; Spectrum Analysis; Plant Leaves; Zea mays
TL;DR:
Results indicate that subtle variations in retardance and diattenuation versus leaf canopy position may be present before they are clearly visible in the spectral transmission, as indicated in the optimization procedure, simulations, and calibration methods.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID
Added: April 11, 2023
2023 review
The Game of Timing: Circadian Rhythms Intersect with Changing Environments
[Review of ]. ANNUAL REVIEW OF PLANT BIOLOGY, 74, 511–538.
author keywords: circadian; rhythms; climate change; signaling networks; environmental adaptation
MeSH headings : Plant Breeding; Circadian Rhythm / physiology; Circadian Clocks; Signal Transduction
TL;DR:
This review examines what the authors know about the circadian clock in diverse plant species, the challenges with extrapolating data from controlled environments, and the need to anticipate how plants will respond to climate change.
(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: June 12, 2023
2023 journal article
Weed-induced changes in the maize root transcriptome reveal transcription factors and physiological processes impacted early in crop-weed interactions
AOB PLANTS, 15(3).
author keywords: plant-plant interaction; gene regulation; network analysis
TL;DR:
Investigating the impact of signals from a below-ground competitor on the maize root transcriptome when most vulnerable to weed pressure found the role of several specific proteins involved in ABA signalling as being important for the initiation of the early response of maize to weeds.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
15. Life on Land
(Web of Science)
Sources: Web Of Science, ORCID
Added: June 5, 2023
2022 article
Arabidopsis cell suspension culture that lacks circadian rhythms can be recovered by constitutive ELF3 expression
Laosuntisuk, K., Desai, J. S., & Doherty, C. J. (2022, May 13). (Vol. 5). Vol. 5.
TL;DR:
This work shows that while callus and cell suspension cultures can be valuable tools for investigating plant responses, careful evaluation of their phenotype is important and the altered circadian rhythms under constant light and temperature cycles in the AT2 callus could be useful backgrounds to understand the connections driving circadian oscillators and light andTemperature sensing at the cellular level.
(via Semantic Scholar)
Source: ORCID
Added: May 20, 2022
2022 article
Assessing the Nucleotide-Level Impact of Spaceflight Stress using RNA-Sequencing Data
Knight, M. S., Doherty, C. J., & Nielsen, D. M. (2022, December 2).
TL;DR:
GeneLab data is used to examine DNA sequence variants linked to spaceflight stress exposure and provides a baseline for the types of mutations that could be detected, demonstrating that RNA-Seq data is a useful resource for evaluating DNA damage from spaceflight.
(via Semantic Scholar)
Source: ORCID
Added: December 3, 2022
2022 article
Evaluating the Effects of the Circadian Clock and Time of Day on Plant Gravitropic Responses
PLANT GRAVITROPISM, Vol. 2368, pp. 301–319.
author keywords: Circadian; Gravistimulation; Time of day; Diel; Simulated microgravity
MeSH headings : Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Circadian Clocks; Circadian Rhythm; Gene Expression Regulation, Plant; Gravitropism; Photoperiod
TL;DR:
It is critical to consider the time of day when performing gravitropism experiments, even if the circadian clock is not a focus of study.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
13. Climate Action
(Web of Science)
Sources: ORCID, Web Of Science
Added: October 14, 2021
2022 journal article
Multistatic fiber-based system for measuring the Mueller matrix bidirectional reflectance distribution function
APPLIED OPTICS, 61(33), 9832–9842.
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: December 12, 2022
2022 review
The intersection between circadian and heat-responsive regulatory networks controls plant responses to increasing temperatures
[Review of ]. BIOCHEMICAL SOCIETY TRANSACTIONS, 50(3), 1151–1165.
MeSH headings : Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Circadian Clocks / genetics; Circadian Rhythm; Gene Expression Regulation, Plant; Hypocotyl / metabolism; Temperature; Transcription Factors / metabolism
TL;DR:
The network responses to increased temperatures, heat stress, and the impacts on the mechanisms of gene expression from transcription to translation are reviewed, highlighting the intersections between the elevated temperature and heat stress response pathways and circadian signaling.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Web Of Science
Added: June 28, 2022
2021 article
Fieldable Mueller matrix imaging spectropolarimeter using a hybrid spatial and temporal modulation scheme
POLARIZATION SCIENCE AND REMOTE SENSING X, Vol. 11833.
author keywords: Mueller matrix; polarimetry; imaging; temporal; spatial; modulation; plants
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID
Added: March 21, 2022
2021 journal article
Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice
SCIENTIFIC REPORTS, 11(1).
MeSH headings : Computational Biology / methods; Edible Grain / genetics; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genetic Association Studies; Genome-Wide Association Study / methods; Oryza / genetics; Phenotype; Stress, Physiological; Temperature
TL;DR:
Integrated physiological, genomic, and gene network-informed approaches indicate that the candidate genes for stay-green trait may be relevant to minimizing HNT-induced yield and quality losses during grain filling in rice by optimizing source-sink relationships.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science
Added: March 25, 2021
2021 journal article
Quantification of gray mold infection in lettuce using a bispectral imaging system under laboratory conditions
PLANT DIRECT, 5(3).
author keywords: disease detection; gray mold; hyperspectral imaging; multispectral imaging; plant pathology; reflectance indexing
TL;DR:
This paper design and build a bispectral imaging system for discriminating between leaf regions infected with gray mold and those that remain unharmed on a lettuce (Lactuca spp.) host using two optimal spectral bands from continuous hyperspectral imagery.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: ORCID, Web Of Science
Added: March 25, 2021
2021 journal article
The Circadian-clock Regulates the Arabidopsis Gravitropic Response
Gravitational and Space Research.
TL;DR:
Gravitropic responses were disrupted in plants with disrupted circadian clocks, including plants overexpressing Circadian-clock Associated 1 (CCA1) and elf3-2, in the reorientation assay and on a 2D clinostat suggesting the variation is circadian-regulated.
(via Semantic Scholar)
Source: ORCID
Added: January 6, 2022
2021 journal article
Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots
LIFE-BASEL, 11(10).
author keywords: spaceflight; fractional gravity; RNA-seq; Arabidopsis; gene expression; heat shock proteins
TL;DR:
A subset of genes whose expression correlates with changes in fractional g include those encoding transcription factors, defense, and cell wall-related proteins and heat shock proteins, which are likely to be responsive to gravity changes.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Web Of Science
Added: September 28, 2021
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).
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: ORCID, Web Of Science
Added: June 22, 2021
2020 journal article
A universal method for high-quality RNA extraction from plant tissues rich in starch, proteins and fiber
SCIENTIFIC REPORTS, 10(1).
MeSH headings : Dietary Fiber; Electrophoresis, Polyacrylamide Gel / methods; Plant Proteins; Plants / chemistry; Plants / genetics; RNA, Plant / isolation & purification; Seeds / chemistry; Seeds / genetics; Solid Phase Extraction / methods; Spectrophotometry; Starch
TL;DR:
The modified SDS-LiCl method is a robust and highly reproducible RNA extraction method for plant tissues rich in starch and other secondary metabolites and was demonstrated to be suitable for downstream applications, such as cDNA synthesis, gene amplification, and RT-qPCR.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science
Added: January 25, 2021
2020 journal article
Current status of the multinational Arabidopsis community
Plant Direct, 4(7).
author keywords: Arabidopsis thaliana; collaboration; Research Network; roadmap
TL;DR:
A call for ideas and foci for the “fourth decadal roadmap,” which will advise and coordinate the global activities of the Arabidopsis research community is initiated.
(via Semantic Scholar)
Source: ORCID
Added: April 1, 2022
2020 article
Detection of Gray Mold Infection in Plants Using a Multispectral Imaging System
Scarboro, C. G., Ruzsa, S. M., Doherty, C. J., & Kudenov, M. W. (2020, April 25). (Vol. 4). Vol. 4.
TL;DR:
A multispectral imaging system for discriminating between leaf regions, infected with gray mold, and those that remain unharmed on a lettuce (Lactuca spp.) host is designed and built.
(via Semantic Scholar)
Source: ORCID
Added: April 26, 2020
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
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: June 4, 2019
2019 journal article
Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future
PLANT DIRECT, 3(1).
author keywords: Arabidopsis; informatics; international collaboration; portal; The Arabidopsis Information Resource
TL;DR:
A “one‐stop shop” website, an Arabidopsis “Super‐Portal” to link tools, data resources, programmatic standards, and best practice descriptions for each data type are proposed, which must have community buy‐in and participation in its establishment and development to encourage adoption.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: February 17, 2020
2019 journal article
Directions for research and training in plant omics: Big Questions and Big Data
Plant Direct, 3(4), e00133.
author keywords: genomics; metabolomics; proteomics; training; transcriptomics
TL;DR:
It is hoped that this article will inspire beginning and established scientists, corporations, and funding agencies to pursue directions in research and training identified by this workshop, capitalizing on the reference species Arabidopsis thaliana and other valuable plant systems.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: ORCID, Crossref
Added: June 25, 2019
2019 journal article
New candidate loci and marker genes on chromosome 7 for improved chilling tolerance in sorghum
J. Exp. Bot, 4.
author keywords: Candidate genes; chilling stress; genome-wide association mapping; genomic regions; root-shoot; sorghum
MeSH headings : Chromosome Mapping; Cold Temperature; Crop Production; Genes, Plant; Genetic Markers; Sorghum / genetics; Stress, Physiological / genetics
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
15. Life on Land
(Web of Science)
Source: ORCID
Added: June 25, 2019
2019 journal article
Novel transcriptional responses to heat revealed by turning up the heat at night
Plant Molecular Biology, 101(1-2), 1–19.
author keywords: Heat shock; Diel regulation; Transcriptional networks; Abiotic stress; Gating of plant responses; Circadian clock
MeSH headings : Acclimatization; Arabidopsis / genetics; Arabidopsis / physiology; Circadian Clocks / genetics; Gene Expression Profiling; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks; Genome, Plant / genetics; Heat-Shock Proteins / genetics; Heat-Shock Response / genetics; Hot Temperature; Seedlings / genetics; Seedlings / physiology; Stress, Physiological; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
It is proposed that using time as a perturbagen is an approach that will enhance the understanding of plant regulatory networks and responses to environmental stresses and underpinning new aspects of heat stress responses not previously appreciated.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: ORCID
Added: June 25, 2019
2019 journal article
Only a matter of time: the impact of daily and seasonal rhythms on phytochemicals
Phytochemistry Reviews, 18(6), 1409–1433.
author keywords: Diel; Time of day; Temporal regulation; Circadian rhythms; Photoperiod responses; Environmental regulation; Specialized metabolites; Phenols; Flavonoids; Terpenoids; Alkaloids
TL;DR:
The mechanisms underlying diel and seasonal variations in phytochemical composition are reviewed and examples of temporal regulation of specific compounds within phenol, terpenoid, and alkaloidPhytochemical classes are provided and integrating temporal factors will improve the understanding of the underlying regulatory connections and ultimately improve the quality of phytochemicals.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Source: ORCID
Added: August 15, 2019
2019 article
Warm nights disrupt global transcriptional rhythms in field-grown rice panicles
Desai, J. S., Lawas, L. M. F., Valente, A. M., Leman, A. R., Grinevich, D. O., Jagadish, S. V. K., & Doherty, C. J. (2019, July 16). (Vol. 7). Vol. 7.
TL;DR:
The system-wide transcriptional perturbations suggest that WNT disrupts the tight temporal coordination between internal molecular events and the environment resulting in reduced productivity in rice.
(via Semantic Scholar)
Source: ORCID
Added: July 17, 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.
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
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes
Scientific Reports.
MeSH headings : Algorithms; Animals; Circadian Clocks / genetics; Computational Biology / methods; Gene Regulatory Networks; Humans; Mice; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
ExRANGES improved the identification of experimentally validated transcription factor targets for all species tested, even in unevenly spaced and sparse data sets, and enhances the utility of network inference approaches in non-model species where experimental validation is challenging.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Source: ORCID
Added: June 25, 2019
2017 journal article
Plant Stress Tolerance Requires Auxin-Sensitive Aux/IAA Transcriptional Repressors
CURRENT BIOLOGY, 27(3), 437–444.
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis / physiology; Arabidopsis Proteins / antagonists & inhibitors; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Gene Expression Regulation, Plant / drug effects; Indoleacetic Acids / metabolism; Plant Growth Regulators / metabolism; Plants, Genetically Modified; Repressor Proteins / genetics; Repressor Proteins / metabolism; Stress, Physiological
TL;DR:
It is hypothesized that transcriptional control of Aux/IAA genes plays a central role in the establishment of the auxin-signaling pathways that regulate organogenesis, growth, and environmental response, and it is demonstrated that stress pathways interact with the auxIn gene regulatory network (GRN) through transcription of the Aux/ IAA genes.
(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 article
The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology
Friesner, J., Assmann, S. M., Bastow, R., Bailey-Serres, J., Beynon, J., Brendel, V., … Brady, S. M. (2017, December). PLANT PHYSIOLOGY, Vol. 175, pp. 1499–1509.
MeSH headings : Arabidopsis / genetics; Computational Biology / education; Cooperative Behavior; Faculty; Phenotype; Research / education
TL;DR:
Training for experimental plant biologists needs to combine bioinformatics, quantitative approaches, computational biology, and training in the art of collaboration, best achieved through fully integrated curriculum development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
4. Quality Education
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2016 article
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes
Desai, J. S., Sartor, R. C., Lawas, L. M., Jagadish, S. V. K., & Doherty, C. J. (2016, December 24). (Vol. 12). Vol. 12.
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: June 25, 2019
2015 journal article
Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis.
Proceedings of the National Academy of Sciences of the United States of America.
author keywords: genome-wide; circadian clock; clock-controlled outputs; transcriptional regulation
MeSH headings : Arabidopsis / genetics; Arabidopsis Proteins / genetics; Genome, Plant; Transcription Factors / genetics; Transcriptome
TL;DR:
A genome-wide characterization of the direct targets of a key clock component in Arabidopsis revealed several CCA1 targets that do not cycle in either LL or LD conditions, suggesting that C CA1 plays an important role in regulating a large subset of the rhythmic transcriptome.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2021
2015 journal article
Regulation of the Arabidopsis CBF regulon by a complex low-temperature regulatory network.
The Plant Journal : for Cell and Molecular Biology.
author keywords: CBF regulatory pathway; low-temperature regulatory network; freezing tolerance; Arabidopsis thaliana
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cold Temperature; Gene Expression Regulation, Plant; Regulon / genetics
TL;DR:
The results indicate that cold regulation of the CBF regulon involves extensive co-regulation by other first-wave transcription factors; that the low-temperature regulatory network beyond theCBF pathway is complex and highly interconnected; and that the increase in freezing tolerance that occurs with cold acclimation is only partially dependent on the CBf-CRT/DRE regulatory module.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2021
2014 journal article
A genome-scale resource for the functional characterization of Arabidopsis transcription factors.
Cell Reports.
MeSH headings : Arabidopsis / genetics; Arabidopsis Proteins / genetics; Gene Expression Regulation, Plant; Genome, Plant; Transcription Factors / genetics
TL;DR:
This work presents the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions and identified direct regulators of a key clock gene (CCA1) that provide molecular links between different signaling modules and the circadian clock.
(via Semantic Scholar)
Source: ORCID
Added: June 25, 2019
2012 journal article
Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor.
Proceedings of the National Academy of Sciences of the United States of America.
author keywords: transcriptional regulation; transcriptional potential; gene networks; circadian outputs; diurnal
MeSH headings : Amino Acid Sequence; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Base Sequence; Circadian Clocks / genetics; DNA, Plant / metabolism; DNA-Binding Proteins / chemistry; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Gene Expression Regulation, Plant; Genes, Plant / genetics; Molecular Sequence Data; Promoter Regions, Genetic / genetics; Protein Binding; Protein Structure, Tertiary; Repressor Proteins / metabolism; Transcription Factors / chemistry; Transcription Factors / genetics; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
A biochemical action is defined for the core clock protein TOC1 that acts as a general transcriptional repressor, and that repression activity is in the pseudoreceiver domain of the protein.
(via Semantic Scholar)
Source: ORCID
Added: June 25, 2019
2012 journal article
CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses.
Proceedings of the National Academy of Sciences of the United States of America.
author keywords: redox homeostasis; transcriptional coordination
MeSH headings : Arabidopsis / physiology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Arabidopsis Proteins / physiology; Chromatin Immunoprecipitation; Computational Biology; Gene Expression Regulation, Plant / genetics; Gene Expression Regulation, Plant / physiology; Homeostasis / genetics; Homeostasis / physiology; Luminescent Measurements; Mutation / genetics; Oxidative Stress / physiology; Polymerase Chain Reaction; Reactive Oxygen Species / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism; Transcription Factors / physiology
TL;DR:
This work proposes CCA1 as a master regulator of ROS homeostasis through association with the Evening Element in promoters of ROS genes in vivo to coordinate time-dependent responses to oxidative stress.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2021
2012 journal article
Circadian surprise--it's not all about transcription.
Science (New York, N.Y.).
MeSH headings : Animals; CLOCK Proteins / genetics; Chromatin / metabolism; Circadian Clocks / genetics; Circadian Rhythm / genetics; Cryptochromes / genetics; Epigenesis, Genetic; Gene Expression Regulation; Liver / physiology; Male; RNA-Binding Proteins / metabolism; Transcription, Genetic; Transcriptional Activation
TL;DR:
This issue focuses on the importance of posttranscriptional regulation of messenger RNA levels on the clock, and investigates this problem from opposite ends of the spectrum—a genome-wide discovery approach and the functional characterization of a specific factor.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2021
2011 journal article
A comparison of the low temperature transcriptomes and CBF regulons of three plant species that differ in freezing tolerance: Solanum commersonii, Solanum tuberosum, and Arabidopsis thaliana.
Journal of Experimental Botany.
author keywords: Arabidopsis; CBF regulon; freezing tolerance; low temperature transcriptome; Solanum species
MeSH headings : Acclimatization; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis / physiology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Core Binding Factors / genetics; Core Binding Factors / metabolism; Freezing; Gene Expression Regulation, Plant; Plant Proteins / genetics; Plant Proteins / metabolism; Regulon; Solanum / genetics; Solanum / metabolism; Solanum / physiology; Solanum tuberosum / genetics; Solanum tuberosum / metabolism; Solanum tuberosum / physiology; Species Specificity; Transcription Factors / genetics; Transcription Factors / physiology; Transcription, Genetic / genetics
TL;DR:
It seems likely that these conserved cold-regulated genes—many of which encode transcription factors and proteins of unknown function—have fundamental roles in plant growth and development at low temperature.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2021
2010 journal article
Circadian control of global gene expression patterns.
Annual Review of Genetics.
author keywords: transcriptome; network analysis; transcriptional regulation; microarray analysis; systems biology
MeSH headings : Animals; Arabidopsis / genetics; Arabidopsis / physiology; Circadian Clocks; Circadian Rhythm; Drosophila melanogaster / genetics; Drosophila melanogaster / physiology; Gene Expression Regulation; Humans; Mice
TL;DR:
The impacts transcriptomics have had on the understanding of the clock and how this molecular clock connects with system-level circadian responses are reviewed and the discoveries made possible by high-throughput RNA assays, the network approaches used to investigate these large transcript datasets, and potential future directions are explored.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2021
2009 journal article
Roles for Arabidopsis CAMTA transcription factors in cold-regulated gene expression and freezing tolerance.
The Plant Cell.
MeSH headings : Adaptation, Biological; Arabidopsis / genetics; Arabidopsis / physiology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Base Sequence; Calmodulin-Binding Proteins / genetics; Calmodulin-Binding Proteins / metabolism; Cold Temperature; Freezing; Gene Expression Regulation, Plant; Genes, Reporter; Molecular Sequence Data; Promoter Regions, Genetic; Signal Transduction / physiology; Trans-Activators / genetics; Trans-Activators / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
A role for CAMTA proteins in cold acclimation is established and a possible point of integrating low-temperature calcium and calmodulin signaling with cold-regulated gene expression is provided.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2021
Employment
Updated: August 10th, 2023 09:25
2020 - present
NC State University Raleigh, NC, US
Associate Professor
Molecular and Structural Biochemistry
2014 - 2020
North Carolina State University Raleigh, North Carolina, US
Assistant Professor
Biochemistry
2008 - 2013
University of California San Diego La Jolla, CA, US
Postdoctoral Researcher
Education
Updated: April 10th, 2014 19:43
2002 - 2008
Michigan State University East Lansing, MI, US
PhD
Biochemistry and Molecular Biology
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