Works (37)
Updated: December 16th, 2024 11:10
2024 article
The Black American experience: Answering the global challenge of broadening participation in STEM/agriculture
Haverroth, E., Gobble, M., Bradley, L., Harris-Gilliam, K., Fischer, A., Williams, C., … Sozzani, R. (2024, January 29). PLANT CELL, Vol. 1.
open access via academic.oup.com (publisher PDF)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
3. Good Health and Well-being
(Web of Science)
4. Quality Education
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 1, 2024
2023 journal article
Cellular clarity: a logistic regression approach to identify root epidermal regulators of iron deficiency response
BMC GENOMICS, 24(1).
author keywords: Iron deficiency; Epidermis; Arabidopsis; Logistic regression; Gene regulatory network; RNA-seq
TL;DR:
Machine learning approaches combined with additional static data identified putative regulators of -Fe response that would not have been identified solely through transcriptomic profiles and reveal how developmental and general stress responses within the epidermis may act upstream of more specialized -Fe responses for Fe uptake.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: November 27, 2023
2022 article
BTS Is a Negative Regulator for the Cellular Energy Level and the Expression of Energy Metabolism-Related Genes Encoded by Two Organellar Genomes in Leaf Tissues
Choi, B., Hyeon, D. Y., Lee, J., Long, T. A., Hwang, D., & Hwang, I. (2022, April 15). MOLECULES AND CELLS, Vol. 4.
author keywords: Arabidopsis thaliana; BRUTUS; energy metabolism; shoot tissues
MeSH headings : Adenosine Diphosphate / metabolism; Adenosine Triphosphate / metabolism; Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Energy Metabolism / genetics; Gene Expression Regulation, Plant; Plant Leaves / genetics; Plant Leaves / metabolism; Plant Roots / genetics; Plant Roots / metabolism; Plant Shoots; Starch / metabolism; Ubiquitin-Protein Ligases / metabolism
TL;DR:
The role of BTS is expanded to regulation of energy metabolism in the shoot in addition to its role of iron deficiency response in roots through Comparative transcriptome analysis with shoot and root tissues.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
7. Affordable and Clean Energy
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: April 20, 2022
2022 article
POPEYE intercellular localization mediates cell-specific iron deficiency responses
Muhammad, D. S., Clark, N. M., Haque, S., Williams, C. M., Sozzani, R., & Long, T. A. (2022, August 3). PLANT PHYSIOLOGY, Vol. 8.
MeSH headings : Iron Deficiencies; Arabidopsis Proteins / metabolism; Gene Expression Regulation, Plant; Basic Helix-Loop-Helix Transcription Factors / metabolism; Arabidopsis / metabolism; Iron / metabolism; Plant Roots / genetics; Plant Roots / metabolism
TL;DR:
The findings indicate that PYE acts as a positive regulator of iron deficiency response by regulating iron bioavailability differentially across cells, which may trigger iron uptake from the surrounding rhizosphere and impact root energy metabolism.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: August 13, 2022
2021 journal article
A hybrid model connecting regulatory interactions with stem cell divisions in the root
Quantitative Plant Biology, 2.
TL;DR:
This work proposes a non-cell autonomous role for WOX5 in the cortex endodermis initial (CEI) and identifies a regulator, ANGUSTIFOLIA (AN3)/GRF-INTERACTING FACTOR 1, that coordinates CEI divisions.
(via Semantic Scholar)
Source: ORCID
Added: April 13, 2021
2021 journal article
Broadening the impact of plant science through innovative, integrative, and inclusive outreach
PLANT DIRECT, 5(4).
TL;DR:
This document is expected to guide the formation of community partnerships to scale up currently successful outreach programs, and lead to the design of future programs that effectively engage with a more diverse student body and citizenry.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
4. Quality Education
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 9, 2022
2021 review
Solving the puzzle of Fe homeostasis by integrating molecular, mathematical, and societal models
[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 64.
author keywords: Iron homeostasis; Simulation-based inference (SBI); Inclusivity
MeSH headings : Biological Transport; Gene Expression Regulation, Plant; Homeostasis; Iron / metabolism; Plants / genetics; Plants / metabolism
TL;DR:
This work examines recent advances in the understanding of cellular responses to Fe deficiency and uses intracellular mechanisms of Fe homeostasis to discuss how formalizing cell biology knowledge via a mathematical model can advance discovery even when quantitative data is limited.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: November 27, 2021
2020 chapter
BioVision Tracker: A semi-automated image analysis software for spatiotemporal gene expression tracking in Arabidopsis thaliana
In Methods in Cell Biology (Vol. 160, pp. 419–436).
Contributors: E. Buckner n, I. Madison n, C. Melvin n, n , R. Sozzani n & C. Williams n
MeSH headings : Arabidopsis / genetics; Automation; Gene Expression Regulation, Plant; Image Processing, Computer-Assisted; Plant Roots / anatomy & histology; Software; Time Factors
TL;DR:
A procedure for analyzing 3D microscopy images to track spatiotemporal gene expression signals using the MATLAB-based BioVision Tracker software, which requires either a fluorescence image or a brightfield image to analyze root geometry and afluorescence image to capture and track temporal changes in gene expression.
(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, NC State University Libraries, Crossref
Added: June 17, 2020
2020 journal article
Computational solutions for modeling and controlling plant response to abiotic stresses: a review with focus on iron deficiency
Current Opinion in Plant Biology, 57, 8–15.
MeSH headings : Anemia, Iron-Deficiency; Arabidopsis / metabolism; Droughts; Gene Expression Regulation, Plant; Humans; Plant Proteins / genetics; Plant Proteins / metabolism; Stress, Physiological / genetics
TL;DR:
The increasing development and use of statistical modeling and systematic modeling of transcriptomic data have provided significant insight into the gene regulatory mechanisms associated with abiotic stress responses and facilitated the plant science community's future goals of developing multi-scale models of responses to iron deficiency stress and other abiotic Stress conditions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Source: ORCID
Added: July 1, 2020
2020 article
Exchange of molecular and cellular information: a hybrid model that integrates stem cell divisions and key regulatory interactions
Broeck, L. V., Spurney, R. J., Fisher, A. P., Schwartz, M., Clark, N. M., Nguyen, T. T., … Sozzani, R. (2020, December 1).
TL;DR:
A non-cell autonomous role for WOX5 in the CEI is proposed and a regulator, AN3/GIF1, that coordinates CEI divisions is identified and an interdependency between CEI and QC divisions is shown.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2024
2020 journal article
Iron homeostasis and plant immune responses: Recent insights and translational implications
Journal of Biological Chemistry, 295(39), 13444–13457.
author keywords: Arabidopsis thaliana; host-pathogen interaction; iron metabolism; metal homeostasis; oxygen radicals; plant defense; plant hormone
MeSH headings : Animals; Homeostasis / immunology; Humans; Iron / immunology; Iron / metabolism; Plant Immunity / immunology
TL;DR:
Improved mechanistic understanding of plant iron metabolism suggests that such alterations could promote or impede plant immunity, depending on the nature of the alteration and the virulence strategy of the pathogen.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
Source: ORCID
Added: July 31, 2020
2020 chapter
MAGIC: Live imaging of cellular division in plant seedlings using lightsheet microscopy
In Methods in Cell Biology (Vol. 160, pp. 405–418).
Contributors: I. Madison n, C. Melvin n, E. Buckner n, C. Williams n , R. Sozzani n & n
MeSH headings : Arabidopsis / cytology; Arabidopsis / growth & development; Cell Division; Imaging, Three-Dimensional; Microscopy, Fluorescence / methods; Seedlings / cytology; Seedlings / growth & development
TL;DR:
This chapter describes a detailed method for preparing and imaging Arabidopsis thaliana seedlings for lightsheet microscopy via a Multi-Sample Imaging Growth Chamber (MAGIC), which allows simultaneous imaging of at least four samples.
(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, NC State University Libraries, Crossref
Added: June 17, 2020
2019 journal article
Automated Imaging, Tracking, and Analytics Pipeline for Differentiating Environmental Effects on Root Meristematic Cell Division
Frontiers in Plant Science, 10.
Contributors: E. Buckner n, I. Madison n, H. Chou n, A. Matthiadis n, C. Melvin n, R. Sozzani n , C. Williams n, n
author keywords: light sheet imaging; image analysis; cell cycle progression; heat stress and iron deficiency stresses; combined stresses
TL;DR:
It is observed that iron deficiency, in combination with temporary heat stress, suppresses the expression of iron deficiency-responsive pPYE::LUC (POPEYE::luciferase) and pBTS::L UC (BRUTUS::lUC) reporter genes and root growth was suppressed less under combined iron deficiency and heat stress than under either single stress condition.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: ORCID, Crossref, NC State University Libraries
Added: December 4, 2019
2019 journal article
Dynamic modelling of the iron deficiency modulated transcriptome response in Arabidopsis thaliana roots
In Silico Plants, 1(1).
author keywords: Arabidopsis thaliana; modelling; ODE; Gene Regulatory Network; plant stress response
TL;DR:
A dynamic model of the iron deficiency induced transcriptional response in Arabidopsis thaliana was formulated and trained to approximate the expression behaviour of currently unknown gene regulators, unveil potential synergistic effects between the modulating transcription factors and predict the effect of double regulator mutants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
Sources: ORCID, Crossref, NC State University Libraries
Added: December 10, 2019
2019 review
Hemerythrin E3 Ubiquitin Ligases as Negative Regulators of Iron Homeostasis in Plants
[Review of ]. FRONTIERS IN PLANT SCIENCE, 10.
Contributors: J. Rodríguez-Celma *, H. Chou n, T. Kobayashi *, n & J. Balk *
author keywords: micronutrient; iron deficiency; bHLH; FBXL5; zinc finger; sensor
TL;DR:
A mechanistic model is proposed to help focus future research questions towards a full understanding of the regulatory role of these proteins in Fe homeostasis in plants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: March 4, 2019
2019 review
Keep talking: crosstalk between iron and sulfur networks fine-tunes growth and development to promote survival under iron limitation
[Review of ]. JOURNAL OF EXPERIMENTAL BOTANY, 70(16), 4197–4210.
Contributors: D. Mendoza-Cózatl *, A. Gokul *, M. Carelse *, T. Jobe *, n , M. Keyster *, S. Kopriva
author keywords: Dynamic cell economy; iron sensing; iron use efficiency; nutrient crosstalk; sulfur homeostasis
MeSH headings : Growth and Development; Iron / metabolism; Minerals / metabolism; Plant Proteins / genetics; Plant Proteins / metabolism; Plants / genetics; Plants / metabolism; Sulfur / metabolism
TL;DR:
This review summarizes and discusses recent literature on Fe sensing, allocation, use efficiency, and when pertinent, its relation to S metabolism.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: September 30, 2019
2018 journal article
The E3 ligase BRUTUS facilitates degradation of VOZ1/2 transcription factors
PLANT CELL AND ENVIRONMENT, 41(10), 2463–2474.
Contributors: D. Selote n, A. Matthiadis n, J. Gillikin n, M. Sato * & n
author keywords: abiotic stress; Arabidopsis thaliana; BRUTUS; ubiquitin-proteasome system; VOZ1/2
MeSH headings : Arabidopsis / enzymology; Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Arabidopsis Proteins / physiology; Basic Helix-Loop-Helix Transcription Factors / metabolism; Blotting, Western; FMN Reductase / metabolism; Immunoprecipitation; Plant Roots / metabolism; Real-Time Polymerase Chain Reaction; Stress, Physiological; Subcellular Fractions / metabolism; Transcription Factors / metabolism; Ubiquitin-Protein Ligases / metabolism; Ubiquitin-Protein Ligases / physiology
TL;DR:
It is demonstrated that BTS facilitates the degradation of Vascular plant One-Zinc finger 1/2 (VOZ1/2) protein in the nucleus particularly under drought and cold stress conditions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: October 16, 2018
2018 journal article
The bHLH transcription factor ILR3 modulates multiple stress responses in Arabidopsis
Plant Molecular Biology, 97(4-5), 297–309.
Contributors: R. Samira n, B. Li *, D. Kliebenstein *, C. Li n, E. Davis n, J. Gillikin n, n
author keywords: Arabidopsis thaliana; Glucosinolates; Heterodera schachtii; Iron homeostasis; ILR3; PYE
MeSH headings : Adaptation, Physiological / genetics; Animals; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis / parasitology; Arabidopsis Proteins; Basic Helix-Loop-Helix Transcription Factors; Disease Resistance / genetics; Gene Expression Regulation, Plant; Glucosinolates / metabolism; Homeostasis; Iron / metabolism; Plant Diseases / genetics; Plant Diseases / parasitology; Plant Roots / genetics; Plant Roots / metabolism; Plant Roots / parasitology; Plants, Genetically Modified; Stress, Physiological; Tylenchoidea / physiology
TL;DR:
It is suggested that ILR3 and PYE function in a regulatory network that controls wounding pathogen response in plant roots by modulating GLS accumulation under iron deficiency.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
Sources: ORCID, Crossref
Added: December 4, 2019
2016 journal article
Further insight into BRUTUS domain composition and functionality
PLANT SIGNALING & BEHAVIOR, 11(8).
Contributors: A. Matthiadis n & n
author keywords: Arabidopsis thaliana; BRUTUS (BTS); hemerythrin (HHE); iron homeostasis; multidomain protein; Pirh2; RING E3
MeSH headings : Arabidopsis / enzymology; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Hemerythrin / genetics; Hemerythrin / metabolism; Iron / metabolism; Iron Deficiencies; Ubiquitin-Protein Ligases / genetics; Ubiquitin-Protein Ligases / metabolism
TL;DR:
It is concluded that enzymatic activity of BTS via the RING domain is essential for response to iron deficiency in plants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2016 review
More than meets the eye: Emergent properties of transcription factors networks in Arabidopsis
[Review of ]. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS, 1860(1), 64–74.
Contributors: D. Muhammad n, S. Schmittling n, C. Williams n & n
author keywords: Transcription factor networks (TFNs); Emergent properties; Mathematical modeling
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Computational Biology / methods; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Plant Development / genetics; Stress, Physiological / genetics; Transcription Factors / genetics
TL;DR:
This review highlights literature that provides, in part, experimental and computational techniques for characterizing Transcription Factor Networks and outlines methodologies that have been used to mathematically model the dynamic characteristics of TFNs.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2015 journal article
Clustering and Differential Alignment Algorithm: Identification of Early Stage Regulators in the Arabidopsis thaliana Iron Deficiency Response
PLOS ONE, 10(8).
Contributors: A. Koryachko n, A. Matthiadis n, D. Muhammad n, J. Foret *, S. Brady *, J. Ducoste n , J. Tuck n , n , C. Williams n
MeSH headings : Algorithms; Arabidopsis / genetics; Arabidopsis / metabolism; Databases, Genetic; Gene Expression Regulation, Plant; Iron Deficiencies; Sequence Alignment; Software; Transcriptome
TL;DR:
It is proposed that this tool can be used successfully for similar time course datasets to extract additional information and infer reliable regulatory connections for individual genes, and served as a proof of concept emphasizing the utility of the CDAA for identifying unknown or missing nodes in regulatory cascades.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2015 journal article
Computational approaches to identify regulators of plant stress response using high-throughput gene expression data
Current Plant Biology, 3-4, 20–29.
Contributors: A. Koryachko n, A. Matthiadis n, J. Ducoste n , J. Tuck n , n & C. Williams n
author keywords: Stress response; Transcription factors; Gene regulatory networks; Algorithms; Arabidopsis thaliana
TL;DR:
This review conceptually organizes a wide variety of developed algorithms into a classification system based on desired type of output predictions to describe completed approaches in the literature, with a focus on project goals, overall path of implemented algorithms, and biological insight gained.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Crossref, NC State University Libraries
Added: December 14, 2019
2014 journal article
Chromate alters root system architecture and activates expression of genes involved in iron homeostasis and signaling in Arabidopsis thaliana
PLANT MOLECULAR BIOLOGY, 86(1-2), 35–50.
author keywords: Chromium; Root development; Gene expression; Iron homeostasis; Arabidopsis
MeSH headings : Arabidopsis / drug effects; Arabidopsis / genetics; Arabidopsis / physiology; Chromates / toxicity; Gene Expression Regulation, Plant / drug effects; Homeostasis / drug effects; Iron / metabolism; Plant Roots / drug effects; Plant Roots / genetics; Plant Roots / physiology; Seedlings / drug effects; Seedlings / genetics; Seedlings / physiology; Signal Transduction / drug effects; Soil Pollutants / toxicity
TL;DR:
It is reported that depending upon its concentration, Cr(VI) alters in different ways the architecture of the root system in Arabidopsis thaliana seedlings, and that toxic Cr concentrations activate a low-Fe rescue system.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
11. Sustainable Cities and Communities
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2014 review
Fixating on metals: new insights into the role of metals in nodulation and symbiotic nitrogen fixation
[Review of ]. FRONTIERS IN PLANT SCIENCE, 5(FEB).
Contributors: M. González-Guerrero *, A. Matthiadis n, Á. Sáez * & n
author keywords: symbiotic nitrogen fixation (SNF); metals; legume; rhizobia; nodule; iron; zinc; copper
TL;DR:
Renewed efforts have been undertaken to identify the mechanisms governing metal delivery from soil to the rhizobia, and to determine how metals are used in the nodule and how they are recycled once the nodules are no longer functional.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2014 journal article
Iron-Binding E3 Ligase Mediates Iron Response in Plants by Targeting Basic Helix-Loop-Helix Transcription Factors
PLANT PHYSIOLOGY, 167(1), 273-+.
Contributors: D. Selote n, R. Samira n, A. Matthiadis n, J. Gillikin n & n
MeSH headings : Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis / physiology; Arabidopsis Proteins / metabolism; Arabidopsis Proteins / physiology; Basic Helix-Loop-Helix Transcription Factors / metabolism; Basic Helix-Loop-Helix Transcription Factors / physiology; Iron / metabolism; Iron-Binding Proteins / metabolism; Iron-Binding Proteins / physiology; Plant Roots / growth & development; Plant Roots / physiology; Proteasome Endopeptidase Complex / metabolism; Proteasome Endopeptidase Complex / physiology; Ubiquitin-Protein Ligases / metabolism; Ubiquitin-Protein Ligases / physiology
TL;DR:
This study reveals an important and unique mechanism for plant iron homeostasis whereby an E3 ubiquitin ligase may posttranslationally control components of the transcriptional regulatory network involved in the iron deficiency response.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2013 journal article
A Single Amino Acid Alteration in PGR5 Confers Resistance to Antimycin A in Cyclic Electron Transport around PSI
Plant and Cell Physiology, 54(9), 1525–1534.
Contributors: K. Sugimoto *, Y. Okegawa *, A. Tohri*, n , S. Covert*, T. Hisabori *, T. Shikanai *
author keywords: Antimycin A; Arabidopsis thaliana; Cyclic electron transport; FQR; PGR5; Pinus taeda
MeSH headings : Amino Acid Sequence; Amino Acid Substitution; Antifungal Agents / pharmacology; Antimycin A / pharmacology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Chlorophyll / metabolism; Chloroplasts / drug effects; Chloroplasts / genetics; Chloroplasts / metabolism; Drug Resistance / genetics; Electron Transport / drug effects; Genetic Complementation Test; Immunoblotting; Molecular Sequence Data; Mutation; Photosynthetic Reaction Center Complex Proteins / genetics; Photosynthetic Reaction Center Complex Proteins / metabolism; Photosystem I Protein Complex / genetics; Photosystem I Protein Complex / metabolism; Photosystem II Protein Complex / genetics; Photosystem II Protein Complex / metabolism; Pinus taeda / genetics; Plant Leaves / genetics; Plant Leaves / metabolism; Plant Proteins / genetics; Plant Proteins / metabolism; Plants, Genetically Modified; Sequence Homology, Amino Acid
TL;DR:
It is found that ferredoxin-dependent plastoquinone reduction in ruptured chloroplasts was less sensitive to antimycin A in Arabidopsis that overaccumulated PGR5 (PROTON GRADIENT REGULATION 5) originating from Pinus taeda than that in the wild type.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2020
2013 review
Ironing out the issues: Integrated approaches to understanding iron homeostasis in plants
[Review of ]. PLANT SCIENCE, 210, 250–259.
Contributors: R. Samira n, A. Stallmann n, L. Massenburg * & n
author keywords: Fe homeostasis; Fe translocation; Systems biology; Elemental analysis; Predictive model
MeSH headings : Biological Transport; Gene Expression Regulation, Plant; Genomics; Homeostasis; Iron / metabolism; Iron Deficiencies; Plants / genetics; Plants / metabolism; Signal Transduction; Systems Biology
TL;DR:
A broad perspective of how Fe localization data might one day be integrated with large-scale data to create models for Fe homeostasis is presented, as well as some of the recent advances in understanding mechanisms that control Fe translocation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science; OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: August 6, 2018
2011 journal article
Many needles in a haystack: cell-type specific abiotic stress responses
Current Opinion in Plant Biology, 14(3), 325–331.
MeSH headings : Cell Nucleus / genetics; Flow Cytometry / methods; Gene Expression Profiling; Gene Expression Regulation, Plant / genetics; Genomics; Iron / metabolism; Lasers; Metabolome; Microdissection / methods; Organ Specificity; Plant Cells / classification; Plant Cells / physiology; Plant Epidermis / cytology; Plant Epidermis / metabolism; Plant Roots / cytology; Plants / anatomy & histology; Plants / genetics; Plants / metabolism; Polyribosomes / genetics; Polyribosomes / immunology; RNA, Messenger / immunology; RNA, Messenger / isolation & purification; Stress, Physiological / genetics
TL;DR:
Continuous technological advances in profiling the proteomes, metabolomes, and other biological components of specific cells will continue to broaden the understanding of plant stress responses.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: February 11, 2020
2010 journal article
The bHLH Transcription Factor POPEYE Regulates Response to Iron Deficiency in Arabidopsis Roots
The Plant Cell, 22(7), 2219–2236.
Contributors: * , H. Tsukagoshi *, W. Busch *, B. Lahner*, D. Salt * & P. Benfey *
MeSH headings : Arabidopsis / metabolism; Basic Helix-Loop-Helix Transcription Factors / physiology; Gene Expression Profiling; Homeostasis; Iron / metabolism; Iron Deficiencies; Plant Roots / metabolism; Promoter Regions, Genetic; Transcription, Genetic
TL;DR:
Functional analysis of PYE suggests that it positively regulates growth and development under iron-deficient conditions, and Chromatin immunoprecipitation-on-chip analysis and transcriptional profiling reveal that PYE helps maintain iron homeostasis by regulating the expression of known ironHomeostasis genes and other genes involved in transcription, development, and stress response.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
13. Climate Action
(OpenAlex)
Source: ORCID
Added: February 11, 2020
2009 journal article
Development rooted in interwoven networks
Developmental Biology, 331(2), 386.
TL;DR:
This work has identified several genes that, when knocked down by RNAi, cause various defects in germ cell development, including: impaired testes development; loss of spermatogonial stem cells; meiotic failure; and defects in sperm elongation.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: March 5, 2020
2008 journal article
Cell Identity Mediates the Response of Arabidopsis Roots to Abiotic Stress
Science, 320(5878), 942–945.
Contributors: J. Dinneny *, * , J. Wang*, J. Jung*, D. Mace*, S. Pointer*, C. Barron *, S. Brady *, J. Schiefelbein *, P. Benfey *
MeSH headings : Abscisic Acid / metabolism; Algorithms; Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / physiology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Culture Media; Gene Expression Profiling; Gene Expression Regulation, Plant; Genes, Plant; Iron / metabolism; Mutation; Plant Epidermis / cytology; Plant Epidermis / genetics; Plant Epidermis / physiology; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Plant Roots / physiology; Promoter Regions, Genetic; Response Elements; Salinity; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
The transcriptional response to high salinity of different cell layers and developmental stages of the Arabidopsis root is characterized and it is found that transcriptional responses are highly constrained by developmental parameters.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2020
2008 journal article
Conserved role of PROTON GRADIENT REGULATION 5 in the regulation of PSI cyclic electron transport
Planta, 228(6), 907–918.
Contributors: * , Y. Okegawa *, T. Shikanai *, G. Schmidt & S. Covert
author keywords: Arabidopsis; Cyclic electron transport; Nonphotochemical quenching; Photosynthesis; PGR5; Stress tolerance
MeSH headings : Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis / physiology; Arabidopsis Proteins / analysis; Arabidopsis Proteins / physiology; Electron Transport; Glucuronidase / analysis; Light; Photosynthetic Reaction Center Complex Proteins / analysis; Photosynthetic Reaction Center Complex Proteins / physiology; Photosystem I Protein Complex / physiology; Pinus taeda / metabolism; Pinus taeda / physiology
TL;DR:
PGR5 has a developmentally-regulated, conserved role in mediating CET, and is cloned from a species which apparently lacks NDH, loblolly pine, and overexpressed it in Arabidopsis to investigate the conserved function of PGR5.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: February 11, 2020
2008 journal article
Systems Approaches to Identifying Gene Regulatory Networks in Plants
Annual Review of Cell and Developmental Biology, 24, 81–103.
Contributors: * , S. Brady * & P. Benfey *
author keywords: systems biology; Arabidopsis; transcription factors; emergent properties; modeling; genomics
MeSH headings : Biological Clocks / physiology; Circadian Rhythm / physiology; Databases, Genetic; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Indoleacetic Acids / metabolism; Models, Genetic; Plant Development; Plants / anatomy & histology; Plants / metabolism; Systems Biology; Transcription, Genetic
TL;DR:
Methods that researchers are using to obtain large-scale data sets and examples of gene regulatory networks modeled with these data are highlighted, and emergent properties revealed by the use of these network models are discussed.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2020
2007 journal article
A Balanced PGR5 Level is Required for Chloroplast Development and Optimum Operation of Cyclic Electron Transport Around Photosystem I
Plant and Cell Physiology, 48(10), 1462–1471.
Contributors: Y. Okegawa *, * , M. Iwano *, S. Takayama *, Y. Kobayashi*, S. Covert*, T. Shikanai *
author keywords: antimycin A; Arabidopsis; ferredoxin; NPQ; PGR5; PSI; cyclic electron transport
MeSH headings : Antimycin A / pharmacology; Arabidopsis / drug effects; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Chloroplasts / metabolism; Cotyledon / metabolism; Electron Transport / physiology; Gene Expression Regulation, Plant; Light; Oxidation-Reduction; Photosynthetic Reaction Center Complex Proteins / genetics; Photosynthetic Reaction Center Complex Proteins / metabolism; Photosystem I Protein Complex / metabolism; Time Factors
TL;DR:
It is proposed that a balanced PGR5 level is required for efficient regulation of the rate of antimycin A-sensitive PSI cyclic electron transport, although the rate is probably also regulated by other factors during steady-state photosynthesis.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2020
2006 journal article
Transcription factors and hormones: new insights into plant cell differentiation
Current Opinion in Cell Biology, 18(6), 710–714.
Contributors: * & P. Benfey *
MeSH headings : Cell Differentiation / genetics; Gene Expression Regulation, Developmental / genetics; Gene Expression Regulation, Plant / genetics; Hormones / genetics; Hormones / metabolism; Meristem / cytology; Meristem / embryology; Meristem / metabolism; Plant Leaves / cytology; Plant Leaves / embryology; Plant Leaves / metabolism; Plant Shoots / cytology; Plant Shoots / embryology; Plant Shoots / metabolism; Seeds / cytology; Seeds / genetics; Seeds / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
Several recent studies provide new insight into how transcription factors and phytohormones interact within meristems to control cell proliferation and differentiation.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: February 11, 2020
2006 journal article
Unraveling the Dynamic Transcriptome
The Plant Cell, 18(9), 2101–2111.
Contributors: S. Brady *, * & P. Benfey *
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis / metabolism; Cluster Analysis; Gene Expression Profiling / methods; Gene Expression Regulation, Plant; Genomics; Oligonucleotide Array Sequence Analysis; Plant Development; Plants / genetics; Plants / metabolism; RNA, Messenger / metabolism
TL;DR:
The advent of large-scale transcriptional profiling techniques signalled a new age in biology, and the field of transcriptomics allows the examination of whole transcriptome changes across a variety of biological conditions.
(via Semantic Scholar)
Source: ORCID
Added: February 11, 2020
1998 journal article
Intragenic Recombination and Diversifying Selection Contribute to the Evolution of Downy Mildew Resistance at the RPP8 Locus of Arabidopsis
The Plant Cell, 10(11), 1861–1874.
Contributors: J. McDowell *, M. Dhandaydham*, * , M. Aarts *, S. Goff, E. Holub, J. Dangl *
MeSH headings : Alleles; Amino Acid Sequence; Arabidopsis / genetics; Arabidopsis / microbiology; Base Sequence; Chromosome Mapping; DNA, Plant / genetics; Evolution, Molecular; Genes, Plant; Genetic Complementation Test; Molecular Sequence Data; Mutation; Oomycetes / pathogenicity; Phenotype; Plant Diseases / genetics; Plant Diseases / microbiology; Plant Proteins / genetics; Plants, Genetically Modified; Recombination, Genetic; Selection, Genetic; Sequence Homology, Amino Acid
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: February 11, 2020
Employment
Updated: August 7th, 2020 23:03
North Carolina State University Raleigh, NC, US
Associate Professor
Plant and Microbial Biology
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