Works (71)
Updated: April 3rd, 2024 19:04
2024 article
Cell-material interactions in 3D bioprinted plant cells
Madison, I., Tahir, M., Broeck, L. V., Phan, L., Horn, T., & Sozzani, R. (2024, February 1).
TL;DR:
A study in which 3D bioprinting parameters, such as needle gauge, extrusion pressure, and scaffold type, were all tested in 3D bioprinted Tobacco BY-2 cells revealed an optimal range of extrusion pressures and needle gauges that resulted in an optimum cell viability.
(via Semantic Scholar)
doi.org (repository)
Source: ORCID
Added: February 2, 2024
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.
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: February 1, 2024
2023 journal article
Functional annotation of proteins for signaling network inference in non-model species
Nature Communications, 14(1).
TL;DR:
A multi-layer neural network that determines protein functionality directly from the protein sequence is developed that shows generalization and scalability and extends to Oryza sativa, Zea mays, Sorghum bicolor, and Triticum aestivum.
(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, NC State University Libraries, ORCID, Crossref
Added: September 5, 2023
2023 article
Obituary Philip N. Benfey (1953-2023)
Bennett, M. J., Brady, S. M., Dinneny, J. R., Helariutta, Y., & Sozzani, R. (2023, November 20). DEVELOPMENTAL CELL, Vol. 58, pp. 2413–2415.
Sources: Web Of Science, NC State University Libraries
Added: January 2, 2024
2023 article
Phosphate starvation: response mechanisms and solutions
Madison, I., Gillan, L., Peace, J., Gabrieli, F., Broeck, L., Jones, J. L., & Sozzani, R. (2023, August 23). (D. Ort, Ed.). JOURNAL OF EXPERIMENTAL BOTANY, Vol. 8.
Ed(s): D. Ort
author keywords: Nutrient uptake; nutrient sensing; phosphorus; Pi
TL;DR:
This review describes regulatory mechanisms used by specific tissues in the root apical meristem to sense and uptake phosphate from the rhizosphere and overviews the major mechanism of plant systemic phosphate starvation responses.
(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: September 18, 2023
2023 conference paper
Prediction and functional characterization of transcriptional activation domains
Mahatma, S., Broeck, L. V., Morffy, N., Staller, M. V., Strader, L. C., & Sozzani, R. (2023, March 22).
TL;DR:
This work used an unsupervised learning approach to classify the ADs into 10 subclasses, which can be explored for AA specificity and AD functionality, and shed light on the non-linear properties of ADs.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2024
2023 article
Quantitative Modeling of the Short-Term Response to Nitrogen Availability that Coordinates Early Events in Lateral Root Initiation
Gaudinier, A., Broeck, L. V., Moreno-Risueño, M., Rodriguez-Medina, J., Sozzani, R., & Brady, S. M. (2023, December 6).
TL;DR:
Linking the N time course transcriptomics, LR mutant phenotypes, and cell-type specific single cell profiling, these approaches provide multiple lines of evidence to find and test the roles of TFs that are involved in early root patterning responses to N conditions.
(via Semantic Scholar)
Source: ORCID
Added: January 25, 2024
2023 article
The ALOG family members OsG1L1 and OsG1L2 regulate inflorescence branching in rice
Beretta, V. M., Franchini, E., Din, I. U., Lacchini, E., Broeck, L., Sozzani, R., … Kater, M. M. (2023, April 21). PLANT JOURNAL, Vol. 4.
author keywords: Oryza sativa; transcription factor; inflorescence architecture; meristem identity; transcriptome analysis; CRISPR mutants; gene regulatory network; ALOG
TL;DR:
The spatio-temporal expression profiling and phenotypical analysis of CRISPR loss-of-function mutants of OsHOX14 suggests that the proposed GRN indeed serves as a valuable resource for the identification of new players involved in rice inflorescence development.
(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: May 9, 2023
2022 journal article
Field-grown soybean shows genotypic variation in physiological and seed composition responses to heat stress during seed development
Environmental and Experimental Botany, 195, 104768.
author keywords: Photosynthesis; V-cmax; Respiration; Yield; Seed composition
UN Sustainable Development Goal Categories
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: March 14, 2022
2022 journal article
Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation
PLANT CELL, 34(1), 535–556.
MeSH headings : Capsicum / genetics; Capsicum / physiology; Gene Expression Regulation, Plant / physiology; Gene Regulatory Networks; Homeodomain Proteins / genetics; Homeodomain Proteins / metabolism; Solanum lycopersicum / genetics; Solanum lycopersicum / physiology; Plant Proteins / genetics; Plant Proteins / metabolism
TL;DR:
A model system with Solanum lycopersicum ‘tomato’ and Capsicum annuum ‘pepper’ heterografting is developed, which expresses signs of anatomical junction failure within the first week of grafting, and SlWOX4 is the first gene to be functionally implicated in vegetable crop grafting.
(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: February 7, 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: Web Of Science, NC State University Libraries, ORCID
Added: August 13, 2022
2022 journal article
RNA-Seq and Gene Regulatory Network Analyses Uncover Candidate Genes in the Early Defense to Two Hemibiotrophic Colletorichum spp. in Strawberry
FRONTIERS IN GENETICS, 12.
author keywords: Colletotrichum acutatum; Colletotrichum gloeosporioides; Fragaria x ananassa; rate-reducing resistance; gene regulatory network
TL;DR:
Comparison transcriptome analyses and Gene regulatory network inference analysis revealed candidate transcription factors (TFs) such as GATA5 and MYB-10, and their downstream targets were upregulated in resistant interactions, which can provide valuable insights into transcriptional changes during resistant and susceptible interactions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
3. Good Health and Well-being
(OpenAlex)
13. Climate Action
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: April 25, 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
Cell-by-cell dissection of phloem development links a maturation gradient to cell specialization
SCIENCE, 374(6575), 1577-+.
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Differentiation; GTP-Binding Proteins / genetics; GTP-Binding Proteins / metabolism; Meristem / cytology; Phloem / cytology; Phloem / genetics; Phloem / growth & development; Phloem / metabolism; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Plant Roots / metabolism; RNA-Seq; Signal Transduction; Single-Cell Analysis; Transcription Factors / genetics; Transcription Factors / metabolism; Transcriptome
TL;DR:
The ability to connect cellular development such as lineage bifurcation and enucleation to molecular states using scRNA-seq allowed us to uncover genetic mechanisms that coordinate cellular maturation, and revealed the importance of RHO of PLANTS GTPase signaling during early phloem development when the protophloem cell lineage b ifurcates to generate metaphloem sieve element and procambium.
(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
Added: February 7, 2022
2021 review
Divide and Conquer: The Initiation and Proliferation of Meristems
[Review of ]. CRITICAL REVIEWS IN PLANT SCIENCES, 40(2), 147–156.
Contributors: L. Broeck n
author keywords: Founder cells; meristem initiation; meristem maintenance; procambium; root apical meristem; shoot apical meristem
TL;DR:
This review focuses on the various plant meristems, how cells within theseMeristems maintain their identity, and particularly the molecular players that regulate stem cell maintenance, including pericycle and rachis founder cells.
(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: May 10, 2021
2021 journal article
Down-regulation of Fra a 1.02 in strawberry fruits causes transcriptomic and metabolic changes compatible with an altered defense response
HORTICULTURE RESEARCH, 8(1).
TL;DR:
Gene ontology (GO) analysis of the genes differentially expressed indicated that oxidation/reduction was the most represented biological process and redox state was not apparently altered since no changes were found in ascorbic acid and glutathione reduced/oxidized ratio, but GSH content was reduced in the silenced fruits.
(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
Added: April 19, 2021
2021 article
Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation
Thomas, H., Broeck, L. V., Spurney, R., Sozzani, R., & Frank, M. (2021, February 27). (Vol. 2). Vol. 2.
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: October 21, 2022
2021 journal article
Integrated omics networks reveal the temporal signaling events of brassinosteroid response in Arabidopsis
NATURE COMMUNICATIONS, 12(1).
MeSH headings : Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Brassinosteroids / metabolism; Cell Division; DNA-Binding Proteins / genetics; DNA-Binding Proteins / metabolism; Gene Expression Regulation, Plant; Nuclear Proteins / metabolism; Plant Growth Regulators / metabolism; Protein Kinases / genetics; Protein Kinases / metabolism; Proteomics; Seedlings / metabolism; Signal Transduction; Steroids, Heterocyclic; Transcription Factors / metabolism
TL;DR:
By integrating multiple omics datasets and inferring networks, the authors profile BR signaling in Arabidopsis and characterize BRONTOSAURUS, a BR-regulated transcription factor that impacts cell division in roots.
(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
Added: October 26, 2021
2021 journal article
Precise transcriptional control of cellular quiescence by BRAVO/WOX5 complex in Arabidopsis roots
MOLECULAR SYSTEMS BIOLOGY, 17(6).
author keywords: BRAVO; mathematical modelling; quiescent centre; root growth; WOX5
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Division; Gene Expression Regulation, Plant; Homeodomain Proteins / genetics; Meristem / genetics; Meristem / metabolism; Nitriles; Plant Roots / genetics; Plant Roots / metabolism
TL;DR:
It is found that BRAVO and WOX5 regulate each other besides forming a transcription factor complex in the QC necessary to preserve overall root growth and architecture, unveiling the importance of transcriptional regulatory circuits at the quiescent and stem cells to the control of organ initiation and growth of plant tissues.
(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
Added: July 12, 2021
2021 article
Spatiotemporal Gene Expression Profiling and Network Inference: A Roadmap for Analysis, Visualization, and Key Gene Identification
MODELING TRANSCRIPTIONAL REGULATION, Vol. 2328, pp. 47–65.
author keywords: Gene regulatory network inference; RNA sequencing; Bioinformatics; Network visualization
MeSH headings : Algorithms; Amino Acid Motifs / genetics; Cluster Analysis; Computational Biology / methods; Gene Expression Profiling / methods; Gene Expression Regulation / genetics; Gene Regulatory Networks / genetics; Multigene Family; RNA-Seq / methods; Software; Spatio-Temporal Analysis; Workflow
TL;DR:
This chapter aims to present a workflow feasible and accessible for plant biologists without a bioinformatics or computer science background and chooses TuxNet, a user-friendly graphical user interface that integrates RNA sequencing data analysis with GRN inference, for the purpose of providing a detailed tutorial.
(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
Added: October 4, 2021
2020 journal article
BAM1/2 receptor kinase signaling drives CLE peptide-mediated formative cell divisions in Arabidopsis roots
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 117(51), 32750–32756.
author keywords: Arabidopsis; receptor kinase; cell cycle; SHORT-ROOT; CLE peptide
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Division; Gene Expression Regulation, Plant; Green Fluorescent Proteins / genetics; Green Fluorescent Proteins / metabolism; Plant Cells / metabolism; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / metabolism; Plants, Genetically Modified; Protein Serine-Threonine Kinases / genetics; Protein Serine-Threonine Kinases / metabolism; Signal Transduction; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
It is shown that key cell divisions that generate the plant root are controlled by cell-to-cell signaling peptides which act through plant-specific receptor kinases to control expression of a specific cyclinD cell cycle regulatory gene.
(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
Added: January 19, 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, T. Long n , 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: Crossref, NC State University Libraries, Web Of Science, ORCID
Added: June 17, 2020
2020 article
Editorial overview: Directionality and precision - how signaling and gene regulation drive plant development and growth
Van Norman, J. M., Strader, L. C., & Sozzani, R. (2020, October). CURRENT OPINION IN PLANT BIOLOGY, Vol. 57, pp. A1–A3.
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: January 19, 2021
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
Gene Regulatory Network Inference: Connecting Plant Biology and Mathematical Modeling
Frontiers in Genetics, 11.
author keywords: gene regulatory network; network properties; network inference; machine learning; experimental methodologies
TL;DR:
This review provides examples of experimental methodologies commonly used to identify regulatory interactions and generate GRNs, and describes network inference techniques that leverage gene expression data to predict regulatory interactions.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Crossref, NC State University Libraries, Web Of Science, ORCID
Added: July 13, 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 , n & T. Long 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: Crossref, NC State University Libraries, Web Of Science, ORCID
Added: June 17, 2020
2020 journal article
Novel Imaging Modalities Shedding Light on Plant Biology: Start Small and Grow Big
Annual Review of Plant Biology, 71(1), 789–816.
author keywords: Forster resonance energy transfer; scanning fluorescent correlation spectroscopy; microfluid devices; light sheet microscopy; imaging of macroscopic traits; multiscale imaging techniques
MeSH headings : Biology; Plant Development; Plants
TL;DR:
New imaging modalities are presented and how they have enabled a better understanding of plant growth from the microscopic to the macroscopic scale are reviewed to enable unprecedented systems-level computational modeling.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Crossref, NC State University Libraries, Web Of Science, ORCID
Added: September 14, 2020
2020 journal article
Protein complex stoichiometry and expression dynamics of transcription factors modulate stem cell division
Proceedings of the National Academy of Sciences, 117(26), 15332–15342.
author keywords: protein complex stoichiometry; intercellular protein movement; mathematical modeling; expression dynamics; transcription factor
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / metabolism; Biomarkers; Cell Differentiation; Gene Expression Regulation, Plant / physiology; Models, Biological; Mutation; Stem Cells / physiology; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
It is suggested that SHR-SCR protein complex stoichiometry and regulation of SHR transcription modulate the division timing of two different specialized cell types in the root stem cell niche.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Crossref, NC State University Libraries, ORCID
Added: September 14, 2020
2020 journal article
tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks
PLANT JOURNAL, 101(3), 716–730.
author keywords: Arabidopsis thaliana; gene regulatory network inference; graphical user interface; RNA sequencing processing; stem cell maintenance; technical advance
MeSH headings : Algorithms; Arabidopsis / genetics; Bayes Theorem; Computational Biology; Gene Expression Regulation, Plant; Gene Regulatory Networks / genetics; Genome, Plant / genetics; Sequence Analysis, RNA; Transcriptome
UN Sustainable Development Goal Categories
2. Zero Hunger
(Web of Science)
13. Climate Action
(Web of Science)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: December 9, 2019
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, n , C. Williams n, T. Long 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: Crossref, NC State University Libraries, ORCID
Added: December 4, 2019
2019 journal article
Characterizing the involvement of FaMADS9 in the regulation of strawberry fruit receptacle development
Plant Biotechnology Journal, 18(4), 929–943.
MeSH headings : Bayes Theorem; Fragaria / genetics; Fragaria / growth & development; Fruit / growth & development; Gene Expression Regulation, Plant; Gene Silencing; MADS Domain Proteins / genetics; Metabolome; Plant Proteins / genetics; Plants, Genetically Modified
TL;DR:
The inference of a gene regulatory network, based on a dynamic Bayesian approach, among the genes differentially expressed in the transgenic receptacles at the white and red stages, identified the genes KAN1, DIV, ZFN2 and GTE7 as putative targets of FaMADS9.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, Crossref
Added: November 11, 2019
2019 journal article
Computational prediction of gene regulatory networks in plant growth and development
Current Opinion in Plant Biology, 47, 96–105.
MeSH headings : Computational Biology / methods; Gene Regulatory Networks; Models, Genetic; Plant Development / genetics; Reproducibility of Results
TL;DR:
Computational frameworks integrating large-scale heterogeneous datasets are needed for a more accurate and comprehensive inference of gene regulatory networks, or GRNs, in the context of plant growth and development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
16. Peace, Justice and Strong Institutions
(OpenAlex)
Sources: Web Of Science, NC State University Libraries, ORCID, Crossref
Added: February 8, 2019
2019 journal article
DOF2.1 Controls Cytokinin-Dependent Vascular Cell Proliferation Downstream of TMO5/LHW
CURRENT BIOLOGY, 29(3), 520-+.
MeSH headings : Arabidopsis / genetics; Arabidopsis / physiology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Basic Helix-Loop-Helix Transcription Factors / genetics; Basic Helix-Loop-Helix Transcription Factors / metabolism; Cambium / physiology; Cell Proliferation / genetics; Cytokinins / metabolism; Plant Roots / genetics; Plant Roots / growth & development; Trans-Activators / genetics; Trans-Activators / metabolism; Transcription Factors, General / genetics; Transcription Factors, General / metabolism; Xylem / physiology
TL;DR:
The results suggest that DOF2.1 and its closest homologs control vascular cell proliferation, thus leading to radial expansion of the root.
(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
Added: February 18, 2019
2019 journal article
Mobile PEAR transcription factors integrate hormone and miRNA cues to prime cambial growth
Nature, 565(7740), 490–494.
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis Proteins / biosynthesis; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cambium / cytology; Cambium / genetics; Cambium / growth & development; Cambium / metabolism; Cell Division / genetics; Cues; Cytokinins / metabolism; Gene Expression Regulation, Plant; Indoleacetic Acids / metabolism; MicroRNAs / genetics; MicroRNAs / metabolism; Phloem / cytology; Phloem / metabolism; Plant Growth Regulators / metabolism; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Plant Roots / metabolism; Signal Transduction; Transcription Factors / biosynthesis; Transcription Factors / genetics; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
During root procambial development there exists a network in which a module that links PEAR and HD-ZIP III transcription factors integrates spatial information of the hormonal domains and miRNA gradients to provide adjacent zones of dividing and more-quiescent cells, which forms a foundation for further radial growth.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
2019 journal article
Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana
MOLECULAR CELL, 76(1), 177-+.
MeSH headings : Arabidopsis / drug effects; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Nucleus / metabolism; Cytoplasm / metabolism; Gene Expression Regulation, Plant; Indoleacetic Acids / pharmacology; Intrinsically Disordered Proteins / chemistry; Intrinsically Disordered Proteins / genetics; Intrinsically Disordered Proteins / metabolism; Plant Growth Regulators / pharmacology; Protein Binding; Protein Folding; Protein Interaction Domains and Motifs; Structure-Activity Relationship; Transcription Factors / chemistry; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
The data suggest a model in which ARF nucleo-cytoplasmic partitioning regulates auxin responsiveness, providing a mechanism for cellular competence for auxin signaling.
(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
Added: October 21, 2019
2019 journal article
Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks
NATURE COMMUNICATIONS, 10.
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Asymmetric Cell Division / genetics; Asymmetric Cell Division / physiology; Cell Differentiation; Cell Division; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Stem Cells / cytology; Stem Cells / metabolism; Transcription Factors / metabolism; Transcriptome; Ubiquitination / genetics; Ubiquitins / genetics
TL;DR:
In the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks and orchestrates the coordinated division of different stem cell types.
(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
Added: December 30, 2019
2019 journal article
The Lateral Root Cap Acts as an Auxin Sink that Controls Meristem Size
CURRENT BIOLOGY, 29(7), 1199-+.
MeSH headings : Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cytokinins / genetics; Cytokinins / metabolism; Indoleacetic Acids / metabolism; Meristem / growth & development; Meristem / metabolism; Plant Roots / growth & development; Plant Roots / metabolism
TL;DR:
Overall, the results indicate that the lateral root cap serves as an auxin sink that, under the control of cytokinin, regulates meristem size and root growth.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: April 15, 2019
2018 journal article
Exposure to heavy metal stress triggers changes in plasmodesmatal permeability via deposition and breakdown of callose
JOURNAL OF EXPERIMENTAL BOTANY, 69(15), 3715–3728.
author keywords: Callose; copper; iron; nutrient stress; plasmodesmata; root development
MeSH headings : Arabidopsis / drug effects; Arabidopsis / physiology; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Glucan 1,3-beta-Glucosidase / genetics; Glucan 1,3-beta-Glucosidase / metabolism; Glucans / metabolism; Glucosyltransferases / genetics; Glucosyltransferases / metabolism; Metals, Heavy / toxicity; Permeability / drug effects; Plant Roots / drug effects; Plant Roots / physiology; Plasmodesmata / drug effects; Plasmodesmata / metabolism
TL;DR:
It is shown that significant changes in plasmodesmatal permeability underlie root responses to nutrient stress and this results in new insights into how plants modify their growth to adapt to changes in their environment.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2018 journal article
GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis
DEVELOPMENT, 145(3).
author keywords: Root hair; Cell growth; Trihelix transcription factor; Gene regulatory network
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Basic Helix-Loop-Helix Transcription Factors / genetics; Basic Helix-Loop-Helix Transcription Factors / metabolism; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Indoleacetic Acids / metabolism; Models, Biological; Mutation; Plant Growth Regulators / metabolism; Plant Roots / growth & development; Plant Roots / metabolism; Plants, Genetically Modified; Promoter Regions, Genetic; Signal Transduction; Transcription Factors / genetics; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
This study uncovers a core regulatory module that fine-tunes the extent of root hair growth by the orchestrated actions of opposing transcription factors.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2018 chapter
Identifying Differentially Expressed Genes Using Fluorescence-Activated Cell Sorting (FACS) and RNA Sequencing from Low Input Samples
In L. von Stechow & A. Santos Delgado (Eds.), Computational Cell Biology (pp. 139–151).
Ed(s): L. Stechow & A. Santos Delgado
author keywords: Protoplasting; Fluorescence activated cell sorting; RNA sequencing; Differential expression; Low input samples
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / metabolism; Cytoplasm / metabolism; Flow Cytometry / methods; Gene Expression Regulation, Plant / physiology; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / metabolism; RNA, Plant / biosynthesis; RNA, Plant / genetics; Sequence Analysis, RNA / methods
TL;DR:
FACS is described to perform fluorescence-activated cell sorting on Arabidopsis root protoplasts to isolate specific cell types in the root and how to extract and process RNA from a very low number of cells for RNA sequencing (RNA seq).
(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
Added: February 8, 2019
2018 conference paper
Tracking Gene Expression via Light Sheet Microscopy and Computer Vision in Living Organisms
2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), 818–821.
Event: 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)
MeSH headings : Arabidopsis; Cell Nucleus; Microscopy; Proteins
TL;DR:
The solution indicates, segments, and tracks gene expression using a fluorescent imaging channel of a light sheet microscope while determining gene expression location within an organism from a Brightfield (non-fluorescent) imaging channel.
(via Semantic Scholar)
Sources: NC State University Libraries, NC State University Libraries
Added: February 8, 2019
2017 journal article
Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(36), E7641–E7649.
author keywords: plant hormones; cell differentiation; root meristem; computational modeling
MeSH headings : Arabidopsis / metabolism; Arabidopsis / physiology; Arabidopsis Proteins / metabolism; Biological Transport / physiology; Cell Differentiation / physiology; Cell Division / physiology; Cytokinins / metabolism; Gene Expression Regulation, Plant / physiology; Indoleacetic Acids / metabolism; Meristem / metabolism; Meristem / physiology; Plant Growth Regulators / metabolism; Plant Roots / metabolism; Plant Roots / physiology; Signal Transduction / physiology
TL;DR:
Computational modeling and molecular genetics show that boundary formation is dependent on cytokinin’s control on auxin polar transport and degradation, and the regulation of both processes shapes the auxin profile in a well-defined auxin minimum.
(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
Added: August 6, 2018
2017 journal article
Dose-Duration Reciprocity for G protein activation: Modulation of kinase to substrate ratio alters cell signaling
PLOS ONE, 12(12).
MeSH headings : Arabidopsis / enzymology; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; GTP-Binding Proteins / metabolism; Genotype; Phosphorylation; Phosphotransferases / metabolism; Signal Transduction; Substrate Specificity
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2017 journal article
Framework for gradual progression of cell ontogeny in the Arabidopsis root meristem
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(42), E8922–E8929.
author keywords: plant development; root meristem; Arabidopsis; transcriptional regulation
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / genetics; Flow Cytometry / methods; Gene Expression Regulation, Plant; Green Fluorescent Proteins / genetics; Meristem / cytology; Meristem / genetics; Plant Cells; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Plants, Genetically Modified
TL;DR:
It is proposed that cells in the Arabidopsis root meristem gradually transition from stem cell activity toward differentiation, by opposing gradients.
(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
Added: August 6, 2018
2017 journal article
Genetic Architecture and Molecular Networks Underlying Leaf Thickness in Desert-Adapted Tomato Solanum pennellii
PLANT PHYSIOLOGY, 175(1), 376–391.
MeSH headings : Adaptation, Physiological / genetics; Bayes Theorem; Desert Climate; Gene Regulatory Networks; Organ Specificity; Phenotype; Plant Leaves / anatomy & histology; Plant Leaves / genetics; Plant Leaves / growth & development; Plant Leaves / physiology; Quantitative Trait Loci / genetics; Sequence Analysis, RNA; Solanum / anatomy & histology; Solanum / genetics; Solanum / growth & development; Solanum / physiology
TL;DR:
A custom-built confocal profilometer was used to directly measure leaf thickness in a set of introgression lines (ILs) derived from the desert tomato Solanum pennellii and identified quantitative trait loci to establish a framework of genetic, anatomical, and molecular mechanisms that pattern leaf thicknessIn desert-adapted tomato.
(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
Added: August 6, 2018
2017 chapter
Inferring Gene Regulatory Networks in the Arabidopsis Root Using a Dynamic Bayesian Network Approach
In K. Kaufmann & B. Mueller-Roeber (Eds.), Plant Gene Regulatory Networks (pp. 331–348).
Ed(s): K. Kaufmann & B. Mueller-Roeber
author keywords: Gene regulatory network; Dynamic Bayesian network; Ordinary differential equation; Arabidopsis root
MeSH headings : Algorithms; Arabidopsis / genetics; Bayes Theorem; Computational Biology / methods; Databases, Genetic; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene Regulatory Networks; Plant Roots / genetics; Reproducibility of Results
TL;DR:
The basic steps to implement a simple but computationally efficient algorithm to infer GRNs based on dynamic Bayesian networks (DBNs) are shown, and how to approximate DBN-based GRN models with continuous models is explained.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
2017 chapter
Measuring Protein Movement, Oligomerization State, and Protein–Protein Interaction in Arabidopsis Roots Using Scanning Fluorescence Correlation Spectroscopy (Scanning FCS)
In W. Busch (Ed.), Plant Genomics (pp. 251–266).
Ed(s): W. Busch
author keywords: Scanning fluorescence correlation spectroscopy; Diffusion coefficient; Protein movement; Oligomerization state; Protein stoichiometry
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Green Fluorescent Proteins / genetics; Green Fluorescent Proteins / metabolism; Plant Roots / metabolism; Spectrometry, Fluorescence / methods
TL;DR:
The scanning FCS techniques of raster image correlation spectroscopy and pair correlation function (pCF) and number and brightness (N&B) and cross-correlation analyses can be used to determine oligomerization state and binding ratios of protein complexes.
(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
Added: February 8, 2019
2017 journal article
Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(36), E7632–E7640.
author keywords: root stem cell; root development; cell-type expression profile; gene regulatory network; modeling
MeSH headings : Algorithms; Arabidopsis / genetics; Bayes Theorem; Cluster Analysis; Computational Biology / methods; Gene Expression Profiling / methods; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Plant Roots / genetics; Stem Cells / metabolism; Transcription Factors / genetics; Transcriptome / genetics
TL;DR:
A computational pipeline that uses gene expression datasets for inferring relationships among genes and predicting their importance and a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference that identified PERIANTHIA as an important molecular regulator of quiescent center function.
(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
Added: August 6, 2018
2016 journal article
Gene and networks regulating the root stem cell niche of Arabidopsis
Curr Opin Plant Biol, 29, 38–43.
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / growth & development; Asymmetric Cell Division; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Stem Cells / cytology
TL;DR:
This review will discuss several studies that characterized many of the genetic programs and molecular mechanisms regulating stem cell ACD and their identity in the Arabidopsis root and highlight how the growing use of mathematical modeling provides a comprehensive and quantitative perspective on the design rules governing stemcell ACDs.
(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
Added: August 6, 2018
2016 journal article
Light sheet microscopy reveals more gradual light attenuation in light-green versus dark-green soybean leaves
JOURNAL OF EXPERIMENTAL BOTANY, 67(15), 4697–4709.
author keywords: Chlorophyll; Glycine max; leaf light environment; light sheet microscopy; light use efficiency; photosynthesis; photosynthetic efficiency; soybean
MeSH headings : Chlorophyll / physiology; Chlorophyll / radiation effects; Chloroplasts / physiology; Chloroplasts / radiation effects; Color; Light; Microscopy / methods; Plant Leaves / physiology; Plant Leaves / radiation effects; Soybeans / physiology; Soybeans / radiation effects
TL;DR:
Highlight Light sheet microscopy, a novel approach to quantifying light profiles, showed more gradual light attenuation in light- green soybean leaves compared to dark-green soybean.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2016 journal article
Multi-sample Arabidopsis Growth and Imaging Chamber (MAGIC) for long term imaging in the ZEISS Lightsheet Z.1
Developmental Biology, 419(1), 19–25.
author keywords: Arabidopsis root; Light sheet; 3D printing; Time-lapse imaging
MeSH headings : Arabidopsis / ultrastructure; Arabidopsis Proteins / analysis; Cell Division; Computer-Aided Design; Cyclin B / analysis; Equipment Design; Green Fluorescent Proteins / analysis; Image Processing, Computer-Assisted / methods; Microscopy, Fluorescence / instrumentation; Microscopy, Fluorescence / methods; Plant Roots / ultrastructure; Printing, Three-Dimensional; Recombinant Fusion Proteins / analysis; Time-Lapse Imaging / instrumentation; Time-Lapse Imaging / methods
TL;DR:
A Multi-sample Arabidopsis Growth and Imaging Chamber (MAGIC) is developed that provides near-physiological imaging conditions and allows high-throughput time-course imaging experiments in the ZEISS Lightsheet Z.1, and its imaging capabilities are illustrated by following cell divisions, as an indicator of plant growth and development, over prolonged time periods.
(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
Added: August 6, 2018
2016 journal article
Tracking transcription factor mobility and interaction in Arabidopsis roots with fluorescence correlation spectroscopy
Elife, 5.
Source: NC State University Libraries
Added: August 6, 2018
2015 journal article
Bird and Scarecrow proteins organize tissue formation in Arabidopsis roots
Science, 350(6259), 426–430.
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / metabolism; Cell Division / genetics; Cell Lineage / genetics; Gene Expression Regulation, Plant; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Transcription Factors / metabolism; Transcription, Genetic
TL;DR:
It is shown that the BIRDs and SCARECROW regulate lineage identity, positional signals, patterning, and formative divisions throughout Arabidopsis root growth, ensuring developmental plasticity.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
Sources: Web Of Science, NC State University Libraries
Added: August 6, 2018
2014 review
Advanced imaging techniques for the study of plant growth and development
[Review of ]. TRENDS IN PLANT SCIENCE, 19(5), 304–310.
author keywords: imaging techniques; plant growth and development; systems-level modeling.
MeSH headings : Image Processing, Computer-Assisted / methods; Models, Biological; Phenotype; Plant Development; Plants / genetics; Systems Biology; Time Factors
TL;DR:
Advances in parallelized and automated image acquisition enable the throughput to capture images from large populations of plants under specific growth conditions, and facilitate the integration of imaging data with genome-wide molecular data to enable systems-level modeling.
(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
Added: August 6, 2018
2014 review
Experimental data and computational modeling link auxin gradient and development in the Arabidopsis root
[Review of ]. Frontiers in Plant Science, 5.
Source: NC State University Libraries
Added: August 6, 2018
2014 article
Intercellular Protein Movement: Deciphering the Language of Development
ANNUAL REVIEW OF CELL AND DEVELOPMENTAL BIOLOGY, VOL 30, Vol. 30, pp. 207–233.
author keywords: Arabidopsis development; plasmodesmata; non-cell-autonomous proteins; cell-to-cell signaling
TL;DR:
This work reviews some of the transcriptional regulators that traffic between cells, as well as how changes in symplasmic continuity affect and are affected by development, and considers challenges in and new tools for studying protein movement.
(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
Added: August 6, 2018
2014 review
Omics and modelling approaches for understanding regulation of asymmetric cell divisions in arabidopsis and other angiosperm plants
[Review of ]. ANNALS OF BOTANY, 113(7), 1083–1105.
author keywords: Asymmetric cell division; embryo; root; stomata; lateral root; cortex endodermis initial; omics; Arabidopsis thaliana; Zea mays; maize
MeSH headings : Arabidopsis / embryology; Arabidopsis / genetics; Arabidopsis / growth & development; Asymmetric Cell Division; Genomics; Magnoliopsida / embryology; Magnoliopsida / genetics; Magnoliopsida / growth & development; Models, Genetic; Plant Roots / embryology; Plant Roots / genetics; Plant Roots / growth & development; Plant Shoots / embryology; Plant Shoots / genetics; Plant Shoots / growth & development
TL;DR:
This review describes how asymmetric cell divisions are regulated during development and in different cell types in both the root and the shoot of plants, and highlights ways in which omics and modelling approaches have been used to elucidate these regulatory mechanisms.
(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
Added: August 6, 2018
2014 review
Postembryonic control of root meristem growth and development
[Review of ]. CURRENT OPINION IN PLANT BIOLOGY, 17, 7–12.
MeSH headings : Biological Transport; Cell Differentiation / genetics; Cell Division / genetics; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Indoleacetic Acids / metabolism; Meristem / cytology; Meristem / genetics; Meristem / growth & development; Plant Roots / cytology; Plant Roots / genetics; Plant Roots / growth & development; Stem Cell Niche
TL;DR:
Recent advances in the understanding of postembryonic root stem cell maintenance and control of meristem size are reviewed.
(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
Added: August 6, 2018
2013 journal article
Spatial Coordination between Stem Cell Activity and Cell Differentiation in the Root Meristem
Developmental Cell, 26(4), 405–415.
MeSH headings : Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Differentiation / drug effects; Cytokinins / pharmacology; Gene Expression Regulation, Plant / drug effects; Green Fluorescent Proteins / metabolism; Indoleacetic Acids / metabolism; Meristem / cytology; Meristem / drug effects; Meristem / metabolism; Models, Biological; Stem Cell Niche / drug effects; Stem Cell Niche / genetics; Stem Cells / cytology; Stem Cells / drug effects; Stem Cells / metabolism
TL;DR:
It is shown that in Arabidopsis, the gene SCR presides over this spatial coordination of stem cell activity with differentiation of their progeny, ensuring coherent root growth.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
2012 journal article
A bistable circuit involving SCARECROW-RETINOBLASTOMA integrates cues to inform asymmetric stem cell division
Cell, 150(5), 1002–1015.
MeSH headings : Amino Acid Sequence; Arabidopsis / cytology; Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Asymmetric Cell Division; Cyclin D / metabolism; Cyclin-Dependent Kinases / metabolism; Indoleacetic Acids / metabolism; Mesophyll Cells / metabolism; Molecular Sequence Data; Phosphorylation; Plant Roots / cytology; Plant Roots / metabolism; Sequence Alignment
TL;DR:
This work investigates tissue-generating asymmetric divisions in a stem cell daughter within the Arabidopsis root and shows that ACDs are only switched on after integration of radial and longitudinal information, determined by SHR and auxin distribution, respectively.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
2012 journal article
Integrative systems biology: an attempt to describe a simple weed
Current Opinion in Plant Biology, 15(2), 162–167.
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Genome, Plant / genetics; Genomics / methods; Metabolomics / methods; Proteomics / methods; Systems Biology / methods
TL;DR:
This review proposes that 'triangulation' among transcriptomics, proteomics and metabolomics is a meaningful approach for beginning this integrative analysis and uncovering a systems level perspective of Arabidopsis biology.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
2011 journal article
Arabidopsis homologs of the petunia hairy meristem gene are required for maintenance of shoot and root indeterminacy
Plant Physiology, 155(2), 735–750.
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Gene Expression Regulation, Plant; Gene Knockout Techniques; Inflorescence / genetics; Inflorescence / growth & development; Mutation; Phenotype; Phylogeny; Plant Roots / genetics; Plant Roots / growth & development; Plant Shoots / genetics; Plant Shoots / growth & development; RNA, Plant / genetics
TL;DR:
Arabidopsis mutants triply homozygous for knockout alleles in three Arabidopsis HAM orthologs exhibit loss of indeterminacy in both the shoot and root, which is fundamental to the generation of plant architecture and a central component of the plant life strategy.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
2011 journal article
High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype
Genome Biology, 12(3), 219.
MeSH headings : Animals; Automation, Laboratory; Biotechnology; Caenorhabditis elegans / genetics; Caenorhabditis elegans / metabolism; Genetic Association Studies / methods; High-Throughput Screening Assays / methods; Mice; Phenotype; Plants / genetics; Plants / metabolism; RNA Interference
TL;DR:
High-throughput phenotyping approaches (phenomics) are being combined with genome-wide genetic screens to identify alterations in phenotype that result from gene inactivation in multicellular organisms.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
2010 journal article
Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth
Nature, 466(7302), 128–132.
MeSH headings : Arabidopsis / cytology; Arabidopsis / embryology; Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Body Patterning / genetics; Body Patterning / physiology; Cell Cycle / genetics; Cell Cycle / physiology; Cell Division / genetics; Cyclin D / genetics; Cyclin D / metabolism; Cyclin-Dependent Kinases / metabolism; Gene Expression Regulation, Plant; Genes, cdc / physiology; Organogenesis / genetics; Organogenesis / physiology; Plant Roots / cytology; Plant Roots / embryology; Plant Roots / genetics; Plant Roots / growth & development; Time Factors; Transcription Factors / genetics; Transcription Factors / metabolism
TL;DR:
This work shows, using cell-type-specific transcriptional effects of SHR and SCR combined with data from chromatin immunoprecipitation-based microarray experiments, that SHR regulates the spatiotemporal activation of specific genes involved in cell division.
(via Semantic Scholar)
Sources: Crossref, NC State University Libraries
Added: March 5, 2020
2010 journal article
The E2FD/DEL2 factor is a component of a regulatory network controlling cell proliferation and development in Arabidopsis
Plant Molecular Biology, 72(4-5), 381–395.
author keywords: Arabidopsis; Auxin; E2F transcription factors; Plant cell cycle; Plant development
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Base Sequence; Cell Cycle / genetics; Cell Proliferation; DNA, Plant / genetics; E2F Transcription Factors / genetics; E2F Transcription Factors / metabolism; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Indoleacetic Acids / metabolism; Molecular Sequence Data; Mutation; Plants, Genetically Modified; Protein Processing, Post-Translational
TL;DR:
The analysis of mutant and transgenic plants characterized by altered expression of E2FD/DEL2 has revealed that this atypical E2F can affect plant growth by promoting cell proliferation and repressing cell elongation and these results suggest that E2 FD/D EL2 is part of a regulatory network that controls the balance betweencell proliferation and development in Arabidopsis.
(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
Added: August 6, 2018
2010 journal article
The SHR/SCR pathway directly activates genes involved in asymmetric cell division in the Arabidopsis root
Nature, 466(7302), 128–132.
Source: NC State University Libraries
Added: February 8, 2019
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
2009 journal article
The Arabidopsis MCM2 gene is essential to embryo development and its over-expression alters root meristem function
The New Phytologist, 184(2), 311–322.
author keywords: AtMCM3; DNA replication; lateral root initiation; minichromosome maintenance; root meristem function
TL;DR:
Evidence is provided for the involvement of AtMCM2 in DNA replication, and suggest that it plays a crucial role in root meristem function, in Arabidopsis.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
2008 journal article
Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection
Plant Physiology, 148(1), 436–454.
MeSH headings : Arabidopsis / physiology; Arabidopsis / virology; Cell Cycle; DNA Repair; DNA Replication; E2F Transcription Factors / metabolism; Geminiviridae / physiology; Gene Expression; Gene Expression Profiling; Genes, Plant; Host-Parasite Interactions; Oligonucleotide Array Sequence Analysis; Plant Diseases; Plant Leaves / metabolism; Plant Leaves / virology; RNA Viruses / physiology; Signal Transduction
TL;DR:
Geminiviruses modulate plant cell cycle status by differentially impacting the CYCD/retinoblastoma-related protein/E2F regulatory network and facilitating progression into the endocycle.
(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
Added: February 8, 2019
2006 journal article
Interplay between Arabidopsis Activating Factors E2Fb and E2Fa in Cell Cycle Progression and Development
Plant Physiology, 140(4), 1355–1366.
MeSH headings : Arabidopsis / genetics; Arabidopsis / growth & development; Arabidopsis / metabolism; Arabidopsis Proteins / metabolism; Arabidopsis Proteins / physiology; Cell Cycle / physiology; Cell Line; Cotyledon / cytology; Cotyledon / metabolism; E2F Transcription Factors / metabolism; E2F Transcription Factors / physiology; Genetic Markers; Phenotype; Plant Leaves / cytology; Plant Leaves / metabolism; Plant Roots / cytology; Plant Roots / metabolism; Plants, Genetically Modified / metabolism; Up-Regulation
TL;DR:
Overexpression of AtE2Fb in transgenic Arabidopsis plants led to striking modifications of the morphology of roots, cotyledons, and leaves that can be ascribed to stimulation of cell division.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
2006 journal article
Two cell-cycle regulated SET-domain proteins interact with proliferating cell nuclear antigen (PCNA) in Arabidopsis
The Plant Journal: For Cell and Molecular Biology, 47(3), 395–407.
author keywords: cell cycle; S phase; AtE2F; SET domain; proliferating cell nuclear antigen
MeSH headings : Amino Acid Motifs; Arabidopsis / cytology; Arabidopsis / genetics; Arabidopsis / metabolism; Arabidopsis Proteins / chemistry; Arabidopsis Proteins / genetics; Arabidopsis Proteins / metabolism; Cell Cycle / physiology; Cell Cycle Proteins / chemistry; Cell Cycle Proteins / genetics; Cell Cycle Proteins / metabolism; Cell Nucleus / metabolism; Cell Proliferation; DNA Replication; E2F Transcription Factors / metabolism; E2F Transcription Factors / physiology; Flowers / growth & development; Flowers / metabolism; Gene Expression Regulation, Plant; Green Fluorescent Proteins / analysis; Nuclear Proteins / chemistry; Nuclear Proteins / genetics; Nuclear Proteins / metabolism; Plant Infertility; Plastids / metabolism; Proliferating Cell Nuclear Antigen / metabolism; Protein Structure, Tertiary; Recombinant Fusion Proteins / analysis; Two-Hybrid System Techniques
TL;DR:
The results suggest that both proteins may play a role in the cell cycle or DNA replication, and that the activity of ATXR5 may be regulated via its subcellular localization.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries
Added: February 8, 2019
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